diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..34e122cd --- /dev/null +++ b/.gitattributes @@ -0,0 +1,5 @@ +*.yml filter=ignorelines + +# to delete lines commented with # gitignore in yaml files +# git config --global filter.ignorelines.clean "sed '/^# gitignore/d'" +# git config --global filter.ignorelines.smudge cat \ No newline at end of file diff --git a/README.md b/README.md index 8212a03b..5ccf7b6c 100644 --- a/README.md +++ b/README.md @@ -48,8 +48,10 @@ at the forefront of biomedical research. Discover the power and versatility of the PHYLOViZ Web Platform, and unlock new insights into phylogenetic data analysis, by visiting the [PHYLOViZ Web Platform](https://web.phyloviz.net/) website. -To see a demo of the PHYLOViZ Web Platform in action, check out this [video](https://www.youtube.com/watch?v=761A27KgHIY). -It provides an overview of the platform's features and showcases its capabilities for phylogenetic analysis and visualization. +To see a demo of the PHYLOViZ Web Platform in action, check out +this [video](https://www.youtube.com/watch?v=761A27KgHIY). +It provides an overview of the platform's features and showcases its capabilities for phylogenetic analysis and +visualization. --- diff --git a/docker-compose.yml b/docker-compose.yml index 74bffc88..63a375e1 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -74,60 +74,25 @@ services: depends_on: - tool_registry - administration: + core: build: - context: ./src/backend/microservices/administration + context: ./src/backend/core dockerfile: Dockerfile ports: - '8088:8088' network_mode: host depends_on: - mongodb - - cache - - compute: - build: - context: ./src/backend/microservices/compute - dockerfile: Dockerfile - ports: - - '8086:8086' - network_mode: host - depends_on: - - mongodb - - cache - - file-transfer: - build: - context: ./src/backend/microservices/file-transfer - dockerfile: Dockerfile - ports: - - '8089:8089' - network_mode: host - depends_on: - - mongodb - - cache gateway: build: - context: ./src/backend/microservices/gateway + context: ./src/backend/gateway dockerfile: Dockerfile ports: - '8083:8083' network_mode: host depends_on: - mongodb - - cache - - visualization: - build: - context: ./src/backend/microservices/visualization - dockerfile: Dockerfile - ports: - - '8085:8085' - network_mode: host - depends_on: - - mongodb - - cache volumes: keycloak_db_data: diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 4fce725d..4d4ed5de 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -1,6 +1,8 @@ # Contributing to PHYLOViZ Web Platform -Thank you for your interest in contributing to the PHYLOViZ Web Platform! We welcome contributions from the community to help improve and enhance the platform's functionality. This guide will provide you with an overview of the contribution process. +Thank you for your interest in contributing to the PHYLOViZ Web Platform! We welcome contributions from the community to +help improve and enhance the platform's functionality. This guide will provide you with an overview of the contribution +process. ## Table of Contents @@ -16,8 +18,10 @@ Thank you for your interest in contributing to the PHYLOViZ Web Platform! We wel Before you start contributing to the PHYLOViZ Web Platform, please take a moment to review the following guidelines: 1. Familiarize yourself with the project by exploring the documentation, codebase, and existing issues. -2. If you plan to work on a new feature or significant changes, it's recommended to discuss it with the project maintainers beforehand to ensure it aligns with the project's goals and roadmap. -3. Make sure to follow the coding style and conventions used in the project. Adhering to consistent code formatting will make the review process smoother. +2. If you plan to work on a new feature or significant changes, it's recommended to discuss it with the project + maintainers beforehand to ensure it aligns with the project's goals and roadmap. +3. Make sure to follow the coding style and conventions used in the project. Adhering to consistent code formatting will + make the review process smoother. 4. Test your changes thoroughly to ensure they don't introduce any regressions or issues. 5. Document your code updates and any new features or changes you introduce. 6. Respect the existing contributors and maintain a positive and inclusive attitude towards other community members. @@ -37,7 +41,8 @@ To contribute to the PHYLOViZ Web Platform, follow these steps: ## Submitting a Contribution -Once you have made your changes and pushed them to your forked repository, you can submit your contribution by following these steps: +Once you have made your changes and pushed them to your forked repository, you can submit your contribution by following +these steps: 1. Navigate to the original repository on GitHub. 2. Locate the "Pull Requests" tab. @@ -49,36 +54,46 @@ Once you have made your changes and pushed them to your forked repository, you c ## Code Review Process -After submitting a pull request, the project maintainers will review your code and provide feedback. Here's what you can expect during the review process: +After submitting a pull request, the project maintainers will review your code and provide feedback. Here's what you can +expect during the review process: 1. The maintainers will review your code for adherence to coding standards, functionality, and any potential issues. -2. They may request changes or improvements to your code. Please address these requests promptly and make the necessary updates. -3. Once your code meets the project's requirements and standards, it will be approved and merged into the main repository. -4. If there are any conflicts or issues during the review process, maintain an open and collaborative mindset to resolve them. +2. They may request changes or improvements to your code. Please address these requests promptly and make the necessary + updates. +3. Once your code meets the project's requirements and standards, it will be approved and merged into the main + repository. +4. If there are any conflicts or issues during the review process, maintain an open and collaborative mindset to resolve + them. ## Community Guidelines To ensure a positive and inclusive community environment, we kindly request that you adhere to the following guidelines: -1. Treat all community members with respect and courtesy. Avoid any form of harassment, discrimination, or offensive behavior. +1. Treat all community members with respect and courtesy. Avoid any form of harassment, discrimination, or offensive + behavior. 2. Be considerate of others' opinions and perspectives, even if they differ from your own. 3. Provide constructive feedback and suggestions to help improve the project. 4. Help others in the community by sharing your knowledge and expertise. 5. Avoid spamming, advertising, or promoting unrelated content within the community channels. -6. If you encounter any issues or have concerns about the project or community, reach out to the project maintainers privately. +6. If you encounter any issues or have concerns about the project or community, reach out to the project maintainers + privately. ## Contact Information -If you have any questions, concerns, or need assistance, you can reach out to the authors of the PHYLOViZ Web Platform through the following emails: +If you have any questions, concerns, or need assistance, you can reach out to the authors of the PHYLOViZ Web Platform +through the following emails: - André Jesus: [andre.jesus.pilar@gmail.com](mailto:andre.jesus.pilar@gmail.com) - André Páscoa: [andre@pascoa.org](mailto:andre@pascoa.org) - Nyckollas Brandão: [nyckbrandao1236@gmail.com](mailto:nyckbrandao1236@gmail.com) -Please feel free to contact any of the authors if you have any inquiries related to the PHYLOViZ Web Platform. They will be happy to assist you. +Please feel free to contact any of the authors if you have any inquiries related to the PHYLOViZ Web Platform. They will +be happy to assist you. -If you encounter any bugs, have feature requests, or would like to report any issues, please visit the [Issues](https://github.com/phyloviz/phyloviz-web-platform/issues) section -on GitHub and create a new issue. +If you encounter any bugs, have feature requests, or would like to report any issues, please visit +the [Issues](https://github.com/phyloviz/phyloviz-web-platform/issues) section +on GitHub and create a new issue. Your feedback and contributions are valuable to us, and we appreciate your help in improving the platform. -We appreciate your interest and contribution to the PHYLOViZ Web Platform. Thank you for helping us improve the platform and make it even better for the community! +We appreciate your interest and contribution to the PHYLOViZ Web Platform. 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\"gastroenteritis\",\n \"penner\": \"NT\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"1564\",\n \"curator\": \"1\",\n \"town_or_city\": \"Preston\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": \"2001-02-12\"\n }\n },\n {\n \"id\": \"112\",\n \"profileId\": \"93\",\n \"row\": {\n \"continent\": \"Europe\",\n \"country\": \"UK [England]\",\n \"disease\": \"gastroenteritis\",\n \"penner\": \"4c\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"1715\",\n \"curator\": \"1\",\n \"town_or_city\": \"Blackpool\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": \"2001-02-12\"\n }\n },\n {\n \"id\": \"113\",\n \"profileId\": \"93\",\n \"row\": {\n \"continent\": \"Europe\",\n \"country\": \"UK [England]\",\n \"disease\": \"gastroenteritis\",\n \"penner\": \"4c\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"2017\",\n \"curator\": \"1\",\n \"town_or_city\": \"Poole\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": \"2001-02-12\"\n }\n },\n {\n \"id\": \"114\",\n \"profileId\": \"93\",\n \"row\": {\n \"continent\": \"Europe\",\n \"country\": \"UK [England]\",\n \"disease\": \"gastroenteritis\",\n \"penner\": \"4c\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"2035\",\n \"curator\": \"1\",\n \"town_or_city\": \"Bath\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": 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"cookie": [], - "body": "{\r\n \"profiles\": [\r\n {\r\n \"id\": \"1\",\r\n \"profile\": [\r\n \"2\",\r\n \"1\",\r\n \"54\",\r\n \"3\",\r\n \"4\",\r\n \"1\",\r\n \"5\"\r\n ]\r\n },\r\n {\r\n \"id\": \"2\",\r\n \"profile\": [\r\n \"4\",\r\n \"7\",\r\n \"51\",\r\n \"4\",\r\n \"1\",\r\n \"7\",\r\n \"1\"\r\n ]\r\n }\r\n ],\r\n \"totalCount\": 2\r\n}" - } - ] - } - ] - } - ] - } - ] - } - ] - }, - { - "name": "Extra", - "item": [ - { - "name": "Keycloak", - "item": [ - { - "name": "Nyck Keycloak", - "item": [ - { - "name": "Keycloak create access token with password grant type", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "gmaFeUwf9AXnxMaQyTuXEtTAgbJlBpgy", - "type": "text" - }, - { - "key": "grant_type", - "value": "password", - "type": "text" - }, - { - "key": "scope", - "value": "openid email roles profile", - "type": "text" - }, - { - "key": "username", - "value": "nyckoka", - "type": "text" - }, - { - "key": "password", - "value": "andrepascoa", - "type": "text" - } - ] - }, - "url": { - "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - }, - { - "name": "Create access token with device grant", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"device_code\"]){\r", - " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", - "type": "text" - } - ] - }, - "url": { - "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "auth", - "device" - ] - } - }, - "response": [] - }, - { - "name": "Poll Keycloak token", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "device_code", - "value": "{{test_device_code}}", - "type": "text" - }, - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", - "type": "text" - }, - { - "key": "grant_type", - "value": "urn:ietf:params:oauth:grant-type:device_code", - "type": "text" - } - ] - }, - "url": { - "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - } - ] - }, - { - "name": "Páscoa Keycloak", - "item": [ - { - "name": "Keycloak create access token with password grant type", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", - "type": "text" - }, - { - "key": "grant_type", - "value": "password", - "type": "text" - }, - { - "key": "scope", - "value": "openid email roles profile", - "type": "text" - }, - { - "key": "username", - "value": "devandrepascoa", - "type": "text" - }, - { - "key": "password", - "value": "andrepascoa", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - }, - { - "name": "Create access token with device grant", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"device_code\"]){\r", - " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "auth", - "device" - ] - } - }, - "response": [] - }, - { - "name": "Poll Keycloak token", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "device_code", - "value": "{{test_device_code}}", - "type": "text" - }, - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", - "type": "text" - }, - { - "key": "grant_type", - "value": "urn:ietf:params:oauth:grant-type:device_code", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - } - ] - }, - { - "name": "Jesus Keycloak", - "item": [ - { - "name": "Keycloak create access token with password grant type", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", - "type": "text" - }, - { - "key": "grant_type", - "value": "password", - "type": "text" - }, - { - "key": "scope", - "value": "openid email roles profile", - "type": "text" - }, - { - "key": "username", - "value": "devandrepascoa", - "type": "text" - }, - { - "key": "password", - "value": "andrepascoa", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - }, - { - "name": "Create access token with device grant", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"device_code\"]){\r", - " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "auth", - "device" - ] - } - }, - "response": [] - }, - { - "name": "Poll Keycloak token", - "event": [ - { - "listen": "test", - "script": { - "exec": [ - "const json = JSON.parse(responseBody);\r", - "\r", - "if (json[\"access_token\"]){\r", - " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", - "}" - ], - "type": "text/javascript" - } - } - ], - "request": { - "method": "POST", - "header": [ - { - "key": "Content-Type", - "value": "application/x-www-form-urlencoded" - } - ], - "body": { - "mode": "urlencoded", - "urlencoded": [ - { - "key": "device_code", - "value": "{{test_device_code}}", - "type": "text" - }, - { - "key": "client_id", - "value": "{{KEYCLOAK_CLIENT_ID}}", - "type": "text" - }, - { - "key": "client_secret", - "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", - "type": "text" - }, - { - "key": "grant_type", - "value": "urn:ietf:params:oauth:grant-type:device_code", - "type": "text" - } - ] - }, - "url": { - "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", - "protocol": "http", - "host": [ - "{{KEYCLOAK_URL}}" - ], - "path": [ - "realms", - "phyloviz-web-platform", - "protocol", - "openid-connect", - "token" - ] - } - }, - "response": [] - } - ] - } - ] - }, - { - "name": "Openstack", - "item": [ - { - "name": "Login", - "request": { - "method": "POST", - "header": [], - "body": { - "mode": "raw", - "raw": "{\r\n \"auth\": {\r\n \"identity\": {\r\n \"methods\": [\"password\"],\r\n \"password\": {\r\n \"user\": {\r\n \"name\": \"admin\",\r\n \"domain\": {\r\n \"name\": \"Default\"\r\n },\r\n \"password\": \"secret\"\r\n }\r\n }\r\n },\r\n \"scope\": \"unscoped\"\r\n }\r\n}", - "options": { - "raw": { - "language": "json" - } - } - }, - "url": { - "raw": "http://{{OPENSTACK_URL}}/identity/v3/auth/tokens", - "protocol": "http", - "host": [ - "{{OPENSTACK_URL}}" - ], - "path": [ - "identity", - "v3", - "auth", - "tokens" - ] - } - }, - "response": [] - } - 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\"row\": {\n \"continent\": \"Europe\",\n \"country\": \"UK [England]\",\n \"disease\": \"gastroenteritis\",\n \"penner\": \"4c\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"2017\",\n \"curator\": \"1\",\n \"town_or_city\": \"Poole\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": \"2001-02-12\"\n }\n },\n {\n \"id\": \"114\",\n \"profileId\": \"93\",\n \"row\": {\n \"continent\": \"Europe\",\n \"country\": \"UK [England]\",\n \"disease\": \"gastroenteritis\",\n \"penner\": \"4c\",\n \"year\": \"1992\",\n \"source\": \"human stool\",\n \"datestamp\": \"2001-02-12\",\n \"epidemiology\": \"sporadic case\",\n \"isolate\": \"2035\",\n \"curator\": \"1\",\n \"town_or_city\": \"Bath\",\n \"clonal_complex (MLST)\": \"ST-61 complex\",\n \"sender\": \"2\",\n \"species\": \"Campylobacter jejuni\",\n \"date_entered\": \"2001-02-12\"\n }\n }\n ],\n \"totalCount\": 100\n}" + } + ] + } + ] + }, + { + "name": "Typing Data", + "item": [ + { + "name": "Get Typing Data Schema", + "request": { + "method": "GET", + "header": [], + "url": { + "raw": "{{visualization_url}}/projects/:projectId/files/typing-data/:typingDataId", + "host": [ + "{{visualization_url}}" + ], + "path": [ + "projects", + ":projectId", + "files", + "typing-data", + ":typingDataId" + ], + "variable": [ + { + "key": "projectId", + "value": "646279adbc88522eee347ab1" + }, + { + "key": "typingDataId", + "value": "bff2decd-9b60-4508-93b4-f1e55985e78b" + } + ] + } + }, + "response": [ + { + "name": "Get Typing Data Schema", + "originalRequest": { + "method": "GET", + "header": [], + "url": { + "raw": "{{visualization_url}}/projects/:projectId/files/typing-data/:typingDataId", + "host": [ + "{{visualization_url}}" + ], + "path": [ + "projects", + ":projectId", + "files", + "typing-data", + ":typingDataId" + ], + "variable": [ + { + "key": "projectId", + "value": null + }, + { + "key": "typingDataId", + "value": null + } + ] + } + }, + "status": "OK", + "code": 200, + "_postman_previewlanguage": "json", + "header": [ + { + "key": "Content-Type", + "value": "application/json", + "name": "Content-Type", + "description": "", + "type": "text" + } + ], + "cookie": [], + "body": "{\r\n \"type\": \"mlst7\",\r\n \"loci\": [\r\n \"aspA\",\r\n \"glnA\",\r\n \"gltA\",\r\n \"glyA\",\r\n \"pgm\",\r\n \"tkt\",\r\n \"uncA\"\r\n ]\r\n}" + } + ] + }, + { + "name": "Get Typing Data Profiles", + "request": { + "method": "GET", + "header": [], + "url": { + "raw": "{{visualization_url}}/projects/:projectId/files/typing-data/:typingDataId/profiles?limit=100000&offset=0", + "host": [ + "{{visualization_url}}" + ], + "path": [ + "projects", + ":projectId", + "files", + "typing-data", + ":typingDataId", + "profiles" + ], + "query": [ + { + "key": "limit", + "value": "100000" + }, + { + "key": "offset", + "value": "0" + } + ], + "variable": [ + { + "key": "projectId", + "value": "646279adbc88522eee347ab1" + }, + { + "key": "typingDataId", + "value": "bff2decd-9b60-4508-93b4-f1e55985e78b" + } + ] + } + }, + "response": [ + { + "name": "Get Typing Data Profiles", + "originalRequest": { + "method": "GET", + "header": [], + "url": { + "raw": "{{visualization_url}}/projects/:projectId/files/typing-data/:typingDataId/profiles?limit=100&offset=0", + "host": [ + "{{visualization_url}}" + ], + "path": [ + "projects", + ":projectId", + "files", + "typing-data", + ":typingDataId", + "profiles" + ], + "query": [ + { + "key": "limit", + "value": "100" + }, + { + "key": "offset", + "value": "0" + } + ], + "variable": [ + { + "key": "projectId", + "value": null + }, + { + "key": "typingDataId", + "value": null + } + ] + } + }, + "status": "OK", + "code": 200, + "_postman_previewlanguage": "json", + "header": [ + { + "key": "Content-Type", + "value": "application/json", + "name": "Content-Type", + "description": "", + "type": "text" + } + ], + "cookie": [], + "body": "{\r\n \"profiles\": [\r\n {\r\n \"id\": \"1\",\r\n \"profile\": [\r\n \"2\",\r\n \"1\",\r\n \"54\",\r\n \"3\",\r\n \"4\",\r\n \"1\",\r\n \"5\"\r\n ]\r\n },\r\n {\r\n \"id\": \"2\",\r\n \"profile\": [\r\n \"4\",\r\n \"7\",\r\n \"51\",\r\n \"4\",\r\n \"1\",\r\n \"7\",\r\n \"1\"\r\n ]\r\n }\r\n ],\r\n \"totalCount\": 2\r\n}" + } + ] + } + ] + } + ] + } + ] + } + ] + }, + { + "name": "Extra", + "item": [ + { + "name": "Keycloak", + "item": [ + { + "name": "Nyck Keycloak", + "item": [ + { + "name": "Keycloak create access token with password grant type", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "gmaFeUwf9AXnxMaQyTuXEtTAgbJlBpgy", + "type": "text" + }, + { + "key": "grant_type", + "value": "password", + "type": "text" + }, + { + "key": "scope", + "value": "openid email roles profile", + "type": "text" + }, + { + "key": "username", + "value": "nyckoka", + "type": "text" + }, + { + "key": "password", + "value": "andrepascoa", + "type": "text" + } + ] + }, + "url": { + "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + }, + { + "name": "Create access token with device grant", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"device_code\"]){\r", + " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "text" + } + ] + }, + "url": { + "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "auth", + "device" + ] + } + }, + "response": [] + }, + { + "name": "Poll Keycloak token", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "device_code", + "value": "{{test_device_code}}", + "type": "text" + }, + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "text" + }, + { + "key": "grant_type", + "value": "urn:ietf:params:oauth:grant-type:device_code", + "type": "text" + } + ] + }, + "url": { + "raw": "{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + } + ] + }, + { + "name": "Páscoa Keycloak", + "item": [ + { + "name": "Keycloak create access token with password grant type", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", + "type": "text" + }, + { + "key": "grant_type", + "value": "password", + "type": "text" + }, + { + "key": "scope", + "value": "openid email roles profile", + "type": "text" + }, + { + "key": "username", + "value": "devandrepascoa", + "type": "text" + }, + { + "key": "password", + "value": "andrepascoa", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + }, + { + "name": "Create access token with device grant", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"device_code\"]){\r", + " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "auth", + "device" + ] + } + }, + "response": [] + }, + { + "name": "Poll Keycloak token", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "device_code", + "value": "{{test_device_code}}", + "type": "text" + }, + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "whCCD9r37qj8mx9H7R4mzIrSezYf3H7R", + "type": "text" + }, + { + "key": "grant_type", + "value": "urn:ietf:params:oauth:grant-type:device_code", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + } + ] + }, + { + "name": "Jesus Keycloak", + "item": [ + { + "name": "Keycloak create access token with password grant type", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "text" + }, + { + "key": "grant_type", + "value": "password", + "type": "text" + }, + { + "key": "scope", + "value": "openid email roles profile", + "type": "text" + }, + { + "key": "username", + "value": "devandrepascoa", + "type": "text" + }, + { + "key": "password", + "value": "andrepascoa", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + }, + { + "name": "Create access token with device grant", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"device_code\"]){\r", + " pm.collectionVariables.set(\"test_device_code\", json[\"device_code\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/auth/device", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "auth", + "device" + ] + } + }, + "response": [] + }, + { + "name": "Poll Keycloak token", + "event": [ + { + "listen": "test", + "script": { + "exec": [ + "const json = JSON.parse(responseBody);\r", + "\r", + "if (json[\"access_token\"]){\r", + " pm.collectionVariables.set(\"test_access_token\", json[\"access_token\"]);\r", + "}" + ], + "type": "text/javascript" + } + } + ], + "request": { + "method": "POST", + "header": [ + { + "key": "Content-Type", + "value": "application/x-www-form-urlencoded" + } + ], + "body": { + "mode": "urlencoded", + "urlencoded": [ + { + "key": "device_code", + "value": "{{test_device_code}}", + "type": "text" + }, + { + "key": "client_id", + "value": "{{KEYCLOAK_CLIENT_ID}}", + "type": "text" + }, + { + "key": "client_secret", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "text" + }, + { + "key": "grant_type", + "value": "urn:ietf:params:oauth:grant-type:device_code", + "type": "text" + } + ] + }, + "url": { + "raw": "http://{{KEYCLOAK_URL}}/realms/phyloviz-web-platform/protocol/openid-connect/token", + "protocol": "http", + "host": [ + "{{KEYCLOAK_URL}}" + ], + "path": [ + "realms", + "phyloviz-web-platform", + "protocol", + "openid-connect", + "token" + ] + } + }, + "response": [] + } + ] + } + ] + }, + { + "name": "Openstack", + "item": [ + { + "name": "Login", + "request": { + "method": "POST", + "header": [], + "body": { + "mode": "raw", + "raw": "{\r\n \"auth\": {\r\n \"identity\": {\r\n \"methods\": [\"password\"],\r\n \"password\": {\r\n \"user\": {\r\n \"name\": \"admin\",\r\n \"domain\": {\r\n \"name\": \"Default\"\r\n },\r\n \"password\": \"secret\"\r\n }\r\n }\r\n },\r\n \"scope\": \"unscoped\"\r\n }\r\n}", + "options": { + "raw": { + "language": "json" + } + } + }, + "url": { + "raw": "http://{{OPENSTACK_URL}}/identity/v3/auth/tokens", + "protocol": "http", + "host": [ + "{{OPENSTACK_URL}}" + ], + "path": [ + "identity", + "v3", + "auth", + "tokens" + ] + } + }, + "response": [] + } + ] + } + ] + } + ], + "auth": { + "type": "bearer", + "bearer": [ + { + "key": "token", + "value": "{{test_access_token}}", + "type": "string" + } + ] + }, + "event": [ + { + "listen": "prerequest", + "script": { + "type": "text/javascript", + "exec": [ + "" + ] + } + }, + { + "listen": "test", + "script": { + "type": "text/javascript", + "exec": [ + "" + ] + } + } + ], + "variable": [ + { + "key": "visualization_url", + "value": "localhost:8085", + "type": "string" + }, + { + "key": "compute_url", + "value": "localhost:8086", + "type": "string" + }, + { + "key": "downloader_url", + "value": "localhost:8087", + "type": "string" + }, + { + "key": "administration_url", + "value": "localhost:8088", + "type": "string" + }, + { + "key": "file_transfer_url", + "value": "localhost:8089", + "type": "string" + }, + { + "key": "test_device_code", + "value": "" + }, + { + "key": "test_access_token", + "value": "" + }, + { + "key": "KEYCLOAK_URL", + "value": "localhost:8082", + "type": "string" + }, + { + "key": "KEYCLOAK_CLIENT_ID", + "value": "phyloviz-web-platform-client", + "type": "string" + }, + { + "key": "KEYCLOAK_CLIENT_SECRET", + "value": "pZW9kZ05jHjLiOlYYhBAa9CGk1uL7bob", + "type": "string" + }, + { + "key": "OPENSTACK_URL", + "value": "192.168.1.93", + "type": "string" + } + ] } \ No newline at end of file diff --git a/src/backend/microservices/compute/Dockerfile b/src/backend/core/Dockerfile similarity index 56% rename from src/backend/microservices/compute/Dockerfile rename to src/backend/core/Dockerfile index c89e0065..75c743a6 100644 --- a/src/backend/microservices/compute/Dockerfile +++ b/src/backend/core/Dockerfile @@ -1,4 +1,4 @@ FROM openjdk:17-jdk-alpine -COPY build/libs/compute-0.0.1-SNAPSHOT.jar /app.jar +COPY build/libs/pwp-0.0.1-SNAPSHOT.jar /app.jar ENTRYPOINT ["java", "-jar", "/app.jar"] \ No newline at end of file diff --git a/src/backend/microservices/compute/build.gradle b/src/backend/core/build.gradle similarity index 81% rename from src/backend/microservices/compute/build.gradle rename to src/backend/core/build.gradle index ac9c1b48..38d063c2 100644 --- a/src/backend/microservices/compute/build.gradle +++ b/src/backend/core/build.gradle @@ -18,13 +18,11 @@ repositories { } dependencies { - implementation project(path: ':microservices:shared-phylodb') - implementation project(path: ':microservices:shared') - testImplementation 'org.springframework.boot:spring-boot-starter-test' testImplementation 'org.junit.jupiter:junit-jupiter-api' version { jupiterVersion } testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine' version { jupiterVersion } + implementation 'org.springframework.boot:spring-boot-starter-data-rest' implementation 'org.springframework.boot:spring-boot-starter-data-mongodb' implementation 'org.springframework.boot:spring-boot-starter-web' implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server' @@ -38,6 +36,12 @@ dependencies { implementation 'org.apache.commons:commons-text:1.10.0' implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' + testImplementation 'junit:junit:4.13.1' + + implementation 'software.amazon.awssdk:s3:2.20.28' + implementation 'software.amazon.awssdk:s3-transfer-manager:2.20.28' + + implementation 'org.reflections:reflections:0.10.2' } test { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/ComputeMicroserviceApplication.java b/src/backend/core/src/main/java/org/phyloviz/pwp/PWPApplication.java similarity index 50% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/ComputeMicroserviceApplication.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/PWPApplication.java index ae89e11b..d5a3eae9 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/ComputeMicroserviceApplication.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/PWPApplication.java @@ -1,20 +1,20 @@ -package org.phyloviz.pwp.compute; +package org.phyloviz.pwp; import org.springframework.boot.SpringApplication; import org.springframework.boot.autoconfigure.SpringBootApplication; /** - * Main class for the Compute Microservice of the PHYLOViZ Web Platform. + * Main class for the PHYLOViZ Web Platform. */ @SpringBootApplication -public class ComputeMicroserviceApplication { +public class PWPApplication { /** - * Entry point for the Compute Microservice. + * Entry point for the PHYLOViZ Web Platform. * * @param args arguments passed to the application */ public static void main(String[] args) { - SpringApplication.run(ComputeMicroserviceApplication.class, args); + SpringApplication.run(PWPApplication.class, args); } } diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/config/DataRepositoryConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/DataRepositoryConfig.java new file mode 100644 index 00000000..f5e3ac15 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/DataRepositoryConfig.java @@ -0,0 +1,86 @@ +package org.phyloviz.pwp.config; + + +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.DistanceMatrixS3DataRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataS3DataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistryImpl; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistryImpl; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryRegistryImpl; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryRegistryImpl; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryRegistryImpl; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.TreeS3DataRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.TreeViewS3DataRepository; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataS3DataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; +import org.springframework.context.ApplicationContext; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import java.util.Map; + +/** + * Configuration class for the Data Repositories. + */ +@Configuration +public class DataRepositoryConfig { + + @Bean + public TypingDataDataRepositoryRegistry typingDataDataRepositoryRegistry(ApplicationContext context) { + return new TypingDataDataRepositoryRegistryImpl(context, Map.of( + TypingDataDataRepositoryId.S3, TypingDataS3DataRepository.class + ), Map.of( + TypingDataDataRepositoryId.S3, TypingDataS3DataRepositorySpecificData.class + )); + } + + @Bean + public IsolateDataDataRepositoryRegistry isolateDataDataRepositoryRegistry(ApplicationContext context) { + return new IsolateDataDataRepositoryRegistryImpl(context, Map.of( + IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepository.class + + ), Map.of( + IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepositorySpecificData.class + )); + } + + @Bean + public DistanceMatrixDataRepositoryRegistry distanceMatrixDataRepositoryRegistry(ApplicationContext context) { + return new DistanceMatrixDataRepositoryRegistryImpl(context, Map.of( + DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepository.class + ), Map.of( + DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepositorySpecificData.class + )); + } + + @Bean + public TreeDataRepositoryRegistry treeDataRepositoryRegistry(ApplicationContext context) { + return new TreeDataRepositoryRegistryImpl(context, Map.of( + TreeDataRepositoryId.S3, TreeS3DataRepository.class + ), Map.of( + TreeDataRepositoryId.S3, TreeS3DataRepositorySpecificData.class + )); + } + + @Bean + public TreeViewDataRepositoryRegistry treeViewDataRepositoryRegistry(ApplicationContext context) { + return new TreeViewDataRepositoryRegistryImpl(context, Map.of( + TreeViewDataRepositoryId.S3, TreeViewS3DataRepository.class + ), Map.of( + TreeViewDataRepositoryId.S3, TreeViewS3DataRepositorySpecificData.class + )); + } +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/FilterChainConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/FilterChainConfig.java similarity index 96% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/FilterChainConfig.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/config/FilterChainConfig.java index eea7e0db..23b73a87 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/FilterChainConfig.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/FilterChainConfig.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.config; +package org.phyloviz.pwp.config; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.annotation.Bean; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/MongoConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/MongoConfig.java similarity index 58% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/MongoConfig.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/config/MongoConfig.java index 38946db5..9b214052 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/MongoConfig.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/MongoConfig.java @@ -1,30 +1,25 @@ -package org.phyloviz.pwp.shared.config; +package org.phyloviz.pwp.config; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.converters.DistanceMatrixMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataSerializer; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.converters.TreeMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters.TreeViewMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters.TreeViewMetadataSerializer; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters.TypingDataMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters.TypingDataMetadataSerializer; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.converters.DistanceMatrixMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataSerializer; +import org.phyloviz.pwp.repository.metadata.tree.documents.converters.TreeMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.converters.TreeViewMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.converters.TreeViewMetadataSerializer; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.converters.TypingDataMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.converters.TypingDataMetadataSerializer; import org.springframework.beans.factory.BeanFactory; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.core.convert.converter.Converter; import org.springframework.data.mongodb.MongoDatabaseFactory; -import org.springframework.data.mongodb.core.convert.DbRefResolver; -import org.springframework.data.mongodb.core.convert.DefaultDbRefResolver; -import org.springframework.data.mongodb.core.convert.DefaultMongoTypeMapper; -import org.springframework.data.mongodb.core.convert.MappingMongoConverter; -import org.springframework.data.mongodb.core.convert.MongoConverter; -import org.springframework.data.mongodb.core.convert.MongoCustomConversions; +import org.springframework.data.mongodb.core.convert.*; import org.springframework.data.mongodb.core.mapping.MongoMappingContext; import org.springframework.data.mongodb.repository.config.EnableMongoRepositories; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/config/ComputeConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/PWPConfig.java similarity index 65% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/config/ComputeConfig.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/config/PWPConfig.java index f0ccaa63..9c019e01 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/config/ComputeConfig.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/PWPConfig.java @@ -1,24 +1,22 @@ -package org.phyloviz.pwp.compute.config; +package org.phyloviz.pwp.config; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters.AccessTemplateDeserializer; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters.AccessTemplateSerializer; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters.CaseInsensitiveEnumDeserializerFactory; -import org.phyloviz.pwp.compute.service.flowviz.FLOWViZClient; -import org.phyloviz.pwp.shared.config.ResourceServerSharedConfig; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.converters.DistanceMatrixMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataSerializer; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.converters.TreeMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters.TreeViewMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters.TreeViewMetadataSerializer; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters.TypingDataMetadataDeserializer; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters.TypingDataMetadataSerializer; -import org.phyloviz.pwp.shared_phylodb.config.ResourceServerSharedPhylodbConfig; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.converters.AccessTemplateDeserializer; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.converters.AccessTemplateSerializer; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.converters.CaseInsensitiveEnumDeserializerFactory; +import org.phyloviz.pwp.service.flowviz.FLOWViZClient; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.converters.DistanceMatrixMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters.IsolateDataMetadataSerializer; +import org.phyloviz.pwp.repository.metadata.tree.documents.converters.TreeMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.converters.TreeViewMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.converters.TreeViewMetadataSerializer; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.converters.TypingDataMetadataDeserializer; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.converters.TypingDataMetadataSerializer; import org.springframework.beans.factory.BeanFactory; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; @@ -30,23 +28,17 @@ import org.springframework.core.convert.support.GenericConversionService; import org.springframework.data.mongodb.MongoDatabaseFactory; import org.springframework.data.mongodb.MongoTransactionManager; -import org.springframework.data.mongodb.core.convert.DbRefResolver; -import org.springframework.data.mongodb.core.convert.DefaultDbRefResolver; -import org.springframework.data.mongodb.core.convert.DefaultMongoTypeMapper; -import org.springframework.data.mongodb.core.convert.MappingMongoConverter; -import org.springframework.data.mongodb.core.convert.MongoConverter; -import org.springframework.data.mongodb.core.convert.MongoCustomConversions; +import org.springframework.data.mongodb.core.convert.*; import org.springframework.data.mongodb.core.mapping.MongoMappingContext; import java.util.List; /** - * Configuration class for the Compute Microservice. + * Configuration class for the PHYLOViZ web platform (PWP). + * Contains beans for the FLOWViZ client, the Mongo transaction manager, and the Mongo custom conversions. */ @Configuration -@Import({ResourceServerSharedConfig.class, ResourceServerSharedPhylodbConfig.class}) -public class ComputeConfig { - +public class PWPConfig { private final String flowVizUsername; private final String flowVizPassword; private final String flowVizUrl; @@ -56,7 +48,7 @@ public class ComputeConfig { private final TreeDataRepositoryRegistry treeDataRepositoryRegistry; private final TreeViewDataRepositoryRegistry treeViewDataRepositoryRegistry; - public ComputeConfig( + public PWPConfig( @Value("${flowviz.username}") String flowVizUsername, @Value("${flowviz.password}") String flowVizPassword, @Value("${flowviz.url}") String flowVizUrl, diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ProblemJsonConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/ProblemJsonConfig.java similarity index 93% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ProblemJsonConfig.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/config/ProblemJsonConfig.java index ce10d9b2..770f1c53 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ProblemJsonConfig.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/ProblemJsonConfig.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.config; +package org.phyloviz.pwp.config; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/UserArgumentResolverConfig.java b/src/backend/core/src/main/java/org/phyloviz/pwp/config/UserArgumentResolverConfig.java similarity index 85% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/UserArgumentResolverConfig.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/config/UserArgumentResolverConfig.java index 16b1b922..f58418d7 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/UserArgumentResolverConfig.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/config/UserArgumentResolverConfig.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.shared.config; +package org.phyloviz.pwp.config; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.http.pipeline.UserArgumentResolver; +import org.phyloviz.pwp.http.pipeline.UserArgumentResolver; import org.springframework.context.annotation.Configuration; import org.springframework.web.method.support.HandlerMethodArgumentResolver; import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/domain/User.java b/src/backend/core/src/main/java/org/phyloviz/pwp/domain/User.java similarity index 93% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/domain/User.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/domain/User.java index a13cc5df..f827b553 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/domain/User.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/domain/User.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.domain; +package org.phyloviz.pwp.domain; import lombok.Data; import org.springframework.security.oauth2.server.resource.authentication.BearerTokenAuthentication; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/ComputeController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/ComputeController.java new file mode 100644 index 00000000..cb0c5eca --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/ComputeController.java @@ -0,0 +1,118 @@ +//package org.phyloviz.pwp.http.controllers; +// +//import lombok.RequiredArgsConstructor; +//import org.phyloviz.pwp.http.models.create_workflow.CreateWorkflowInputModel; +//import org.phyloviz.pwp.http.models.create_workflow.CreateWorkflowOutputModel; +//import org.phyloviz.pwp.http.models.get_workflow.GetWorkflowOutputModel; +//import org.phyloviz.pwp.http.models.get_workflow_status.GetWorkflowStatusOutputModel; +//import org.phyloviz.pwp.http.models.get_workflows.GetWorkflowsOutputModel; +//import org.phyloviz.pwp.service.ComputeService; +//import org.phyloviz.pwp.service.dtos.create_workflow.CreateWorkflowOutput; +//import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowOutput; +//import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowStatusOutput; +//import org.phyloviz.pwp.domain.User; +//import org.springframework.http.ResponseEntity; +//import org.springframework.web.bind.annotation.*; +// +//import java.util.List; +// +///** +// * Controller for the Compute Microservice. +// */ +//@RestController +//@RequiredArgsConstructor +//public class ComputeController { +// +// private final ComputeService computeService; +// +// /** +// * Create a new workflow. +// * +// * @param inputModel input model for the workflow +// * @param projectId the project id of the project to which the workflow belongs +// * @param user the user who is creating the workflow +// * @return information about the created workflow +// */ +// @PostMapping("/projects/{projectId}/workflows") +// public ResponseEntity createWorkflow( +// @PathVariable String projectId, +// @RequestBody CreateWorkflowInputModel inputModel, +// User user +// ) { +// CreateWorkflowOutput createWorkflowOutput = computeService.createWorkflow( +// projectId, inputModel.getType(), inputModel.getProperties(), user.getId() +// ); +// +// return ResponseEntity +// .accepted() +// .body(new CreateWorkflowOutputModel(createWorkflowOutput)); +// } +// +// /** +// * Gets the status of a workflow. +// * +// * @param projectId the project id of the project to which the workflow belongs +// * @param workflowId the id of the workflow +// * @param user the user who is requesting the workflow status +// * @return information about the workflow +// */ +// @GetMapping("/projects/{projectId}/workflows/{workflowId}/status") +// public GetWorkflowStatusOutputModel getWorkflowStatus( +// @PathVariable String projectId, +// @PathVariable String workflowId, +// User user +// ) { +// GetWorkflowStatusOutput getWorkflowStatusOutput = computeService.getWorkflowStatus( +// projectId, workflowId, user.getId() +// ); +// +// return new GetWorkflowStatusOutputModel(getWorkflowStatusOutput); +// } +// +// /** +// * Gets the workflow. +// * +// * @param projectId the project id of the project to which the workflow belongs +// * @param workflowId the id of the workflow +// * @param user the user who is requesting the workflow status +// * @return information about the workflow +// */ +// @GetMapping("/projects/{projectId}/workflows/{workflowId}") +// public GetWorkflowOutputModel getWorkflow( +// @PathVariable String projectId, +// @PathVariable String workflowId, +// User user +// ) { +// GetWorkflowOutput getWorkflowOutput = computeService.getWorkflow( +// projectId, workflowId, user.getId() +// ); +// +// return new GetWorkflowOutputModel(getWorkflowOutput); +// } +// +// /** +// * Gets the workflows of a project. +// * +// * @param projectId the project id of the project to which the workflow belongs +// * @param running whether to get only running workflows or not running workflows +// * @param user the user who is requesting the workflows +// * @return information about the workflows +// */ +// @GetMapping("/projects/{projectId}/workflows") +// public GetWorkflowsOutputModel getWorkflows( +// @PathVariable String projectId, +// @RequestParam(required = false) Boolean running, +// User user +// ) { +// List getWorkflowStatusOutputList; +// +// if (running == null) +// getWorkflowStatusOutputList = computeService.getAllWorkflows(projectId, user.getId()); +// else if (running) +// getWorkflowStatusOutputList = computeService.getAllRunningWorkflows(projectId, user.getId()); +// else +// getWorkflowStatusOutputList = computeService.getAllNotRunningWorkflows(projectId, user.getId()); +// +// return new GetWorkflowsOutputModel(getWorkflowStatusOutputList); +// } +//} diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/controllers/FileTransferController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/FileTransferController.java similarity index 83% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/controllers/FileTransferController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/FileTransferController.java index e2a81c3e..ec4e0476 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/controllers/FileTransferController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/FileTransferController.java @@ -1,19 +1,15 @@ -package org.phyloviz.pwp.file_transfer.http.controllers; +package org.phyloviz.pwp.http.controllers; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.file_transfer.http.models.isolate_data.UploadIsolateDataOutputModel; -import org.phyloviz.pwp.file_transfer.http.models.typing_data.UploadTypingDataOutputModel; -import org.phyloviz.pwp.file_transfer.service.FileTransferService; -import org.phyloviz.pwp.shared.domain.User; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.UploadIsolateDataOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.UploadTypingDataOutput; +import org.phyloviz.pwp.http.models.isolate_data.UploadIsolateDataOutputModel; +import org.phyloviz.pwp.http.models.typing_data.UploadTypingDataOutputModel; +import org.phyloviz.pwp.service.FileTransferService; +import org.phyloviz.pwp.domain.User; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UploadIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UploadTypingDataOutput; import org.springframework.http.MediaType; import org.springframework.http.ResponseEntity; -import org.springframework.web.bind.annotation.GetMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.PostMapping; -import org.springframework.web.bind.annotation.RequestPart; -import org.springframework.web.bind.annotation.RestController; +import org.springframework.web.bind.annotation.