From 31307b0806ba90ab1da17c74a0bfee2ff6de62bf Mon Sep 17 00:00:00 2001 From: Seyit Zor Date: Thu, 16 Nov 2023 13:13:34 +0000 Subject: [PATCH 01/10] template and dependency updates --- .deprecated_files | 1 + .devcontainer/devcontainer.json | 36 ++- .editorconfig | 14 -- .gitignore | 6 + .mandatory_files | 2 - .readme_template.md | 23 +- .static_files | 2 +- pyproject.toml | 8 +- requirements-dev.txt | 223 +++++++++++++----- requirements.txt | 205 +++++++++++----- scripts/license_checker.py | 3 + scripts/update_config_docs.py | 9 +- .../accession_registry/accession_registry.py | 17 +- .../accession_registry/accession_store.py | 3 +- src/metldata/artifacts_rest/config.py | 5 +- src/metldata/artifacts_rest/models.py | 7 +- .../add_accessions/config.py | 3 +- .../aggregate/config.py | 5 +- .../custom_embeddings/config.py | 5 +- .../delete_slots/config.py | 15 +- .../infer_references/config.py | 37 +-- .../infer_references/path/path.py | 8 +- .../infer_references/reference.py | 8 +- .../merge_slots/config.py | 7 +- .../merge_slots/models.py | 9 +- .../event_handling/artifact_events.py | 4 +- src/metldata/event_handling/event_handling.py | 3 +- .../event_handling/submission_events.py | 3 +- src/metldata/load/collect.py | 4 +- src/metldata/load/event_publisher.py | 19 +- src/metldata/model_utils/config.py | 3 +- src/metldata/submission_registry/models.py | 4 +- .../submission_registry/submission_store.py | 5 +- src/metldata/transform/base.py | 13 +- src/metldata/transform/handling.py | 2 +- tests/artifact_rest/test_api_factory.py | 6 +- tests/fixtures/load/config.py | 2 +- tests/transform/test_base.py | 7 +- 38 files changed, 479 insertions(+), 257 deletions(-) delete mode 100644 .editorconfig diff --git a/.deprecated_files b/.deprecated_files index ca3684e0..af2a4cf8 100644 --- a/.deprecated_files +++ b/.deprecated_files @@ -21,3 +21,4 @@ setup.cfg .pylintrc .flake8 +.editorconfig diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index eda6e100..89ff58f8 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,7 +2,7 @@ // https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres // Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.8, 3.7, 3.6 { - "name": "metldata", + "name": "${localWorkspaceFolderBasename}", "dockerComposeFile": "docker-compose.yml", "service": "app", "workspaceFolder": "/workspace", @@ -10,6 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { + "files.eol": "\n", "terminal.integrated.profiles.linux": { "bash": { "path": "/bin/bash" @@ -17,19 +18,11 @@ }, "python.pythonPath": "/usr/local/bin/python", "python.languageServer": "Pylance", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8", - "python.formatting.blackPath": "/usr/local/py-utils/bin/black", - "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf", - "python.formatting.provider": "black", "python.analysis.typeCheckingMode": "basic", - "python.linting.banditPath": "/usr/local/py-utils/bin/bandit", - "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy", - "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle", - "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle", - "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint", "python.testing.pytestPath": "/usr/local/py-utils/bin/pytest", + "python.testing.pytestArgs": [ + "--profile" + ], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, "editor.formatOnSave": true, @@ -37,6 +30,7 @@ "editor.rulers": [ 88 ], + "editor.defaultFormatter": "ms-python.black-formatter", "licenser.license": "Custom", "licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt" }, @@ -45,7 +39,6 @@ "mikestead.dotenv", "ms-azuretools.vscode-docker", "ms-python.python", - "ms-python.isort", "ms-python.vscode-pylance", "ms-toolsai.jupyter", "njpwerner.autodocstring", @@ -58,7 +51,9 @@ "yzhang.markdown-all-in-one", "visualstudioexptteam.vscodeintellicode", "ymotongpoo.licenser", - "editorconfig.editorconfig" + "charliermarsh.ruff", + "ms-python.black-formatter", + "ms-python.mypy-type-checker" ] } }, @@ -68,12 +63,13 @@ "postCreateCommand": "dev_install", // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root. "remoteUser": "vscode", + "containerEnv": { + // for testcontainers to connect to the docker host: + "TC_HOST": "host.docker.internal", + "DOCKER_HOST": "unix:///var/run/docker.sock" + }, "features": { - "ghcr.io/devcontainers/features/docker-in-docker:2": { - "version": "latest", - "enableNonRootDocker": "true", - "moby": true, - "azureDnsAutoDetection": false - } + // details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {} } } diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 3fa06b52..00000000 --- a/.editorconfig +++ /dev/null @@ -1,14 +0,0 @@ -# Top-most EditorConfig file. -root = true - -# For all files ... -[*] - -# Unix-style LF newlines. -end_of_line = lf - -# Force a newline at the end of the file. -insert_final_newline = true - -# Use UTF-8. -charset = utf-8 diff --git a/.gitignore b/.gitignore index a71cfd2a..d9ba6145 100644 --- a/.gitignore +++ b/.gitignore @@ -133,6 +133,12 @@ dmypy.json # ignore VS Code settings: .vscode/ +# key stores +*.key +*.rnd +.keystore +.ssl/ + # desktop settings and thumbnails .DS_Store desktop.ini diff --git a/.mandatory_files b/.mandatory_files index c0b51fb1..ba9f6c31 100644 --- a/.mandatory_files +++ b/.mandatory_files @@ -6,9 +6,7 @@ # may differ from that of the template repository. .devcontainer/dev_launcher -.devcontainer/devcontainer.json .devcontainer/docker-compose.yml -.devcontainer/Dockerfile tests/__init__.py tests/fixtures/__init__.py diff --git a/.readme_template.md b/.readme_template.md index dd8b1844..10e3e612 100644 --- a/.readme_template.md +++ b/.readme_template.md @@ -1,5 +1,5 @@ -[![tests](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml) +[![tests](https://github.com/ghga-de/$name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/tests.yaml) [![Coverage Status](https://coveralls.io/repos/github/ghga-de/$name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$name?branch=main) # $title @@ -11,6 +11,7 @@ $summary $description ## Installation + We recommend using the provided Docker container. A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name): @@ -42,6 +43,7 @@ $shortname --help ``` ## Configuration + ### Parameters The service requires the following configuration parameters: @@ -77,19 +79,20 @@ $openapi_doc $design_description ## Development + For setting up the development environment, we rely on the -[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode +[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of VS Code in combination with Docker Compose. -To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers" +To use it, you have to have Docker Compose as well as VS Code with its "Remote - Containers" extension (`ms-vscode-remote.remote-containers`) installed. -Then open this repository in vscode and run the command -`Remote-Containers: Reopen in Container` from the vscode "Command Palette". +Then open this repository in VS Code and run the command +`Remote-Containers: Reopen in Container` from the VS Code "Command Palette". This will give you a full-fledged, pre-configured development environment including: - infrastructural dependencies of the service (databases, etc.) -- all relevant vscode extensions pre-installed -- pre-configured linting and auto-formating +- all relevant VS Code extensions pre-installed +- pre-configured linting and auto-formatting - a pre-configured debugger - automatic license-header insertion @@ -101,9 +104,11 @@ if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the [`./requirements-dev.txt`](./requirements-dev.txt), please run it again. ## License + This repository is free to use and modify according to the [Apache 2.0 License](./LICENSE). -## Readme Generation -This readme is autogenerate, please see [`readme_generation.md`](./readme_generation.md) +## README Generation + +This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md) for details. diff --git a/.static_files b/.static_files index e3c8f767..5f035a96 100644 --- a/.static_files +++ b/.static_files @@ -11,6 +11,7 @@ .devcontainer/dev_install .devcontainer/license_header.txt .devcontainer/Dockerfile +.devcontainer/devcontainer.json scripts/script_utils/__init__.py scripts/script_utils/cli.py @@ -39,7 +40,6 @@ scripts/README.md example_data/README.md .coveragerc -.editorconfig .gitattributes .gitignore .mypy.ini diff --git a/pyproject.toml b/pyproject.toml index 65503bd2..e16ef130 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,10 +21,10 @@ classifiers = [ "Intended Audience :: Developers", ] dependencies = [ - "hexkit[akafka,mongodb]>=0.10.2", - "ghga-service-commons[api,auth]>=0.5.0", - "ghga-event-schemas>=0.13.4", - "typer>=0.7.0", + "hexkit[akafka,mongodb]~=1.0.0", + "ghga-service-commons[api,auth]~=1.1.0", + "ghga-event-schemas~=1.0.0", + "typer~=0.9.0", "linkml==1.6.1", "linkml-runtime==1.6.0", "linkml-validator==0.4.5", diff --git a/requirements-dev.txt b/requirements-dev.txt index 596f35b7..97c91940 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,7 +2,7 @@ # This file is autogenerated by pip-compile with Python 3.9 # by the following command: # -# pip-compile --generate-hashes --output-file=/workspace/requirements-dev.txt /tmp/tmpu62427re/pyproject.toml /workspace/requirements-dev.in +# pip-compile --generate-hashes --output-file=/workspace/requirements-dev.txt /tmp/tmph8bxvet7/pyproject.toml /workspace/requirements-dev.in # aiokafka==0.8.0 \ --hash=sha256:021e9f0027ca63c6c04daccfdd0e985f7a56d51bd0d43f482f674a58fada52f5 \ @@ -37,16 +37,21 @@ aiokafka==0.8.0 \ --hash=sha256:f0a216a27f05b050d5a5308fb3444014fa6bca5f0cd63468eaa169c5f19ea1dd \ --hash=sha256:f3f96301337fa7f7242f46651619b8e9e8fa8f23902dc11416fe764436d662d3 # via hexkit +annotated-types==0.6.0 \ + --hash=sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43 \ + --hash=sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d + # via pydantic antlr4-python3-runtime==4.9.3 \ --hash=sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b # via # linkml # pyjsg # pyshexc -anyio==4.0.0 \ - --hash=sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f \ - --hash=sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a +anyio==3.7.1 \ + --hash=sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780 \ + --hash=sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5 # via + # fastapi # httpcore # starlette # watchfiles @@ -326,7 +331,9 @@ coverage[toml]==7.3.2 \ --hash=sha256:f94b734214ea6a36fe16e96a70d941af80ff3bfd716c141300d95ebc85339738 \ --hash=sha256:fa28e909776dc69efb6ed975a63691bc8172b64ff357e663a1bb06ff3c9b589a \ --hash=sha256:fe494faa90ce6381770746077243231e0b83ff3f17069d748f645617cefe19d4 - # via pytest-cov + # via + # coverage + # pytest-cov cryptography==41.0.4 \ --hash=sha256:004b6ccc95943f6a9ad3142cfabcc769d7ee38a3f60fb0dddbfb431f818c3a67 \ --hash=sha256:047c4603aeb4bbd8db2756e38f5b8bd7e94318c047cfe4efeb5d715e08b49311 \ @@ -447,7 +454,6 @@ dnspython==2.3.0 \ --hash=sha256:89141536394f909066cabd112e3e1a37e4e654db00a25308b0f130bc3152eb46 # via # email-validator - # ghga-event-schemas # pymongo docker==6.1.3 \ --hash=sha256:aa6d17830045ba5ef0168d5eaa34d37beeb113948c413affe1d5991fc11f9a20 \ @@ -467,9 +473,9 @@ exceptiongroup==1.1.3 \ # via # anyio # pytest -fastapi==0.96.1 \ - --hash=sha256:22d773ce95f14f04f8f37a0c8998fc163e67af83b65510d2879de6cbaaa10215 \ - --hash=sha256:5c1d243030e63089ccfc0aec69c2da6d619943917727e8e82ee502358d5119bf +fastapi==0.103.2 \ + --hash=sha256:3270de872f0fe9ec809d4bd3d4d890c6d5cc7b9611d721d6438f9dacc8c4ef2e \ + --hash=sha256:75a11f6bfb8fc4d2bec0bd710c2d5f2829659c0e8c0afd5560fdda6ce25ec653 # via ghga-service-commons filelock==3.12.4 \ --hash=sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4 \ @@ -479,14 +485,16 @@ fqdn==1.5.1 \ --hash=sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f \ --hash=sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014 # via jsonschema -ghga-event-schemas==0.13.5 \ - --hash=sha256:1ce129c7c969fe2b263483d55c500a3d7f75b6c97e0acb6f49ddd84eca1e1974 \ - --hash=sha256:c5fb0abab7d06512b2470bb84247473528051d109200ba69a87b6701e3384d6c - # via metldata (pyproject.toml) -ghga-service-commons[api,auth]==0.7.1 \ - --hash=sha256:70a6bc39d3ab8309524dfbcd4c29e5f37de118c41107fb42054834e5dcf8decc \ - --hash=sha256:888a789cbea86bcd7433e0b848c137928eea87bd9194de3504a3c25a36ac983c +ghga-event-schemas==1.0.0 \ + --hash=sha256:34e3dcfc97025dcf9c05de73f3d40cf3c1cb361ba74f4cb2ef621de16bc158c2 \ + --hash=sha256:9f006151bb19064eb135313967e8ca6c07382ecfe0a273884e96236ffd01f3ea # via metldata (pyproject.toml) +ghga-service-commons[api,auth]==1.1.0 \ + --hash=sha256:2502ac05e429f988d066303b53147691b86c9915455c375c79a4c73d65060e8a \ + --hash=sha256:a198195e731c0239e2c248e8f40c3918ebb6087f1d0fb8f55eef91479c7ea287 + # via + # ghga-service-commons + # metldata (pyproject.toml) gprof2dot==2022.7.29 \ --hash=sha256:45b4d298bd36608fccf9511c3fd88a773f7a1abc04d6cd39445b11ba43133ec5 \ --hash=sha256:f165b3851d3c52ee4915eb1bd6cca571e5759823c2cd0f71a79bda93c2dc85d6 @@ -572,11 +580,12 @@ hbreader==0.9.1 \ # jsonasobj2 # linkml # linkml-runtime -hexkit[akafka,mongodb,test-mongodb]==0.10.2 \ - --hash=sha256:1495f2bc6ae7423874bc20367dd28555cd15a74ccf5cb4997e0fb8307757987e \ - --hash=sha256:436ea50e706ab616803eb85a9a9f5e7bec727379b750b966650d6e64d4ea5ef0 +hexkit[akafka,mongodb,test-mongodb]==1.0.0 \ + --hash=sha256:767e9cda5433f8e0c74e8f0b0376dccbfee8db1efecd2dc75e3f2b841dc99c60 \ + --hash=sha256:a88afb9d8ff9c1672fe81a233501b2ae369e155b72aae46ff5ae83f7bb252b6b # via # -r /workspace/requirements-dev.in + # hexkit # metldata (pyproject.toml) httpcore==0.16.3 \ --hash=sha256:c5d6f04e2fc530f39e0c077e6a30caa53f1451096120f1f38b954afd0b17c0cb \ @@ -701,6 +710,7 @@ jsonschema[format]==4.19.1 \ # via # ghga-event-schemas # hexkit + # jsonschema # linkml # linkml-runtime jsonschema-specifications==2023.7.1 \ @@ -906,43 +916,9 @@ pycparser==2.21 \ --hash=sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9 \ --hash=sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206 # via cffi -pydantic[email]==1.10.6 \ - --hash=sha256:012c99a9c0d18cfde7469aa1ebff922e24b0c706d03ead96940f5465f2c9cf62 \ - --hash=sha256:0abd9c60eee6201b853b6c4be104edfba4f8f6c5f3623f8e1dba90634d63eb35 \ - --hash=sha256:12e837fd320dd30bd625be1b101e3b62edc096a49835392dcf418f1a5ac2b832 \ - --hash=sha256:163e79386c3547c49366e959d01e37fc30252285a70619ffc1b10ede4758250a \ - --hash=sha256:189318051c3d57821f7233ecc94708767dd67687a614a4e8f92b4a020d4ffd06 \ - --hash=sha256:1c84583b9df62522829cbc46e2b22e0ec11445625b5acd70c5681ce09c9b11c4 \ - --hash=sha256:3091d2eaeda25391405e36c2fc2ed102b48bac4b384d42b2267310abae350ca6 \ - --hash=sha256:32937835e525d92c98a1512218db4eed9ddc8f4ee2a78382d77f54341972c0e7 \ - --hash=sha256:3a2be0a0f32c83265fd71a45027201e1278beaa82ea88ea5b345eea6afa9ac7f \ - --hash=sha256:3ac1cd4deed871dfe0c5f63721e29debf03e2deefa41b3ed5eb5f5df287c7b70 \ - --hash=sha256:3ce13a558b484c9ae48a6a7c184b1ba0e5588c5525482681db418268e5f86186 \ - --hash=sha256:415a3f719ce518e95a92effc7ee30118a25c3d032455d13e121e3840985f2efd \ - --hash=sha256:43cdeca8d30de9a897440e3fb8866f827c4c31f6c73838e3a01a14b03b067b1d \ - --hash=sha256:476f6674303ae7965730a382a8e8d7fae18b8004b7b69a56c3d8fa93968aa21c \ - --hash=sha256:4c19eb5163167489cb1e0161ae9220dadd4fc609a42649e7e84a8fa8fff7a80f \ - --hash=sha256:4ca83739c1263a044ec8b79df4eefc34bbac87191f0a513d00dd47d46e307a65 \ - --hash=sha256:528dcf7ec49fb5a84bf6fe346c1cc3c55b0e7603c2123881996ca3ad79db5bfc \ - --hash=sha256:53de12b4608290992a943801d7756f18a37b7aee284b9ffa794ee8ea8153f8e2 \ - --hash=sha256:587d92831d0115874d766b1f5fddcdde0c5b6c60f8c6111a394078ec227fca6d \ - --hash=sha256:60184e80aac3b56933c71c48d6181e630b0fbc61ae455a63322a66a23c14731a \ - --hash=sha256:6195ca908045054dd2d57eb9c39a5fe86409968b8040de8c2240186da0769da7 \ - --hash=sha256:61f1f08adfaa9cc02e0cbc94f478140385cbd52d5b3c5a657c2fceb15de8d1fb \ - --hash=sha256:72cb30894a34d3a7ab6d959b45a70abac8a2a93b6480fc5a7bfbd9c935bdc4fb \ - --hash=sha256:751f008cd2afe812a781fd6aa2fb66c620ca2e1a13b6a2152b1ad51553cb4b77 \ - --hash=sha256:89f15277d720aa57e173954d237628a8d304896364b9de745dcb722f584812c7 \ - --hash=sha256:8c32b6bba301490d9bb2bf5f631907803135e8085b6aa3e5fe5a770d46dd0160 \ - --hash=sha256:acc6783751ac9c9bc4680379edd6d286468a1dc8d7d9906cd6f1186ed682b2b0 \ - --hash=sha256:b1eb6610330a1dfba9ce142ada792f26bbef1255b75f538196a39e9e90388bf4 \ - --hash=sha256:b243b564cea2576725e77aeeda54e3e0229a168bc587d536cd69941e6797543d \ - --hash=sha256:b41822064585fea56d0116aa431fbd5137ce69dfe837b599e310034171996084 \ - --hash=sha256:bbd5c531b22928e63d0cb1868dee76123456e1de2f1cb45879e9e7a3f3f1779b \ - --hash=sha256:cf95adb0d1671fc38d8c43dd921ad5814a735e7d9b4d9e437c088002863854fd \ - --hash=sha256:e277bd18339177daa62a294256869bbe84df1fb592be2716ec62627bb8d7c81d \ - --hash=sha256:ea4e2a7cb409951988e79a469f609bba998a576e6d7b9791ae5d1e0619e1c0f2 \ - --hash=sha256:f9289065611c48147c1dd1fd344e9d57ab45f1d99b0fb26c51f1cf72cd9bcd31 \ - --hash=sha256:fd9b9e98068fa1068edfc9eabde70a7132017bdd4f362f8b4fd0abed79c33083 +pydantic[email]==2.4.2 \ + --hash=sha256:94f336138093a5d7f426aac732dcfe7ab4eb4da243c88f891d65deb4a2556ee7 \ + --hash=sha256:bc3ddf669d234f4220e6e1c4d96b061abe0998185a8d7855c0126782b7abc8c1 # via # curies # fastapi @@ -952,6 +928,119 @@ pydantic[email]==1.10.6 \ # linkml # linkml-runtime # linkml-validator + # pydantic-settings +pydantic-core==2.10.1 \ + --hash=sha256:042462d8d6ba707fd3ce9649e7bf268633a41018d6a998fb5fbacb7e928a183e \ + --hash=sha256:0523aeb76e03f753b58be33b26540880bac5aa54422e4462404c432230543f33 \ + --hash=sha256:05560ab976012bf40f25d5225a58bfa649bb897b87192a36c6fef1ab132540d7 \ + --hash=sha256:0675ba5d22de54d07bccde38997e780044dcfa9a71aac9fd7d4d7a1d2e3e65f7 \ + --hash=sha256:073d4a470b195d2b2245d0343569aac7e979d3a0dcce6c7d2af6d8a920ad0bea \ + --hash=sha256:07ec6d7d929ae9c68f716195ce15e745b3e8fa122fc67698ac6498d802ed0fa4 \ + --hash=sha256:0880e239827b4b5b3e2ce05e6b766a7414e5f5aedc4523be6b68cfbc7f61c5d0 \ + --hash=sha256:0c27f38dc4fbf07b358b2bc90edf35e82d1703e22ff2efa4af4ad5de1b3833e7 \ + --hash=sha256:0d8a8adef23d86d8eceed3e32e9cca8879c7481c183f84ed1a8edc7df073af94 \ + --hash=sha256:0e2a35baa428181cb2270a15864ec6286822d3576f2ed0f4cd7f0c1708472aff \ + --hash=sha256:0f8682dbdd2f67f8e1edddcbffcc29f60a6182b4901c367fc8c1c40d30bb0a82 \ + --hash=sha256:0fa467fd300a6f046bdb248d40cd015b21b7576c168a6bb20aa22e595c8ffcdd \ + --hash=sha256:128552af70a64660f21cb0eb4876cbdadf1a1f9d5de820fed6421fa8de07c893 \ + --hash=sha256:1396e81b83516b9d5c9e26a924fa69164156c148c717131f54f586485ac3c15e \ + --hash=sha256:149b8a07712f45b332faee1a2258d8ef1fb4a36f88c0c17cb687f205c5dc6e7d \ + --hash=sha256:14ac492c686defc8e6133e3a2d9eaf5261b3df26b8ae97450c1647286750b901 \ + --hash=sha256:14cfbb00959259e15d684505263d5a21732b31248a5dd4941f73a3be233865b9 \ + --hash=sha256:14e09ff0b8fe6e46b93d36a878f6e4a3a98ba5303c76bb8e716f4878a3bee92c \ + --hash=sha256:154ea7c52e32dce13065dbb20a4a6f0cc012b4f667ac90d648d36b12007fa9f7 \ + --hash=sha256:15d6bca84ffc966cc9976b09a18cf9543ed4d4ecbd97e7086f9ce9327ea48891 \ + --hash=sha256:1d40f55222b233e98e3921df7811c27567f0e1a4411b93d4c5c0f4ce131bc42f \ + --hash=sha256:25bd966103890ccfa028841a8f30cebcf5875eeac8c4bde4fe221364c92f0c9a \ + --hash=sha256:2cf5bb4dd67f20f3bbc1209ef572a259027c49e5ff694fa56bed62959b41e1f9 \ + --hash=sha256:2e0e2959ef5d5b8dc9ef21e1a305a21a36e254e6a34432d00c72a92fdc5ecda5 \ + --hash=sha256:320f14bd4542a04ab23747ff2c8a778bde727158b606e2661349557f0770711e \ + --hash=sha256:3625578b6010c65964d177626fde80cf60d7f2e297d56b925cb5cdeda6e9925a \ + --hash=sha256:39215d809470f4c8d1881758575b2abfb80174a9e8daf8f33b1d4379357e417c \ + --hash=sha256:3f0ac9fb8608dbc6eaf17956bf623c9119b4db7dbb511650910a82e261e6600f \ + --hash=sha256:417243bf599ba1f1fef2bb8c543ceb918676954734e2dcb82bf162ae9d7bd514 \ + --hash=sha256:420a692b547736a8d8703c39ea935ab5d8f0d2573f8f123b0a294e49a73f214b \ + --hash=sha256:443fed67d33aa85357464f297e3d26e570267d1af6fef1c21ca50921d2976302 \ + --hash=sha256:48525933fea744a3e7464c19bfede85df4aba79ce90c60b94d8b6e1eddd67096 \ + --hash=sha256:485a91abe3a07c3a8d1e082ba29254eea3e2bb13cbbd4351ea4e5a21912cc9b0 \ + --hash=sha256:4a5be350f922430997f240d25f8219f93b0c81e15f7b30b868b2fddfc2d05f27 \ + --hash=sha256:4d966c47f9dd73c2d32a809d2be529112d509321c5310ebf54076812e6ecd884 \ + --hash=sha256:524ff0ca3baea164d6d93a32c58ac79eca9f6cf713586fdc0adb66a8cdeab96a \ + --hash=sha256:53df009d1e1ba40f696f8995683e067e3967101d4bb4ea6f667931b7d4a01357 \ + --hash=sha256:5994985da903d0b8a08e4935c46ed8daf5be1cf217489e673910951dc533d430 \ + --hash=sha256:5cabb9710f09d5d2e9e2748c3e3e20d991a4c5f96ed8f1132518f54ab2967221 \ + --hash=sha256:5fdb39f67c779b183b0c853cd6b45f7db84b84e0571b3ef1c89cdb1dfc367325 \ + --hash=sha256:600d04a7b342363058b9190d4e929a8e2e715c5682a70cc37d5ded1e0dd370b4 \ + --hash=sha256:631cb7415225954fdcc2a024119101946793e5923f6c4d73a5914d27eb3d3a05 \ + --hash=sha256:63974d168b6233b4ed6a0046296803cb13c56637a7b8106564ab575926572a55 \ + --hash=sha256:64322bfa13e44c6c30c518729ef08fda6026b96d5c0be724b3c4ae4da939f875 \ + --hash=sha256:655f8f4c8d6a5963c9a0687793da37b9b681d9ad06f29438a3b2326d4e6b7970 \ + --hash=sha256:6835451b57c1b467b95ffb03a38bb75b52fb4dc2762bb1d9dbed8de31ea7d0fc \ + --hash=sha256:6db2eb9654a85ada248afa5a6db5ff1cf0f7b16043a6b070adc4a5be68c716d6 \ + --hash=sha256:7c4d1894fe112b0864c1fa75dffa045720a194b227bed12f4be7f6045b25209f \ + --hash=sha256:7eb037106f5c6b3b0b864ad226b0b7ab58157124161d48e4b30c4a43fef8bc4b \ + --hash=sha256:8282bab177a9a3081fd3d0a0175a07a1e2bfb7fcbbd949519ea0980f8a07144d \ + --hash=sha256:82f55187a5bebae7d81d35b1e9aaea5e169d44819789837cdd4720d768c55d15 \ + --hash=sha256:8572cadbf4cfa95fb4187775b5ade2eaa93511f07947b38f4cd67cf10783b118 \ + --hash=sha256:8cdbbd92154db2fec4ec973d45c565e767ddc20aa6dbaf50142676484cbff8ee \ + --hash=sha256:8f6e6aed5818c264412ac0598b581a002a9f050cb2637a84979859e70197aa9e \ + --hash=sha256:92f675fefa977625105708492850bcbc1182bfc3e997f8eecb866d1927c98ae6 \ + --hash=sha256:962ed72424bf1f72334e2f1e61b68f16c0e596f024ca7ac5daf229f7c26e4208 \ + --hash=sha256:9badf8d45171d92387410b04639d73811b785b5161ecadabf056ea14d62d4ede \ + --hash=sha256:9c120c9ce3b163b985a3b966bb701114beb1da4b0468b9b236fc754783d85aa3 \ + --hash=sha256:9f6f3e2598604956480f6c8aa24a3384dbf6509fe995d97f6ca6103bb8c2534e \ + --hash=sha256:a1254357f7e4c82e77c348dabf2d55f1d14d19d91ff025004775e70a6ef40ada \ + --hash=sha256:a1392e0638af203cee360495fd2cfdd6054711f2db5175b6e9c3c461b76f5175 \ + --hash=sha256:a1c311fd06ab3b10805abb72109f01a134019739bd3286b8ae1bc2fc4e50c07a \ + --hash=sha256:a5cb87bdc2e5f620693148b5f8f842d293cae46c5f15a1b1bf7ceeed324a740c \ + --hash=sha256:a7a7902bf75779bc12ccfc508bfb7a4c47063f748ea3de87135d433a4cca7a2f \ + --hash=sha256:aad7bd686363d1ce4ee930ad39f14e1673248373f4a9d74d2b9554f06199fb58 \ + --hash=sha256:aafdb89fdeb5fe165043896817eccd6434aee124d5ee9b354f92cd574ba5e78f \ + --hash=sha256:ae8a8843b11dc0b03b57b52793e391f0122e740de3df1474814c700d2622950a \ + --hash=sha256:b00bc4619f60c853556b35f83731bd817f989cba3e97dc792bb8c97941b8053a \ + --hash=sha256:b1f22a9ab44de5f082216270552aa54259db20189e68fc12484873d926426921 \ + --hash=sha256:b3c01c2fb081fced3bbb3da78510693dc7121bb893a1f0f5f4b48013201f362e \ + --hash=sha256:b3dcd587b69bbf54fc04ca157c2323b8911033e827fffaecf0cafa5a892a0904 \ + --hash=sha256:b4a6db486ac8e99ae696e09efc8b2b9fea67b63c8f88ba7a1a16c24a057a0776 \ + --hash=sha256:bec7dd208a4182e99c5b6c501ce0b1f49de2802448d4056091f8e630b28e9a52 \ + --hash=sha256:c0877239307b7e69d025b73774e88e86ce82f6ba6adf98f41069d5b0b78bd1bf \ + --hash=sha256:caa48fc31fc7243e50188197b5f0c4228956f97b954f76da157aae7f67269ae8 \ + --hash=sha256:cfe1090245c078720d250d19cb05d67e21a9cd7c257698ef139bc41cf6c27b4f \ + --hash=sha256:d43002441932f9a9ea5d6f9efaa2e21458221a3a4b417a14027a1d530201ef1b \ + --hash=sha256:d64728ee14e667ba27c66314b7d880b8eeb050e58ffc5fec3b7a109f8cddbd63 \ + --hash=sha256:d6495008733c7521a89422d7a68efa0a0122c99a5861f06020ef5b1f51f9ba7c \ + --hash=sha256:d8f1ebca515a03e5654f88411420fea6380fc841d1bea08effb28184e3d4899f \ + --hash=sha256:d99277877daf2efe074eae6338453a4ed54a2d93fb4678ddfe1209a0c93a2468 \ + --hash=sha256:da01bec0a26befab4898ed83b362993c844b9a607a86add78604186297eb047e \ + --hash=sha256:db9a28c063c7c00844ae42a80203eb6d2d6bbb97070cfa00194dff40e6f545ab \ + --hash=sha256:dda81e5ec82485155a19d9624cfcca9be88a405e2857354e5b089c2a982144b2 \ + --hash=sha256:e357571bb0efd65fd55f18db0a2fb0ed89d0bb1d41d906b138f088933ae618bb \ + --hash=sha256:e544246b859f17373bed915182ab841b80849ed9cf23f1f07b73b7c58baee5fb \ + --hash=sha256:e562617a45b5a9da5be4abe72b971d4f00bf8555eb29bb91ec2ef2be348cd132 \ + --hash=sha256:e570ffeb2170e116a5b17e83f19911020ac79d19c96f320cbfa1fa96b470185b \ + --hash=sha256:e6f31a17acede6a8cd1ae2d123ce04d8cca74056c9d456075f4f6f85de055607 \ + --hash=sha256:e9121b4009339b0f751955baf4543a0bfd6bc3f8188f8056b1a25a2d45099934 \ + --hash=sha256:ebedb45b9feb7258fac0a268a3f6bec0a2ea4