*; import org.springframework.web.multipart.MultipartFile; import org.springframework.web.servlet.support.ServletUriComponentsBuilder; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/controllers/VisualizationController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/VisualizationController.java similarity index 80% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/controllers/VisualizationController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/VisualizationController.java index 3b463a0a..cdd9bfb6 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/controllers/VisualizationController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/VisualizationController.java @@ -1,26 +1,21 @@ -package org.phyloviz.pwp.visualization.http.controllers; +package org.phyloviz.pwp.http.controllers; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.domain.User; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewOutput; -import org.phyloviz.pwp.visualization.http.models.get_tree_view.GetTreeViewOutputModel; -import org.phyloviz.pwp.visualization.http.models.isolate_data.get_isolate_data_rows.GetIsolateDataRowsOutputModel; -import org.phyloviz.pwp.visualization.http.models.isolate_data.get_isolate_data_schema.GetIsolateDataKeysOutputModel; -import org.phyloviz.pwp.visualization.http.models.save_tree_view.SaveTreeViewInputModel; -import org.phyloviz.pwp.visualization.http.models.save_tree_view.SaveTreeViewOutputModel; -import org.phyloviz.pwp.visualization.http.models.typing_data.get_typing_data_profiles.GetTypingDataProfilesOutputModel; -import org.phyloviz.pwp.visualization.http.models.typing_data.get_typing_data_schema.GetTypingDataSchemaOutputModel; -import org.phyloviz.pwp.visualization.service.VisualizationService; -import org.springframework.web.bind.annotation.GetMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.PostMapping; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RequestParam; -import org.springframework.web.bind.annotation.RestController; +import org.phyloviz.pwp.http.models.get_tree_view.GetTreeViewOutputModel; +import org.phyloviz.pwp.http.models.isolate_data.get_isolate_data_rows.GetIsolateDataRowsOutputModel; +import org.phyloviz.pwp.http.models.isolate_data.get_isolate_data_schema.GetIsolateDataKeysOutputModel; +import org.phyloviz.pwp.http.models.save_tree_view.SaveTreeViewInputModel; +import org.phyloviz.pwp.http.models.save_tree_view.SaveTreeViewOutputModel; +import org.phyloviz.pwp.http.models.typing_data.get_typing_data_profiles.GetTypingDataProfilesOutputModel; +import org.phyloviz.pwp.http.models.typing_data.get_typing_data_schema.GetTypingDataSchemaOutputModel; +import org.phyloviz.pwp.service.VisualizationService; +import org.phyloviz.pwp.domain.User; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewOutput; +import org.springframework.web.bind.annotation.*; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/ProjectsController.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/ProjectsController.java index 408dad95..1783ead4 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/ProjectsController.java @@ -1,27 +1,21 @@ -package org.phyloviz.pwp.administration.http.controllers.projects; +package org.phyloviz.pwp.http.controllers.projects; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.projects.create_project.CreateProjectInputModel; -import org.phyloviz.pwp.administration.http.models.projects.create_project.CreateProjectOutputModel; -import org.phyloviz.pwp.administration.http.models.projects.delete_project.DeleteProjectOutputModel; -import org.phyloviz.pwp.administration.http.models.projects.get_project.GetProjectOutputModel; -import org.phyloviz.pwp.administration.http.models.projects.get_projects.GetProjectsOutputModel; -import org.phyloviz.pwp.administration.http.models.projects.update_project.UpdateProjectInputModel; -import org.phyloviz.pwp.administration.http.models.projects.update_project.UpdateProjectOutputModel; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; -import org.phyloviz.pwp.administration.service.dtos.project.UpdateProjectOutput; -import org.phyloviz.pwp.administration.service.project.ProjectService; -import org.phyloviz.pwp.shared.domain.User; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.http.models.projects.create_project.CreateProjectInputModel; +import org.phyloviz.pwp.http.models.projects.create_project.CreateProjectOutputModel; +import org.phyloviz.pwp.http.models.projects.delete_project.DeleteProjectOutputModel; +import org.phyloviz.pwp.http.models.projects.get_project.GetProjectOutputModel; +import org.phyloviz.pwp.http.models.projects.get_projects.GetProjectsOutputModel; +import org.phyloviz.pwp.http.models.projects.update_project.UpdateProjectInputModel; +import org.phyloviz.pwp.http.models.projects.update_project.UpdateProjectOutputModel; +import org.phyloviz.pwp.service.dtos.project.CreateProjectOutput; +import org.phyloviz.pwp.service.dtos.project.FullProjectInfo; +import org.phyloviz.pwp.service.dtos.project.UpdateProjectOutput; +import org.phyloviz.pwp.service.project.ProjectService; +import org.phyloviz.pwp.domain.User; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import org.springframework.http.ResponseEntity; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.GetMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.PostMapping; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.springframework.web.bind.annotation.*; import org.springframework.web.servlet.support.ServletUriComponentsBuilder; import java.net.URI; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/DatasetsController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/DatasetsController.java similarity index 75% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/DatasetsController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/DatasetsController.java index c593dcef..c338da56 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/DatasetsController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/DatasetsController.java @@ -1,29 +1,23 @@ -package org.phyloviz.pwp.administration.http.controllers.projects.datasets; +package org.phyloviz.pwp.http.controllers.projects.datasets; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.datasets.create_dataset.CreateDatasetInputModel; -import org.phyloviz.pwp.administration.http.models.datasets.create_dataset.CreateDatasetOutputModel; -import org.phyloviz.pwp.administration.http.models.datasets.delete_dataset.DeleteDatasetOutputModel; -import org.phyloviz.pwp.administration.http.models.datasets.get_dataset.GetDatasetOutputModel; -import org.phyloviz.pwp.administration.http.models.datasets.get_datasets.GetDatasetsOutputModel; -import org.phyloviz.pwp.administration.http.models.datasets.set_isolate_data_of_dataset.SetIsolateDataOfDatasetInputModel; -import org.phyloviz.pwp.administration.http.models.datasets.set_isolate_data_of_dataset.SetIsolateDataOfDatasetOutputModel; -import org.phyloviz.pwp.administration.http.models.datasets.update_dataset.UpdateDatasetInputModel; -import org.phyloviz.pwp.administration.http.models.datasets.update_dataset.UpdateDatasetOutputModel; -import org.phyloviz.pwp.administration.service.dtos.dataset.CreateDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; -import org.phyloviz.pwp.administration.service.dtos.dataset.SetIsolateDataOfDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.UpdateDatasetOutput; -import org.phyloviz.pwp.administration.service.project.dataset.DatasetService; -import org.phyloviz.pwp.shared.domain.User; +import org.phyloviz.pwp.http.models.datasets.create_dataset.CreateDatasetInputModel; +import org.phyloviz.pwp.http.models.datasets.create_dataset.CreateDatasetOutputModel; +import org.phyloviz.pwp.http.models.datasets.delete_dataset.DeleteDatasetOutputModel; +import org.phyloviz.pwp.http.models.datasets.get_dataset.GetDatasetOutputModel; +import org.phyloviz.pwp.http.models.datasets.get_datasets.GetDatasetsOutputModel; +import org.phyloviz.pwp.http.models.datasets.set_isolate_data_of_dataset.SetIsolateDataOfDatasetInputModel; +import org.phyloviz.pwp.http.models.datasets.set_isolate_data_of_dataset.SetIsolateDataOfDatasetOutputModel; +import org.phyloviz.pwp.http.models.datasets.update_dataset.UpdateDatasetInputModel; +import org.phyloviz.pwp.http.models.datasets.update_dataset.UpdateDatasetOutputModel; +import org.phyloviz.pwp.service.dtos.dataset.CreateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.service.dtos.dataset.SetIsolateDataOfDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.UpdateDatasetOutput; +import org.phyloviz.pwp.service.project.dataset.DatasetService; +import org.phyloviz.pwp.domain.User; import org.springframework.http.ResponseEntity; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.GetMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.PostMapping; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.springframework.web.bind.annotation.*; import org.springframework.web.servlet.support.ServletUriComponentsBuilder; import java.net.URI; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java similarity index 70% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java index b2ecec63..bed3e33f 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/distance_matrices/DistanceMatricesController.java @@ -1,17 +1,13 @@ -package org.phyloviz.pwp.administration.http.controllers.projects.datasets.distance_matrices; +package org.phyloviz.pwp.http.controllers.projects.datasets.distance_matrices; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.distance_matrices.delete_distance_matrix.DeleteDistanceMatrixOutputModel; -import org.phyloviz.pwp.administration.http.models.distance_matrices.update_distance_matrix.UpdateDistanceMatrixInputModel; -import org.phyloviz.pwp.administration.http.models.distance_matrices.update_distance_matrix.UpdateDistanceMatrixOutputModel; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; -import org.phyloviz.pwp.administration.service.project.dataset.distance_matrix.DistanceMatrixService; -import org.phyloviz.pwp.shared.domain.User; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.phyloviz.pwp.http.models.distance_matrices.delete_distance_matrix.DeleteDistanceMatrixOutputModel; +import org.phyloviz.pwp.http.models.distance_matrices.update_distance_matrix.UpdateDistanceMatrixInputModel; +import org.phyloviz.pwp.http.models.distance_matrices.update_distance_matrix.UpdateDistanceMatrixOutputModel; +import org.phyloviz.pwp.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; +import org.phyloviz.pwp.service.project.dataset.distance_matrix.DistanceMatrixService; +import org.phyloviz.pwp.domain.User; +import org.springframework.web.bind.annotation.*; /** * Controller that handles requests related to distance matrices. diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/tree_views/TreeViewsController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/tree_views/TreeViewsController.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/tree_views/TreeViewsController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/tree_views/TreeViewsController.java index 1dc4d94c..de6c652c 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/tree_views/TreeViewsController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/tree_views/TreeViewsController.java @@ -1,17 +1,13 @@ -package org.phyloviz.pwp.administration.http.controllers.projects.datasets.tree_views; +package org.phyloviz.pwp.http.controllers.projects.datasets.tree_views; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.tree_views.delete_tree_view.DeleteTreeViewOutputModel; -import org.phyloviz.pwp.administration.http.models.tree_views.update_tree_view.UpdateTreeViewInputModel; -import org.phyloviz.pwp.administration.http.models.tree_views.update_tree_view.UpdateTreeViewOutputModel; -import org.phyloviz.pwp.administration.service.dtos.tree_view.UpdateTreeViewOutput; -import org.phyloviz.pwp.administration.service.project.dataset.tree_view.TreeViewService; -import org.phyloviz.pwp.shared.domain.User; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.phyloviz.pwp.http.models.tree_views.delete_tree_view.DeleteTreeViewOutputModel; +import org.phyloviz.pwp.http.models.tree_views.update_tree_view.UpdateTreeViewInputModel; +import org.phyloviz.pwp.http.models.tree_views.update_tree_view.UpdateTreeViewOutputModel; +import org.phyloviz.pwp.service.dtos.tree_view.UpdateTreeViewOutput; +import org.phyloviz.pwp.service.project.dataset.tree_view.TreeViewService; +import org.phyloviz.pwp.domain.User; +import org.springframework.web.bind.annotation.*; /** * Controller that handles requests related to tree views. diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/trees/TreesController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/trees/TreesController.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/trees/TreesController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/trees/TreesController.java index a7909970..5cbb9aa7 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/datasets/trees/TreesController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/datasets/trees/TreesController.java @@ -1,17 +1,13 @@ -package org.phyloviz.pwp.administration.http.controllers.projects.datasets.trees; +package org.phyloviz.pwp.http.controllers.projects.datasets.trees; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.trees.delete_tree.DeleteTreeOutputModel; -import org.phyloviz.pwp.administration.http.models.trees.update_tree_view.UpdateTreeInputModel; -import org.phyloviz.pwp.administration.http.models.trees.update_tree_view.UpdateTreeOutputModel; -import org.phyloviz.pwp.administration.service.dtos.tree.UpdateTreeOutput; -import org.phyloviz.pwp.administration.service.project.dataset.tree.TreeService; -import org.phyloviz.pwp.shared.domain.User; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.phyloviz.pwp.http.models.trees.delete_tree.DeleteTreeOutputModel; +import org.phyloviz.pwp.http.models.trees.update_tree_view.UpdateTreeInputModel; +import org.phyloviz.pwp.http.models.trees.update_tree_view.UpdateTreeOutputModel; +import org.phyloviz.pwp.service.dtos.tree.UpdateTreeOutput; +import org.phyloviz.pwp.service.project.dataset.tree.TreeService; +import org.phyloviz.pwp.domain.User; +import org.springframework.web.bind.annotation.*; /** * Controller that handles requests related to trees. diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/files/FilesController.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/files/FilesController.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/files/FilesController.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/files/FilesController.java index a84be807..528fe725 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/controllers/projects/files/FilesController.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/controllers/projects/files/FilesController.java @@ -1,22 +1,18 @@ -package org.phyloviz.pwp.administration.http.controllers.projects.files; +package org.phyloviz.pwp.http.controllers.projects.files; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.http.models.files.isolate_data.delete_isolate_data.DeleteIsolateDataOutputModel; -import org.phyloviz.pwp.administration.http.models.files.isolate_data.update_isolate_data.UpdateIsolateDataInputModel; -import org.phyloviz.pwp.administration.http.models.files.isolate_data.update_isolate_data.UpdateIsolateDataOutputModel; -import org.phyloviz.pwp.administration.http.models.files.typing_data.delete_typing_data.DeleteTypingDataOutputModel; -import org.phyloviz.pwp.administration.http.models.files.typing_data.update_typing_data.UpdateTypingDataInputModel; -import org.phyloviz.pwp.administration.http.models.files.typing_data.update_typing_data.UpdateTypingDataOutputModel; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.UpdateIsolateDataOutput; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.UpdateTypingDataOutput; -import org.phyloviz.pwp.administration.service.project.file.IsolateDataService; -import org.phyloviz.pwp.administration.service.project.file.TypingDataService; -import org.phyloviz.pwp.shared.domain.User; -import org.springframework.web.bind.annotation.DeleteMapping; -import org.springframework.web.bind.annotation.PatchMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RestController; +import org.phyloviz.pwp.http.models.files.isolate_data.delete_isolate_data.DeleteIsolateDataOutputModel; +import org.phyloviz.pwp.http.models.files.isolate_data.update_isolate_data.UpdateIsolateDataInputModel; +import org.phyloviz.pwp.http.models.files.isolate_data.update_isolate_data.UpdateIsolateDataOutputModel; +import org.phyloviz.pwp.http.models.files.typing_data.delete_typing_data.DeleteTypingDataOutputModel; +import org.phyloviz.pwp.http.models.files.typing_data.update_typing_data.UpdateTypingDataInputModel; +import org.phyloviz.pwp.http.models.files.typing_data.update_typing_data.UpdateTypingDataOutputModel; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UpdateIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UpdateTypingDataOutput; +import org.phyloviz.pwp.service.project.file.IsolateDataService; +import org.phyloviz.pwp.service.project.file.TypingDataService; +import org.phyloviz.pwp.domain.User; +import org.springframework.web.bind.annotation.*; /** * Controller that handles requests related to files. diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowInputModel.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowInputModel.java index d576bd17..4ceb74b1 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.http.models.create_workflow; +package org.phyloviz.pwp.http.models.create_workflow; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowOutputModel.java similarity index 63% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowOutputModel.java index 4139fab2..ad2c1f0b 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/create_workflow/CreateWorkflowOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/create_workflow/CreateWorkflowOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.http.models.create_workflow; +package org.phyloviz.pwp.http.models.create_workflow; import lombok.Data; -import org.phyloviz.pwp.compute.service.dtos.create_workflow.CreateWorkflowOutput; +import org.phyloviz.pwp.service.dtos.create_workflow.CreateWorkflowOutput; @Data public class CreateWorkflowOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/DatasetModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/DatasetModel.java similarity index 74% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/DatasetModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/DatasetModel.java index f4cacdee..de07ad68 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/DatasetModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/DatasetModel.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.administration.http.models.datasets; +package org.phyloviz.pwp.http.models.datasets; import lombok.Data; -import org.phyloviz.pwp.administration.http.models.distance_matrices.DistanceMatrixOutputModel; -import org.phyloviz.pwp.administration.http.models.tree_views.TreeViewOutputModel; -import org.phyloviz.pwp.administration.http.models.trees.TreeOutputModel; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.http.models.distance_matrices.DistanceMatrixOutputModel; +import org.phyloviz.pwp.http.models.tree_views.TreeViewOutputModel; +import org.phyloviz.pwp.http.models.trees.TreeOutputModel; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetInputModel.java similarity index 74% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetInputModel.java index 72eabffd..c999b01a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.datasets.create_dataset; +package org.phyloviz.pwp.http.models.datasets.create_dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetOutputModel.java similarity index 68% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetOutputModel.java index facfb555..bbb76d76 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/create_dataset/CreateDatasetOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/create_dataset/CreateDatasetOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.datasets.create_dataset; +package org.phyloviz.pwp.http.models.datasets.create_dataset; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.dataset.CreateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.CreateDatasetOutput; @Data public class CreateDatasetOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java similarity index 70% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java index 6a2bacd8..f7602487 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/delete_dataset/DeleteDatasetOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.datasets.delete_dataset; +package org.phyloviz.pwp.http.models.datasets.delete_dataset; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_dataset/GetDatasetOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_dataset/GetDatasetOutputModel.java new file mode 100644 index 00000000..c761e188 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_dataset/GetDatasetOutputModel.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.http.models.datasets.get_dataset; + +import org.phyloviz.pwp.http.models.datasets.DatasetModel; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; + +public class GetDatasetOutputModel extends DatasetModel { + public GetDatasetOutputModel(FullDatasetInfo fullDatasetInfo) { + super(fullDatasetInfo); + } +} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_datasets/GetDatasetsOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_datasets/GetDatasetsOutputModel.java similarity index 56% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_datasets/GetDatasetsOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_datasets/GetDatasetsOutputModel.java index b0e86c90..85cdbd23 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_datasets/GetDatasetsOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/get_datasets/GetDatasetsOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.administration.http.models.datasets.get_datasets; +package org.phyloviz.pwp.http.models.datasets.get_datasets; import lombok.Data; -import org.phyloviz.pwp.administration.http.models.datasets.DatasetModel; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.http.models.datasets.DatasetModel; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java similarity index 62% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java index 1bb4d259..7a3e3de6 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.datasets.set_isolate_data_of_dataset; +package org.phyloviz.pwp.http.models.datasets.set_isolate_data_of_dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java index bbbc7dd2..d703aa87 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/set_isolate_data_of_dataset/SetIsolateDataOfDatasetOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.datasets.set_isolate_data_of_dataset; +package org.phyloviz.pwp.http.models.datasets.set_isolate_data_of_dataset; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.dataset.SetIsolateDataOfDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.SetIsolateDataOfDatasetOutput; @Data public class SetIsolateDataOfDatasetOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetInputModel.java similarity index 62% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetInputModel.java index a9c72bef..d51fd2e6 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.datasets.update_dataset; +package org.phyloviz.pwp.http.models.datasets.update_dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java similarity index 83% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java index b24270dd..f07fdeff 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/datasets/update_dataset/UpdateDatasetOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.datasets.update_dataset; +package org.phyloviz.pwp.http.models.datasets.update_dataset; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.dataset.UpdateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.UpdateDatasetOutput; @Data public class UpdateDatasetOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixOutputModel.java similarity index 74% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixOutputModel.java index e7a3b3b4..5d2cfee3 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices; +package org.phyloviz.pwp.http.models.distance_matrices; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixSourceFunctionInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixSourceFunctionInfo; @Data public class DistanceMatrixOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java similarity index 67% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java index 85e50934..26f39ec0 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceFunctionOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices; +package org.phyloviz.pwp.http.models.distance_matrices; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixSourceFunctionInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixSourceFunctionInfo; @Data public class DistanceMatrixSourceFunctionOutputModel implements DistanceMatrixSourceOutputModel { diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java new file mode 100644 index 00000000..ed68b7bc --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.http.models.distance_matrices; + +public interface DistanceMatrixSourceOutputModel { +} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java similarity index 70% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java index 2d81ef13..a913a3b2 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/delete_distance_matrix/DeleteDistanceMatrixOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices.delete_distance_matrix; +package org.phyloviz.pwp.http.models.distance_matrices.delete_distance_matrix; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java similarity index 51% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java index 2b055b43..1cbcdfa2 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices.update_distance_matrix; +package org.phyloviz.pwp.http.models.distance_matrices.update_distance_matrix; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java index 3aa094e4..03d71c47 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/distance_matrices/update_distance_matrix/UpdateDistanceMatrixOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices.update_distance_matrix; +package org.phyloviz.pwp.http.models.distance_matrices.update_distance_matrix; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; +import org.phyloviz.pwp.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; @Data public class UpdateDistanceMatrixOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/FilesModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/FilesModel.java similarity index 58% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/FilesModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/FilesModel.java index 0a9025a4..fe17ed1a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/FilesModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/FilesModel.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.http.models.files; +package org.phyloviz.pwp.http.models.files; import lombok.Data; -import org.phyloviz.pwp.administration.http.models.files.isolate_data.IsolateDataModel; -import org.phyloviz.pwp.administration.http.models.files.typing_data.TypingDataModel; -import org.phyloviz.pwp.administration.service.dtos.files.FilesInfo; +import org.phyloviz.pwp.http.models.files.isolate_data.IsolateDataModel; +import org.phyloviz.pwp.http.models.files.typing_data.TypingDataModel; +import org.phyloviz.pwp.service.dtos.files.FilesInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/IsolateDataModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/IsolateDataModel.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/IsolateDataModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/IsolateDataModel.java index dd66ee40..45fb36d6 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/IsolateDataModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/IsolateDataModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.files.isolate_data; +package org.phyloviz.pwp.http.models.files.isolate_data; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.IsolateDataInfo; +import org.phyloviz.pwp.service.dtos.files.isolate_data.IsolateDataInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java similarity index 67% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java index 2100459f..f76db29b 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/delete_isolate_data/DeleteIsolateDataOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.files.isolate_data.delete_isolate_data; +package org.phyloviz.pwp.http.models.files.isolate_data.delete_isolate_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java similarity index 51% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java index 8a4ff145..9580f76c 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.files.isolate_data.update_isolate_data; +package org.phyloviz.pwp.http.models.files.isolate_data.update_isolate_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java index 61a70ef1..d6540ec8 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/isolate_data/update_isolate_data/UpdateIsolateDataOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.files.isolate_data.update_isolate_data; +package org.phyloviz.pwp.http.models.files.isolate_data.update_isolate_data; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.UpdateIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UpdateIsolateDataOutput; @Data public class UpdateIsolateDataOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/TypingDataModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/TypingDataModel.java similarity index 65% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/TypingDataModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/TypingDataModel.java index 6ed9f12f..612f1cc8 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/TypingDataModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/TypingDataModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.files.typing_data; +package org.phyloviz.pwp.http.models.files.typing_data; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.TypingDataInfo; +import org.phyloviz.pwp.service.dtos.files.typing_data.TypingDataInfo; @Data public class TypingDataModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java similarity index 67% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java index a5bd90b2..153f1220 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/delete_typing_data/DeleteTypingDataOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.files.typing_data.delete_typing_data; +package org.phyloviz.pwp.http.models.files.typing_data.delete_typing_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java similarity index 51% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java index 1ccce795..61b9285d 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.files.typing_data.update_typing_data; +package org.phyloviz.pwp.http.models.files.typing_data.update_typing_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java index 8739c5f7..f79538f4 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/files/typing_data/update_typing_data/UpdateTypingDataOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.files.typing_data.update_typing_data; +package org.phyloviz.pwp.http.models.files.typing_data.update_typing_data; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.UpdateTypingDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UpdateTypingDataOutput; @Data public class UpdateTypingDataOutputModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/EdgeModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/EdgeModel.java similarity index 68% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/EdgeModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/EdgeModel.java index 9ccf3983..299d99b2 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/EdgeModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/EdgeModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.visualization.http.models.get_tree_view; +package org.phyloviz.pwp.http.models.get_tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Edge; +import org.phyloviz.pwp.service.dtos.tree_view.Edge; @Data public class EdgeModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/GetTreeViewOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/GetTreeViewOutputModel.java similarity index 80% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/GetTreeViewOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/GetTreeViewOutputModel.java index 87e47962..c621c25d 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/GetTreeViewOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/GetTreeViewOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.get_tree_view; +package org.phyloviz.pwp.http.models.get_tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.visualization.http.models.save_tree_view.TransformationsModel; +import org.phyloviz.pwp.http.models.save_tree_view.TransformationsModel; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/NodeModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/NodeModel.java similarity index 80% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/NodeModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/NodeModel.java index 567a9e06..55e18ce2 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/get_tree_view/NodeModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_tree_view/NodeModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.get_tree_view; +package org.phyloviz.pwp.http.models.get_tree_view; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Node; +import org.phyloviz.pwp.service.dtos.tree_view.Node; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow/GetWorkflowOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow/GetWorkflowOutputModel.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow/GetWorkflowOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow/GetWorkflowOutputModel.java index af20cab5..5a87e87e 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow/GetWorkflowOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow/GetWorkflowOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.http.models.get_workflow; +package org.phyloviz.pwp.http.models.get_workflow; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowOutput; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowOutput; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java similarity index 76% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java index 3f7b679e..3a963d2e 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflow_status/GetWorkflowStatusOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.http.models.get_workflow_status; +package org.phyloviz.pwp.http.models.get_workflow_status; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowStatusOutput; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowStatusOutput; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflows/GetWorkflowsOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflows/GetWorkflowsOutputModel.java similarity index 60% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflows/GetWorkflowsOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflows/GetWorkflowsOutputModel.java index 04b9d672..9ab8c118 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/models/get_workflows/GetWorkflowsOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/get_workflows/GetWorkflowsOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.http.models.get_workflows; +package org.phyloviz.pwp.http.models.get_workflows; import lombok.Data; -import org.phyloviz.pwp.compute.http.models.get_workflow_status.GetWorkflowStatusOutputModel; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowStatusOutput; +import org.phyloviz.pwp.http.models.get_workflow_status.GetWorkflowStatusOutputModel; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowStatusOutput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/IsolateDataRowModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/IsolateDataRowModel.java similarity index 74% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/IsolateDataRowModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/IsolateDataRowModel.java index 8001aaa2..204c4d96 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/IsolateDataRowModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/IsolateDataRowModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.visualization.http.models.isolate_data; +package org.phyloviz.pwp.http.models.isolate_data; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.IsolateDataRow; +import org.phyloviz.pwp.service.dtos.files.isolate_data.IsolateDataRow; import java.util.Map; diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/isolate_data/UploadIsolateDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/UploadIsolateDataOutputModel.java similarity index 70% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/isolate_data/UploadIsolateDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/UploadIsolateDataOutputModel.java index 8b31eb79..562e41ff 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/isolate_data/UploadIsolateDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/UploadIsolateDataOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.file_transfer.http.models.isolate_data; +package org.phyloviz.pwp.http.models.isolate_data; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.UploadIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UploadIsolateDataOutput; @Data public class UploadIsolateDataOutputModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java similarity index 63% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java index d21d02e1..1696d49c 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_rows/GetIsolateDataRowsOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.isolate_data.get_isolate_data_rows; +package org.phyloviz.pwp.http.models.isolate_data.get_isolate_data_rows; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; -import org.phyloviz.pwp.visualization.http.models.isolate_data.IsolateDataRowModel; +import org.phyloviz.pwp.http.models.isolate_data.IsolateDataRowModel; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java similarity index 68% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java index 9aebf598..f39b58c0 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/isolate_data/get_isolate_data_schema/GetIsolateDataKeysOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.visualization.http.models.isolate_data.get_isolate_data_schema; +package org.phyloviz.pwp.http.models.isolate_data.get_isolate_data_schema; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/ProjectModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/ProjectModel.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/ProjectModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/ProjectModel.java index a5475dc6..2f27f0ac 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/ProjectModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/ProjectModel.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.http.models.projects; +package org.phyloviz.pwp.http.models.projects; import lombok.Data; -import org.phyloviz.pwp.administration.http.models.datasets.DatasetModel; -import org.phyloviz.pwp.administration.http.models.files.FilesModel; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; +import org.phyloviz.pwp.http.models.datasets.DatasetModel; +import org.phyloviz.pwp.http.models.files.FilesModel; +import org.phyloviz.pwp.service.dtos.project.FullProjectInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectInputModel.java similarity index 62% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectInputModel.java index 3db16488..2066de50 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.projects.create_project; +package org.phyloviz.pwp.http.models.projects.create_project; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectOutputModel.java similarity index 60% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectOutputModel.java index d8ff03c1..bcb57a0f 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/create_project/CreateProjectOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/create_project/CreateProjectOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.projects.create_project; +package org.phyloviz.pwp.http.models.projects.create_project; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; +import org.phyloviz.pwp.service.dtos.project.CreateProjectOutput; @Data public class CreateProjectOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/delete_project/DeleteProjectOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/delete_project/DeleteProjectOutputModel.java similarity index 66% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/delete_project/DeleteProjectOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/delete_project/DeleteProjectOutputModel.java index ec58fbb2..ecb892da 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/delete_project/DeleteProjectOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/delete_project/DeleteProjectOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.projects.delete_project; +package org.phyloviz.pwp.http.models.projects.delete_project; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_project/GetProjectOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_project/GetProjectOutputModel.java new file mode 100644 index 00000000..99b78139 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_project/GetProjectOutputModel.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.http.models.projects.get_project; + +import org.phyloviz.pwp.http.models.projects.ProjectModel; +import org.phyloviz.pwp.service.dtos.project.FullProjectInfo; + +public class GetProjectOutputModel extends ProjectModel { + public GetProjectOutputModel(FullProjectInfo fullProjectInfo) { + super(fullProjectInfo); + } +} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsOutputModel.java similarity index 66% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsOutputModel.java index b89e9450..9d68871e 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.projects.get_projects; +package org.phyloviz.pwp.http.models.projects.get_projects; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsProjectModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsProjectModel.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsProjectModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsProjectModel.java index 51428d6d..48b0c8f2 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_projects/GetProjectsProjectModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/get_projects/GetProjectsProjectModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.projects.get_projects; +package org.phyloviz.pwp.http.models.projects.get_projects; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; @Data public class GetProjectsProjectModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectInputModel.java similarity index 62% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectInputModel.java index c5a4718a..3908ab79 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.projects.update_project; +package org.phyloviz.pwp.http.models.projects.update_project; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectOutputModel.java similarity index 83% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectOutputModel.java index 2006ea74..edeab13a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/update_project/UpdateProjectOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/projects/update_project/UpdateProjectOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.projects.update_project; +package org.phyloviz.pwp.http.models.projects.update_project; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.project.UpdateProjectOutput; +import org.phyloviz.pwp.service.dtos.project.UpdateProjectOutput; @Data public class UpdateProjectOutputModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewInputModel.java similarity index 64% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewInputModel.java index 8d15dbc0..824403d8 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewInputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.save_tree_view; +package org.phyloviz.pwp.http.models.save_tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewInput; -import org.phyloviz.pwp.visualization.http.models.get_tree_view.NodeModel; +import org.phyloviz.pwp.http.models.get_tree_view.NodeModel; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewInput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewOutputModel.java similarity index 77% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewOutputModel.java index d2831e01..9c36929e 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/SaveTreeViewOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/SaveTreeViewOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.visualization.http.models.save_tree_view; +package org.phyloviz.pwp.http.models.save_tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewOutput; /** * Output model for the save tree view endpoint. diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/TransformationsModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/TransformationsModel.java similarity index 92% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/TransformationsModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/TransformationsModel.java index 22f87364..be2053cf 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/save_tree_view/TransformationsModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/save_tree_view/TransformationsModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.save_tree_view; +package org.phyloviz.pwp.http.models.save_tree_view; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Transformations; +import org.phyloviz.pwp.service.dtos.tree_view.Transformations; /** * Transformations model for the Tree View. diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewOutputModel.java similarity index 77% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewOutputModel.java index d9d752a9..d859e5f7 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.tree_views; +package org.phyloviz.pwp.http.models.tree_views; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewInfo; +import org.phyloviz.pwp.service.dtos.tree_view.TreeViewInfo; @Data public class TreeViewOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewSourceOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewSourceOutputModel.java similarity index 61% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewSourceOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewSourceOutputModel.java index ee016743..de18543e 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/TreeViewSourceOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/TreeViewSourceOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.tree_views; +package org.phyloviz.pwp.http.models.tree_views; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewSourceInfo; +import org.phyloviz.pwp.service.dtos.tree_view.TreeViewSourceInfo; @Data public class TreeViewSourceOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java index 5a30f54b..2fd571d4 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/delete_tree_view/DeleteTreeViewOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.tree_views.delete_tree_view; +package org.phyloviz.pwp.http.models.tree_views.delete_tree_view; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java similarity index 53% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java index b8cb5a26..8c256b09 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.tree_views.update_tree_view; +package org.phyloviz.pwp.http.models.tree_views.update_tree_view; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java similarity index 73% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java index 59889908..ef8a18d6 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/tree_views/update_tree_view/UpdateTreeViewOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.tree_views.update_tree_view; +package org.phyloviz.pwp.http.models.tree_views.update_tree_view; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree_view.UpdateTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.UpdateTreeViewOutput; @Data public class UpdateTreeViewOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeOutputModel.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeOutputModel.java index be0c8911..0c51274c 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeOutputModel.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.administration.http.models.trees; +package org.phyloviz.pwp.http.models.trees; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceAlgorithmDistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceAlgorithmTypingDataInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceFileInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceAlgorithmDistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceAlgorithmTypingDataInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceFileInfo; @Data public class TreeOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java similarity index 79% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java index fe0bb4c5..7e73f793 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmDistanceMatrixOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.trees; +package org.phyloviz.pwp.http.models.trees; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceAlgorithmDistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceAlgorithmDistanceMatrixInfo; @Data public class TreeSourceAlgorithmDistanceMatrixOutputModel implements TreeSourceOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java similarity index 79% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java index 983e4cbc..b1160394 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceAlgorithmTypingDataOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.trees; +package org.phyloviz.pwp.http.models.trees; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceAlgorithmTypingDataInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceAlgorithmTypingDataInfo; @Data public class TreeSourceAlgorithmTypingDataOutputModel implements TreeSourceOutputModel { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceFileOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceFileOutputModel.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceFileOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceFileOutputModel.java index e6744387..b520418d 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceFileOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceFileOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.trees; +package org.phyloviz.pwp.http.models.trees; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeSourceFileInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeSourceFileInfo; @Data public class TreeSourceFileOutputModel implements TreeSourceOutputModel { diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceOutputModel.java new file mode 100644 index 00000000..85ee2169 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/TreeSourceOutputModel.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.http.models.trees; + +public interface TreeSourceOutputModel { +} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/delete_tree/DeleteTreeOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/delete_tree/DeleteTreeOutputModel.java similarity index 74% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/delete_tree/DeleteTreeOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/delete_tree/DeleteTreeOutputModel.java index 197883f0..75f04bc7 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/delete_tree/DeleteTreeOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/delete_tree/DeleteTreeOutputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.trees.delete_tree; +package org.phyloviz.pwp.http.models.trees.delete_tree; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeInputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeInputModel.java similarity index 54% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeInputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeInputModel.java index 321f69ec..8d4ffe92 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeInputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeInputModel.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.http.models.trees.update_tree_view; +package org.phyloviz.pwp.http.models.trees.update_tree_view; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeOutputModel.java similarity index 73% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeOutputModel.java index 4de420fd..84db3043 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/update_tree_view/UpdateTreeOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/trees/update_tree_view/UpdateTreeOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.http.models.trees.update_tree_view; +package org.phyloviz.pwp.http.models.trees.update_tree_view; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.tree.UpdateTreeOutput; +import org.phyloviz.pwp.service.dtos.tree.UpdateTreeOutput; @Data public class UpdateTreeOutputModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/TypingDataProfileModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/TypingDataProfileModel.java similarity index 72% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/TypingDataProfileModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/TypingDataProfileModel.java index be518b4b..f793e06d 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/TypingDataProfileModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/TypingDataProfileModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.visualization.http.models.typing_data; +package org.phyloviz.pwp.http.models.typing_data; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.TypingDataProfile; +import org.phyloviz.pwp.service.dtos.files.typing_data.TypingDataProfile; import java.util.List; diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/typing_data/UploadTypingDataOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/UploadTypingDataOutputModel.java similarity index 70% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/typing_data/UploadTypingDataOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/UploadTypingDataOutputModel.java index f947ce4a..485204cf 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/models/typing_data/UploadTypingDataOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/UploadTypingDataOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.file_transfer.http.models.typing_data; +package org.phyloviz.pwp.http.models.typing_data; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.UploadTypingDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UploadTypingDataOutput; @Data public class UploadTypingDataOutputModel { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java similarity index 67% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java index 889668b6..b8156591 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_profiles/GetTypingDataProfilesOutputModel.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.visualization.http.models.typing_data.get_typing_data_profiles; +package org.phyloviz.pwp.http.models.typing_data.get_typing_data_profiles; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.visualization.http.models.typing_data.TypingDataProfileModel; +import org.phyloviz.pwp.http.models.typing_data.TypingDataProfileModel; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java similarity index 72% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java index 50138588..a702dd12 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/models/typing_data/get_typing_data_schema/GetTypingDataSchemaOutputModel.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.visualization.http.models.typing_data.get_typing_data_schema; +package org.phyloviz.pwp.http.models.typing_data.get_typing_data_schema; import lombok.Data; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/pipeline/AdministrationExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/AdministrationExceptionHandler.java similarity index 75% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/pipeline/AdministrationExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/AdministrationExceptionHandler.java index b8b4e355..401cdf98 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/pipeline/AdministrationExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/AdministrationExceptionHandler.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.administration.http.pipeline; +package org.phyloviz.pwp.http.pipeline; -import org.phyloviz.pwp.administration.service.exceptions.DeniedFileDeletionException; -import org.phyloviz.pwp.administration.service.exceptions.DeniedResourceDeletionException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataDoesNotExistException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataDoesNotExistException; +import org.phyloviz.pwp.service.exceptions.DeniedFileDeletionException; +import org.phyloviz.pwp.service.exceptions.DeniedResourceDeletionException; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.IsolateDataDoesNotExistException; +import org.phyloviz.pwp.service.exceptions.TypingDataDoesNotExistException; import org.springframework.web.bind.annotation.ExceptionHandler; import org.springframework.web.bind.annotation.RestControllerAdvice; import org.zalando.problem.Problem; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/pipeline/ComputeExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/ComputeExceptionHandler.java similarity index 65% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/pipeline/ComputeExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/ComputeExceptionHandler.java index a15ebc48..65d41fc4 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/pipeline/ComputeExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/ComputeExceptionHandler.java @@ -1,11 +1,6 @@ -package org.phyloviz.pwp.compute.http.pipeline; +package org.phyloviz.pwp.http.pipeline; -import org.phyloviz.pwp.compute.service.exceptions.DatasetDoesNotExistException; -import org.phyloviz.pwp.compute.service.exceptions.DistanceMatrixDoesNotExistException; -import org.phyloviz.pwp.compute.service.exceptions.InvalidWorkflowException; -import org.phyloviz.pwp.compute.service.exceptions.TreeDoesNotExistException; -import org.phyloviz.pwp.compute.service.exceptions.TreeViewDoesNotExistException; -import org.phyloviz.pwp.compute.service.exceptions.WorkflowInstanceNotFoundException; +import org.phyloviz.pwp.service.exceptions.*; import org.springframework.web.bind.annotation.ExceptionHandler; import org.springframework.web.bind.annotation.RestControllerAdvice; import org.zalando.problem.Problem; diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/pipeline/FileTransferExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/FileTransferExceptionHandler.java similarity index 95% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/pipeline/FileTransferExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/FileTransferExceptionHandler.java index ade1228c..bd8bf39a 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/http/pipeline/FileTransferExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/FileTransferExceptionHandler.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.file_transfer.http.pipeline; +package org.phyloviz.pwp.http.pipeline; import org.springframework.beans.factory.annotation.Value; import org.springframework.web.bind.annotation.ExceptionHandler; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/UserArgumentResolver.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/UserArgumentResolver.java similarity index 92% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/UserArgumentResolver.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/UserArgumentResolver.java index c244c28d..2ffafaf0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/UserArgumentResolver.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/UserArgumentResolver.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.http.pipeline; +package org.phyloviz.pwp.http.pipeline; -import org.phyloviz.pwp.shared.domain.User; +import org.phyloviz.pwp.domain.User; import org.springframework.core.MethodParameter; import org.springframework.security.oauth2.server.resource.authentication.BearerTokenAuthentication; import org.springframework.stereotype.Component; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/pipeline/VisualizationExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/VisualizationExceptionHandler.java similarity index 85% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/pipeline/VisualizationExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/VisualizationExceptionHandler.java index 7ff089c9..1c518895 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/http/pipeline/VisualizationExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/VisualizationExceptionHandler.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.visualization.http.pipeline; +package org.phyloviz.pwp.http.pipeline; -import org.phyloviz.pwp.visualization.service.exceptions.IndexingNeededException; +import org.phyloviz.pwp.service.exceptions.IndexingNeededException; import org.springframework.web.bind.annotation.ExceptionHandler; import org.springframework.web.bind.annotation.RestControllerAdvice; import org.zalando.problem.Problem; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java similarity index 97% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java index d2f5b080..7f28a525 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/ProblemJsonResponseBodyAdvice.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.http.pipeline.advice; +package org.phyloviz.pwp.http.pipeline.advice; import org.springframework.core.MethodParameter; import org.springframework.http.HttpStatus; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java index d332386a..ca1b2f88 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/AuthenticationExceptionHandler.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.http.pipeline.advice.exception.handlers; +package org.phyloviz.pwp.http.pipeline.advice.exception.handlers; import org.springframework.security.core.AuthenticationException; import org.springframework.web.bind.annotation.ExceptionHandler; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java similarity index 84% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java index 4220d207..20bedfb0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/http/pipeline/advice/exception/handlers/SharedExceptionHandler.java @@ -1,19 +1,10 @@ -package org.phyloviz.pwp.shared.http.pipeline.advice.exception.handlers; +package org.phyloviz.pwp.http.pipeline.advice.exception.handlers; import com.fasterxml.jackson.core.JsonParseException; import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.exc.IgnoredPropertyException; import com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.DistanceMatrixNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.FileCorruptedException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeViewNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.UnauthorizedException; +import org.phyloviz.pwp.service.exceptions.*; import org.springframework.http.converter.HttpMessageNotReadableException; import org.springframework.web.bind.annotation.ExceptionHandler; import org.springframework.web.bind.annotation.RestControllerAdvice; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepository.java similarity index 81% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepository.java index 222f0b11..a4f177d2 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepository.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data; +package org.phyloviz.pwp.repository.data; import org.springframework.web.multipart.MultipartFile; @@ -28,11 +28,4 @@ public interface S3FileRepository { * @return true if the file was deleted successfully, false otherwise */ boolean delete(String url); - - /** - * Get location of the repository. - * - * @return location of the repository - */ - String getLocation(); } diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepositoryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepositoryImpl.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepositoryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepositoryImpl.java index 47633495..a791bc31 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/S3FileRepositoryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/S3FileRepositoryImpl.java @@ -1,12 +1,11 @@ -package org.phyloviz.pwp.shared.repository.data; +package org.phyloviz.pwp.repository.data; -import org.phyloviz.pwp.shared.service.exceptions.FileCorruptedException; -import org.phyloviz.pwp.shared.service.exceptions.MultipartFileReadException; +import org.phyloviz.pwp.service.exceptions.FileCorruptedException; +import org.phyloviz.pwp.service.exceptions.MultipartFileReadException; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Repository; import org.springframework.web.multipart.MultipartFile; import software.amazon.awssdk.auth.credentials.AwsBasicCredentials; -import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider; import software.amazon.awssdk.core.BytesWrapper; import software.amazon.awssdk.core.async.AsyncRequestBody; import software.amazon.awssdk.core.async.AsyncResponseTransformer; @@ -28,36 +27,34 @@ @Repository public class S3FileRepositoryImpl implements S3FileRepository { - public static final Region REGION = Region.of("custom"); private final String bucketName; - private final String objectStorageEndpoint; private final S3AsyncClient s3Client; private final S3TransferManager transferManager; private final ExecutorService executorService = Executors.newCachedThreadPool(); public S3FileRepositoryImpl( @Value("${s3.endpoint}") - String objectStorageEndpoint, + String s3endpoint, @Value("${s3.access-key-id}") String accessKeyId, @Value("${s3.secret-access-key}") String secretAccessKey, @Value("${s3.bucket}") - String bucketName + String bucketName, + @Value("${s3.region}") + String region ) { - AwsBasicCredentials awsCredentials = AwsBasicCredentials.create(accessKeyId, secretAccessKey); - S3AsyncClient newS3Client = S3AsyncClient.builder() - .credentialsProvider(StaticCredentialsProvider.create(awsCredentials)) - .endpointOverride(URI.create(objectStorageEndpoint)) - .region(REGION) + .forcePathStyle(true) + .endpointOverride(URI.create(s3endpoint)) + .credentialsProvider(() -> AwsBasicCredentials.create(accessKeyId, secretAccessKey)) + .region(Region.of(region)) .build(); newS3Client.createBucket(r -> r.bucket(bucketName)); this.s3Client = newS3Client; this.bucketName = bucketName; - this.objectStorageEndpoint = objectStorageEndpoint; this.transferManager = S3TransferManager.builder().s3Client(newS3Client).build(); } @@ -81,15 +78,14 @@ public boolean upload(String url, MultipartFile multipartFile) { upload.completionFuture().join(); + // s3Client.listBuckets().join() -> lists all buckets, currently only one with name "phyloviz-web-platform" + return true; } @Override public String download(String url) { - if (!url.startsWith(getLocation())) - throw new IllegalArgumentException("URL does not start with the object storage endpoint"); - - String key = url.substring(getLocation().length()); + String key = url; /*s3Client.listObjectsV2(ListObjectsV2Request.builder().bucket(bucketName).build()) .thenAccept(response -> { @@ -131,21 +127,13 @@ public String download(String url) { @Override public boolean delete(String url) { - if (!url.startsWith(getLocation())) - throw new IllegalArgumentException("URL does not start with the object storage endpoint"); - DeleteObjectRequest deleteObjectRequest = DeleteObjectRequest.builder() .bucket(bucketName) - .key(url.substring(getLocation().length())) + .key(url) .build(); s3Client.deleteObject(deleteObjectRequest); // TODO throw exception if not successful return true; } - - @Override - public String getLocation() { - return objectStorageEndpoint + "/" + bucketName.substring(0, bucketName.length() - 1); - } } diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java new file mode 100644 index 00000000..91fee1a5 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java @@ -0,0 +1,5 @@ +package org.phyloviz.pwp.repository.data.distance_matrix; + +public enum DistanceMatrixDataRepositoryId { + S3 +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java similarity index 57% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java index 296b143b..a54ca8dc 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixDataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.data.distance_matrix.repository; +package org.phyloviz.pwp.repository.data.distance_matrix.repository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; public interface DistanceMatrixDataRepository { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java similarity index 69% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java index 28cacd99..ef627e46 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/DistanceMatrixS3DataRepository.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.distance_matrix.repository; +package org.phyloviz.pwp.repository.data.distance_matrix.repository; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.S3FileRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.S3FileRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; import org.springframework.stereotype.Repository; @Repository diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java new file mode 100644 index 00000000..66929fb5 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data; + +public interface DistanceMatrixDataRepositorySpecificData { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java similarity index 70% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java index 6bf06152..43fa77ce 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/distance_matrix/repository/specific_data/DistanceMatrixS3DataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data; +package org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/IsolateDataDataRepositoryId.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/IsolateDataDataRepositoryId.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/IsolateDataDataRepositoryId.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/IsolateDataDataRepositoryId.java index f03a381f..bc8fa7dd 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/IsolateDataDataRepositoryId.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/IsolateDataDataRepositoryId.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data; +package org.phyloviz.pwp.repository.data.isolate_data; public enum IsolateDataDataRepositoryId { S3, diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataDataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataDataRepository.java similarity index 69% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataDataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataDataRepository.java index 89c3d7da..c91e3977 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataDataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataDataRepository.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data.repository; +package org.phyloviz.pwp.repository.data.isolate_data.repository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; import org.springframework.web.multipart.MultipartFile; public interface IsolateDataDataRepository { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java index 3a1a521c..a288f509 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/IsolateDataS3DataRepository.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data.repository; +package org.phyloviz.pwp.repository.data.isolate_data.repository; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.S3FileRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; +import org.phyloviz.pwp.repository.data.S3FileRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; import org.springframework.stereotype.Repository; import org.springframework.web.multipart.MultipartFile; @@ -20,7 +20,7 @@ public IsolateDataDataRepositorySpecificData uploadIsolateData(String projectId, s3FileRepository.upload(url, multipartFile); - return new IsolateDataS3DataRepositorySpecificData(s3FileRepository.getLocation() + "/" + url, multipartFile.getOriginalFilename()); + return new IsolateDataS3DataRepositorySpecificData(url, multipartFile.getOriginalFilename()); } @Override diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java new file mode 100644 index 00000000..8b7b53c7 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data; + +public interface IsolateDataDataRepositorySpecificData { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java index f076b26a..e4a89647 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataPhyloDBDataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data; +package org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java index 56b6c081..3646d4f9 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/isolate_data/repository/specific_data/IsolateDataS3DataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data; +package org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/AbstractDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/AbstractDataRepositoryRegistry.java similarity index 97% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/AbstractDataRepositoryRegistry.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/AbstractDataRepositoryRegistry.java index 1d9ce5d7..e2e58d4b 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/AbstractDataRepositoryRegistry.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/AbstractDataRepositoryRegistry.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.registry; +package org.phyloviz.pwp.repository.data.registry; import jakarta.annotation.PostConstruct; import org.springframework.context.ApplicationContext; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryFactory.java similarity index 89% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryFactory.java index e21fe918..d2a8f967 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryFactory.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.registry; +package org.phyloviz.pwp.repository.data.registry; import lombok.RequiredArgsConstructor; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryRegistry.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryRegistry.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryRegistry.java index b888822f..cd54ef29 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/DataRepositoryRegistry.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/DataRepositoryRegistry.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.registry; +package org.phyloviz.pwp.repository.data.registry; public interface DataRepositoryRegistry, R, D> { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java similarity index 50% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java index 0f04af8c..847bfdb1 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryFactory.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.distance_matrix; +package org.phyloviz.pwp.repository.data.registry.distance_matrix; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryFactory; +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryFactory; import org.springframework.stereotype.Component; @Component diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java new file mode 100644 index 00000000..09c1a1b4 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.repository.data.registry.distance_matrix; + +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryRegistry; + +public interface DistanceMatrixDataRepositoryRegistry extends + DataRepositoryRegistry { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java similarity index 62% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java index 2cf1fb61..76764a47 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistryImpl.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.distance_matrix; +package org.phyloviz.pwp.repository.data.registry.distance_matrix; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.AbstractDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.AbstractDataRepositoryRegistry; import org.springframework.context.ApplicationContext; import java.util.Map; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java similarity index 50% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java index 960eac3f..a8049063 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryFactory.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.isolate_data; +package org.phyloviz.pwp.repository.data.registry.isolate_data; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryFactory; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataDataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryFactory; import org.springframework.stereotype.Component; @Component diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java new file mode 100644 index 00000000..51e6ac2e --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.repository.data.registry.isolate_data; + +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataDataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryRegistry; + +public interface IsolateDataDataRepositoryRegistry extends + DataRepositoryRegistry { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java similarity index 62% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java index f11e3aab..44d5e459 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistryImpl.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.isolate_data; +package org.phyloviz.pwp.repository.data.registry.isolate_data; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.AbstractDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataDataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.AbstractDataRepositoryRegistry; import org.springframework.context.ApplicationContext; import java.util.Map; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryFactory.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryFactory.java index 6a4251d5..359c92be 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryFactory.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree; +package org.phyloviz.pwp.repository.data.registry.tree; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryFactory; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.TreeDataRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; import org.springframework.stereotype.Component; @Component diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistry.java new file mode 100644 index 00000000..62c0cb73 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistry.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.repository.data.registry.tree; + +import org.phyloviz.pwp.repository.data.registry.DataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.TreeDataRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; + +public interface TreeDataRepositoryRegistry extends + DataRepositoryRegistry { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java similarity index 62% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java index 22e1637b..5017e56f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree/TreeDataRepositoryRegistryImpl.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree; +package org.phyloviz.pwp.repository.data.registry.tree; -import org.phyloviz.pwp.shared.repository.data.registry.AbstractDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.AbstractDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.TreeDataRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; import org.springframework.context.ApplicationContext; import java.util.Map; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java index 43d8c29e..60b564a8 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryFactory.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree_view; +package org.phyloviz.pwp.repository.data.registry.tree_view; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryFactory; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.TreeViewDataRepository; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; import org.springframework.stereotype.Component; @Component diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java new file mode 100644 index 00000000..503a4dd1 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.repository.data.registry.tree_view; + +import org.phyloviz.pwp.repository.data.registry.DataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.TreeViewDataRepository; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; + +public interface TreeViewDataRepositoryRegistry extends + DataRepositoryRegistry { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java similarity index 62% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java index 632498d8..5ff237ad 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/tree_view/TreeViewDataRepositoryRegistryImpl.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree_view; +package org.phyloviz.pwp.repository.data.registry.tree_view; -import org.phyloviz.pwp.shared.repository.data.registry.AbstractDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.AbstractDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.TreeViewDataRepository; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; import org.springframework.context.ApplicationContext; import java.util.Map; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java index c3260495..0cd671b4 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryFactory.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.typing_data; +package org.phyloviz.pwp.repository.data.registry.typing_data; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.DataRepositoryFactory; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataDataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; import org.springframework.stereotype.Component; @Component diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java new file mode 100644 index 00000000..0d3cad47 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java @@ -0,0 +1,10 @@ +package org.phyloviz.pwp.repository.data.registry.typing_data; + +import org.phyloviz.pwp.repository.data.registry.DataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataDataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; + +public interface TypingDataDataRepositoryRegistry extends + DataRepositoryRegistry { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java similarity index 62% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java index 7f1b6de5..81fa9030 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/registry/typing_data/TypingDataDataRepositoryRegistryImpl.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.registry.typing_data; +package org.phyloviz.pwp.repository.data.registry.typing_data; -import org.phyloviz.pwp.shared.repository.data.registry.AbstractDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.AbstractDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataDataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; import org.springframework.context.ApplicationContext; import java.util.Map; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/TreeDataRepositoryId.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/TreeDataRepositoryId.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/TreeDataRepositoryId.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/TreeDataRepositoryId.java index baf43251..448f57f7 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/TreeDataRepositoryId.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/TreeDataRepositoryId.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree; +package org.phyloviz.pwp.repository.data.tree; public enum TreeDataRepositoryId { PHYLODB, diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeDataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeDataRepository.java similarity index 54% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeDataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeDataRepository.java index d22d757b..a17f52b3 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeDataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeDataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.data.tree.repository; +package org.phyloviz.pwp.repository.data.tree.repository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; public interface TreeDataRepository { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeS3DataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeS3DataRepository.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeS3DataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeS3DataRepository.java index 8cea1ef7..37f61f81 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/TreeS3DataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/TreeS3DataRepository.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.tree.repository; +package org.phyloviz.pwp.repository.data.tree.repository; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.S3FileRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.S3FileRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; import org.springframework.stereotype.Repository; @Repository diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java new file mode 100644 index 00000000..c1806160 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.data.tree.repository.specific_data; + +public interface TreeDataRepositorySpecificData { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java index fdc93792..9a665a6c 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreePhyloDBDataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data; +package org.phyloviz.pwp.repository.data.tree.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java similarity index 71% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java index a3464943..cccd0c2e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree/repository/specific_data/TreeS3DataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data; +package org.phyloviz.pwp.repository.data.tree.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/TreeViewDataRepositoryId.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/TreeViewDataRepositoryId.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/TreeViewDataRepositoryId.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/TreeViewDataRepositoryId.java index e6d523b9..3ef54c6a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/TreeViewDataRepositoryId.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/TreeViewDataRepositoryId.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view; +package org.phyloviz.pwp.repository.data.tree_view; public enum TreeViewDataRepositoryId { PHYLODB, diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewDataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewDataRepository.java similarity index 54% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewDataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewDataRepository.java index 491b48d9..0521a6bf 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewDataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewDataRepository.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view.repository; +package org.phyloviz.pwp.repository.data.tree_view.repository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Node; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.Node; import java.util.List; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewS3DataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewS3DataRepository.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewS3DataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewS3DataRepository.java index c9826616..48ade0e3 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/TreeViewS3DataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/TreeViewS3DataRepository.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view.repository; +package org.phyloviz.pwp.repository.data.tree_view.repository; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Node; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.Node; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java new file mode 100644 index 00000000..7a793749 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.data.tree_view.repository.specific_data; + +public interface TreeViewDataRepositorySpecificData { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java similarity index 78% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java index 39b12028..f169a9b0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewPhyloDBDataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data; +package org.phyloviz.pwp.repository.data.tree_view.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java similarity index 71% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java index c5181aae..cac460ad 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/tree_view/repository/specific_data/TreeViewS3DataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data; +package org.phyloviz.pwp.repository.data.tree_view.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/TypingDataDataRepositoryId.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/TypingDataDataRepositoryId.java similarity index 51% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/TypingDataDataRepositoryId.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/TypingDataDataRepositoryId.java index c314cdf6..522065b4 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/TypingDataDataRepositoryId.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/TypingDataDataRepositoryId.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data; +package org.phyloviz.pwp.repository.data.typing_data; public enum TypingDataDataRepositoryId { S3, diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataDataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataDataRepository.java similarity index 67% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataDataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataDataRepository.java index d9fd0b21..84cc989e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataDataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataDataRepository.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data.repository; +package org.phyloviz.pwp.repository.data.typing_data.repository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; import org.springframework.web.multipart.MultipartFile; public interface TypingDataDataRepository { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataS3DataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataS3DataRepository.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataS3DataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataS3DataRepository.java index ce802019..4a269f61 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/TypingDataS3DataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/TypingDataS3DataRepository.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data.repository; +package org.phyloviz.pwp.repository.data.typing_data.repository; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.S3FileRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.repository.data.S3FileRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; import org.springframework.stereotype.Repository; import org.springframework.web.multipart.MultipartFile; @@ -21,7 +21,7 @@ public TypingDataDataRepositorySpecificData uploadTypingData(String projectId, S s3FileRepository.upload(url, multipartFile); - return new TypingDataS3DataRepositorySpecificData(s3FileRepository.getLocation() + "/" + url, multipartFile.getOriginalFilename()); + return new TypingDataS3DataRepositorySpecificData(url, multipartFile.getOriginalFilename()); } @Override diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java new file mode 100644 index 00000000..3b079b34 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.data.typing_data.repository.specific_data; + +public interface TypingDataDataRepositorySpecificData { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java index c65f51d6..0575dd41 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataPhyloDBDataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data; +package org.phyloviz.pwp.repository.data.typing_data.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java index efa254b4..6557ef9c 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/data/typing_data/repository/specific_data/TypingDataS3DataRepositorySpecificData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data; +package org.phyloviz.pwp.repository.data.typing_data.repository.specific_data; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/DocumentConversionException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/DocumentConversionException.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/DocumentConversionException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/DocumentConversionException.java index 68c21062..083c08dc 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/DocumentConversionException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/DocumentConversionException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata; +package org.phyloviz.pwp.repository.metadata; public class DocumentConversionException extends RuntimeException { public DocumentConversionException(String message) { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/DatasetRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/DatasetRepository.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/DatasetRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/DatasetRepository.java index 91a0adf5..2326c30e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/DatasetRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/DatasetRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.dataset; +package org.phyloviz.pwp.repository.metadata.dataset; -import org.phyloviz.pwp.shared.repository.metadata.dataset.documents.Dataset; +import org.phyloviz.pwp.repository.metadata.dataset.documents.Dataset; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/documents/Dataset.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/documents/Dataset.java similarity index 92% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/documents/Dataset.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/documents/Dataset.java index a56a04e9..464bbb9d 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/documents/Dataset.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/documents/Dataset.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.dataset.documents; +package org.phyloviz.pwp.repository.metadata.dataset.documents; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetMongoRepository.java similarity index 84% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetMongoRepository.java index 84177cb2..58ce1360 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.dataset.mongo; +package org.phyloviz.pwp.repository.metadata.dataset.mongo; -import org.phyloviz.pwp.shared.repository.metadata.dataset.documents.Dataset; +import org.phyloviz.pwp.repository.metadata.dataset.documents.Dataset; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java index b0fc90d1..92f20b9d 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/dataset/mongo/DatasetRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.dataset.mongo; +package org.phyloviz.pwp.repository.metadata.dataset.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.dataset.documents.Dataset; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.dataset.documents.Dataset; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java index 638903cd..3ea0341f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/DistanceMatrixMetadataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix; +package org.phyloviz.pwp.repository.metadata.distance_matrix; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java index ea276958..d3edca2b 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/DistanceMatrixMetadata.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents; +package org.phyloviz.pwp.repository.metadata.distance_matrix.documents; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSource; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSource; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java index 4f32e784..5d3a92a0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/converters/DistanceMatrixMetadataDeserializer.java @@ -1,14 +1,14 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.converters; +package org.phyloviz.pwp.repository.metadata.distance_matrix.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSource; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSource; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java new file mode 100644 index 00000000..542a9054 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source; + +public interface DistanceMatrixSource { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java similarity index 73% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java index ffafedf1..576ea499 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceFunction.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source; +package org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java index 4698b9b2..b1fce8f6 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/documents/source/DistanceMatrixSourceType.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source; +package org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source; import lombok.Getter; import lombok.RequiredArgsConstructor; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java index 29f2db1d..4cbc04cf 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.mongo; +package org.phyloviz.pwp.repository.metadata.distance_matrix.mongo; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java index 28aba5a7..86f72f39 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/distance_matrix/mongo/DistanceMatrixMetadataRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.mongo; +package org.phyloviz.pwp.repository.metadata.distance_matrix.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/IsolateDataMetadataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/IsolateDataMetadataRepository.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/IsolateDataMetadataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/IsolateDataMetadataRepository.java index d364f0ca..f7cefed0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/IsolateDataMetadataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/IsolateDataMetadataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data; +package org.phyloviz.pwp.repository.metadata.isolate_data; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/IsolateDataMetadata.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/IsolateDataMetadata.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/IsolateDataMetadata.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/IsolateDataMetadata.java index 72c1ca79..967de8c7 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/IsolateDataMetadata.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/IsolateDataMetadata.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents; +package org.phyloviz.pwp.repository.metadata.isolate_data.documents; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java index fb15cf5d..2996435a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataDeserializer.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters; +package org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java similarity index 87% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java index ecf24e45..16d62e0a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/documents/converters/IsolateDataMetadataSerializer.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.converters; +package org.phyloviz.pwp.repository.metadata.isolate_data.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.WritingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java index f9d9d8fb..ab6af236 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data.mongo; +package org.phyloviz.pwp.repository.metadata.isolate_data.mongo; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java similarity index 87% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java index 20e7257b..ebfbb544 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/isolate_data/mongo/IsolateDataMetadataRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.isolate_data.mongo; +package org.phyloviz.pwp.repository.metadata.isolate_data.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.isolate_data.IsolateDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/ProjectRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/ProjectRepository.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/ProjectRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/ProjectRepository.java index 9fd12d98..85366cb2 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/ProjectRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/ProjectRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.project; +package org.phyloviz.pwp.repository.metadata.project; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/FileIds.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/FileIds.java similarity index 78% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/FileIds.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/FileIds.java index 2b7a56c8..1f8a50da 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/FileIds.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/FileIds.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.project.documents; +package org.phyloviz.pwp.repository.metadata.project.documents; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/Project.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/Project.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/Project.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/Project.java index f29c703b..341e4531 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/documents/Project.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/documents/Project.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.project.documents; +package org.phyloviz.pwp.repository.metadata.project.documents; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectMongoRepository.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectMongoRepository.java index ab4a8340..0e48f7d5 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectMongoRepository.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.shared.repository.metadata.project.mongo; +package org.phyloviz.pwp.repository.metadata.project.mongo; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectRepositoryMongo.java similarity index 83% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectRepositoryMongo.java index b797f619..dbfe1b5f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/project/mongo/ProjectRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/project/mongo/ProjectRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.project.mongo; +package org.phyloviz.pwp.repository.metadata.project.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/ToolTemplateRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/ToolTemplateRepository.java similarity index 51% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/ToolTemplateRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/ToolTemplateRepository.java index e637c0a9..e218f094 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/ToolTemplateRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/ToolTemplateRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template; +package org.phyloviz.pwp.repository.metadata.templates.tool_template; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplate; import org.springframework.stereotype.Repository; import java.util.Optional; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java similarity index 71% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java index d35d72ff..c6e86ce7 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateDeserializer.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; import org.jetbrains.annotations.NotNull; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessTypeTemplate; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessTypeTemplate; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java similarity index 74% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java index 0ae8b332..31c13648 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/AccessTemplateSerializer.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.converters; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.JsonObject; import lombok.SneakyThrows; import org.bson.Document; import org.jetbrains.annotations.NotNull; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessTemplate; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.WritingConverter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java similarity index 93% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java index c64ab2fe..f8aed5a6 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumDeserializerFactory.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.converters; import org.jetbrains.annotations.NotNull; import org.springframework.core.convert.converter.Converter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java similarity index 78% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java index 58fac089..8b24481e 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/converters/CaseInsensitiveEnumSerializer.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.converters; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.converters; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.WritingConverter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/GeneralTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/GeneralTemplate.java similarity index 70% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/GeneralTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/GeneralTemplate.java index 9f9864d6..ce67e44d 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/GeneralTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/GeneralTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.General; +import org.phyloviz.pwp.service.flowviz.models.tool.General; @Data @Builder diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplate.java similarity index 75% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplate.java index 4186c17b..98407c50 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplate.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.library.LibraryTemplate; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.Tool; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.library.LibraryTemplate; +import org.phyloviz.pwp.service.flowviz.models.tool.Tool; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplateData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplateData.java similarity index 95% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplateData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplateData.java index 5940275c..ccf254d2 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/ToolTemplateData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/ToolTemplateData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents; import lombok.Getter; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java new file mode 100644 index 00000000..ab7d7d9f --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java @@ -0,0 +1,7 @@ +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access; + +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessDetails; + +public interface AccessDetailsTemplate { + AccessDetails build(); +} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java similarity index 67% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java index c481ef6e..6cac5aa3 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTemplate.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplateData; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.library.LibraryAccessDetailsTemplate; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.Access; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplateData; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.library.LibraryAccessDetailsTemplate; +import org.phyloviz.pwp.service.flowviz.models.tool.access.Access; import org.springframework.data.mongodb.core.mapping.Field; @Data diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java new file mode 100644 index 00000000..47bc0aec --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java @@ -0,0 +1,22 @@ +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access; + +import lombok.Getter; +import lombok.RequiredArgsConstructor; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.api.ApiAccessDetailsTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.library.LibraryAccessDetailsTemplate; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessType; + +@RequiredArgsConstructor +public enum AccessTypeTemplate { + LIBRARY(LibraryAccessDetailsTemplate.class), + API(ApiAccessDetailsTemplate.class); + + @Getter + private final Class detailsClass; + + public AccessType build() { + return AccessType.valueOf(this.name()); + } +} + + diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java similarity index 53% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java index 2ad74fea..ec5ae289 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/api/ApiAccessDetailsTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.api; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.api; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.api.ApiAccessDetails; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; +import org.phyloviz.pwp.service.flowviz.models.tool.access.api.ApiAccessDetails; @Data public class ApiAccessDetailsTemplate implements AccessDetailsTemplate { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java similarity index 58% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java index f75db6ba..c7d0b20e 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerAutoRemoveTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.library; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.library; import lombok.Getter; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.DockerAutoRemove; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.DockerAutoRemove; @Getter @RequiredArgsConstructor diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java index 6f22b567..88f8e352 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/DockerVolumeTemplate.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.library; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.library; import lombok.Builder; import lombok.Data; import org.apache.commons.text.StringSubstitutor; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplateData; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.DockerVolume; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.VolumeType; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplateData; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.DockerVolume; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.VolumeType; import org.springframework.data.mongodb.core.mapping.Field; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java similarity index 81% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java index 9f2ee563..be85097a 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/access/library/LibraryAccessDetailsTemplate.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.library; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.library; import lombok.AllArgsConstructor; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplateData; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.LibraryAccessDetails; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplateData; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessDetailsTemplate; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.LibraryAccessDetails; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java similarity index 82% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java index cb493cae..35a8fce4 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/CommandTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.library; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.library; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.library.Command; +import org.phyloviz.pwp.service.flowviz.models.tool.library.Command; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java similarity index 78% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java index ac00964e..fc1c7f47 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/documents/library/LibraryTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.library; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.library; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.library.Library; +import org.phyloviz.pwp.service.flowviz.models.tool.library.Library; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java similarity index 63% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java index 64b1a6b8..21638123 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.mongo; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.mongo; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplate; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java similarity index 62% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java index 9fabd346..521dd7c4 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/tool_template/mongo/ToolTemplateRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.mongo; +package org.phyloviz.pwp.repository.metadata.templates.tool_template.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.ToolTemplateRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.ToolTemplateRepository; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplate; import org.springframework.stereotype.Repository; import java.util.Optional; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java index 9636f0bc..e0e24efc 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/WorkflowInstanceRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances; +package org.phyloviz.pwp.repository.metadata.templates.workflow_instances; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java index 8721f67d..18eacec8 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowInstance.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents; +package org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.Workflow; +import org.phyloviz.pwp.service.flowviz.models.workflow.Workflow; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java new file mode 100644 index 00000000..0ef3a6e2 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java @@ -0,0 +1,7 @@ +package org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents; + +public enum WorkflowStatus { + RUNNING, + SUCCESS, + FAILED +} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java index 397df1f7..7ff28a50 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.mongo; +package org.phyloviz.pwp.repository.metadata.templates.workflow_instances.mongo; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.data.mongodb.repository.Query; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java similarity index 79% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java index 3bf3eb93..6b5d5d2c 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_instances/mongo/WorkflowInstanceRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.mongo; +package org.phyloviz.pwp.repository.metadata.templates.workflow_instances.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.WorkflowInstanceRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.WorkflowInstanceRepository; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java similarity index 73% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java index e9afb396..6521fba5 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/WorkflowTemplateRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/ActionTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/ActionTemplate.java similarity index 75% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/ActionTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/ActionTemplate.java index 72b01ed5..ac9a9260 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/ActionTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/ActionTemplate.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents; import lombok.Builder; import lombok.Data; import org.apache.commons.text.StringSubstitutor; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.tasks.Action; +import org.phyloviz.pwp.service.flowviz.models.workflow.tasks.Action; @Data @Builder diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/TaskTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/TaskTemplate.java similarity index 79% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/TaskTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/TaskTemplate.java index 862bb793..2a61c147 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/TaskTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/TaskTemplate.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.tasks.Task; +import org.phyloviz.pwp.service.flowviz.models.workflow.tasks.Task; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java similarity index 89% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java index b5d6ffc1..d64e92f0 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplate.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.arguments.WorkflowTemplateArgumentProperties; -import org.phyloviz.pwp.compute.service.exceptions.WorkflowTemplateConfigurationException; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.Workflow; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.arguments.WorkflowTemplateArgumentProperties; +import org.phyloviz.pwp.service.exceptions.WorkflowTemplateConfigurationException; +import org.phyloviz.pwp.service.flowviz.models.workflow.Workflow; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java similarity index 95% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java index 299a317d..c45874cb 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/WorkflowTemplateData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents; import lombok.Getter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java similarity index 86% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java index 3064cd6b..dc9211cc 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentProperties.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.arguments; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.arguments; import lombok.Getter; -import org.phyloviz.pwp.compute.service.exceptions.WorkflowTemplateConfigurationException; +import org.phyloviz.pwp.service.exceptions.WorkflowTemplateConfigurationException; import org.springframework.data.mongodb.core.mapping.Field; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java similarity index 62% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java index 73bba66c..8c755ffd 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/documents/arguments/WorkflowTemplateArgumentType.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.arguments; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.arguments; public enum WorkflowTemplateArgumentType { OBJECTID, diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java similarity index 70% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java index d19af6ee..8e5c8c14 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.mongo; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.mongo; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java similarity index 64% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java index 3a8e8d90..c525da76 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/templates/workflow_template/mongo/WorkflowTemplateRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.mongo; +package org.phyloviz.pwp.repository.metadata.templates.workflow_template.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.WorkflowTemplateRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.WorkflowTemplateRepository; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; import org.springframework.stereotype.Repository; import java.util.List; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/TreeMetadataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/TreeMetadataRepository.java similarity index 91% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/TreeMetadataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/TreeMetadataRepository.java index 7fd8b9ae..541ec151 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/TreeMetadataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/TreeMetadataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree; +package org.phyloviz.pwp.repository.metadata.tree; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/TreeMetadata.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/TreeMetadata.java similarity index 72% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/TreeMetadata.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/TreeMetadata.java index 3fb4d354..412da763 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/TreeMetadata.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/TreeMetadata.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents; +package org.phyloviz.pwp.repository.metadata.tree.documents; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSource; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceType; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSource; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceType; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java index f791efc5..944dcc20 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/converters/TreeMetadataDeserializer.java @@ -1,14 +1,14 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.converters; +package org.phyloviz.pwp.repository.metadata.tree.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSource; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceType; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSource; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceType; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSource.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSource.java new file mode 100644 index 00000000..b53412d3 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSource.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.repository.metadata.tree.documents.source; + +public interface TreeSource { +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java similarity index 80% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java index 3c465782..ff5eeb5b 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmDistanceMatrix.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.source; +package org.phyloviz.pwp.repository.metadata.tree.documents.source; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java index d820a68b..0f4e1269 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceAlgorithmTypingData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.source; +package org.phyloviz.pwp.repository.metadata.tree.documents.source; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceFile.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceFile.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceFile.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceFile.java index 638b3a6c..2e377b70 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceFile.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceFile.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.source; +package org.phyloviz.pwp.repository.metadata.tree.documents.source; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceType.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceType.java similarity index 82% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceType.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceType.java index 84a934ac..4e52733f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSourceType.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/documents/source/TreeSourceType.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.source; +package org.phyloviz.pwp.repository.metadata.tree.documents.source; import lombok.Getter; import lombok.RequiredArgsConstructor; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java similarity index 91% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java index 78a84a31..39f3394c 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.mongo; +package org.phyloviz.pwp.repository.metadata.tree.mongo; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.data.mongodb.repository.Query; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java similarity index 89% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java index 6c8ab99c..569dd63e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree/mongo/TreeMetadataRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.mongo; +package org.phyloviz.pwp.repository.metadata.tree.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree.TreeMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/TreeViewMetadataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/TreeViewMetadataRepository.java similarity index 91% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/TreeViewMetadataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/TreeViewMetadataRepository.java index 814cf17a..adaeb567 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/TreeViewMetadataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/TreeViewMetadataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view; +package org.phyloviz.pwp.repository.metadata.tree_view; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/TreeViewMetadata.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/TreeViewMetadata.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/TreeViewMetadata.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/TreeViewMetadata.java index fd09e118..55278984 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/TreeViewMetadata.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/TreeViewMetadata.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.documents; +package org.phyloviz.pwp.repository.metadata.tree_view.documents; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.source.TreeViewSource; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Transformations; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.source.TreeViewSource; +import org.phyloviz.pwp.service.dtos.tree_view.Transformations; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java similarity index 78% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java index 4f5fc35f..273ebf06 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataDeserializer.java @@ -1,14 +1,14 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters; +package org.phyloviz.pwp.repository.metadata.tree_view.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.source.TreeViewSource; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Transformations; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.source.TreeViewSource; +import org.phyloviz.pwp.service.dtos.tree_view.Transformations; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java index 91df0a52..724286e0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/converters/TreeViewMetadataSerializer.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.converters; +package org.phyloviz.pwp.repository.metadata.tree_view.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; import org.bson.types.ObjectId; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.WritingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/source/TreeViewSource.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/source/TreeViewSource.java similarity index 70% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/source/TreeViewSource.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/source/TreeViewSource.java index 7fcdb01e..bd2c1a9e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/documents/source/TreeViewSource.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/documents/source/TreeViewSource.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.source; +package org.phyloviz.pwp.repository.metadata.tree_view.documents.source; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java similarity index 91% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java index 6d330b05..44d8d565 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.mongo; +package org.phyloviz.pwp.repository.metadata.tree_view.mongo; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.data.mongodb.repository.Query; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java similarity index 89% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java index c56d1456..24d645f6 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/tree_view/mongo/TreeViewMetadataRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree_view.mongo; +package org.phyloviz.pwp.repository.metadata.tree_view.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.TreeViewMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/TypingDataMetadataRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/TypingDataMetadataRepository.java similarity index 90% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/TypingDataMetadataRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/TypingDataMetadataRepository.java index 7cafbc1d..e60f9a2a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/TypingDataMetadataRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/TypingDataMetadataRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data; +package org.phyloviz.pwp.repository.metadata.typing_data; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; import java.util.List; import java.util.Optional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/TypingDataMetadata.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/TypingDataMetadata.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/TypingDataMetadata.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/TypingDataMetadata.java index ce964512..30995929 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/TypingDataMetadata.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/TypingDataMetadata.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data.documents; +package org.phyloviz.pwp.repository.metadata.typing_data.documents; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; import org.springframework.data.annotation.Id; import org.springframework.data.mongodb.core.mapping.Document; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java index 58f8572c..93c052d0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataDeserializer.java @@ -1,12 +1,12 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters; +package org.phyloviz.pwp.repository.metadata.typing_data.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.ReadingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java similarity index 87% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java index 201f4a89..48ebe893 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/documents/converters/TypingDataMetadataSerializer.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.converters; +package org.phyloviz.pwp.repository.metadata.typing_data.documents.converters; import lombok.RequiredArgsConstructor; import org.bson.Document; -import org.phyloviz.pwp.shared.repository.metadata.DocumentConversionException; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.metadata.DocumentConversionException; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; import org.springframework.core.convert.converter.Converter; import org.springframework.data.convert.WritingConverter; import org.springframework.data.mongodb.core.convert.MongoConverter; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java similarity index 88% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java index 0f01158e..043d638a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataMongoRepository.java @@ -1,6 +1,6 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data.mongo; +package org.phyloviz.pwp.repository.metadata.typing_data.mongo; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; import org.springframework.data.mongodb.repository.MongoRepository; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java similarity index 87% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java index 90df75d7..f06b59ef 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/repository/metadata/typing_data/mongo/TypingDataMetadataRepositoryMongo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.shared.repository.metadata.typing_data.mongo; +package org.phyloviz.pwp.repository.metadata.typing_data.mongo; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.metadata.typing_data.TypingDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; import org.springframework.context.annotation.Primary; import org.springframework.stereotype.Repository; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeService.java similarity index 89% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeService.java index 78d0872c..bff744cb 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeService.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.service; +package org.phyloviz.pwp.service; -import org.phyloviz.pwp.compute.service.dtos.create_workflow.CreateWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowStatusOutput; +import org.phyloviz.pwp.service.dtos.create_workflow.CreateWorkflowOutput; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowOutput; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowStatusOutput; import java.util.List; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeServiceImpl.java similarity index 86% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeServiceImpl.java index 85cea232..d937c6ad 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/ComputeServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/ComputeServiceImpl.java @@ -1,34 +1,34 @@ -package org.phyloviz.pwp.compute.service; +package org.phyloviz.pwp.service; import org.bson.types.ObjectId; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.ToolTemplateRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.ToolTemplateData; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.AccessTypeTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.WorkflowInstanceRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.WorkflowTemplateRepository; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.TaskTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.WorkflowTemplateData; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_template.documents.arguments.WorkflowTemplateArgumentProperties; -import org.phyloviz.pwp.compute.service.dtos.create_workflow.CreateWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowStatusOutput; -import org.phyloviz.pwp.compute.service.exceptions.InvalidWorkflowException; -import org.phyloviz.pwp.compute.service.exceptions.TemplateNotFound; -import org.phyloviz.pwp.compute.service.exceptions.WorkflowInstanceNotFoundException; -import org.phyloviz.pwp.compute.service.flowviz.FLOWViZClient; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.UnexpectedResponseException; -import org.phyloviz.pwp.compute.service.flowviz.models.get_workflow.AirflowWorkflowStatus; -import org.phyloviz.pwp.compute.service.flowviz.models.get_workflow.GetWorkflowResponse; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.Tool; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.GetWorkflowTaskLogResponse; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.Workflow; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.utils.UUIDUtils; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.ToolTemplateRepository; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplate; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.ToolTemplateData; +import org.phyloviz.pwp.repository.metadata.templates.tool_template.documents.access.AccessTypeTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.WorkflowInstanceRepository; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowInstance; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.WorkflowTemplateRepository; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.TaskTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.WorkflowTemplate; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.WorkflowTemplateData; +import org.phyloviz.pwp.repository.metadata.templates.workflow_template.documents.arguments.WorkflowTemplateArgumentProperties; +import org.phyloviz.pwp.service.dtos.create_workflow.CreateWorkflowOutput; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowOutput; +import org.phyloviz.pwp.service.dtos.get_workflow.GetWorkflowStatusOutput; +import org.phyloviz.pwp.service.exceptions.InvalidWorkflowException; +import org.phyloviz.pwp.service.exceptions.TemplateNotFound; +import org.phyloviz.pwp.service.exceptions.WorkflowInstanceNotFoundException; +import org.phyloviz.pwp.service.flowviz.FLOWViZClient; +import org.phyloviz.pwp.service.flowviz.exceptions.UnexpectedResponseException; +import org.phyloviz.pwp.service.flowviz.models.get_workflow.AirflowWorkflowStatus; +import org.phyloviz.pwp.service.flowviz.models.get_workflow.GetWorkflowResponse; +import org.phyloviz.pwp.service.flowviz.models.tool.Tool; +import org.phyloviz.pwp.service.flowviz.models.workflow.GetWorkflowTaskLogResponse; +import org.phyloviz.pwp.service.flowviz.models.workflow.Workflow; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.utils.UUIDUtils; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; @@ -36,8 +36,8 @@ import java.util.List; import java.util.Map; -@Service -@Transactional +//@Service +//@Transactional public class ComputeServiceImpl implements ComputeService { private final ProjectRepository projectRepository; diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferService.java similarity index 89% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferService.java index 3179dde3..3faddc8f 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.file_transfer.service; +package org.phyloviz.pwp.service; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.UploadIsolateDataOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.UploadTypingDataOutput; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UploadIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UploadTypingDataOutput; import org.springframework.web.multipart.MultipartFile; /** diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferServiceImpl.java similarity index 76% rename from src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferServiceImpl.java index db7ca265..40ebd41d 100644 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/service/FileTransferServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/FileTransferServiceImpl.java @@ -1,26 +1,22 @@ -package org.phyloviz.pwp.file_transfer.service; +package org.phyloviz.pwp.service; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.UploadIsolateDataOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.UploadTypingDataOutput; -import org.phyloviz.pwp.shared.service.exceptions.FileCorruptedException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.MultipartFileReadException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataNotFoundException; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataDataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataDataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.isolate_data.IsolateDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.TypingDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UploadIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.UploadTypingDataOutput; +import org.phyloviz.pwp.service.exceptions.*; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationService.java similarity index 87% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationService.java index 9423fe48..edbf45ca 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationService.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.visualization.service; +package org.phyloviz.pwp.service; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewInput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewOutput; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewInput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewOutput; import java.util.List; diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationServiceImpl.java similarity index 72% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationServiceImpl.java index 59e88352..99135ae3 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/VisualizationServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/VisualizationServiceImpl.java @@ -1,52 +1,46 @@ -package org.phyloviz.pwp.visualization.service; +package org.phyloviz.pwp.service; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewInput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.SaveTreeViewOutput; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.DistanceMatrixNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeViewNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataNotFoundException; -import org.phyloviz.pwp.visualization.service.exceptions.IndexingNeededException; +import org.phyloviz.pwp.service.exceptions.IndexingNeededException; +import org.phyloviz.pwp.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; +import org.phyloviz.pwp.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.isolate_data.IsolateDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.isolate_data.repository.IsolateDataDataRepository; +import org.phyloviz.pwp.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.data.tree.TreeDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree.repository.TreeDataRepository; +import org.phyloviz.pwp.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.tree_view.TreeViewDataRepositoryId; +import org.phyloviz.pwp.repository.data.tree_view.repository.TreeViewDataRepository; +import org.phyloviz.pwp.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; +import org.phyloviz.pwp.repository.data.typing_data.TypingDataDataRepositoryId; +import org.phyloviz.pwp.repository.data.typing_data.repository.TypingDataDataRepository; +import org.phyloviz.pwp.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.isolate_data.IsolateDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.tree.TreeMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.TreeViewMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.typing_data.TypingDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataProfilesOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.GetTypingDataSchemaOutput; +import org.phyloviz.pwp.service.dtos.tree_view.GetTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewInput; +import org.phyloviz.pwp.service.dtos.tree_view.SaveTreeViewOutput; +import org.phyloviz.pwp.service.exceptions.*; import org.springframework.beans.factory.annotation.Value; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/create_workflow/CreateWorkflowOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/create_workflow/CreateWorkflowOutput.java similarity index 62% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/create_workflow/CreateWorkflowOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/create_workflow/CreateWorkflowOutput.java index 1b3cf703..cfb90eec 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/create_workflow/CreateWorkflowOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/create_workflow/CreateWorkflowOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.dtos.create_workflow; +package org.phyloviz.pwp.service.dtos.create_workflow; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/CreateDatasetOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/CreateDatasetOutput.java similarity index 68% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/CreateDatasetOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/CreateDatasetOutput.java index 8a31e7b1..015deb99 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/CreateDatasetOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/CreateDatasetOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.dataset; +package org.phyloviz.pwp.service.dtos.dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/FullDatasetInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/FullDatasetInfo.java similarity index 61% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/FullDatasetInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/FullDatasetInfo.java index bdd4c4d5..8bdccae0 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/FullDatasetInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/FullDatasetInfo.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.service.dtos.dataset; +package org.phyloviz.pwp.service.dtos.dataset; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeInfo; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.tree.TreeInfo; +import org.phyloviz.pwp.service.dtos.tree_view.TreeViewInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java index 46e3e7cb..a05e14c9 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/SetIsolateDataOfDatasetOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.dataset; +package org.phyloviz.pwp.service.dtos.dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/UpdateDatasetOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/UpdateDatasetOutput.java similarity index 78% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/UpdateDatasetOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/UpdateDatasetOutput.java index 9d64f280..15c28c15 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/dataset/UpdateDatasetOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/dataset/UpdateDatasetOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.dataset; +package org.phyloviz.pwp.service.dtos.dataset; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixInfo.java similarity index 66% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixInfo.java index faa869b3..173f4844 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixInfo.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.service.dtos.distance_matrix; +package org.phyloviz.pwp.service.dtos.distance_matrix; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceFunction; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceFunction; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; @Data public class DistanceMatrixInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java similarity index 64% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java index 98f3900d..0a2d9133 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceFunctionInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.distance_matrix; +package org.phyloviz.pwp.service.dtos.distance_matrix; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceFunction; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceFunction; @Data public class DistanceMatrixSourceFunctionInfo implements DistanceMatrixSourceInfo { diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java new file mode 100644 index 00000000..0390593b --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.service.dtos.distance_matrix; + +public interface DistanceMatrixSourceInfo { +} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java similarity index 67% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java index eb71728b..343fe9ed 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/distance_matrix/UpdateDistanceMatrixOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.distance_matrix; +package org.phyloviz.pwp.service.dtos.distance_matrix; import lombok.Data; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/FilesInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/FilesInfo.java new file mode 100644 index 00000000..4965b618 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/FilesInfo.java @@ -0,0 +1,13 @@ +package org.phyloviz.pwp.service.dtos.files; + +import lombok.Data; +import org.phyloviz.pwp.service.dtos.files.isolate_data.IsolateDataInfo; +import org.phyloviz.pwp.service.dtos.files.typing_data.TypingDataInfo; + +import java.util.List; + +@Data +public class FilesInfo { + private final List typingData; + private final List isolateData; +} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java index 82e3af64..634650fe 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/GetIsolateDataRowsOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.isolate_data; +package org.phyloviz.pwp.service.dtos.files.isolate_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/IsolateDataInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataInfo.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/IsolateDataInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataInfo.java index 96a2fc09..f0df3fac 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/IsolateDataInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.files.isolate_data; +package org.phyloviz.pwp.service.dtos.files.isolate_data; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; import java.util.List; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/IsolateDataRow.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataRow.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/IsolateDataRow.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataRow.java index 4393018e..e7fbf1be 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/IsolateDataRow.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/IsolateDataRow.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.isolate_data; +package org.phyloviz.pwp.service.dtos.files.isolate_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java similarity index 66% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java index c70df625..acea6425 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UpdateIsolateDataOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.files.isolate_data; +package org.phyloviz.pwp.service.dtos.files.isolate_data; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/UploadIsolateDataOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UploadIsolateDataOutput.java similarity index 69% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/UploadIsolateDataOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UploadIsolateDataOutput.java index 79922869..a97c3c53 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/isolate_data/UploadIsolateDataOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/isolate_data/UploadIsolateDataOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.isolate_data; +package org.phyloviz.pwp.service.dtos.files.isolate_data; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java similarity index 78% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java index 3337a7a5..c583d2d7 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataProfilesOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java similarity index 77% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java index 16c1213c..e5559730 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/GetTypingDataSchemaOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/TypingDataInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataInfo.java similarity index 65% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/TypingDataInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataInfo.java index 9eb25fd5..41714252 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/TypingDataInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; @Data public class TypingDataInfo { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/TypingDataProfile.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataProfile.java similarity index 75% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/TypingDataProfile.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataProfile.java index ee3580a0..6cbeba7b 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/TypingDataProfile.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/TypingDataProfile.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/UpdateTypingDataOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UpdateTypingDataOutput.java similarity index 66% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/UpdateTypingDataOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UpdateTypingDataOutput.java index e991f322..3169f216 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/typing_data/UpdateTypingDataOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UpdateTypingDataOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/UploadTypingDataOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UploadTypingDataOutput.java similarity index 69% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/UploadTypingDataOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UploadTypingDataOutput.java index 606f2536..f53b2349 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/files/typing_data/UploadTypingDataOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/files/typing_data/UploadTypingDataOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.files.typing_data; +package org.phyloviz.pwp.service.dtos.files.typing_data; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowOutput.java similarity index 69% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowOutput.java index 137b6e4d..e7f3a2a1 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowOutput.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.service.dtos.get_workflow; +package org.phyloviz.pwp.service.dtos.get_workflow; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowStatusOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowStatusOutput.java similarity index 67% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowStatusOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowStatusOutput.java index 0ec89070..2325f2de 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/dtos/get_workflow/GetWorkflowStatusOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/get_workflow/GetWorkflowStatusOutput.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.service.dtos.get_workflow; +package org.phyloviz.pwp.service.dtos.get_workflow; import lombok.Data; -import org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; +import org.phyloviz.pwp.repository.metadata.templates.workflow_instances.documents.WorkflowStatus; import java.util.Map; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/CreateProjectOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/CreateProjectOutput.java similarity index 61% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/CreateProjectOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/CreateProjectOutput.java index eb657c9c..0485bbac 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/CreateProjectOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/CreateProjectOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.project; +package org.phyloviz.pwp.service.dtos.project; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/FullProjectInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/FullProjectInfo.java similarity index 59% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/FullProjectInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/FullProjectInfo.java index 2144fa70..d2c39165 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/FullProjectInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/FullProjectInfo.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.administration.service.dtos.project; +package org.phyloviz.pwp.service.dtos.project; import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; -import org.phyloviz.pwp.administration.service.dtos.files.FilesInfo; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.service.dtos.files.FilesInfo; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/UpdateProjectOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/UpdateProjectOutput.java similarity index 78% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/UpdateProjectOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/UpdateProjectOutput.java index 182114ce..d9a2e1df 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/project/UpdateProjectOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/project/UpdateProjectOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.project; +package org.phyloviz.pwp.service.dtos.project; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeInfo.java similarity index 64% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeInfo.java index 8da0c5cc..68a94cfe 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeInfo.java @@ -1,11 +1,11 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; +package org.phyloviz.pwp.service.dtos.tree; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceAlgorithmDistanceMatrix; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceAlgorithmTypingData; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceFile; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceType; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceAlgorithmDistanceMatrix; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceAlgorithmTypingData; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceFile; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceType; @Data public class TreeInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java similarity index 78% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java index 03a117c7..d5d29430 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmDistanceMatrixInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; +package org.phyloviz.pwp.service.dtos.tree; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceAlgorithmDistanceMatrix; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceAlgorithmDistanceMatrix; @Data public class TreeSourceAlgorithmDistanceMatrixInfo implements TreeSourceInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java similarity index 77% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java index 53803063..c1f9d53a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceAlgorithmTypingDataInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; +package org.phyloviz.pwp.service.dtos.tree; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceAlgorithmTypingData; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceAlgorithmTypingData; @Data public class TreeSourceAlgorithmTypingDataInfo implements TreeSourceInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceFileInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceFileInfo.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceFileInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceFileInfo.java index b5b33cee..96b3b5c3 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceFileInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceFileInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; +package org.phyloviz.pwp.service.dtos.tree; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceFile; +import org.phyloviz.pwp.repository.metadata.tree.documents.source.TreeSourceFile; @Data public class TreeSourceFileInfo implements TreeSourceInfo { diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceInfo.java new file mode 100644 index 00000000..c4e308a4 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/TreeSourceInfo.java @@ -0,0 +1,5 @@ +package org.phyloviz.pwp.service.dtos.tree; + +public interface TreeSourceInfo { +} + diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/UpdateTreeOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/UpdateTreeOutput.java similarity index 69% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/UpdateTreeOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/UpdateTreeOutput.java index 10533a88..9c1b3b37 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/UpdateTreeOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree/UpdateTreeOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; +package org.phyloviz.pwp.service.dtos.tree; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Edge.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Edge.java similarity index 71% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Edge.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Edge.java index 307f5892..81f98195 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Edge.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Edge.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/GetTreeViewOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/GetTreeViewOutput.java similarity index 85% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/GetTreeViewOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/GetTreeViewOutput.java index 911e7c3d..d12e6f95 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/GetTreeViewOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/GetTreeViewOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Node.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Node.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Node.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Node.java index a252bd1c..8237fb1f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Node.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Node.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewInput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewInput.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewInput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewInput.java index 59fc26f1..df58845e 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewInput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewInput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewOutput.java similarity index 79% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewOutput.java index 71e8805d..a0fe184b 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/SaveTreeViewOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/SaveTreeViewOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Transformations.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Transformations.java similarity index 91% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Transformations.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Transformations.java index fe368c43..a2b54b1f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/dtos/tree_view/Transformations.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/Transformations.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewInfo.java similarity index 76% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewInfo.java index 6991b161..76da434f 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; @Data public class TreeViewInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewSourceInfo.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewSourceInfo.java similarity index 57% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewSourceInfo.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewSourceInfo.java index 1f9aeadd..a2e52bd2 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/TreeViewSourceInfo.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/TreeViewSourceInfo.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.source.TreeViewSource; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.source.TreeViewSource; @Data public class TreeViewSourceInfo { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/UpdateTreeViewOutput.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/UpdateTreeViewOutput.java similarity index 68% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/UpdateTreeViewOutput.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/UpdateTreeViewOutput.java index e5b95b22..7d0218ab 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree_view/UpdateTreeViewOutput.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/dtos/tree_view/UpdateTreeViewOutput.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.dtos.tree_view; +package org.phyloviz.pwp.service.dtos.tree_view; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DatasetDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetDoesNotExistException.java similarity index 74% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DatasetDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetDoesNotExistException.java index 0c1574cc..ddc4c5cb 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DatasetDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DatasetDoesNotExistException extends RuntimeException { public DatasetDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DatasetNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetNotFoundException.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DatasetNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetNotFoundException.java index 28843aef..fe12b54d 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DatasetNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DatasetNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DatasetNotFoundException extends RuntimeException { public DatasetNotFoundException() { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedFileDeletionException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedFileDeletionException.java similarity index 71% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedFileDeletionException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedFileDeletionException.java index 4a1c53bd..749bf4f0 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedFileDeletionException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedFileDeletionException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DeniedFileDeletionException extends RuntimeException { public DeniedFileDeletionException(String msg) { diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedResourceDeletionException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedResourceDeletionException.java similarity index 72% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedResourceDeletionException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedResourceDeletionException.java index d82b7d80..98e54fd6 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/exceptions/DeniedResourceDeletionException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DeniedResourceDeletionException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.administration.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DeniedResourceDeletionException extends RuntimeException { public DeniedResourceDeletionException(String msg) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DistanceMatrixDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixDoesNotExistException.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DistanceMatrixDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixDoesNotExistException.java index 2eb10873..2e54fad0 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/DistanceMatrixDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DistanceMatrixDoesNotExistException extends RuntimeException { public DistanceMatrixDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DistanceMatrixNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixNotFoundException.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DistanceMatrixNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixNotFoundException.java index 78148b44..2ee8a4d4 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/DistanceMatrixNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/DistanceMatrixNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class DistanceMatrixNotFoundException extends RuntimeException { public DistanceMatrixNotFoundException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/FileCorruptedException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/FileCorruptedException.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/FileCorruptedException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/FileCorruptedException.java index ca2f33d0..b3639f28 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/FileCorruptedException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/FileCorruptedException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class FileCorruptedException extends RuntimeException { public FileCorruptedException(String message) { diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/exceptions/IndexingNeededException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IndexingNeededException.java similarity index 71% rename from src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/exceptions/IndexingNeededException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IndexingNeededException.java index 82e0738d..3630b920 100644 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/service/exceptions/IndexingNeededException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IndexingNeededException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.visualization.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class IndexingNeededException extends RuntimeException { public IndexingNeededException(String message) { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/InvalidArgumentException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidArgumentException.java similarity index 73% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/InvalidArgumentException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidArgumentException.java index 0a2f9ccb..ff0d7fdb 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/InvalidArgumentException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidArgumentException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class InvalidArgumentException extends RuntimeException { public InvalidArgumentException(String msg) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/InvalidWorkflowException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidWorkflowException.java similarity index 73% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/InvalidWorkflowException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidWorkflowException.java index 0053119d..3c0bab93 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/InvalidWorkflowException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/InvalidWorkflowException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class InvalidWorkflowException extends RuntimeException { public InvalidWorkflowException(String msg) { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataDoesNotExistException.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataDoesNotExistException.java index 84ad41e4..1d4c45af 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class IsolateDataDoesNotExistException extends RuntimeException { public IsolateDataDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataNotFoundException.java similarity index 75% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataNotFoundException.java index e46f7561..38eb59fa 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/IsolateDataNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/IsolateDataNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class IsolateDataNotFoundException extends RuntimeException { public IsolateDataNotFoundException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/MultipartFileReadException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/MultipartFileReadException.java similarity index 75% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/MultipartFileReadException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/MultipartFileReadException.java index 0405eb90..b9c39d1a 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/MultipartFileReadException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/MultipartFileReadException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class MultipartFileReadException extends RuntimeException { public MultipartFileReadException(String msg, Throwable e) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/ProjectDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectDoesNotExistException.java similarity index 74% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/ProjectDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectDoesNotExistException.java index e03790d1..8d3c2986 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/ProjectDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class ProjectDoesNotExistException extends RuntimeException { public ProjectDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/ProjectNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectNotFoundException.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/ProjectNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectNotFoundException.java index 36f01c83..ed3102d6 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/ProjectNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/ProjectNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class ProjectNotFoundException extends RuntimeException { public ProjectNotFoundException() { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TemplateNotFound.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TemplateNotFound.java similarity index 70% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TemplateNotFound.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TemplateNotFound.java index 6b49c2a7..55126c45 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TemplateNotFound.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TemplateNotFound.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TemplateNotFound extends RuntimeException { public TemplateNotFound(String msg) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeDoesNotExistException.java similarity index 73% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeDoesNotExistException.java index bf1d9268..79cc34fe 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TreeDoesNotExistException extends RuntimeException { public TreeDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeNotFoundException.java similarity index 73% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeNotFoundException.java index e7d062d7..c764a4b1 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TreeNotFoundException extends RuntimeException { public TreeNotFoundException() { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeViewDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewDoesNotExistException.java similarity index 75% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeViewDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewDoesNotExistException.java index 7d244e43..b411ba06 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/TreeViewDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TreeViewDoesNotExistException extends RuntimeException { public TreeViewDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeViewNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewNotFoundException.java similarity index 74% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeViewNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewNotFoundException.java index 3fa186a8..ee79e0d8 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TreeViewNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TreeViewNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TreeViewNotFoundException extends RuntimeException { public TreeViewNotFoundException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataDoesNotExistException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataDoesNotExistException.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataDoesNotExistException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataDoesNotExistException.java index a8b4eec6..8240a7f0 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataDoesNotExistException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataDoesNotExistException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TypingDataDoesNotExistException extends RuntimeException { public TypingDataDoesNotExistException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataNotFoundException.java similarity index 75% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataNotFoundException.java index acda88c9..03d64376 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/TypingDataNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/TypingDataNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class TypingDataNotFoundException extends RuntimeException { public TypingDataNotFoundException() { diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/UnauthorizedException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/UnauthorizedException.java similarity index 76% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/UnauthorizedException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/UnauthorizedException.java index bdefbd8c..94a0db0f 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/service/exceptions/UnauthorizedException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/UnauthorizedException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class UnauthorizedException extends RuntimeException { public UnauthorizedException() { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowInstanceNotFoundException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowInstanceNotFoundException.java similarity index 76% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowInstanceNotFoundException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowInstanceNotFoundException.java index 952d5155..cbb58b71 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowInstanceNotFoundException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowInstanceNotFoundException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class WorkflowInstanceNotFoundException extends RuntimeException { public WorkflowInstanceNotFoundException() { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowTemplateConfigurationException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowTemplateConfigurationException.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowTemplateConfigurationException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowTemplateConfigurationException.java index 197b380f..8a0f3a51 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/exceptions/WorkflowTemplateConfigurationException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/exceptions/WorkflowTemplateConfigurationException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.exceptions; +package org.phyloviz.pwp.service.exceptions; public class WorkflowTemplateConfigurationException extends RuntimeException { public WorkflowTemplateConfigurationException(String message) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClient.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClient.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClient.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClient.java index f650f106..214df548 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClient.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClient.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.compute.service.flowviz; +package org.phyloviz.pwp.service.flowviz; import lombok.Getter; -import org.phyloviz.pwp.compute.service.flowviz.identity.Credentials; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.ToolService; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.WorkflowService; +import org.phyloviz.pwp.service.flowviz.identity.Credentials; +import org.phyloviz.pwp.service.flowviz.models.tool.ToolService; +import org.phyloviz.pwp.service.flowviz.models.workflow.WorkflowService; /** * Client for the FLOWViZ API. diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClientBuilder.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClientBuilder.java similarity index 85% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClientBuilder.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClientBuilder.java index 1100c37a..ea17c107 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZClientBuilder.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZClientBuilder.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.compute.service.flowviz; +package org.phyloviz.pwp.service.flowviz; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.AuthenticationException; -import org.phyloviz.pwp.compute.service.flowviz.identity.Credentials; +import org.phyloviz.pwp.service.flowviz.exceptions.AuthenticationException; +import org.phyloviz.pwp.service.flowviz.identity.Credentials; /** * Builder for the {@link FLOWViZClient}. diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZHttpService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZHttpService.java similarity index 88% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZHttpService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZHttpService.java index 14d753c5..ca5e5574 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/FLOWViZHttpService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/FLOWViZHttpService.java @@ -1,25 +1,20 @@ -package org.phyloviz.pwp.compute.service.flowviz; +package org.phyloviz.pwp.service.flowviz; import com.google.gson.Gson; import com.google.gson.GsonBuilder; import com.google.gson.JsonSyntaxException; import com.google.gson.stream.JsonReader; -import okhttp3.MediaType; -import okhttp3.OkHttpClient; -import okhttp3.Request; -import okhttp3.RequestBody; -import okhttp3.Response; -import okhttp3.ResponseBody; -import org.phyloviz.pwp.compute.service.flowviz.adapters.AccessDeserializer; -import org.phyloviz.pwp.compute.service.flowviz.adapters.AccessSerializer; -import org.phyloviz.pwp.compute.service.flowviz.adapters.LocalDateTimeDeserializer; -import org.phyloviz.pwp.compute.service.flowviz.adapters.LocalDateTimeSerializer; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.AuthenticationException; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.ConnectionRefusedException; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.UnexpectedResponseException; -import org.phyloviz.pwp.compute.service.flowviz.identity.Credentials; -import org.phyloviz.pwp.compute.service.flowviz.identity.Token; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.Access; +import okhttp3.*; +import org.phyloviz.pwp.service.flowviz.adapters.AccessDeserializer; +import org.phyloviz.pwp.service.flowviz.adapters.AccessSerializer; +import org.phyloviz.pwp.service.flowviz.adapters.LocalDateTimeDeserializer; +import org.phyloviz.pwp.service.flowviz.adapters.LocalDateTimeSerializer; +import org.phyloviz.pwp.service.flowviz.exceptions.AuthenticationException; +import org.phyloviz.pwp.service.flowviz.exceptions.ConnectionRefusedException; +import org.phyloviz.pwp.service.flowviz.exceptions.UnexpectedResponseException; +import org.phyloviz.pwp.service.flowviz.identity.Credentials; +import org.phyloviz.pwp.service.flowviz.identity.Token; +import org.phyloviz.pwp.service.flowviz.models.tool.access.Access; import java.io.IOException; import java.time.LocalDateTime; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessDeserializer.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessDeserializer.java index 58ab7c29..e334ef23 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessDeserializer.java @@ -1,15 +1,11 @@ -package org.phyloviz.pwp.compute.service.flowviz.adapters; - -import com.google.gson.JsonDeserializationContext; -import com.google.gson.JsonDeserializer; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; -import com.google.gson.JsonParseException; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.Access; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessDetails; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessType; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.api.ApiAccessDetails; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.LibraryAccessDetails; +package org.phyloviz.pwp.service.flowviz.adapters; + +import com.google.gson.*; +import org.phyloviz.pwp.service.flowviz.models.tool.access.Access; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessType; +import org.phyloviz.pwp.service.flowviz.models.tool.access.api.ApiAccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.LibraryAccessDetails; import java.lang.reflect.Type; import java.util.Map; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessSerializer.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessSerializer.java index d2e79788..03ecf659 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/AccessSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/AccessSerializer.java @@ -1,13 +1,13 @@ -package org.phyloviz.pwp.compute.service.flowviz.adapters; +package org.phyloviz.pwp.service.flowviz.adapters; import com.google.gson.JsonElement; import com.google.gson.JsonObject; import com.google.gson.JsonSerializationContext; import com.google.gson.JsonSerializer; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.Access; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessDetails; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.api.ApiAccessDetails; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library.LibraryAccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.Access; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.api.ApiAccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.library.LibraryAccessDetails; import java.lang.reflect.Type; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeDeserializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeDeserializer.java similarity index 91% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeDeserializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeDeserializer.java index c47a56fd..9ea4e966 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeDeserializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeDeserializer.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.adapters; +package org.phyloviz.pwp.service.flowviz.adapters; import com.google.gson.JsonDeserializationContext; import com.google.gson.JsonDeserializer; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeSerializer.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeSerializer.java similarity index 92% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeSerializer.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeSerializer.java index f4215ba9..20b0694b 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/adapters/LocalDateTimeSerializer.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/adapters/LocalDateTimeSerializer.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.adapters; +package org.phyloviz.pwp.service.flowviz.adapters; import com.google.gson.JsonElement; import com.google.gson.JsonPrimitive; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/AuthenticationException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/AuthenticationException.java similarity index 71% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/AuthenticationException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/AuthenticationException.java index f7094bad..ed46d03a 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/AuthenticationException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/AuthenticationException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.exceptions; +package org.phyloviz.pwp.service.flowviz.exceptions; public class AuthenticationException extends RuntimeException { public AuthenticationException(String message) { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/ConnectionRefusedException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/ConnectionRefusedException.java similarity index 76% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/ConnectionRefusedException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/ConnectionRefusedException.java index 87a9f110..b8e4d924 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/ConnectionRefusedException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/ConnectionRefusedException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.exceptions; +package org.phyloviz.pwp.service.flowviz.exceptions; import java.io.IOException; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/UnexpectedResponseException.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/UnexpectedResponseException.java similarity index 83% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/UnexpectedResponseException.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/UnexpectedResponseException.java index f8da5606..1cb6cbd0 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/exceptions/UnexpectedResponseException.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/exceptions/UnexpectedResponseException.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.exceptions; +package org.phyloviz.pwp.service.flowviz.exceptions; import lombok.Getter; import okhttp3.Response; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Credentials.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Credentials.java similarity index 68% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Credentials.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Credentials.java index ebdbf13b..b550d38d 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Credentials.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Credentials.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.identity; +package org.phyloviz.pwp.service.flowviz.identity; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Token.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Token.java similarity index 72% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Token.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Token.java index 221ea674..480e0c7a 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/identity/Token.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/identity/Token.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.identity; +package org.phyloviz.pwp.service.flowviz.identity; import com.google.gson.annotations.SerializedName; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowData.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowData.java similarity index 65% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowData.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowData.java index 4c842bd5..bf751de9 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowData.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowData.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.get_workflow; +package org.phyloviz.pwp.service.flowviz.models.get_workflow; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java similarity index 75% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java index 13190bc1..2813b130 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/AirflowWorkflowStatus.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.get_workflow; +package org.phyloviz.pwp.service.flowviz.models.get_workflow; import com.google.gson.annotations.SerializedName; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/GetWorkflowResponse.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/GetWorkflowResponse.java similarity index 58% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/GetWorkflowResponse.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/GetWorkflowResponse.java index 80e6c1d5..af4b3e85 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/GetWorkflowResponse.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/GetWorkflowResponse.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.get_workflow; +package org.phyloviz.pwp.service.flowviz.models.get_workflow; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/WorkflowState.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/WorkflowState.java similarity index 76% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/WorkflowState.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/WorkflowState.java index 950b0d49..7d0e2bc6 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/get_workflow/WorkflowState.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/get_workflow/WorkflowState.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.get_workflow; +package org.phyloviz.pwp.service.flowviz.models.get_workflow; import lombok.Getter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/General.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/General.java similarity index 71% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/General.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/General.java index b4677cba..11706987 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/General.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/General.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool; +package org.phyloviz.pwp.service.flowviz.models.tool; import lombok.Builder; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/Tool.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/Tool.java similarity index 50% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/Tool.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/Tool.java index bab95fab..aac17bce 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/Tool.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/Tool.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool; +package org.phyloviz.pwp.service.flowviz.models.tool; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.Access; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.library.Library; +import org.phyloviz.pwp.service.flowviz.models.tool.access.Access; +import org.phyloviz.pwp.service.flowviz.models.tool.library.Library; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/ToolService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/ToolService.java similarity index 59% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/ToolService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/ToolService.java index 06186c69..4e7b30c5 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/ToolService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/ToolService.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool; +package org.phyloviz.pwp.service.flowviz.models.tool; -import org.phyloviz.pwp.compute.service.flowviz.FLOWViZHttpService; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.ConnectionRefusedException; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.UnexpectedResponseException; +import org.phyloviz.pwp.service.flowviz.FLOWViZHttpService; +import org.phyloviz.pwp.service.flowviz.exceptions.ConnectionRefusedException; +import org.phyloviz.pwp.service.flowviz.exceptions.UnexpectedResponseException; public class ToolService extends FLOWViZHttpService { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/Access.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/Access.java similarity index 69% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/Access.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/Access.java index 88128d0a..a3a87d28 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/Access.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/Access.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access; +package org.phyloviz.pwp.service.flowviz.models.tool.access; import lombok.Builder; import lombok.Data; diff --git a/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessDetails.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessDetails.java new file mode 100644 index 00000000..f92e59d3 --- /dev/null +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessDetails.java @@ -0,0 +1,4 @@ +package org.phyloviz.pwp.service.flowviz.models.tool.access; + +public interface AccessDetails { +} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessType.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessType.java similarity index 76% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessType.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessType.java index 6b54823a..468c6dde 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessType.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/AccessType.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access; +package org.phyloviz.pwp.service.flowviz.models.tool.access; import com.google.gson.annotations.SerializedName; import lombok.RequiredArgsConstructor; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/api/ApiAccessDetails.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/api/ApiAccessDetails.java similarity index 54% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/api/ApiAccessDetails.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/api/ApiAccessDetails.java index 8ceb6005..0bd16fa3 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/api/ApiAccessDetails.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/api/ApiAccessDetails.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access.api; +package org.phyloviz.pwp.service.flowviz.models.tool.access.api; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessDetails; @Data @Builder diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerAutoRemove.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerAutoRemove.java similarity index 79% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerAutoRemove.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerAutoRemove.java index 93037e60..8999c971 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerAutoRemove.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerAutoRemove.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library; +package org.phyloviz.pwp.service.flowviz.models.tool.access.library; import com.google.gson.annotations.SerializedName; import lombok.Getter; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerVolume.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerVolume.java similarity index 78% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerVolume.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerVolume.java index baeeae0e..14c560fb 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/DockerVolume.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/DockerVolume.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library; +package org.phyloviz.pwp.service.flowviz.models.tool.access.library; import com.google.gson.annotations.SerializedName; import lombok.Builder; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/LibraryAccessDetails.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/LibraryAccessDetails.java similarity index 75% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/LibraryAccessDetails.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/LibraryAccessDetails.java index bea04533..16126471 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/LibraryAccessDetails.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/LibraryAccessDetails.java @@ -1,8 +1,8 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library; +package org.phyloviz.pwp.service.flowviz.models.tool.access.library; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessDetails; +import org.phyloviz.pwp.service.flowviz.models.tool.access.AccessDetails; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/VolumeType.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/VolumeType.java similarity index 74% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/VolumeType.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/VolumeType.java index 061c6b3f..8feef59b 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/library/VolumeType.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/access/library/VolumeType.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access.library; +package org.phyloviz.pwp.service.flowviz.models.tool.access.library; import com.google.gson.annotations.SerializedName; import lombok.RequiredArgsConstructor; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Command.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Command.java similarity index 82% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Command.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Command.java index 1aeaac16..4ac93a12 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Command.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Command.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.library; +package org.phyloviz.pwp.service.flowviz.models.tool.library; import lombok.Builder; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Library.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Library.java similarity index 80% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Library.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Library.java index 766ba8ed..912b024f 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/library/Library.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/tool/library/Library.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.library; +package org.phyloviz.pwp.service.flowviz.models.tool.library; import lombok.Builder; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java similarity index 60% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java index be6f1f46..fdcdd1f7 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/GetWorkflowTaskLogResponse.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.workflow; +package org.phyloviz.pwp.service.flowviz.models.workflow; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/Workflow.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/Workflow.java similarity index 73% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/Workflow.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/Workflow.java index a11ab209..dfdc4207 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/Workflow.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/Workflow.java @@ -1,10 +1,10 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.workflow; +package org.phyloviz.pwp.service.flowviz.models.workflow; import com.google.gson.annotations.SerializedName; import lombok.Builder; import lombok.Data; -import org.phyloviz.pwp.compute.service.flowviz.models.workflow.tasks.Task; +import org.phyloviz.pwp.service.flowviz.models.workflow.tasks.Task; import java.time.LocalDateTime; import java.util.List; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/WorkflowService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/WorkflowService.java similarity index 66% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/WorkflowService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/WorkflowService.java index a91d99b6..243175bc 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/WorkflowService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/WorkflowService.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.workflow; +package org.phyloviz.pwp.service.flowviz.models.workflow; -import org.phyloviz.pwp.compute.service.flowviz.FLOWViZHttpService; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.ConnectionRefusedException; -import org.phyloviz.pwp.compute.service.flowviz.exceptions.UnexpectedResponseException; -import org.phyloviz.pwp.compute.service.flowviz.models.get_workflow.GetWorkflowResponse; +import org.phyloviz.pwp.service.flowviz.FLOWViZHttpService; +import org.phyloviz.pwp.service.flowviz.exceptions.ConnectionRefusedException; +import org.phyloviz.pwp.service.flowviz.exceptions.UnexpectedResponseException; +import org.phyloviz.pwp.service.flowviz.models.get_workflow.GetWorkflowResponse; public class WorkflowService extends FLOWViZHttpService { diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Action.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Action.java similarity index 62% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Action.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Action.java index 7e7922b0..2a7143ca 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Action.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Action.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.workflow.tasks; +package org.phyloviz.pwp.service.flowviz.models.workflow.tasks; import lombok.Builder; import lombok.Data; diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Task.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Task.java similarity index 77% rename from src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Task.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Task.java index b34d3f0d..627d8c7a 100644 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/workflow/tasks/Task.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/flowviz/models/workflow/tasks/Task.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.workflow.tasks; +package org.phyloviz.pwp.service.flowviz.models.workflow.tasks; import lombok.Builder; import lombok.Data; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectService.java similarity index 81% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectService.java index 034e6c21..4bdbe88a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectService.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.service.project; +package org.phyloviz.pwp.service.project; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; -import org.phyloviz.pwp.administration.service.dtos.project.UpdateProjectOutput; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.service.dtos.project.CreateProjectOutput; +import org.phyloviz.pwp.service.dtos.project.FullProjectInfo; +import org.phyloviz.pwp.service.dtos.project.UpdateProjectOutput; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectServiceImpl.java similarity index 78% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectServiceImpl.java index d42f241b..92bdff13 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/ProjectServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/ProjectServiceImpl.java @@ -1,17 +1,17 @@ -package org.phyloviz.pwp.administration.service.project; +package org.phyloviz.pwp.service.project; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.files.FilesInfo; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; -import org.phyloviz.pwp.administration.service.dtos.project.UpdateProjectOutput; -import org.phyloviz.pwp.administration.service.project.dataset.DatasetService; -import org.phyloviz.pwp.administration.service.project.file.IsolateDataService; -import org.phyloviz.pwp.administration.service.project.file.TypingDataService; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.dtos.files.FilesInfo; +import org.phyloviz.pwp.service.dtos.project.CreateProjectOutput; +import org.phyloviz.pwp.service.dtos.project.FullProjectInfo; +import org.phyloviz.pwp.service.dtos.project.UpdateProjectOutput; +import org.phyloviz.pwp.service.project.dataset.DatasetService; +import org.phyloviz.pwp.service.project.file.IsolateDataService; +import org.phyloviz.pwp.service.project.file.TypingDataService; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.project.documents.Project; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetService.java similarity index 89% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetService.java index 67881e9c..71eeedda 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetService.java @@ -1,9 +1,9 @@ -package org.phyloviz.pwp.administration.service.project.dataset; +package org.phyloviz.pwp.service.project.dataset; -import org.phyloviz.pwp.administration.service.dtos.dataset.CreateDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; -import org.phyloviz.pwp.administration.service.dtos.dataset.SetIsolateDataOfDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.UpdateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.CreateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.service.dtos.dataset.SetIsolateDataOfDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.UpdateDatasetOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetServiceImpl.java similarity index 85% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetServiceImpl.java index a253b8ff..596db2c3 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/DatasetServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/DatasetServiceImpl.java @@ -1,25 +1,21 @@ -package org.phyloviz.pwp.administration.service.project.dataset; +package org.phyloviz.pwp.service.project.dataset; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.dataset.CreateDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; -import org.phyloviz.pwp.administration.service.dtos.dataset.SetIsolateDataOfDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.UpdateDatasetOutput; -import org.phyloviz.pwp.administration.service.project.dataset.distance_matrix.DistanceMatrixService; -import org.phyloviz.pwp.administration.service.project.dataset.tree.TreeService; -import org.phyloviz.pwp.administration.service.project.dataset.tree_view.TreeViewService; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.dataset.documents.Dataset; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataDoesNotExistException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataDoesNotExistException; -import org.phyloviz.pwp.shared.utils.UUIDUtils; +import org.phyloviz.pwp.service.dtos.dataset.CreateDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.FullDatasetInfo; +import org.phyloviz.pwp.service.dtos.dataset.SetIsolateDataOfDatasetOutput; +import org.phyloviz.pwp.service.dtos.dataset.UpdateDatasetOutput; +import org.phyloviz.pwp.service.project.dataset.distance_matrix.DistanceMatrixService; +import org.phyloviz.pwp.service.project.dataset.tree.TreeService; +import org.phyloviz.pwp.service.project.dataset.tree_view.TreeViewService; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.dataset.documents.Dataset; +import org.phyloviz.pwp.repository.metadata.isolate_data.IsolateDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.TypingDataMetadataRepository; +import org.phyloviz.pwp.service.exceptions.*; +import org.phyloviz.pwp.utils.UUIDUtils; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixService.java similarity index 84% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixService.java index eed7948f..6ac9fc48 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.project.dataset.distance_matrix; +package org.phyloviz.pwp.service.project.dataset.distance_matrix; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java similarity index 76% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java index e7a4b5c6..8b2f8978 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/distance_matrix/DistanceMatrixServiceImpl.java @@ -1,19 +1,19 @@ -package org.phyloviz.pwp.administration.service.project.dataset.distance_matrix; +package org.phyloviz.pwp.service.project.dataset.distance_matrix; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedResourceDeletionException; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.DistanceMatrixNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.dtos.distance_matrix.DistanceMatrixInfo; +import org.phyloviz.pwp.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; +import org.phyloviz.pwp.service.exceptions.DeniedResourceDeletionException; +import org.phyloviz.pwp.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryFactory; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; +import org.phyloviz.pwp.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.tree.TreeMetadataRepository; +import org.phyloviz.pwp.service.exceptions.DatasetNotFoundException; +import org.phyloviz.pwp.service.exceptions.DistanceMatrixNotFoundException; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeService.java similarity index 85% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeService.java index 4eca24ad..9e91c439 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.project.dataset.tree; +package org.phyloviz.pwp.service.project.dataset.tree; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.UpdateTreeOutput; +import org.phyloviz.pwp.service.dtos.tree.TreeInfo; +import org.phyloviz.pwp.service.dtos.tree.UpdateTreeOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeServiceImpl.java similarity index 75% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeServiceImpl.java index bf951bf8..d1945f6d 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree/TreeServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree/TreeServiceImpl.java @@ -1,19 +1,19 @@ -package org.phyloviz.pwp.administration.service.project.dataset.tree; +package org.phyloviz.pwp.service.project.dataset.tree; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.UpdateTreeOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedResourceDeletionException; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeNotFoundException; +import org.phyloviz.pwp.service.dtos.tree.TreeInfo; +import org.phyloviz.pwp.service.dtos.tree.UpdateTreeOutput; +import org.phyloviz.pwp.service.exceptions.DeniedResourceDeletionException; +import org.phyloviz.pwp.repository.data.registry.tree.TreeDataRepositoryFactory; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.tree.TreeMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree.documents.TreeMetadata; +import org.phyloviz.pwp.repository.metadata.tree_view.TreeViewMetadataRepository; +import org.phyloviz.pwp.service.exceptions.DatasetNotFoundException; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.exceptions.TreeNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewService.java similarity index 84% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewService.java index 1b60dc1a..d6a63485 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.project.dataset.tree_view; +package org.phyloviz.pwp.service.project.dataset.tree_view; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewInfo; -import org.phyloviz.pwp.administration.service.dtos.tree_view.UpdateTreeViewOutput; +import org.phyloviz.pwp.service.dtos.tree_view.TreeViewInfo; +import org.phyloviz.pwp.service.dtos.tree_view.UpdateTreeViewOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewServiceImpl.java similarity index 76% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewServiceImpl.java index a19c874a..48cdb2c7 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/dataset/tree_view/TreeViewServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/dataset/tree_view/TreeViewServiceImpl.java @@ -1,17 +1,17 @@ -package org.phyloviz.pwp.administration.service.project.dataset.tree_view; +package org.phyloviz.pwp.service.project.dataset.tree_view; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewInfo; -import org.phyloviz.pwp.administration.service.dtos.tree_view.UpdateTreeViewOutput; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeViewNotFoundException; +import org.phyloviz.pwp.service.dtos.tree_view.TreeViewInfo; +import org.phyloviz.pwp.service.dtos.tree_view.UpdateTreeViewOutput; +import org.phyloviz.pwp.repository.data.registry.tree_view.TreeViewDataRepositoryFactory; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.tree_view.TreeViewMetadataRepository; +import org.phyloviz.pwp.repository.metadata.tree_view.documents.TreeViewMetadata; +import org.phyloviz.pwp.service.exceptions.DatasetNotFoundException; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.exceptions.TreeViewNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataService.java similarity index 60% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataService.java index 0f7eb8a5..feeae9bb 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.project.file; +package org.phyloviz.pwp.service.project.file; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.IsolateDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.UpdateIsolateDataOutput; +import org.phyloviz.pwp.service.dtos.files.isolate_data.IsolateDataInfo; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UpdateIsolateDataOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataServiceImpl.java similarity index 76% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataServiceImpl.java index c985fd7f..8ab78550 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/IsolateDataServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/IsolateDataServiceImpl.java @@ -1,17 +1,17 @@ -package org.phyloviz.pwp.administration.service.project.file; +package org.phyloviz.pwp.service.project.file; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.IsolateDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.UpdateIsolateDataOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedFileDeletionException; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.dtos.files.isolate_data.IsolateDataInfo; +import org.phyloviz.pwp.service.dtos.files.isolate_data.UpdateIsolateDataOutput; +import org.phyloviz.pwp.service.exceptions.DeniedFileDeletionException; +import org.phyloviz.pwp.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.IsolateDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.isolate_data.documents.IsolateDataMetadata; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.IsolateDataNotFoundException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataService.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataService.java similarity index 60% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataService.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataService.java index ebe0ef8a..c1da38c4 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataService.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataService.java @@ -1,7 +1,7 @@ -package org.phyloviz.pwp.administration.service.project.file; +package org.phyloviz.pwp.service.project.file; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.TypingDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.UpdateTypingDataOutput; +import org.phyloviz.pwp.service.dtos.files.typing_data.TypingDataInfo; +import org.phyloviz.pwp.service.dtos.files.typing_data.UpdateTypingDataOutput; import java.util.List; diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataServiceImpl.java b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataServiceImpl.java similarity index 75% rename from src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataServiceImpl.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataServiceImpl.java index fa1da705..effe713a 100644 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/project/file/TypingDataServiceImpl.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/service/project/file/TypingDataServiceImpl.java @@ -1,17 +1,17 @@ -package org.phyloviz.pwp.administration.service.project.file; +package org.phyloviz.pwp.service.project.file; import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.TypingDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.UpdateTypingDataOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedFileDeletionException; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataNotFoundException; +import org.phyloviz.pwp.service.dtos.files.typing_data.TypingDataInfo; +import org.phyloviz.pwp.service.dtos.files.typing_data.UpdateTypingDataOutput; +import org.phyloviz.pwp.service.exceptions.DeniedFileDeletionException; +import org.phyloviz.pwp.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; +import org.phyloviz.pwp.repository.metadata.dataset.DatasetRepository; +import org.phyloviz.pwp.repository.metadata.project.ProjectRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.TypingDataMetadataRepository; +import org.phyloviz.pwp.repository.metadata.typing_data.documents.TypingDataMetadata; +import org.phyloviz.pwp.service.exceptions.InvalidArgumentException; +import org.phyloviz.pwp.service.exceptions.ProjectNotFoundException; +import org.phyloviz.pwp.service.exceptions.TypingDataNotFoundException; import org.springframework.stereotype.Service; import org.springframework.transaction.annotation.Transactional; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/SharedLogger.java b/src/backend/core/src/main/java/org/phyloviz/pwp/utils/SharedLogger.java similarity index 97% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/SharedLogger.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/utils/SharedLogger.java index c3682af8..2ee2a1ff 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/SharedLogger.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/utils/SharedLogger.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.utils; +package org.phyloviz.pwp.utils; import org.slf4j.LoggerFactory; diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/UUIDUtils.java b/src/backend/core/src/main/java/org/phyloviz/pwp/utils/UUIDUtils.java similarity index 94% rename from src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/UUIDUtils.java rename to src/backend/core/src/main/java/org/phyloviz/pwp/utils/UUIDUtils.java index 7b421d0b..f9f52bd8 100644 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/utils/UUIDUtils.java +++ b/src/backend/core/src/main/java/org/phyloviz/pwp/utils/UUIDUtils.java @@ -1,4 +1,4 @@ -package org.phyloviz.pwp.shared.utils; +package org.phyloviz.pwp.utils; import java.util.UUID; diff --git a/src/backend/microservices/gateway/Dockerfile b/src/backend/gateway/Dockerfile similarity index 100% rename from src/backend/microservices/gateway/Dockerfile rename to src/backend/gateway/Dockerfile diff --git a/src/backend/microservices/gateway/build.gradle b/src/backend/gateway/build.gradle similarity index 100% rename from src/backend/microservices/gateway/build.gradle rename to src/backend/gateway/build.gradle diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/GatewayApplication.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/GatewayApplication.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/GatewayApplication.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/GatewayApplication.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/GatewayConfig.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/GatewayConfig.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/GatewayConfig.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/GatewayConfig.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/MicroservicesProperties.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/MicroservicesProperties.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/MicroservicesProperties.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/MicroservicesProperties.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/ProblemJsonResponseBodyResultHandler.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/ProblemJsonResponseBodyResultHandler.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/config/ProblemJsonResponseBodyResultHandler.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/config/ProblemJsonResponseBodyResultHandler.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/NegatePathResourceLookupFunction.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/NegatePathResourceLookupFunction.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/NegatePathResourceLookupFunction.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/NegatePathResourceLookupFunction.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/controllers/AuthController.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/controllers/AuthController.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/controllers/AuthController.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/controllers/AuthController.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/exceptions/AuthenticationException.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/exceptions/AuthenticationException.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/exceptions/AuthenticationException.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/exceptions/AuthenticationException.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/models/get_session/GetSessionOutputModel.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/models/get_session/GetSessionOutputModel.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/models/get_session/GetSessionOutputModel.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/models/get_session/GetSessionOutputModel.java diff --git a/src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/pipeline/GatewayExceptionHandler.java b/src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/pipeline/GatewayExceptionHandler.java similarity index 100% rename from src/backend/microservices/gateway/src/main/java/org/phyloviz/pwp/gateway/http/pipeline/GatewayExceptionHandler.java rename to src/backend/gateway/src/main/java/org/phyloviz/pwp/gateway/http/pipeline/GatewayExceptionHandler.java diff --git a/src/backend/microservices/gateway/src/test/java/org/phyloviz/pwp/gateway/GatewayApplicationTests.java b/src/backend/gateway/src/test/java/org/phyloviz/pwp/gateway/GatewayApplicationTests.java similarity index 100% rename from src/backend/microservices/gateway/src/test/java/org/phyloviz/pwp/gateway/GatewayApplicationTests.java rename to src/backend/gateway/src/test/java/org/phyloviz/pwp/gateway/GatewayApplicationTests.java diff --git a/src/backend/microservices/administration/Dockerfile b/src/backend/microservices/administration/Dockerfile deleted file mode 100644 index 868b03da..00000000 --- a/src/backend/microservices/administration/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM openjdk:17-jdk-alpine -COPY build/libs/administration-0.0.1-SNAPSHOT.jar /app.jar - -ENTRYPOINT ["java", "-jar", "/app.jar"] \ No newline at end of file diff --git a/src/backend/microservices/administration/build.gradle b/src/backend/microservices/administration/build.gradle deleted file mode 100644 index 9efebb93..00000000 --- a/src/backend/microservices/administration/build.gradle +++ /dev/null @@ -1,41 +0,0 @@ -plugins { - id 'application' - id 'org.springframework.boot' version '3.0.4' - id 'io.spring.dependency-management' version '1.1.0' - id "io.freefair.lombok" version "8.0.0-rc2" -} - -group 'phylovizwebplatform' -version '0.0.1-SNAPSHOT' -sourceCompatibility = '17' - -ext { - set('jupiterVersion', "5.8.1") -} - -repositories { - mavenCentral() -} - -dependencies { - implementation project(path: ':microservices:shared-phylodb') - implementation project(path: ':microservices:shared') - - testImplementation 'org.springframework.boot:spring-boot-starter-test' - testImplementation 'org.junit.jupiter:junit-jupiter-api' version { jupiterVersion } - testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine' version { jupiterVersion } - - implementation 'org.springframework.boot:spring-boot-starter-data-mongodb' - implementation 'org.springframework.boot:spring-boot-starter-web' - implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server' - - implementation 'com.fasterxml.jackson.core:jackson-databind:2.14.2' - implementation 'org.zalando:problem-spring-web-starter:0.27.0' - - implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' - testImplementation 'junit:junit:4.13.1' -} - -test { - useJUnitPlatform() -} \ No newline at end of file diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplication.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplication.java deleted file mode 100644 index 26d6f5d2..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplication.java +++ /dev/null @@ -1,20 +0,0 @@ -package org.phyloviz.pwp.administration; - -import org.springframework.boot.SpringApplication; -import org.springframework.boot.autoconfigure.SpringBootApplication; - -/** - * Main class for the Administration Microservice of the PHYLOViZ Web Platform. - */ -@SpringBootApplication -public class AdministrationMicroserviceApplication { - - /** - * Entry point for the Administration Microservice. - * - * @param args arguments passed to the application - */ - public static void main(String[] args) { - SpringApplication.run(AdministrationMicroserviceApplication.class, args); - } -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/config/AdministrationConfig.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/config/AdministrationConfig.java deleted file mode 100644 index a536db07..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/config/AdministrationConfig.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.phyloviz.pwp.administration.config; - -import org.phyloviz.pwp.shared.config.ResourceServerSharedConfig; -import org.phyloviz.pwp.shared_phylodb.config.ResourceServerSharedPhylodbConfig; -import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Import; - -/** - * Configuration class for the Administration Microservice. - */ -@Configuration -@Import({ResourceServerSharedConfig.class, ResourceServerSharedPhylodbConfig.class}) -public class AdministrationConfig { -} \ No newline at end of file diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_dataset/GetDatasetOutputModel.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_dataset/GetDatasetOutputModel.java deleted file mode 100644 index 30042d78..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/datasets/get_dataset/GetDatasetOutputModel.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.administration.http.models.datasets.get_dataset; - -import org.phyloviz.pwp.administration.http.models.datasets.DatasetModel; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; - -public class GetDatasetOutputModel extends DatasetModel { - public GetDatasetOutputModel(FullDatasetInfo fullDatasetInfo) { - super(fullDatasetInfo); - } -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java deleted file mode 100644 index 5c1b4ef9..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/distance_matrices/DistanceMatrixSourceOutputModel.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.administration.http.models.distance_matrices; - -public interface DistanceMatrixSourceOutputModel { -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_project/GetProjectOutputModel.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_project/GetProjectOutputModel.java deleted file mode 100644 index 18cda661..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/projects/get_project/GetProjectOutputModel.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.administration.http.models.projects.get_project; - -import org.phyloviz.pwp.administration.http.models.projects.ProjectModel; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; - -public class GetProjectOutputModel extends ProjectModel { - public GetProjectOutputModel(FullProjectInfo fullProjectInfo) { - super(fullProjectInfo); - } -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceOutputModel.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceOutputModel.java deleted file mode 100644 index 557f90fc..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/http/models/trees/TreeSourceOutputModel.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.administration.http.models.trees; - -public interface TreeSourceOutputModel { -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java deleted file mode 100644 index 681b821e..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/distance_matrix/DistanceMatrixSourceInfo.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.administration.service.dtos.distance_matrix; - -public interface DistanceMatrixSourceInfo { -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/FilesInfo.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/FilesInfo.java deleted file mode 100644 index ec7707c8..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/files/FilesInfo.java +++ /dev/null @@ -1,13 +0,0 @@ -package org.phyloviz.pwp.administration.service.dtos.files; - -import lombok.Data; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.IsolateDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.TypingDataInfo; - -import java.util.List; - -@Data -public class FilesInfo { - private final List typingData; - private final List isolateData; -} diff --git a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceInfo.java b/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceInfo.java deleted file mode 100644 index 3b1f6624..00000000 --- a/src/backend/microservices/administration/src/main/java/org/phyloviz/pwp/administration/service/dtos/tree/TreeSourceInfo.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.phyloviz.pwp.administration.service.dtos.tree; - -public interface TreeSourceInfo { -} - diff --git a/src/backend/microservices/administration/src/main/resources/application.yml b/src/backend/microservices/administration/src/main/resources/application.yml deleted file mode 100644 index fcb987c6..00000000 --- a/src/backend/microservices/administration/src/main/resources/application.yml +++ /dev/null @@ -1,10 +0,0 @@ -server: - port: 8088 - -spring: - config: - import: application-shared.yml - -logging: - level: - root: debug \ No newline at end of file diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplicationTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplicationTests.java deleted file mode 100644 index 0544b6cc..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/AdministrationMicroserviceApplicationTests.java +++ /dev/null @@ -1,12 +0,0 @@ -package org.phyloviz.pwp.administration; - -import org.junit.jupiter.api.Test; -import org.springframework.boot.test.context.SpringBootTest; - -@SpringBootTest -class AdministrationMicroserviceApplicationTests { - - @Test - void contextLoads() { - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsControllerTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsControllerTests.java deleted file mode 100644 index ca1febe0..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/http/controllers/projects/ProjectsControllerTests.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.phyloviz.pwp.administration.http.controllers.projects; - - -import org.junit.jupiter.api.Test; -import org.junit.runner.RunWith; -import org.mockito.Mockito; -import org.phyloviz.pwp.administration.http.models.projects.create_project.CreateProjectInputModel; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; -import org.phyloviz.pwp.administration.service.project.ProjectService; -import org.springframework.boot.test.context.SpringBootTest; -import org.springframework.boot.test.mock.mockito.MockBean; -import org.springframework.test.context.junit4.SpringRunner; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -@RunWith(SpringRunner.class) -@SpringBootTest -class ProjectsControllerTests { - - @MockBean - private ProjectService projectService; - - @Test - void createProjectIsSuccessful() { - CreateProjectInputModel createProjectInputModel = new CreateProjectInputModel(); - createProjectInputModel.setName("project1"); - createProjectInputModel.setDescription("project1 description"); - - String projectId = "projectId"; - String userId = "userId"; - Mockito.when(projectService.createProject( - createProjectInputModel.getName(), - createProjectInputModel.getDescription(), - userId - )).thenReturn( - new CreateProjectOutput(projectId) - ); - - CreateProjectOutput createProjectOutput = projectService.createProject( - createProjectInputModel.getName(), - createProjectInputModel.getDescription(), - userId - ); - - assertEquals(projectId, createProjectOutput.getProjectId()); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/ProjectsServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/ProjectsServiceTests.java deleted file mode 100644 index c0ee79d9..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/ProjectsServiceTests.java +++ /dev/null @@ -1,320 +0,0 @@ -package org.phyloviz.pwp.administration.service; - - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.CsvSource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.project.CreateProjectOutput; -import org.phyloviz.pwp.administration.service.dtos.project.FullProjectInfo; -import org.phyloviz.pwp.administration.service.dtos.project.UpdateProjectOutput; -import org.phyloviz.pwp.administration.service.project.ProjectServiceImpl; -import org.phyloviz.pwp.administration.service.project.dataset.DatasetService; -import org.phyloviz.pwp.administration.service.project.file.IsolateDataService; -import org.phyloviz.pwp.administration.service.project.file.TypingDataService; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.documents.Project; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; - -import java.util.List; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class ProjectsServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetService datasetService; - - @Mock - private TypingDataService typingDataService; - - @Mock - private IsolateDataService isolateDataService; - - @InjectMocks - private ProjectServiceImpl projectService; - - // createProject - @Test - void createProjectIsSuccessful() { - String projectName = "project1"; - String projectDescription = "project1 description"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.save(any(Project.class))) - .thenReturn( - new Project( - projectId, - projectName, - projectDescription, - userId - ) - ); - - CreateProjectOutput createProjectOutput = projectService.createProject( - projectName, - projectDescription, - userId - ); - - assertEquals(projectId, createProjectOutput.getProjectId()); - } - - @Test - void createProjectWithEmptyNameThrowsException() { - String projectName = ""; - String projectDescription = "project1 description"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - assertThrows(InvalidArgumentException.class, () -> - projectService.createProject( - projectName, - projectDescription, - userId - )); - } - - - // getFullProjectInfo - @Test - void getFullProjectInfoIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String projectName = "project1"; - String projectDescription = "project1 description"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn( - Optional.of(new Project( - projectId, - projectName, - projectDescription, - userId - )) - ); - - when(datasetService.getFullDatasetInfos(any(String.class))).thenReturn(List.of()); - when(typingDataService.getTypingDataInfos(any(String.class))).thenReturn(List.of()); - when(isolateDataService.getIsolateDataInfos(any(String.class))).thenReturn(List.of()); - - FullProjectInfo fullProjectInfo = projectService.getFullProjectInfo(projectId, userId); - - assertEquals(projectId, fullProjectInfo.getProjectId()); - assertEquals(projectName, fullProjectInfo.getName()); - assertEquals(projectDescription, fullProjectInfo.getDescription()); - assertEquals(userId, fullProjectInfo.getOwner()); - assertTrue(fullProjectInfo.getDatasets().isEmpty()); - assertTrue(fullProjectInfo.getFiles().getTypingData().isEmpty()); - assertTrue(fullProjectInfo.getFiles().getIsolateData().isEmpty()); - } - - @Test - void getFullProjectInfoWithInexistentProjectIdThrowsException() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(ProjectNotFoundException.class, () -> - projectService.getFullProjectInfo(projectId, userId) - ); - } - - @Test - void getFullProjectInfoWithInexistentUserIdThrowsException() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(ProjectNotFoundException.class, () -> - projectService.getFullProjectInfo(projectId, userId) - ); - } - - - // getProjects - @Test - void getProjectsIsSuccessful() { - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - List projects = List.of( - new Project( - "ec7bae63-3238-4044-8d03-e2d9911f50f8", - "project1", - "project1 description", - userId - ), - new Project( - "ec7bae63-3238-4044-8d03-e2d9911f50f9", - "project2", - "project2 description", - userId - ) - ); - - when(projectRepository.findAllByOwnerId(any(String.class))) - .thenReturn(projects); - - List userProjects = projectService.getProjects(userId); - assertEquals(projects.size(), userProjects.size()); - assertEquals(projects, userProjects); - } - - - // deleteProject - @Test - void deleteProjectIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn( - Optional.of(new Project( - projectId, - "project1", - "project1 description", - userId - )) - ); - - projectService.deleteProject(projectId, userId); - - verify(projectRepository, times(1)).delete(any(Project.class)); - } - - @Test - void deleteProjectWithInexistentProjectIdThrowsException() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(ProjectNotFoundException.class, () -> - projectService.deleteProject(projectId, userId) - ); - } - - @Test - void deleteProjectWithInexistentUserIdThrowsException() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(ProjectNotFoundException.class, () -> - projectService.deleteProject(projectId, userId) - ); - } - - - // updateProject - @Test - void updateProjectIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String projectName = "project1"; - String projectDescription = "project1 description"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - String newProjectName = "project1 updated"; - String newProjectDescription = "project1 description updated"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn( - Optional.of(new Project( - projectId, - projectName, - projectDescription, - userId - )) - ); - - when(projectRepository.save(any(Project.class))) - .thenReturn(new Project( - projectId, - newProjectName, - newProjectDescription, - userId - )); - - UpdateProjectOutput updateProjectOutput = projectService.updateProject( - newProjectName, - newProjectDescription, - projectId, - userId - ); - - assertEquals(projectName, updateProjectOutput.getPreviousName()); - assertEquals(projectDescription, updateProjectOutput.getPreviousDescription()); - assertEquals(newProjectName, updateProjectOutput.getNewName()); - assertEquals(newProjectDescription, updateProjectOutput.getNewDescription()); - } - - @Test - void updateProjectWithInexistentProjectIdThrowsException() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - String newProjectName = "project1 updated"; - String newProjectDescription = "project1 description updated"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(ProjectNotFoundException.class, () -> - projectService.updateProject( - newProjectName, - newProjectDescription, - projectId, - userId - )); - } - - @ParameterizedTest - @CsvSource({ - ",", - "'', description", - "name,''", - }) - void updateProjectWithInvalidFieldsThrowsException(String newProjectName, String newProjectDescription) { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String projectName = "project1"; - String projectDescription = "project1 description"; - String userId = "2da00a2f-21bd-43fd-8c07-0e74725c851a"; - - when(projectRepository.findByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn( - Optional.of(new Project( - projectId, - projectName, - projectDescription, - userId - )) - ); - - assertThrows(InvalidArgumentException.class, () -> - projectService.updateProject( - newProjectName, - newProjectDescription, - projectId, - userId - )); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/DatasetServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/DatasetServiceTests.java deleted file mode 100644 index 12a421c6..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/DatasetServiceTests.java +++ /dev/null @@ -1,562 +0,0 @@ -package org.phyloviz.pwp.administration.service.dataset; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.CsvSource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.dataset.CreateDatasetOutput; -import org.phyloviz.pwp.administration.service.dtos.dataset.FullDatasetInfo; -import org.phyloviz.pwp.administration.service.dtos.dataset.UpdateDatasetOutput; -import org.phyloviz.pwp.administration.service.project.dataset.DatasetServiceImpl; -import org.phyloviz.pwp.administration.service.project.dataset.distance_matrix.DistanceMatrixService; -import org.phyloviz.pwp.administration.service.project.dataset.tree.TreeService; -import org.phyloviz.pwp.administration.service.project.dataset.tree_view.TreeViewService; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.dataset.documents.Dataset; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; - -import java.util.ArrayList; -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class DatasetServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private TypingDataMetadataRepository typingDataMetadataRepository; - - @Mock - private IsolateDataMetadataRepository isolateDataMetadataRepository; - - @Mock - private DistanceMatrixService distanceMatrixService; - - @Mock - private TreeService treeService; - - @Mock - private TreeViewService treeViewService; - - @InjectMocks - private DatasetServiceImpl datasetService; - - - // createDataset - @Test - void createDatasetWithoutIsolateDataIsSuccessfull() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = null; - String isolateDataKey = null; - String projectId = "projectId"; - String userId = "userId"; - String datasetId = "datasetId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(typingDataMetadataRepository.existsByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.save(any())) - .thenReturn(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey - )); - - CreateDatasetOutput createDatasetOutput = datasetService.createDataset( - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey, - projectId, - userId - ); - - assertEquals(datasetId, createDatasetOutput.getDatasetId()); - assertEquals(projectId, createDatasetOutput.getProjectId()); - } - - @Test - void createDatasetWithIsolateDataIsSuccessfull() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "dfb3b1a0-7b9a-4b7e-9b9a-5b8b5b5b5b5b"; - String isolateDataName = "isolateDataName"; - String isolateDataKey = "isolateDataKey"; - String projectId = "projectId"; - String userId = "userId"; - String datasetId = "datasetId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(typingDataMetadataRepository.existsByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(true); - - when(isolateDataMetadataRepository.findByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new IsolateDataMetadata( - projectId, - isolateDataId, - List.of(isolateDataKey), - isolateDataName, - Map.of(IsolateDataDataRepositoryId.S3, new IsolateDataS3DataRepositorySpecificData()) - ))); - - when(datasetRepository.save(any())) - .thenReturn(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey - )); - - CreateDatasetOutput createDatasetOutput = datasetService.createDataset( - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey, - projectId, - userId - ); - - assertEquals(datasetId, createDatasetOutput.getDatasetId()); - assertEquals(projectId, createDatasetOutput.getProjectId()); - } - - - @Test - void createDatasetThrowsWhenIsolateDataKeyIsNull() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "dfb3b1a0-7b9a-4b7e-9b9a-5b8b5b5b5b5b"; - String isolateDataName = "isolateDataName"; - String isolateDataKey = null; - String projectId = "projectId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(typingDataMetadataRepository.existsByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(true); - - List isolateDataKeys = new ArrayList<>(); - isolateDataKeys.add(isolateDataKey); - - assertThrows( - InvalidArgumentException.class, - () -> datasetService.createDataset( - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey, - projectId, - userId - ) - ); - } - - @Test - void createDatasetThrowsWhenProjectDoesNotExist() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = null; - String isolateDataKey = null; - String projectId = "projectId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - datasetService.createDataset( - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey, - projectId, - userId - )); - } - - @ParameterizedTest - @CsvSource({ - ", ec7bae63-3238-4044-8d03-e2d9911f50f8, dh9bae45-3238-4044-8d03-e2d9911f50f8", - "'', ec7bae63-3238-4044-8d03-e2d9911f50f8, dh9bae45-3238-4044-8d03-e2d9911f50f8", - "name,, dh9bae45-3238-4044-8d03-e2d9911f50f8", - "name,'', dh9bae45-3238-4044-8d03-e2d9911f50f8", - "name,invalidUUID, dh9bae45-3238-4044-8d03-e2d9911f50f8", - "name,ec7bae63-3238-4044-8d03-e2d9911f50f8,''", - "name,ec7bae63-3238-4044-8d03-e2d9911f50f8,invalidUUID", - }) - void createDatasetThrowsWhenInvalidArguments(String datasetName, String typingDataId, String isolateDataId) { - String datasetDescription = "datasetDescription"; - String isolateDataKey = "isolateDataKey"; - String projectId = "projectId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(InvalidArgumentException.class, () -> - datasetService.createDataset( - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey, - projectId, - userId - )); - } - - // getFullDatasetInfo - @Test - void getFullDatasetInfoIsSuccessful() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = null; - String isolateDataKey = null; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn( - Optional.of(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey - )) - ); - - when(distanceMatrixService.getDistanceMatrixInfos(any(String.class))).thenReturn(List.of()); - when(treeService.getTreeInfos(any(String.class))).thenReturn(List.of()); - when(treeViewService.getTreeViewInfos(any(String.class))).thenReturn(List.of()); - - FullDatasetInfo fullDatasetInfo = datasetService.getFullDatasetInfo(projectId, datasetId, userId); - - assertEquals(datasetId, fullDatasetInfo.getDatasetId()); - assertEquals(datasetName, fullDatasetInfo.getName()); - assertEquals(datasetDescription, fullDatasetInfo.getDescription()); - assertEquals(typingDataId, fullDatasetInfo.getTypingDataId()); - assertEquals(isolateDataId, fullDatasetInfo.getIsolateDataId()); - assertTrue(fullDatasetInfo.getDistanceMatrices().isEmpty()); - assertTrue(fullDatasetInfo.getTrees().isEmpty()); - assertTrue(fullDatasetInfo.getTreeViews().isEmpty()); - } - - @Test - void getFullDatasetInfoThrowsWhenDatasetDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(DatasetNotFoundException.class, () -> - datasetService.getFullDatasetInfo(projectId, datasetId, userId) - ); - } - - // getFullDatasetInfos - @Test - void getFullDatasetInfosIsSuccessful() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = null; - String isolateDataKey = null; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.findAllByProjectId(any(String.class))) - .thenReturn( - List.of(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey - )) - ); - - when(distanceMatrixService.getDistanceMatrixInfos(any(String.class))).thenReturn(List.of()); - when(treeService.getTreeInfos(any(String.class))).thenReturn(List.of()); - when(treeViewService.getTreeViewInfos(any(String.class))).thenReturn(List.of()); - - List fullDatasetInfos = datasetService.getFullDatasetInfos(projectId, userId); - - assertEquals(1, fullDatasetInfos.size()); - assertEquals(datasetId, fullDatasetInfos.get(0).getDatasetId()); - assertEquals(datasetName, fullDatasetInfos.get(0).getName()); - assertEquals(datasetDescription, fullDatasetInfos.get(0).getDescription()); - assertEquals(typingDataId, fullDatasetInfos.get(0).getTypingDataId()); - assertEquals(isolateDataId, fullDatasetInfos.get(0).getIsolateDataId()); - assertTrue(fullDatasetInfos.get(0).getDistanceMatrices().isEmpty()); - assertTrue(fullDatasetInfos.get(0).getTrees().isEmpty()); - assertTrue(fullDatasetInfos.get(0).getTreeViews().isEmpty()); - } - - @Test - void getFullDatasetInfosThrowsWhenProjectDoesNotExist() { - String projectId = "projectId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - datasetService.getFullDatasetInfos(projectId, userId) - ); - } - - // getFullDatasetInfos - @Test - void getFullDatasetInfosWithProjectIdIsSuccessful() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = null; - String isolateDataKey = null; - String projectId = "projectId"; - String datasetId = "datasetId"; - - when(datasetRepository.findAllByProjectId(any(String.class))) - .thenReturn( - List.of(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - typingDataId, - isolateDataId, - isolateDataKey - )) - ); - - when(distanceMatrixService.getDistanceMatrixInfos(any(String.class))).thenReturn(List.of()); - when(treeService.getTreeInfos(any(String.class))).thenReturn(List.of()); - when(treeViewService.getTreeViewInfos(any(String.class))).thenReturn(List.of()); - - List fullDatasetInfos = datasetService.getFullDatasetInfos(projectId); - - assertEquals(1, fullDatasetInfos.size()); - assertEquals(datasetId, fullDatasetInfos.get(0).getDatasetId()); - assertEquals(datasetName, fullDatasetInfos.get(0).getName()); - assertEquals(datasetDescription, fullDatasetInfos.get(0).getDescription()); - assertEquals(typingDataId, fullDatasetInfos.get(0).getTypingDataId()); - assertEquals(isolateDataId, fullDatasetInfos.get(0).getIsolateDataId()); - assertTrue(fullDatasetInfos.get(0).getDistanceMatrices().isEmpty()); - assertTrue(fullDatasetInfos.get(0).getTrees().isEmpty()); - assertTrue(fullDatasetInfos.get(0).getTreeViews().isEmpty()); - } - - // deleteDataset - // void deleteDataset(String projectId, String datasetId, String userId) - @Test - void deleteDatasetIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new Dataset())); - - datasetService.deleteDataset(projectId, datasetId, userId); - - verify(datasetRepository, times(1)).delete(any(Dataset.class)); - } - - // deleteAllByProjectId - @Test - void deleteAllByProjectIdIsSuccessful() { - String projectId = "projectId"; - - when(datasetRepository.findAllByProjectId(any(String.class))) - .thenReturn(List.of(new Dataset())); - - datasetService.deleteAllByProjectId(projectId); - - verify(datasetRepository, times(1)).delete(any(Dataset.class)); - } - - // updateDataset - @Test - void updateDatasetIsSuccessful() { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String newDatasetName = "newDatasetName"; - String newDatasetDescription = "newDatasetDescription"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - null, - null, - null - ))); - - UpdateDatasetOutput updateDatasetOutput = datasetService.updateDataset( - newDatasetName, - newDatasetDescription, - projectId, - datasetId, - userId - ); - - assertEquals(datasetName, updateDatasetOutput.getPreviousName()); - assertEquals(datasetDescription, updateDatasetOutput.getPreviousDescription()); - assertEquals(newDatasetName, updateDatasetOutput.getNewName()); - assertEquals(newDatasetDescription, updateDatasetOutput.getNewDescription()); - } - - @Test - void updateDatasetThrowsWhenProjectDoesNotExist() { - String newDatasetName = "newDatasetName"; - String newDatasetDescription = "newDatasetDescription"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - datasetService.updateDataset( - newDatasetName, - newDatasetDescription, - projectId, - datasetId, - userId - )); - } - - @Test - void updateDatasetThrowsWhenDatasetDoesNotExist() { - String newDatasetName = "newDatasetName"; - String newDatasetDescription = "newDatasetDescription"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(DatasetNotFoundException.class, () -> - datasetService.updateDataset( - newDatasetName, - newDatasetDescription, - projectId, - datasetId, - userId - )); - } - - @ParameterizedTest - @CsvSource({ - ",", - "'', description", - "name,''", - }) - void updateDatasetThrowsWithInvalidFields(String name, String description) { - String datasetName = "datasetName"; - String datasetDescription = "datasetDescription"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - when(datasetRepository.findByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new Dataset( - datasetId, - projectId, - datasetName, - datasetDescription, - null, - null, - null - ))); - - assertThrows(InvalidArgumentException.class, () -> - datasetService.updateDataset( - name, - description, - projectId, - datasetId, - userId - )); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/distance_matrix/DistanceMatrixServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/distance_matrix/DistanceMatrixServiceTests.java deleted file mode 100644 index 849f7655..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/distance_matrix/DistanceMatrixServiceTests.java +++ /dev/null @@ -1,336 +0,0 @@ -package org.phyloviz.pwp.administration.service.dataset.distance_matrix; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.DistanceMatrixInfo; -import org.phyloviz.pwp.administration.service.dtos.distance_matrix.UpdateDistanceMatrixOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedResourceDeletionException; -import org.phyloviz.pwp.administration.service.project.dataset.distance_matrix.DistanceMatrixServiceImpl; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.DistanceMatrixMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.DistanceMatrixMetadata; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSource; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceFunction; -import org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source.DistanceMatrixSourceType; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.DistanceMatrixNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; - -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class DistanceMatrixServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private DistanceMatrixMetadataRepository distanceMatrixMetadataRepository; - - @Mock - private TreeMetadataRepository treeMetadataRepository; - - @Mock - private DistanceMatrixDataRepositoryFactory distanceMatrixDataRepositoryFactory; - - @InjectMocks - private DistanceMatrixServiceImpl distanceMatrixService; - - - // getDistanceMatrixInfos - @Test - void getDistanceMatrixInfosIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - when(distanceMatrixMetadataRepository.findAllByDatasetId(any(String.class))) - .thenReturn(List.of( - new DistanceMatrixMetadata( - projectId, - datasetId, - distanceMatrixId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - - List distanceMatrixInfos = distanceMatrixService.getDistanceMatrixInfos(datasetId); - - assertEquals(1, distanceMatrixInfos.size()); - assertEquals(name, distanceMatrixInfos.get(0).getName()); - assertEquals(sourceType, distanceMatrixInfos.get(0).getSourceType()); - } - - // deleteDistanceMatrix - @Test - void deleteDistanceMatrixIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn( - Optional.of(new DistanceMatrixMetadata( - projectId, - datasetId, - distanceMatrixId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - when(treeMetadataRepository.existsByDatasetIdAndDistanceMatrixIdSource(datasetId, distanceMatrixId)).thenReturn(false); - - DistanceMatrixDataRepository rep = mock(DistanceMatrixS3DataRepository.class); - - when(distanceMatrixDataRepositoryFactory.getRepository(DistanceMatrixDataRepositoryId.S3)) - .thenReturn(rep); - - - distanceMatrixService.deleteDistanceMatrix(projectId, datasetId, distanceMatrixId, userId); - - verify(distanceMatrixMetadataRepository, times(1)).delete(any(DistanceMatrixMetadata.class)); - } - - @Test - void deleteDistanceMatrixThrowsWhenProjectDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - distanceMatrixService.deleteDistanceMatrix(projectId, datasetId, distanceMatrixId, userId) - ); - } - - @Test - void deleteDistanceMatrixThrowsWhenDatasetDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(false); - - assertThrows(DatasetNotFoundException.class, () -> - distanceMatrixService.deleteDistanceMatrix(projectId, datasetId, distanceMatrixId, userId) - ); - } - - @Test - void deleteDistanceMatrixThrowsWhenDistanceMatrixDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn( - Optional.empty()); - assertThrows(DistanceMatrixNotFoundException.class, () -> - distanceMatrixService.deleteDistanceMatrix(projectId, datasetId, distanceMatrixId, userId) - ); - } - - @Test - void deleteDistanceMatrixThrowsWhenDistanceMatrixIsDependencyOfTree() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn(Optional.of(new DistanceMatrixMetadata( - projectId, - datasetId, - distanceMatrixId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - when(treeMetadataRepository.existsByDatasetIdAndDistanceMatrixIdSource(datasetId, distanceMatrixId)).thenReturn(true); - - assertThrows(DeniedResourceDeletionException.class, () -> - distanceMatrixService.deleteDistanceMatrix(projectId, datasetId, distanceMatrixId, userId) - ); - } - - // deleteAllByProjectIdAndDatasetId - @Test - void deleteAllByProjectIdAndDatasetIdIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - when(distanceMatrixMetadataRepository.findAllByProjectIdAndDatasetId(any(String.class), any(String.class))) - .thenReturn(List.of()); - - distanceMatrixService.deleteAllByProjectIdAndDatasetId(projectId, datasetId); - - verify(distanceMatrixMetadataRepository, times(0)).delete(any(DistanceMatrixMetadata.class)); - } - - // updateDistanceMatrix - @Test - void updateDistanceMatrixIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn(Optional.of(new DistanceMatrixMetadata( - projectId, - datasetId, - distanceMatrixId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - - UpdateDistanceMatrixOutput output = distanceMatrixService.updateDistanceMatrix(name, projectId, datasetId, distanceMatrixId, userId); - - assertEquals(name, output.getPreviousName()); - assertEquals(name, output.getNewName()); - } - - @Test - void updateDistanceMatrixThrowsWhenProjectDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - distanceMatrixService.updateDistanceMatrix(name, projectId, datasetId, distanceMatrixId, userId) - ); - } - - @Test - void updateDistanceMatrixThrowsWhenDistanceMatrixDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - String name = "name"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn(Optional.empty()); - - assertThrows(DistanceMatrixNotFoundException.class, () -> - distanceMatrixService.updateDistanceMatrix(name, projectId, datasetId, distanceMatrixId, userId) - ); - } - - @ParameterizedTest - @NullAndEmptySource - void updateDistanceMatrixThrowsWhenNameIsNullOrEmpty(String name) { - String projectId = "projectId"; - String datasetId = "datasetId"; - String distanceMatrixId = "distanceMatrixId"; - DistanceMatrixSourceType sourceType = DistanceMatrixSourceType.FUNCTION; - DistanceMatrixSource source = new DistanceMatrixSourceFunction("functionName"); - DistanceMatrixDataRepositoryId repositoryId = DistanceMatrixDataRepositoryId.S3; - DistanceMatrixDataRepositorySpecificData repositorySpecificData = new DistanceMatrixS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(projectId, userId)).thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(projectId, datasetId)).thenReturn(true); - when(distanceMatrixMetadataRepository.findByProjectIdAndDatasetIdAndDistanceMatrixId(projectId, datasetId, distanceMatrixId)) - .thenReturn(Optional.of(new DistanceMatrixMetadata( - projectId, - datasetId, - distanceMatrixId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - - assertThrows(InvalidArgumentException.class, () -> - distanceMatrixService.updateDistanceMatrix(name, projectId, datasetId, distanceMatrixId, userId) - ); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree/TreeServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree/TreeServiceTests.java deleted file mode 100644 index f48808cb..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree/TreeServiceTests.java +++ /dev/null @@ -1,346 +0,0 @@ -package org.phyloviz.pwp.administration.service.dataset.tree; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.tree.TreeInfo; -import org.phyloviz.pwp.administration.service.dtos.tree.UpdateTreeOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedResourceDeletionException; -import org.phyloviz.pwp.administration.service.project.dataset.tree.TreeServiceImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.TreeMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.TreeMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSource; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceFile; -import org.phyloviz.pwp.shared.repository.metadata.tree.documents.source.TreeSourceType; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeNotFoundException; - -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class TreeServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private TreeMetadataRepository treeMetadataRepository; - - @Mock - private TreeViewMetadataRepository treeViewMetadataService; - - @Mock - private TreeDataRepositoryFactory treeDataRepositoryFactory; - - @InjectMocks - private TreeServiceImpl treeService; - - - // getTreeInfos - @Test - void getTreeInfosIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String name = "name"; - TreeSourceType sourceType = TreeSourceType.FILE; - TreeSource source = new TreeSourceFile("fileType", "fileName"); - TreeDataRepositoryId repositoryId = TreeDataRepositoryId.S3; - TreeDataRepositorySpecificData repositorySpecificData = new TreeS3DataRepositorySpecificData("url"); - - when(treeMetadataRepository.findAllByDatasetId(any(String.class))) - .thenReturn(List.of( - new TreeMetadata( - projectId, - datasetId, - treeId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ) - )); - - List treeInfos = treeService.getTreeInfos(datasetId); - - assertEquals(1, treeInfos.size()); - assertEquals(name, treeInfos.get(0).getName()); - assertEquals(sourceType, treeInfos.get(0).getSourceType()); - } - - // deleteTree - @Test - void deleteTreeIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String name = "name"; - TreeSourceType sourceType = TreeSourceType.FILE; - TreeSource source = new TreeSourceFile("fileType", "fileName"); - TreeDataRepositoryId repositoryId = TreeDataRepositoryId.S3; - TreeDataRepositorySpecificData repositorySpecificData = new TreeS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of(new TreeMetadata( - projectId, - datasetId, - treeId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - )) - ); - when(treeViewMetadataService.existsByDatasetIdAndTreeIdSource(any(String.class), any(String.class))) - .thenReturn(false); - - TreeDataRepository rep = mock(TreeS3DataRepository.class); - - when(treeDataRepositoryFactory.getRepository(repositoryId)) - .thenReturn(rep); - - - treeService.deleteTree(projectId, datasetId, treeId, userId); - - verify(treeMetadataRepository, times(1)).delete(any(TreeMetadata.class)); - } - - @Test - void deleteTreeThrowsWhenProjectDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - treeService.deleteTree(projectId, datasetId, treeId, userId) - ); - } - - @Test - void deleteTreeThrowsWhenDatasetDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(DatasetNotFoundException.class, () -> - treeService.deleteTree(projectId, datasetId, treeId, userId) - ); - } - - @Test - void deleteTreeThrowsWhenTreeDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(TreeNotFoundException.class, () -> - treeService.deleteTree(projectId, datasetId, treeId, userId) - ); - } - - @Test - void deleteTreeThrowsWhenTreeViewExists() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String name = "name"; - TreeSourceType sourceType = TreeSourceType.FILE; - TreeSource source = new TreeSourceFile("fileType", "fileName"); - TreeDataRepositoryId repositoryId = TreeDataRepositoryId.S3; - TreeDataRepositorySpecificData repositorySpecificData = new TreeS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of(new TreeMetadata( - projectId, - datasetId, - treeId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - )) - ); - when(treeViewMetadataService.existsByDatasetIdAndTreeIdSource(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(DeniedResourceDeletionException.class, () -> - treeService.deleteTree(projectId, datasetId, treeId, userId) - ); - } - - // deleteAllByProjectIdAndDatasetId - @Test - void deleteAllByProjectIdAndDatasetIdIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - when(treeMetadataRepository.findAllByProjectIdAndDatasetId(any(String.class), any(String.class))) - .thenReturn(List.of()); - - treeService.deleteAllByProjectIdAndDatasetId(projectId, datasetId); - - verify(treeMetadataRepository, times(0)).delete(any(TreeMetadata.class)); - } - - // updateTree - @Test - void updateTreeIsSuccessful() { - String newName = "name"; - String projectId = "projectId"; - String userId = "userId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String name = "name"; - TreeSourceType sourceType = TreeSourceType.FILE; - TreeSource source = new TreeSourceFile("fileType", "fileName"); - TreeDataRepositoryId repositoryId = TreeDataRepositoryId.S3; - TreeDataRepositorySpecificData repositorySpecificData = new TreeS3DataRepositorySpecificData("url"); - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of(new TreeMetadata( - projectId, - datasetId, - treeId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - - UpdateTreeOutput updateTreeOutput = treeService.updateTree(newName, projectId, datasetId, treeId, userId); - - assertEquals(newName, updateTreeOutput.getNewName()); - assertEquals(name, updateTreeOutput.getPreviousName()); - } - - @Test - void updateTreeThrowsWhenProjectDoesNotExist() { - String name = "name"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - treeService.updateTree(name, projectId, datasetId, treeId, userId) - ); - } - - @Test - void updateTreeThrowsWhenTreeDoesNotExist() { - String name = "name"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - String userId = "userId"; - - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))).thenReturn(true); - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(TreeNotFoundException.class, () -> - treeService.updateTree(name, projectId, datasetId, treeId, userId) - ); - } - - @ParameterizedTest - @NullAndEmptySource - void updateTreeThrowsWhenNameIsNullOfEmpty(String name) { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeId = "treeId"; - TreeSourceType sourceType = TreeSourceType.FILE; - TreeSource source = new TreeSourceFile("fileType", "fileName"); - TreeDataRepositoryId repositoryId = TreeDataRepositoryId.S3; - TreeDataRepositorySpecificData repositorySpecificData = new TreeS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeMetadataRepository.findByProjectIdAndDatasetIdAndTreeId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of(new TreeMetadata( - projectId, - datasetId, - treeId, - name, - sourceType, - source, - Map.of(repositoryId, repositorySpecificData) - ))); - - assertThrows(InvalidArgumentException.class, () -> - treeService.updateTree(name, projectId, datasetId, treeId, userId) - ); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree_view/TreeViewServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree_view/TreeViewServiceTests.java deleted file mode 100644 index 26c94840..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/dataset/tree_view/TreeViewServiceTests.java +++ /dev/null @@ -1,298 +0,0 @@ -package org.phyloviz.pwp.administration.service.dataset.tree_view; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.tree_view.TreeViewInfo; -import org.phyloviz.pwp.administration.service.dtos.tree_view.UpdateTreeViewOutput; -import org.phyloviz.pwp.administration.service.project.dataset.tree_view.TreeViewServiceImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.TreeViewMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.TreeViewMetadata; -import org.phyloviz.pwp.shared.repository.metadata.tree_view.documents.source.TreeViewSource; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Transformations; -import org.phyloviz.pwp.shared.service.exceptions.DatasetNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TreeViewNotFoundException; - -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class TreeViewServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private TreeViewMetadataRepository treeViewMetadataRepository; - - @Mock - private TreeViewDataRepositoryFactory treeViewDataRepositoryFactory; - - @InjectMocks - private TreeViewServiceImpl treeViewService; - - - // getTreeViewInfos - @Test - void getTreeViewInfosIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String name = "name"; - String layout = "layout"; - TreeViewSource source = new TreeViewSource("treeId"); - TreeViewDataRepositoryId repositoryId = TreeViewDataRepositoryId.S3; - TreeViewDataRepositorySpecificData repositorySpecificData = new TreeViewS3DataRepositorySpecificData("url"); - - when(treeViewMetadataRepository.findAllByDatasetId(any(String.class))) - .thenReturn(List.of( - new TreeViewMetadata( - projectId, - datasetId, - treeViewId, - name, - layout, - source, - Map.of(repositoryId, repositorySpecificData), - new Transformations(1, 1, 1, 1, 1, 1, - 1, 1, true, - 1, 1, false, 1, "absolute") - ) - )); - - List treeViewInfos = treeViewService.getTreeViewInfos(datasetId); - - assertEquals(1, treeViewInfos.size()); - assertEquals(name, treeViewInfos.get(0).getName()); - assertEquals(layout, treeViewInfos.get(0).getLayout()); - } - - // deleteTreeView - @Test - void deleteTreeViewIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String name = "name"; - String layout = "layout"; - TreeViewSource source = new TreeViewSource("treeId"); - TreeViewDataRepositoryId repositoryId = TreeViewDataRepositoryId.S3; - TreeViewDataRepositorySpecificData repositorySpecificData = new TreeViewS3DataRepositorySpecificData("url"); - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeViewMetadataRepository.findByProjectIdAndDatasetIdAndTreeViewId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of(new TreeViewMetadata( - projectId, - datasetId, - treeViewId, - name, - layout, - source, - Map.of(repositoryId, repositorySpecificData), - new Transformations(1, 1, 1, 1, 1, 1, - 1, 1, true, - 1, 1, false, 1, "absolute") - ))); - - TreeViewDataRepository rep = mock(TreeViewS3DataRepository.class); - - when(treeViewDataRepositoryFactory.getRepository(repositoryId)) - .thenReturn(rep); - - treeViewService.deleteTreeView(projectId, datasetId, treeViewId, userId); - - verify(treeViewMetadataRepository, times(1)).delete(any(TreeViewMetadata.class)); - } - - @Test - void deleteTreeViewThrowsWhenProjectDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - treeViewService.deleteTreeView(projectId, datasetId, treeViewId, userId) - ); - } - - @Test - void deleteTreeViewThrowsWhenDatasetDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(DatasetNotFoundException.class, () -> - treeViewService.deleteTreeView(projectId, datasetId, treeViewId, userId) - ); - } - - @Test - void deleteTreeViewThrowsWhenTreeViewDoesNotExist() { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeViewMetadataRepository.findByProjectIdAndDatasetIdAndTreeViewId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(TreeViewNotFoundException.class, () -> - treeViewService.deleteTreeView(projectId, datasetId, treeViewId, userId) - ); - } - - // deleteAllByProjectIdAndDatasetId - @Test - void deleteAllByProjectIdAndDatasetIdIsSuccessful() { - String projectId = "projectId"; - String datasetId = "datasetId"; - when(treeViewMetadataRepository.findAllByProjectIdAndDatasetId(any(String.class), any(String.class))) - .thenReturn(List.of()); - - treeViewService.deleteAllByProjectIdAndDatasetId(projectId, datasetId); - - verify(treeViewMetadataRepository, times(0)).delete(any(TreeViewMetadata.class)); - } - - // updateTreeView - @Test - void updateTreeViewIsSuccessful() { - String newName = "newName"; - String projectId = "projectId"; - String userId = "userId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String name = "name"; - String layout = "layout"; - TreeViewSource source = new TreeViewSource("treeId"); - TreeViewDataRepositoryId repositoryId = TreeViewDataRepositoryId.S3; - TreeViewDataRepositorySpecificData repositorySpecificData = new TreeViewS3DataRepositorySpecificData("url"); - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeViewMetadataRepository.findByProjectIdAndDatasetIdAndTreeViewId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.of( - new TreeViewMetadata( - projectId, - datasetId, - treeViewId, - name, - layout, - source, - Map.of(repositoryId, repositorySpecificData), - new Transformations(1, 1, 1, 1, 1, 1, - 1, 1, true, - 1, 1, false, 1, "absolute") - ) - )); - - UpdateTreeViewOutput updateTreeViewOutput = treeViewService.updateTreeView(newName, projectId, datasetId, treeViewId, userId); - - assertEquals(newName, updateTreeViewOutput.getNewName()); - assertEquals(name, updateTreeViewOutput.getPreviousName()); - } - - @Test - void updateTreeViewThrowsWhenProjectDoesNotExist() { - String name = "name"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - treeViewService.updateTreeView(name, projectId, datasetId, treeViewId, userId) - ); - } - - @Test - void updateTreeViewThrowsWhenTreeViewDoesNotExist() { - String name = "name"; - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeViewMetadataRepository.findByProjectIdAndDatasetIdAndTreeViewId(any(String.class), any(String.class), any(String.class))) - .thenReturn(Optional.empty()); - - assertThrows(TreeViewNotFoundException.class, () -> - treeViewService.updateTreeView(name, projectId, datasetId, treeViewId, userId) - ); - } - - @ParameterizedTest - @NullAndEmptySource - void updateTreeViewThrowsWhenNameIsNullOfEmpty(String name) { - String projectId = "projectId"; - String datasetId = "datasetId"; - String treeViewId = "treeViewId"; - String userId = "userId"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndId(any(String.class), any(String.class))) - .thenReturn(true); - when(treeViewMetadataRepository.findByProjectIdAndDatasetIdAndTreeViewId(projectId, datasetId, treeViewId)) - .thenReturn(Optional.of(new TreeViewMetadata())); - - assertThrows(InvalidArgumentException.class, () -> - treeViewService.updateTreeView(name, projectId, datasetId, treeViewId, userId) - ); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/IsolateDataServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/IsolateDataServiceTests.java deleted file mode 100644 index ac53f7d9..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/IsolateDataServiceTests.java +++ /dev/null @@ -1,223 +0,0 @@ -package org.phyloviz.pwp.administration.service.file; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.IsolateDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.isolate_data.UpdateIsolateDataOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedFileDeletionException; -import org.phyloviz.pwp.administration.service.project.file.IsolateDataServiceImpl; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.IsolateDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.isolate_data.documents.IsolateDataMetadata; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.IsolateDataNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; - -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class IsolateDataServiceTests { - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private IsolateDataMetadataRepository isolateDataMetadataRepository; - - @Mock - private IsolateDataDataRepositoryFactory isolateDataDataRepositoryFactory; - - @InjectMocks - private IsolateDataServiceImpl isolateDataService; - - // getIsolateDataInfos - @Test - void getIsolateDataInfosIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(isolateDataMetadataRepository.findAllByProjectId(any(String.class))) - .thenReturn(List.of()); - - List isolateDataInfos = isolateDataService.getIsolateDataInfos(projectId); - assertTrue(isolateDataInfos.isEmpty()); - } - - // deleteIsolateData - @Test - void deleteIsolateDataIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataMetadataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(false); - when(isolateDataMetadataRepository.findByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of( - new IsolateDataMetadata(isolateDataMetadataId, projectId, isolateDataId, List.of(), "name", Map.of(IsolateDataDataRepositoryId.S3, new IsolateDataS3DataRepositorySpecificData()) - ))); - - IsolateDataDataRepository rep = mock(IsolateDataS3DataRepository.class); - - when(isolateDataDataRepositoryFactory.getRepository(IsolateDataDataRepositoryId.S3)) - .thenReturn(rep); - - isolateDataService.deleteIsolateData(projectId, isolateDataId, userId); - - verify(isolateDataMetadataRepository, times(1)).delete(any(IsolateDataMetadata.class)); - } - - @Test - void deleteIsolateDataThrowsExceptionWhenProjectDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - isolateDataService.deleteIsolateData(projectId, isolateDataId, userId) - ); - } - - @Test - void deleteIsolateDataThrowsExceptionWhenIsolateDataDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(IsolateDataNotFoundException.class, () -> - isolateDataService.deleteIsolateData(projectId, isolateDataId, userId) - ); - } - - @Test - void deleteIsolateDataThrowsExceptionWhenIsolateDataIsUsedByDataset() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(true); - when(isolateDataMetadataRepository.findByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new IsolateDataMetadata())); - - assertThrows(DeniedFileDeletionException.class, () -> - isolateDataService.deleteIsolateData(projectId, isolateDataId, userId) - ); - } - - - // deleteAllByProjectId - @Test - void deleteAllByProjectIdIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(isolateDataMetadataRepository.findAllByProjectId(any(String.class))) - .thenReturn(List.of()); - - isolateDataService.deleteAllByProjectId(projectId); - - verify(isolateDataMetadataRepository, times(0)).delete(any(IsolateDataMetadata.class)); - } - - // updateIsolateData - @Test - void updateIsolateDataIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(isolateDataMetadataRepository.findByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new IsolateDataMetadata())); - when(isolateDataMetadataRepository.save(any(IsolateDataMetadata.class))) - .thenReturn(new IsolateDataMetadata()); - - UpdateIsolateDataOutput updateIsolateDataOutput = isolateDataService.updateIsolateData(newName, projectId, isolateDataId, userId); - assertEquals(newName, updateIsolateDataOutput.getNewName()); - assertNull(updateIsolateDataOutput.getPreviousName()); - } - - @Test - void updateIsolateDataThrowsWhenProjectDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - isolateDataService.updateIsolateData(newName, projectId, isolateDataId, userId) - ); - } - - @Test - void updateIsolateDataThrowsWhenIsolateDataDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(IsolateDataNotFoundException.class, () -> - isolateDataService.updateIsolateData(newName, projectId, isolateDataId, userId) - ); - } - - @ParameterizedTest - @NullAndEmptySource - void updateIsolateDataThrowsWhenNewNameIsInvalid(String newName) { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String isolateDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(isolateDataMetadataRepository.findByProjectIdAndIsolateDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new IsolateDataMetadata())); - - assertThrows(InvalidArgumentException.class, () -> - isolateDataService.updateIsolateData(newName, projectId, isolateDataId, userId) - ); - } -} diff --git a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/TypingDataServiceTests.java b/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/TypingDataServiceTests.java deleted file mode 100644 index 87d51cac..00000000 --- a/src/backend/microservices/administration/src/test/java/org/phyloviz/pwp/administration/service/file/TypingDataServiceTests.java +++ /dev/null @@ -1,228 +0,0 @@ -package org.phyloviz.pwp.administration.service.file; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.mockito.InjectMocks; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.TypingDataInfo; -import org.phyloviz.pwp.administration.service.dtos.files.typing_data.UpdateTypingDataOutput; -import org.phyloviz.pwp.administration.service.exceptions.DeniedFileDeletionException; -import org.phyloviz.pwp.administration.service.project.file.TypingDataServiceImpl; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryFactory; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.metadata.dataset.DatasetRepository; -import org.phyloviz.pwp.shared.repository.metadata.project.ProjectRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.TypingDataMetadataRepository; -import org.phyloviz.pwp.shared.repository.metadata.typing_data.documents.TypingDataMetadata; -import org.phyloviz.pwp.shared.service.exceptions.InvalidArgumentException; -import org.phyloviz.pwp.shared.service.exceptions.ProjectNotFoundException; -import org.phyloviz.pwp.shared.service.exceptions.TypingDataNotFoundException; - -import java.util.List; -import java.util.Map; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.any; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.times; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -@ExtendWith(MockitoExtension.class) -class TypingDataServiceTests { - - @Mock - private ProjectRepository projectRepository; - - @Mock - private DatasetRepository datasetRepository; - - @Mock - private TypingDataMetadataRepository typingDataMetadataRepository; - - @Mock - private TypingDataDataRepositoryFactory typingDataDataRepositoryFactory; - - @InjectMocks - private TypingDataServiceImpl typingDataService; - - // getTypingDataInfos - @Test - void getTypingDataInfosIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(typingDataMetadataRepository.findAllByProjectId(any(String.class))) - .thenReturn(List.of()); - - List typingDataInfos = typingDataService.getTypingDataInfos(projectId); - assertTrue(typingDataInfos.isEmpty()); - } - - // deleteTypingData - @Test - void deleteTypingDataIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String datasetId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(false); - when(typingDataMetadataRepository.findByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of( - new TypingDataMetadata(datasetId, projectId, typingDataId, "type", "name", - Map.of(TypingDataDataRepositoryId.S3, - new TypingDataS3DataRepositorySpecificData("bucket", "key") - )) - )); - - TypingDataDataRepository rep = mock(TypingDataS3DataRepository.class); - - when(typingDataDataRepositoryFactory.getRepository(TypingDataDataRepositoryId.S3)) - .thenReturn(rep); - - - typingDataService.deleteTypingData(projectId, typingDataId, userId); - - verify(typingDataMetadataRepository, times(1)).delete(any(TypingDataMetadata.class)); - } - - @Test - void deleteTypingDataThrowsExceptionWhenProjectDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - typingDataService.deleteTypingData(projectId, typingDataId, userId) - ); - } - - @Test - void deleteTypingDataThrowsExceptionWhenTypingDataDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(TypingDataNotFoundException.class, () -> - typingDataService.deleteTypingData(projectId, typingDataId, userId) - ); - } - - @Test - void deleteTypingDataThrowsExceptionWhenTypingDataIsUsedByDataset() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(datasetRepository.existsByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(true); - when(typingDataMetadataRepository.findByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new TypingDataMetadata())); - - assertThrows(DeniedFileDeletionException.class, () -> - typingDataService.deleteTypingData(projectId, typingDataId, userId) - ); - } - - - // deleteAllByProjectId - @Test - void deleteAllByProjectIdIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(typingDataMetadataRepository.findAllByProjectId(any(String.class))) - .thenReturn(List.of()); - - typingDataService.deleteAllByProjectId(projectId); - - verify(typingDataMetadataRepository, times(0)).delete(any(TypingDataMetadata.class)); - } - - // updateTypingData - @Test - void updateTypingDataIsSuccessful() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(typingDataMetadataRepository.findByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new TypingDataMetadata())); - when(typingDataMetadataRepository.save(any(TypingDataMetadata.class))) - .thenReturn(new TypingDataMetadata()); - - UpdateTypingDataOutput updateTypingDataOutput = typingDataService.updateTypingData(newName, projectId, typingDataId, userId); - assertEquals(newName, updateTypingDataOutput.getNewName()); - assertNull(updateTypingDataOutput.getPreviousName()); - } - - @Test - void updateTypingDataThrowsWhenProjectDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(false); - - assertThrows(ProjectNotFoundException.class, () -> - typingDataService.updateTypingData(newName, projectId, typingDataId, userId) - ); - } - - @Test - void updateTypingDataThrowsWhenTypingDataDoesNotExist() { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String newName = "newName"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - - assertThrows(TypingDataNotFoundException.class, () -> - typingDataService.updateTypingData(newName, projectId, typingDataId, userId) - ); - } - - @ParameterizedTest - @NullAndEmptySource - void updateTypingDataThrowsWhenNewNameIsInvalid(String newName) { - String projectId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String typingDataId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - String userId = "ec7bae63-3238-4044-8d03-e2d9911f50f8"; - - when(projectRepository.existsByIdAndOwnerId(any(String.class), any(String.class))) - .thenReturn(true); - when(typingDataMetadataRepository.findByProjectIdAndTypingDataId(any(String.class), any(String.class))) - .thenReturn(Optional.of(new TypingDataMetadata())); - - assertThrows(InvalidArgumentException.class, () -> - typingDataService.updateTypingData(newName, projectId, typingDataId, userId) - ); - } -} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/controllers/ComputeController.java b/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/controllers/ComputeController.java deleted file mode 100644 index 313dd177..00000000 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/http/controllers/ComputeController.java +++ /dev/null @@ -1,123 +0,0 @@ -package org.phyloviz.pwp.compute.http.controllers; - -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.http.models.create_workflow.CreateWorkflowInputModel; -import org.phyloviz.pwp.compute.http.models.create_workflow.CreateWorkflowOutputModel; -import org.phyloviz.pwp.compute.http.models.get_workflow.GetWorkflowOutputModel; -import org.phyloviz.pwp.compute.http.models.get_workflow_status.GetWorkflowStatusOutputModel; -import org.phyloviz.pwp.compute.http.models.get_workflows.GetWorkflowsOutputModel; -import org.phyloviz.pwp.compute.service.ComputeService; -import org.phyloviz.pwp.compute.service.dtos.create_workflow.CreateWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowOutput; -import org.phyloviz.pwp.compute.service.dtos.get_workflow.GetWorkflowStatusOutput; -import org.phyloviz.pwp.shared.domain.User; -import org.springframework.http.ResponseEntity; -import org.springframework.web.bind.annotation.GetMapping; -import org.springframework.web.bind.annotation.PathVariable; -import org.springframework.web.bind.annotation.PostMapping; -import org.springframework.web.bind.annotation.RequestBody; -import org.springframework.web.bind.annotation.RequestParam; -import org.springframework.web.bind.annotation.RestController; - -import java.util.List; - -/** - * Controller for the Compute Microservice. - */ -@RestController -@RequiredArgsConstructor -public class ComputeController { - - private final ComputeService computeService; - - /** - * Create a new workflow. - * - * @param inputModel input model for the workflow - * @param projectId the project id of the project to which the workflow belongs - * @param user the user who is creating the workflow - * @return information about the created workflow - */ - @PostMapping("/projects/{projectId}/workflows") - public ResponseEntity createWorkflow( - @PathVariable String projectId, - @RequestBody CreateWorkflowInputModel inputModel, - User user - ) { - CreateWorkflowOutput createWorkflowOutput = computeService.createWorkflow( - projectId, inputModel.getType(), inputModel.getProperties(), user.getId() - ); - - return ResponseEntity - .accepted() - .body(new CreateWorkflowOutputModel(createWorkflowOutput)); - } - - /** - * Gets the status of a workflow. - * - * @param projectId the project id of the project to which the workflow belongs - * @param workflowId the id of the workflow - * @param user the user who is requesting the workflow status - * @return information about the workflow - */ - @GetMapping("/projects/{projectId}/workflows/{workflowId}/status") - public GetWorkflowStatusOutputModel getWorkflowStatus( - @PathVariable String projectId, - @PathVariable String workflowId, - User user - ) { - GetWorkflowStatusOutput getWorkflowStatusOutput = computeService.getWorkflowStatus( - projectId, workflowId, user.getId() - ); - - return new GetWorkflowStatusOutputModel(getWorkflowStatusOutput); - } - - /** - * Gets the workflow. - * - * @param projectId the project id of the project to which the workflow belongs - * @param workflowId the id of the workflow - * @param user the user who is requesting the workflow status - * @return information about the workflow - */ - @GetMapping("/projects/{projectId}/workflows/{workflowId}") - public GetWorkflowOutputModel getWorkflow( - @PathVariable String projectId, - @PathVariable String workflowId, - User user - ) { - GetWorkflowOutput getWorkflowOutput = computeService.getWorkflow( - projectId, workflowId, user.getId() - ); - - return new GetWorkflowOutputModel(getWorkflowOutput); - } - - /** - * Gets the workflows of a project. - * - * @param projectId the project id of the project to which the workflow belongs - * @param running whether to get only running workflows or not running workflows - * @param user the user who is requesting the workflows - * @return information about the workflows - */ - @GetMapping("/projects/{projectId}/workflows") - public GetWorkflowsOutputModel getWorkflows( - @PathVariable String projectId, - @RequestParam(required = false) Boolean running, - User user - ) { - List getWorkflowStatusOutputList; - - if (running == null) - getWorkflowStatusOutputList = computeService.getAllWorkflows(projectId, user.getId()); - else if (running) - getWorkflowStatusOutputList = computeService.getAllRunningWorkflows(projectId, user.getId()); - else - getWorkflowStatusOutputList = computeService.getAllNotRunningWorkflows(projectId, user.getId()); - - return new GetWorkflowsOutputModel(getWorkflowStatusOutputList); - } -} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java b/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java deleted file mode 100644 index 8255e3ef..00000000 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessDetailsTemplate.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access; - -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessDetails; - -public interface AccessDetailsTemplate { - AccessDetails build(); -} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java b/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java deleted file mode 100644 index ba811e7f..00000000 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/tool_template/documents/access/AccessTypeTemplate.java +++ /dev/null @@ -1,22 +0,0 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access; - -import lombok.Getter; -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.api.ApiAccessDetailsTemplate; -import org.phyloviz.pwp.compute.repository.metadata.templates.tool_template.documents.access.library.LibraryAccessDetailsTemplate; -import org.phyloviz.pwp.compute.service.flowviz.models.tool.access.AccessType; - -@RequiredArgsConstructor -public enum AccessTypeTemplate { - LIBRARY(LibraryAccessDetailsTemplate.class), - API(ApiAccessDetailsTemplate.class); - - @Getter - private final Class detailsClass; - - public AccessType build() { - return AccessType.valueOf(this.name()); - } -} - - diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java b/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java deleted file mode 100644 index 9d96ede7..00000000 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/repository/metadata/templates/workflow_instances/documents/WorkflowStatus.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.phyloviz.pwp.compute.repository.metadata.templates.workflow_instances.documents; - -public enum WorkflowStatus { - RUNNING, - SUCCESS, - FAILED -} diff --git a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessDetails.java b/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessDetails.java deleted file mode 100644 index 470f5931..00000000 --- a/src/backend/microservices/compute/src/main/java/org/phyloviz/pwp/compute/service/flowviz/models/tool/access/AccessDetails.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.compute.service.flowviz.models.tool.access; - -public interface AccessDetails { -} diff --git a/src/backend/microservices/compute/src/main/resources/application.yml b/src/backend/microservices/compute/src/main/resources/application.yml deleted file mode 100644 index 36451515..00000000 --- a/src/backend/microservices/compute/src/main/resources/application.yml +++ /dev/null @@ -1,15 +0,0 @@ -server: - port: 8086 - -spring: - config: - import: application-shared.yml - -flowviz: - url: http://localhost:3000/flowapi - username: admin - password: admin - -logging: - level: - root: debug \ No newline at end of file diff --git a/src/backend/microservices/compute/src/test/java/org/phyloviz/pwp/compute/service/flowviz/FlowVizClientIntegrationTest.java b/src/backend/microservices/compute/src/test/java/org/phyloviz/pwp/compute/service/flowviz/FlowVizClientIntegrationTest.java deleted file mode 100644 index c2494098..00000000 --- a/src/backend/microservices/compute/src/test/java/org/phyloviz/pwp/compute/service/flowviz/FlowVizClientIntegrationTest.java +++ /dev/null @@ -1,139 +0,0 @@ -package org.phyloviz.pwp.compute.service.flowviz; - -import org.springframework.boot.test.context.SpringBootTest; - -@SpringBootTest -class FlowVizClientIntegrationTest { - - // TODO: Fix this test - // FlowVizClient flowVizClient = FlowVizClient - // .builder() - // .baseUrl("http://localhost:3000/flowapi") - // .credentials("admin", "admin") - // .authenticate(); - // - // Gson gson = new GsonBuilder() - // .registerTypeAdapter(Access.class, new AccessSerializer()) - // .registerTypeAdapter(Access.class, new AccessDeserializer()) - // .create(); - - // @Test - // void toolService() { - // - // Tool tool = Tool.builder() - // .general(General.builder() - // .name("Phylolib") - // .description("The phylolib library") - // .build()) - // .access(Access.builder() - // .type(AccessType.LIBRARY) - // .details(LibraryAccess.builder() - // .address("localhost") - // .dockerUrl("unix://var/run/docker.sock") - // .dockerImage("luanab/phylolib") - // .dockerContainer("phylolib") - // .dockerAutoRemove(DockerAutoRemove.NEVER) - // .dockerNetworkMode("bridge") - // .dockerApiVersion("auto") - // .dockerVolumes(Collections.singletonList(DockerVolume.builder() - // .source("/opt/.phylolibVol") - // .target("/phylolib") - // .type(VolumeType.BIND) - // .build())) - // .build()) - // .build()) - // .library(Arrays.asList( - // Library.builder() - // .name("Arguments") - // .order(0) - // .invocation("-args") - // .allowCommandRep(false) - // .commands(List.of( - // Command.builder().name("help").invocation(List.of("help")).build(), - // Command.builder().name("distance").invocation(List.of("distance")) - // .allowedValues(List.of("hamming", "grapetree", "kimura")) - // .allowedCommandSets(List.of("Options")) - // .build(), - // Command.builder().name("correction").invocation(List.of("correction")) - // .allowedValues(List.of("jukescantor")) - // .allowedCommandSets(List.of("Options")) - // .build(), - // Command.builder().name("algorithm").invocation(List.of("algorithm")) - // .allowedValues(List.of( - // "goeburst", "edmonds", "sl", "cl", "upgma", "upgmc", - // "wpgma", "wpgmc", "saitounei", "studierkepler", "unj")) - // .allowedCommandSets(List.of("Options")) - // .build(), - // Command.builder().name("optimization").invocation(List.of("optimization")) - // .allowedValues(List.of("lbr")) - // .allowedCommandSets(List.of("Options")) - // .build() - // )) - // .build(), - // Library.builder() - // .name("Options") - // .order(1) - // .allowCommandRep(true) - // .commands(List.of( - // Command.builder().name("File Output") - // .description("Output file as : with format being (asymmetric|symmetric|newick|nexus)") - // .invocation(List.of("-o", "--out")) - // .allowedValues(List.of("file")) - // .build(), - // Command.builder().name("Dataset Input") - // .description("Input dataset file as : with format being (fasta|ml|snp)") - // .invocation(List.of("-d", "--dataset")) - // .allowedValues(List.of("file")) - // .build(), - // Command.builder().name("Distance Matrix Input") - // .description("Input distance matrix file as : with format being (asymmetric|symmetric)") - // .invocation(List.of("-m", "--matrix")) - // .allowedValues(List.of("file")) - // .build(), - // Command.builder().name("Phylogenetic Tree Input") - // .description("Input phylogenetic tree file as : with format being (newick|nexus)") - // .invocation(List.of("-t", "--tree")) - // .allowedValues(List.of("file")) - // .build(), - // Command.builder().name("Limit of focus variants") - // .description("Limit of locus variants to consider using goeBURST algorithm [default: 3]") - // .invocation(List.of("-l", "--lvs")) - // .allowedValues(List.of("file")) - // .build() - // )) - // .build() - // )) - // .build(); - // - // flowVizClient.toolService().postTool(tool); - // } - // - // @Test - // void workflowService() { - // Workflow workflow = Workflow.builder() - // .name("PhylolibWorkflow") - // .description("A test workflow for Phylolib") - // .startDate(OffsetDateTime.parse("2022-11-29T19:45:00.000Z").toLocalDateTime()) - // .tasks(Arrays.asList( - // Task.builder() - // .id("hamming") - // .tool("Phylolib") - // .action(Action.builder() - // .command("distance hamming --dataset=ml:/phylolib/data/datasets/10.txt --out=symmetric:/phylolib/out.txt") - // .build()) - // .children(Collections.singletonList("upgma")) - // .build(), - // Task.builder() - // .id("upgma") - // .tool("Phylolib") - // .action(Action.builder() - // .command("algorithm upgma --out=newick:/phylolib/tree.txt --matrix=symmetric:/phylolib/out.txt") - // .build()) - // .children(Collections.emptyList()) - // .build() - // )) - // .build(); - // - // this.flowVizClient.workflowService().postWorkflow(workflow); - // } -} \ No newline at end of file diff --git a/src/backend/microservices/file-transfer/Dockerfile b/src/backend/microservices/file-transfer/Dockerfile deleted file mode 100644 index c007539a..00000000 --- a/src/backend/microservices/file-transfer/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM openjdk:17-jdk-alpine -COPY build/libs/file-transfer-0.0.1-SNAPSHOT.jar /app.jar - -ENTRYPOINT ["java", "-jar", "/app.jar"] \ No newline at end of file diff --git a/src/backend/microservices/file-transfer/build.gradle b/src/backend/microservices/file-transfer/build.gradle deleted file mode 100644 index deb3302b..00000000 --- a/src/backend/microservices/file-transfer/build.gradle +++ /dev/null @@ -1,39 +0,0 @@ -plugins { - id 'application' - id 'org.springframework.boot' version '3.0.4' - id 'io.spring.dependency-management' version '1.1.0' - id "io.freefair.lombok" version "8.0.0-rc2" -} - -group 'phylovizwebplatform' -version '0.0.1-SNAPSHOT' -sourceCompatibility = '17' - -ext { - set('jupiterVersion', "5.8.1") -} - -repositories { - mavenCentral() -} - -dependencies { - implementation project(path: ':microservices:shared') - - testImplementation 'org.springframework.boot:spring-boot-starter-test' - testImplementation 'org.junit.jupiter:junit-jupiter-api' version { jupiterVersion } - testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine' version { jupiterVersion } - - implementation 'org.springframework.boot:spring-boot-starter-data-mongodb' - implementation 'org.springframework.boot:spring-boot-starter-web' - implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server' - - implementation 'com.fasterxml.jackson.core:jackson-databind:2.14.2' - implementation 'org.zalando:problem-spring-web-starter:0.27.0' - - implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' -} - -test { - useJUnitPlatform() -} \ No newline at end of file diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/FileTransferMicroserviceApplication.java b/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/FileTransferMicroserviceApplication.java deleted file mode 100644 index d58f4222..00000000 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/FileTransferMicroserviceApplication.java +++ /dev/null @@ -1,20 +0,0 @@ -package org.phyloviz.pwp.file_transfer; - -import org.springframework.boot.SpringApplication; -import org.springframework.boot.autoconfigure.SpringBootApplication; - -/** - * Main class for the FileTransfer Microservice of the PHYLOViZ Web Platform. - */ -@SpringBootApplication -public class FileTransferMicroserviceApplication { - - /** - * Entry point for the FileTransfer Microservice. - * - * @param args arguments passed to the application - */ - public static void main(String[] args) { - SpringApplication.run(FileTransferMicroserviceApplication.class, args); - } -} diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/DataRepositoryConfig.java b/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/DataRepositoryConfig.java deleted file mode 100644 index 6329b550..00000000 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/DataRepositoryConfig.java +++ /dev/null @@ -1,92 +0,0 @@ -package org.phyloviz.pwp.file_transfer.config; - -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreePhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; -import org.springframework.context.ApplicationContext; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; - -import java.util.Map; - -/** - * Configuration class for the Data Repositories. - */ -@Configuration -public class DataRepositoryConfig { - - @Bean - public TypingDataDataRepositoryRegistry typingDataDataRepositoryRegistry(ApplicationContext context) { - return new TypingDataDataRepositoryRegistryImpl(context, Map.of( - TypingDataDataRepositoryId.S3, TypingDataS3DataRepository.class - ), Map.of( - TypingDataDataRepositoryId.S3, TypingDataS3DataRepositorySpecificData.class, - TypingDataDataRepositoryId.PHYLODB, TypingDataPhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public IsolateDataDataRepositoryRegistry isolateDataDataRepositoryRegistry(ApplicationContext context) { - return new IsolateDataDataRepositoryRegistryImpl(context, Map.of( - IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepository.class - ), Map.of( - IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepositorySpecificData.class, - IsolateDataDataRepositoryId.PHYLODB, IsolateDataPhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public DistanceMatrixDataRepositoryRegistry distanceMatrixDataRepositoryRegistry(ApplicationContext context) { - return new DistanceMatrixDataRepositoryRegistryImpl(context, Map.of( - DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepository.class - ), Map.of( - DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepositorySpecificData.class - )); - } - - @Bean - public TreeDataRepositoryRegistry treeDataRepositoryRegistry(ApplicationContext context) { - return new TreeDataRepositoryRegistryImpl(context, Map.of( - TreeDataRepositoryId.S3, TreeS3DataRepository.class - ), Map.of( - TreeDataRepositoryId.S3, TreeS3DataRepositorySpecificData.class, - TreeDataRepositoryId.PHYLODB, TreePhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public TreeViewDataRepositoryRegistry treeViewDataRepositoryRegistry(ApplicationContext context) { - return new TreeViewDataRepositoryRegistryImpl(context, Map.of( - TreeViewDataRepositoryId.S3, TreeViewS3DataRepository.class - ), Map.of( - TreeViewDataRepositoryId.S3, TreeViewS3DataRepositorySpecificData.class, - TreeViewDataRepositoryId.PHYLODB, TreeViewPhyloDBDataRepositorySpecificData.class - )); - } -} diff --git a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/FileTransferConfig.java b/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/FileTransferConfig.java deleted file mode 100644 index 5c17105f..00000000 --- a/src/backend/microservices/file-transfer/src/main/java/org/phyloviz/pwp/file_transfer/config/FileTransferConfig.java +++ /dev/null @@ -1,13 +0,0 @@ -package org.phyloviz.pwp.file_transfer.config; - -import org.phyloviz.pwp.shared.config.ResourceServerSharedConfig; -import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Import; - -/** - * Configuration class for the FileTransfer Microservice. - */ -@Configuration -@Import({ResourceServerSharedConfig.class}) -public class FileTransferConfig { -} \ No newline at end of file diff --git a/src/backend/microservices/file-transfer/src/main/resources/application.yml b/src/backend/microservices/file-transfer/src/main/resources/application.yml deleted file mode 100644 index c3be64b6..00000000 --- a/src/backend/microservices/file-transfer/src/main/resources/application.yml +++ /dev/null @@ -1,20 +0,0 @@ -server: - port: 8089 - -spring: - config: - import: application-shared.yml - servlet: - multipart: - max-file-size: 1GB - max-request-size: 1GB - -data-repositories: - upload-typing-data-repository: S3 - download-typing-data-repository: S3 - upload-isolate-data-repository: S3 - download-isolate-data-repository: S3 - -logging: - level: - root: debug \ No newline at end of file diff --git a/src/backend/microservices/gateway/src/main/resources/application.yml b/src/backend/microservices/gateway/src/main/resources/application.yml index 2be2cb15..90ce4041 100644 --- a/src/backend/microservices/gateway/src/main/resources/application.yml +++ b/src/backend/microservices/gateway/src/main/resources/application.yml @@ -56,7 +56,7 @@ pwp: path: /projects/{projectId}/files/isolate-data/{isolateDataId} compute: - uri: http://localhost:8086 + uri: http://localhost:8088 routes: - method: POST path: /projects/{projectId}/workflows @@ -66,7 +66,7 @@ pwp: path: /projects/{projectId}/workflows/{workflowId} visualization: - uri: http://localhost:8085 + uri: http://localhost:8088 routes: - method: GET path: /projects/{projectId}/datasets/{datasetId}/trees/{treeId} @@ -86,7 +86,7 @@ pwp: path: /projects/{projectId}/files/typing-data/{typingDataId}/profiles file-transfer: - uri: http://localhost:8089 + uri: http://localhost:8088 routes: - method: POST path: /projects/{projectId}/files/typing-data diff --git a/src/backend/microservices/pwp/src/main/resources/application.yml b/src/backend/microservices/pwp/src/main/resources/application.yml new file mode 100644 index 00000000..16729f78 --- /dev/null +++ b/src/backend/microservices/pwp/src/main/resources/application.yml @@ -0,0 +1,52 @@ +server: + port: 8088 + +s3: + access-key-id: AKIATCKANASTL7VVHAEK + secret-access-key: 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 + bucket: phyloviz-web-platform + region: eu-west-3 + endpoint: https://s3.eu-west-3.amazonaws.com + +spring: + data: + mongodb: + host: localhost + port: 28017 + database: phyloviz-web-platform + authentication-database: admin + auto-index-creation: true + security: + oauth2: + resourceserver: + opaquetoken: + introspection-uri: http://localhost:8082/realms/phyloviz-web-platform/protocol/openid-connect/token/introspect + client-id: phyloviz-web-platform-client + client-secret: 3rG9M1rnH7gKX29QujY7HQedPs7KT1Iu +# jwt: +# jwk-set-uri: http://localhost:8082/realms/phyloviz-web-platform/protocol/openid-connect/certs + servlet: + multipart: + max-file-size: 1GB + max-request-size: 1GB + +data-repositories: + upload-typing-data-repository: S3 + download-typing-data-repository: S3 + upload-isolate-data-repository: S3 + download-isolate-data-repository: S3 + + get-distance-matrix-repository: S3 + get-tree-repository: S3 + get-tree-view-repository: S3 + get-typing-data-repository: S3 + get-isolate-data-repository: S3 + +flowviz: + url: http://localhost:3000/flowapi + username: admin + password: admin + +logging: + level: + root: debug \ No newline at end of file diff --git a/src/backend/microservices/shared-phylodb/build.gradle b/src/backend/microservices/shared-phylodb/build.gradle deleted file mode 100644 index fb79c9ca..00000000 --- a/src/backend/microservices/shared-phylodb/build.gradle +++ /dev/null @@ -1,36 +0,0 @@ -plugins { - id 'java-library' - id 'org.springframework.boot' version '3.0.4' - id 'io.spring.dependency-management' version '1.1.0' - id "io.freefair.lombok" version "8.0.0-rc2" -} - -group 'phylovizwebplatform' -version '0.0.1-SNAPSHOT' -sourceCompatibility = '17' - -repositories { - mavenCentral() -} - -dependencies { - implementation project(path: ':microservices:shared') - - implementation files('libs/phylodb-1.0.0.jar') - implementation 'org.springframework.boot:spring-boot-starter-data-neo4j' - - implementation 'org.springframework.boot:spring-boot-starter-web' - testImplementation 'org.springframework.boot:spring-boot-starter-test' -} - -test { - useJUnitPlatform() -} - -bootJar { - enabled = false -} - -jar { - enabled = true -} \ No newline at end of file diff --git a/src/backend/microservices/shared-phylodb/libs/phylodb-1.0.0.jar b/src/backend/microservices/shared-phylodb/libs/phylodb-1.0.0.jar deleted file mode 100644 index d668385c..00000000 Binary files a/src/backend/microservices/shared-phylodb/libs/phylodb-1.0.0.jar and /dev/null differ diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/DataRepositoryConfig.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/DataRepositoryConfig.java deleted file mode 100644 index 1e6aa5a8..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/DataRepositoryConfig.java +++ /dev/null @@ -1,98 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.config; - -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.distance_matrix.DistanceMatrixDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.isolate_data.IsolateDataDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree.TreeDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.tree_view.TreeViewDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.registry.typing_data.TypingDataDataRepositoryRegistryImpl; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreePhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataS3DataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataS3DataRepositorySpecificData; -import org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.isolate_data.IsolateDataPhyloDBDataRepository; -import org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.tree.TreePhyloDBDataRepository; -import org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.tree_view.TreeViewPhyloDBDataRepository; -import org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.typing_data.TypingDataPhyloDBDataRepository; -import org.springframework.context.ApplicationContext; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.Configuration; - -import java.util.Map; - -@Configuration -public class DataRepositoryConfig { - - @Bean - public DistanceMatrixDataRepositoryRegistry distanceMatrixDataRepositoryRegistry(ApplicationContext context) { - return new DistanceMatrixDataRepositoryRegistryImpl(context, Map.of( - DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepository.class - ), Map.of( - DistanceMatrixDataRepositoryId.S3, DistanceMatrixS3DataRepositorySpecificData.class - )); - } - - @Bean - public IsolateDataDataRepositoryRegistry isolateDataDataRepositoryRegistry(ApplicationContext context) { - return new IsolateDataDataRepositoryRegistryImpl(context, Map.of( - IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepository.class, - IsolateDataDataRepositoryId.PHYLODB, IsolateDataPhyloDBDataRepository.class - - ), Map.of( - IsolateDataDataRepositoryId.S3, IsolateDataS3DataRepositorySpecificData.class, - IsolateDataDataRepositoryId.PHYLODB, IsolateDataPhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public TreeDataRepositoryRegistry treeDataRepositoryRegistry(ApplicationContext context) { - return new TreeDataRepositoryRegistryImpl(context, Map.of( - TreeDataRepositoryId.S3, TreeS3DataRepository.class, - TreeDataRepositoryId.PHYLODB, TreePhyloDBDataRepository.class - ), Map.of( - TreeDataRepositoryId.S3, TreeS3DataRepositorySpecificData.class, - TreeDataRepositoryId.PHYLODB, TreePhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public TreeViewDataRepositoryRegistry treeViewDataRepositoryRegistry(ApplicationContext context) { - return new TreeViewDataRepositoryRegistryImpl(context, Map.of( - TreeViewDataRepositoryId.S3, TreeViewS3DataRepository.class, - TreeViewDataRepositoryId.PHYLODB, TreeViewPhyloDBDataRepository.class - ), Map.of( - TreeViewDataRepositoryId.S3, TreeViewS3DataRepositorySpecificData.class, - TreeViewDataRepositoryId.PHYLODB, TreeViewPhyloDBDataRepositorySpecificData.class - )); - } - - @Bean - public TypingDataDataRepositoryRegistry typingDataDataRepositoryRegistry(ApplicationContext context) { - return new TypingDataDataRepositoryRegistryImpl(context, Map.of( - TypingDataDataRepositoryId.S3, TypingDataS3DataRepository.class, - TypingDataDataRepositoryId.PHYLODB, TypingDataPhyloDBDataRepository.class - ), Map.of( - TypingDataDataRepositoryId.S3, TypingDataS3DataRepositorySpecificData.class, - TypingDataDataRepositoryId.PHYLODB, TypingDataPhyloDBDataRepositorySpecificData.class - )); - } -} diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/ResourceServerSharedPhylodbConfig.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/ResourceServerSharedPhylodbConfig.java deleted file mode 100644 index aba141d9..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/config/ResourceServerSharedPhylodbConfig.java +++ /dev/null @@ -1,13 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.config; - -import org.phyloviz.pwp.shared.config.ResourceServerSharedConfig; -import org.springframework.context.annotation.ComponentScan; -import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Import; - -@Configuration -@Import({ResourceServerSharedConfig.class}) -@ComponentScan(basePackages = {"org.phyloviz.pwp.shared_phylodb", "pt.ist.meic.phylodb"}) -public class ResourceServerSharedPhylodbConfig { - -} \ No newline at end of file diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/isolate_data/IsolateDataPhyloDBDataRepository.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/isolate_data/IsolateDataPhyloDBDataRepository.java deleted file mode 100644 index ef2ca087..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/isolate_data/IsolateDataPhyloDBDataRepository.java +++ /dev/null @@ -1,65 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.isolate_data; - -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.GetIsolateDataRowsOutput; -import org.phyloviz.pwp.shared.service.dtos.files.isolate_data.IsolateDataRow; -import org.springframework.stereotype.Repository; -import org.springframework.web.multipart.MultipartFile; -import pt.ist.meic.phylodb.typing.isolate.IsolateRepository; -import pt.ist.meic.phylodb.typing.isolate.model.Ancillary; -import pt.ist.meic.phylodb.typing.isolate.model.Isolate; - -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; - -@Repository -@RequiredArgsConstructor -public class IsolateDataPhyloDBDataRepository implements IsolateDataDataRepository { - private final IsolateRepository isolateRepository; - - @Override - public IsolateDataDataRepositorySpecificData uploadIsolateData(String projectId, String isolateDataId, MultipartFile multipartFile) { - throw new UnsupportedOperationException("Not supported."); - } - - @Override - public String downloadIsolateData(IsolateDataDataRepositorySpecificData isolateDataDataRepositorySpecificData) { - throw new UnsupportedOperationException("Not supported."); - } - - @Override - public GetIsolateDataRowsOutput getIsolateDataRows(IsolateDataDataRepositorySpecificData isolateDataDataRepositorySpecificData, int limit, int offset) { - IsolateDataPhyloDBDataRepositorySpecificData repositorySpecificData = - (IsolateDataPhyloDBDataRepositorySpecificData) isolateDataDataRepositorySpecificData; - - List isolates = isolateRepository.findAll( - offset, - limit, - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetIds().get(0) - ).orElseThrow(() -> new RuntimeException("Isolates not found in PhyloDB")); - - return new GetIsolateDataRowsOutput( - isolates.stream() - .filter(isolate -> isolate.getProfile() != null) - .map(isolate -> new IsolateDataRow( - isolate.getPrimaryKey().getId(), - isolate.getProfile().getPrimaryKey().getId(), - Arrays.stream(isolate.getAncillaries()).collect( - Collectors.toMap(Ancillary::getKey, Ancillary::getValue) - ) - ) - ).toList(), - isolates.size() - ); - } - - @Override - public void deleteIsolateData(IsolateDataDataRepositorySpecificData isolateDataDataRepositorySpecificData) { - // throw new UnsupportedOperationException("Not implemented yet."); TODO: implement - } -} diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree/TreePhyloDBDataRepository.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree/TreePhyloDBDataRepository.java deleted file mode 100644 index 73006f7f..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree/TreePhyloDBDataRepository.java +++ /dev/null @@ -1,23 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.tree; - -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; -import org.springframework.stereotype.Repository; -import pt.ist.meic.phylodb.analysis.inference.InferenceService; - -@Repository -@RequiredArgsConstructor -public class TreePhyloDBDataRepository implements TreeDataRepository { - private final InferenceService inferenceService; - - @Override - public String getTree(TreeDataRepositorySpecificData treeDataRepositorySpecificData) { - throw new UnsupportedOperationException("Not implemented yet"); - } - - @Override - public void deleteTree(TreeDataRepositorySpecificData treeDataRepositorySpecificData) { - // throw new UnsupportedOperationException("Not implemented yet."); TODO: implement - } -} diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree_view/TreeViewPhyloDBDataRepository.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree_view/TreeViewPhyloDBDataRepository.java deleted file mode 100644 index 2c0c808a..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/tree_view/TreeViewPhyloDBDataRepository.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.tree_view; - -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Edge; -import org.phyloviz.pwp.shared.service.dtos.tree_view.GetTreeViewOutput; -import org.phyloviz.pwp.shared.service.dtos.tree_view.Node; -import org.springframework.stereotype.Repository; -import pt.ist.meic.phylodb.analysis.inference.InferenceService; -import pt.ist.meic.phylodb.analysis.inference.model.Inference; -import pt.ist.meic.phylodb.analysis.visualization.VisualizationRepository; -import pt.ist.meic.phylodb.analysis.visualization.VisualizationService; -import pt.ist.meic.phylodb.analysis.visualization.model.Visualization; -import pt.ist.meic.phylodb.typing.profile.ProfileRepository; -import pt.ist.meic.phylodb.typing.profile.model.Profile; - -import java.util.HashMap; -import java.util.List; - -@Repository -@RequiredArgsConstructor -public class TreeViewPhyloDBDataRepository implements TreeViewDataRepository { - - private final VisualizationService visualizationService; - private final InferenceService inferenceService; - private final ProfileRepository profileRepository; - private final VisualizationRepository visualizationRepository; - - @Override - public GetTreeViewOutput getTreeView(TreeViewDataRepositorySpecificData treeViewDataRepositorySpecificData) { - TreeViewPhyloDBDataRepositorySpecificData repositorySpecificData = - (TreeViewPhyloDBDataRepositorySpecificData) treeViewDataRepositorySpecificData; - - Inference inference = inferenceService.getInference( - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetId(), - repositorySpecificData.getInferenceId() - ).orElseThrow(() -> new RuntimeException("Inference not found in PhyloDB")); - - Visualization visualization = visualizationService.getVisualization( - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetId(), - repositorySpecificData.getInferenceId(), - repositorySpecificData.getVisualizationId() - ).orElseThrow(() -> new RuntimeException("Visualization not found in PhyloDB")); - - List edges = inference.getEdges().stream().map(edge -> new Edge( - edge.getFrom().getPrimaryKey().getId(), - edge.getTo().getPrimaryKey().getId(), - edge.getWeight() - )).toList(); - - List profiles = profileRepository.findAll( - 0, - Integer.MAX_VALUE, - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetId() - ).orElseThrow(() -> new RuntimeException("Profiles not found in PhyloDB")); - - HashMap profilesMap = new HashMap<>(); - - profiles.forEach(profile -> profilesMap.put(profile.getPrimaryKey().getId(), profile)); - - List nodes = visualization.getCoordinates().stream().map(coordinate -> { - Profile.PrimaryKey profileKey = coordinate.getProfile(); - - Profile profile = profilesMap.get(profileKey.getId()); - - return new Node( - profileKey.getId(), - new double[]{coordinate.getX(), coordinate.getY()}, - profile.getAllelesReferences().stream().map(alleleReference -> - alleleReference.getPrimaryKey().getId() - ).toList() // TODO add ancillary data - ); - }).toList(); - - return new GetTreeViewOutput( - nodes, - nodes.size(), - edges, - edges.size(), - null - ); - } - - @Override - public void saveTreeView(TreeViewDataRepositorySpecificData treeViewDataRepositorySpecificData, List nodes) { - // TODO implement save visualization in PhyloDB - - /*TreeViewPhyloDBDataRepositorySpecificData repositorySpecificData = - (TreeViewPhyloDBDataRepositorySpecificData) treeViewDataRepositorySpecificData; - - Visualization visualization = visualizationService.getVisualization( - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetId(), - repositorySpecificData.getInferenceId(), - repositorySpecificData.getVisualizationId() - ).orElseThrow(() -> new RuntimeException("Visualization not found in PhyloDB")); - - List newCoordinates = nodes.stream().map(node -> new Coordinate( - new Profile.PrimaryKey( - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetId(), - node.getSt() - ), - 0, - node.getCoordinates()[0], - node.getCoordinates()[1] - )).toList(); - - visualizationRepository.save(new Visualization( - visualization.getPrimaryKey().getProjectId(), - visualization.getPrimaryKey().getDatasetId(), - visualization.getPrimaryKey().getInferenceId(), - visualization.getPrimaryKey().getId(), - visualization.isDeprecated(), - visualization.getAlgorithm(), - newCoordinates - ));*/ - } - - @Override - public void deleteTreeView(TreeViewDataRepositorySpecificData treeViewDataRepositorySpecificData) { - // throw new UnsupportedOperationException("Not implemented yet."); // TODO: Implement - } -} diff --git a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/typing_data/TypingDataPhyloDBDataRepository.java b/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/typing_data/TypingDataPhyloDBDataRepository.java deleted file mode 100644 index aeb88ffd..00000000 --- a/src/backend/microservices/shared-phylodb/src/main/java/org/phyloviz/pwp/shared_phylodb/repository/data/phylodb/typing_data/TypingDataPhyloDBDataRepository.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.phyloviz.pwp.shared_phylodb.repository.data.phylodb.typing_data; - -import lombok.RequiredArgsConstructor; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataPhyloDBDataRepositorySpecificData; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataProfilesOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.GetTypingDataSchemaOutput; -import org.phyloviz.pwp.shared.service.dtos.files.typing_data.TypingDataProfile; -import org.springframework.stereotype.Repository; -import org.springframework.web.multipart.MultipartFile; -import pt.ist.meic.phylodb.typing.dataset.model.Dataset; -import pt.ist.meic.phylodb.typing.profile.ProfileRepository; -import pt.ist.meic.phylodb.typing.profile.model.Profile; -import pt.ist.meic.phylodb.typing.schema.SchemaRepository; -import pt.ist.meic.phylodb.typing.schema.model.Schema; - -import java.util.List; - -@Repository -@RequiredArgsConstructor -public class TypingDataPhyloDBDataRepository implements TypingDataDataRepository { - private final ProfileRepository profileRepository; - private final SchemaRepository schemaRepository; - - @Override - public TypingDataDataRepositorySpecificData uploadTypingData(String projectId, String typingDataId, MultipartFile multipartFile) { - throw new UnsupportedOperationException("Not supported."); - } - - @Override - public String downloadTypingData(TypingDataDataRepositorySpecificData typingDataDataRepositorySpecificData) { - throw new UnsupportedOperationException("Not supported."); - } - - @Override - public GetTypingDataSchemaOutput getTypingDataSchema(TypingDataDataRepositorySpecificData typingDataDataRepositorySpecificData) { - TypingDataPhyloDBDataRepositorySpecificData repositorySpecificData = - (TypingDataPhyloDBDataRepositorySpecificData) typingDataDataRepositorySpecificData; - - Schema schema = schemaRepository.find(new Dataset.PrimaryKey( - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetIds().get(0)) - ).orElseThrow(() -> new RuntimeException("Schema not found in PhyloDB")); - - return new GetTypingDataSchemaOutput( - schema.getType().getName(), - schema.getLociIds() - ); - } - - @Override - public GetTypingDataProfilesOutput getTypingDataProfiles(TypingDataDataRepositorySpecificData typingDataDataRepositorySpecificData, int limit, int offset) { - TypingDataPhyloDBDataRepositorySpecificData repositorySpecificData = - (TypingDataPhyloDBDataRepositorySpecificData) typingDataDataRepositorySpecificData; - - List profiles = profileRepository.findAll( - offset, - limit, - repositorySpecificData.getProjectId(), - repositorySpecificData.getDatasetIds().get(0) - ).orElseThrow(() -> new RuntimeException("Profiles not found in PhyloDB")); - - return new GetTypingDataProfilesOutput( - profiles.stream().map(profile -> new TypingDataProfile( - profile.getPrimaryKey().getId(), - profile.getAllelesReferences().stream().map(alleleReference -> - alleleReference.getPrimaryKey().getId() - ).toList() - ) - ).toList(), - profiles.size() - ); - } - - @Override - public void deleteTypingData(TypingDataDataRepositorySpecificData typingDataDataRepositorySpecificData) { - // throw new UnsupportedOperationException("Not implemented yet."); TODO: implement - } -} diff --git a/src/backend/microservices/shared/build.gradle b/src/backend/microservices/shared/build.gradle deleted file mode 100644 index c123e211..00000000 --- a/src/backend/microservices/shared/build.gradle +++ /dev/null @@ -1,47 +0,0 @@ -plugins { - id 'java-library' - id 'org.springframework.boot' version '3.0.4' - id 'io.spring.dependency-management' version '1.1.0' - id "io.freefair.lombok" version "8.0.0-rc2" -} - -group 'phylovizwebplatform' -version '0.0.1-SNAPSHOT' -sourceCompatibility = '17' - -repositories { - mavenCentral() -} - -dependencies { - testImplementation 'org.junit.jupiter:junit-jupiter-api:5.8.1' - testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.8.1' - - implementation 'org.springframework.boot:spring-boot-starter-data-mongodb' - implementation 'org.springframework.boot:spring-boot-starter-web' - implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server' - testImplementation 'org.springframework.boot:spring-boot-starter-test' - - implementation 'com.fasterxml.jackson.core:jackson-databind:2.14.2' - implementation 'org.zalando:problem-spring-web-starter:0.27.0' - - implementation 'software.amazon.awssdk:s3:2.20.28' - implementation 'software.amazon.awssdk:s3-transfer-manager:2.20.28' - - implementation 'org.reflections:reflections:0.10.2' - - implementation 'org.springframework.boot:spring-boot-starter-data-rest' - implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' -} - -test { - useJUnitPlatform() -} - -bootJar { - enabled = false -} - -jar { - enabled = true -} \ No newline at end of file diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ResourceServerSharedConfig.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ResourceServerSharedConfig.java deleted file mode 100644 index 6fe56ef7..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/config/ResourceServerSharedConfig.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.phyloviz.pwp.shared.config; - - -import org.springframework.context.annotation.ComponentScan; -import org.springframework.context.annotation.Configuration; - -@Configuration -@ComponentScan(basePackages = {"org.phyloviz.pwp.shared"}) -public class ResourceServerSharedConfig { - -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java deleted file mode 100644 index 5286e47b..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/DistanceMatrixDataRepositoryId.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.distance_matrix; - -public enum DistanceMatrixDataRepositoryId { - S3 -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java deleted file mode 100644 index 35b70094..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/distance_matrix/repository/specific_data/DistanceMatrixDataRepositorySpecificData.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data; - -public interface DistanceMatrixDataRepositorySpecificData { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java deleted file mode 100644 index 8c82eaed..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/isolate_data/repository/specific_data/IsolateDataDataRepositorySpecificData.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data; - -public interface IsolateDataDataRepositorySpecificData { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java deleted file mode 100644 index b8cacacf..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/distance_matrix/DistanceMatrixDataRepositoryRegistry.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.registry.distance_matrix; - -import org.phyloviz.pwp.shared.repository.data.distance_matrix.DistanceMatrixDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.DistanceMatrixDataRepository; -import org.phyloviz.pwp.shared.repository.data.distance_matrix.repository.specific_data.DistanceMatrixDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryRegistry; - -public interface DistanceMatrixDataRepositoryRegistry extends - DataRepositoryRegistry { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java deleted file mode 100644 index d6c1a337..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/isolate_data/IsolateDataDataRepositoryRegistry.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.registry.isolate_data; - -import org.phyloviz.pwp.shared.repository.data.isolate_data.IsolateDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.IsolateDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.isolate_data.repository.specific_data.IsolateDataDataRepositorySpecificData; -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryRegistry; - -public interface IsolateDataDataRepositoryRegistry extends - DataRepositoryRegistry { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistry.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistry.java deleted file mode 100644 index f4c9bbe7..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree/TreeDataRepositoryRegistry.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree; - -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree.TreeDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree.repository.TreeDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data.TreeDataRepositorySpecificData; - -public interface TreeDataRepositoryRegistry extends - DataRepositoryRegistry { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java deleted file mode 100644 index f2121c0d..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/tree_view/TreeViewDataRepositoryRegistry.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.registry.tree_view; - -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.tree_view.TreeViewDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.TreeViewDataRepository; -import org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data.TreeViewDataRepositorySpecificData; - -public interface TreeViewDataRepositoryRegistry extends - DataRepositoryRegistry { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java deleted file mode 100644 index 5a0df3ea..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/registry/typing_data/TypingDataDataRepositoryRegistry.java +++ /dev/null @@ -1,10 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.registry.typing_data; - -import org.phyloviz.pwp.shared.repository.data.registry.DataRepositoryRegistry; -import org.phyloviz.pwp.shared.repository.data.typing_data.TypingDataDataRepositoryId; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.TypingDataDataRepository; -import org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data.TypingDataDataRepositorySpecificData; - -public interface TypingDataDataRepositoryRegistry extends - DataRepositoryRegistry { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java deleted file mode 100644 index f6411629..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree/repository/specific_data/TreeDataRepositorySpecificData.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.tree.repository.specific_data; - -public interface TreeDataRepositorySpecificData { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java deleted file mode 100644 index 5867fe7b..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/tree_view/repository/specific_data/TreeViewDataRepositorySpecificData.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.tree_view.repository.specific_data; - -public interface TreeViewDataRepositorySpecificData { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java deleted file mode 100644 index c356480c..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/data/typing_data/repository/specific_data/TypingDataDataRepositorySpecificData.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.data.typing_data.repository.specific_data; - -public interface TypingDataDataRepositorySpecificData { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java deleted file mode 100644 index 5219ef39..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/distance_matrix/documents/source/DistanceMatrixSource.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.metadata.distance_matrix.documents.source; - -public interface DistanceMatrixSource { -} diff --git a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSource.java b/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSource.java deleted file mode 100644 index 3309283c..00000000 --- a/src/backend/microservices/shared/src/main/java/org/phyloviz/pwp/shared/repository/metadata/tree/documents/source/TreeSource.java +++ /dev/null @@ -1,4 +0,0 @@ -package org.phyloviz.pwp.shared.repository.metadata.tree.documents.source; - -public interface TreeSource { -} diff --git a/src/backend/microservices/shared/src/main/resources/application-shared.yml b/src/backend/microservices/shared/src/main/resources/application-shared.yml deleted file mode 100644 index 11f9cf83..00000000 --- a/src/backend/microservices/shared/src/main/resources/application-shared.yml +++ /dev/null @@ -1,23 +0,0 @@ -s3: - access-key-id: AKIAIOSFODNN7EXAMPLE - secret-access-key: wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY - bucket: phyloviz-web-platform/ - endpoint: http://localhost:9444 - -spring: - data: - mongodb: - host: localhost - port: 28017 - database: phyloviz-web-platform - authentication-database: admin - auto-index-creation: true - security: - oauth2: - resourceserver: - opaquetoken: - introspection-uri: http://localhost:8082/realms/phyloviz-web-platform/protocol/openid-connect/token/introspect - client-id: phyloviz-web-platform-client - client-secret: whCCD9r37qj8mx9H7R4mzIrSezYf3H7R -# jwt: -# jwk-set-uri: http://localhost:8082/realms/phyloviz-web-platform/protocol/openid-connect/certs \ No newline at end of file diff --git a/src/backend/microservices/visualization/Dockerfile b/src/backend/microservices/visualization/Dockerfile deleted file mode 100644 index c0ff91c6..00000000 --- a/src/backend/microservices/visualization/Dockerfile +++ /dev/null @@ -1,4 +0,0 @@ -FROM openjdk:17-jdk-alpine -COPY build/libs/visualization-0.0.1-SNAPSHOT.jar /app.jar - -ENTRYPOINT ["java", "-jar", "/app.jar"] \ No newline at end of file diff --git a/src/backend/microservices/visualization/build.gradle b/src/backend/microservices/visualization/build.gradle deleted file mode 100644 index b2bd2bac..00000000 --- a/src/backend/microservices/visualization/build.gradle +++ /dev/null @@ -1,41 +0,0 @@ -plugins { - id 'application' - id 'org.springframework.boot' version '3.0.4' - id 'io.spring.dependency-management' version '1.1.0' - id "io.freefair.lombok" version "8.0.0-rc2" -} - -group 'phylovizwebplatform' -version '0.0.1-SNAPSHOT' -sourceCompatibility = '17' - -ext { - set('jupiterVersion', "5.8.1") -} - -repositories { - mavenCentral() -} - -dependencies { - implementation project(path: ':microservices:shared-phylodb') - implementation project(path: ':microservices:shared') - - testImplementation 'org.springframework.boot:spring-boot-starter-test' - testImplementation 'org.junit.jupiter:junit-jupiter-api' version { jupiterVersion } - testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine' version { jupiterVersion } - - implementation 'org.springframework.boot:spring-boot-starter-data-mongodb' - implementation 'org.springframework.boot:spring-boot-starter-web' - implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server' - implementation 'org.springframework.boot:spring-boot-starter-actuator' - - implementation 'com.fasterxml.jackson.core:jackson-databind:2.14.2' - implementation 'org.zalando:problem-spring-web-starter:0.27.0' - - implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.6' -} - -test { - useJUnitPlatform() -} \ No newline at end of file diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplication.java b/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplication.java deleted file mode 100644 index d2355e57..00000000 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplication.java +++ /dev/null @@ -1,21 +0,0 @@ -package org.phyloviz.pwp.visualization; - -import org.springframework.boot.SpringApplication; -import org.springframework.boot.autoconfigure.SpringBootApplication; - -/** - * Main class for the Visualization Microservice of the PHYLOViZ Web Platform. - */ -@SpringBootApplication -public class VisualizationMicroserviceApplication { - - - /** - * Entry point for the Visualization Microservice. - * - * @param args arguments passed to the application - */ - public static void main(String[] args) { - SpringApplication.run(VisualizationMicroserviceApplication.class, args); - } -} diff --git a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/config/VisualizationConfig.java b/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/config/VisualizationConfig.java deleted file mode 100644 index 20d26e33..00000000 --- a/src/backend/microservices/visualization/src/main/java/org/phyloviz/pwp/visualization/config/VisualizationConfig.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.phyloviz.pwp.visualization.config; - -import org.phyloviz.pwp.shared.config.ResourceServerSharedConfig; -import org.phyloviz.pwp.shared_phylodb.config.ResourceServerSharedPhylodbConfig; -import org.springframework.context.annotation.Configuration; -import org.springframework.context.annotation.Import; - -/** - * Configuration class for the Visualization Microservice. - */ -@Configuration -@Import({ResourceServerSharedConfig.class, ResourceServerSharedPhylodbConfig.class}) -public class VisualizationConfig { -} \ No newline at end of file diff --git a/src/backend/microservices/visualization/src/main/resources/application.yml b/src/backend/microservices/visualization/src/main/resources/application.yml deleted file mode 100644 index aca9a1e1..00000000 --- a/src/backend/microservices/visualization/src/main/resources/application.yml +++ /dev/null @@ -1,17 +0,0 @@ -server: - port: 8085 - -spring: - config: - import: application-shared.yml - -data-repositories: - get-distance-matrix-repository: S3 - get-tree-repository: S3 - get-tree-view-repository: PHYLODB - get-typing-data-repository: PHYLODB - get-isolate-data-repository: PHYLODB - -logging: - level: - root: debug \ No newline at end of file diff --git a/src/backend/microservices/visualization/src/test/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplicationTests.java b/src/backend/microservices/visualization/src/test/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplicationTests.java deleted file mode 100644 index a404876d..00000000 --- a/src/backend/microservices/visualization/src/test/java/org/phyloviz/pwp/visualization/VisualizationMicroserviceApplicationTests.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.phyloviz.pwp.visualization; - -import org.springframework.boot.test.context.SpringBootTest; - -@SpringBootTest -class VisualizationMicroserviceApplicationTests { - - /*@Test - void contextLoads() { - }*/ -} diff --git a/src/backend/settings.gradle b/src/backend/settings.gradle index 500ba60b..f1603b38 100644 --- a/src/backend/settings.gradle +++ b/src/backend/settings.gradle @@ -1,10 +1,3 @@ rootProject.name = 'phyloviz-web-platform' -include 'microservices:visualization' -include 'microservices:compute' -include 'microservices:gateway' -include 'microservices:shared' -include 'microservices:administration' -include 'microservices:file-transfer' -include 'microservices:shared-phylodb' -findProject(':microservices:shared-phylodb')?.name = 'shared-phylodb' - +include 'gateway' +include 'core' diff --git a/test/.env b/test/.env deleted file mode 100644 index be13d82a..00000000 --- a/test/.env +++ /dev/null @@ -1 +0,0 @@ -COMPOSE_PROJECT_NAME=phyloviz-web-platform-test diff --git a/test/docker-compose.yml b/test/docker-compose.yml deleted file mode 100644 index ce8ec212..00000000 --- a/test/docker-compose.yml +++ /dev/null @@ -1,9 +0,0 @@ -version: '3.9' -services: - s3ninja: - container_name: s3ninja - image: scireum/s3-ninja:latest - ports: - - "9444:9000" - volumes: - - "./s3ninja-data:/data" \ No newline at end of file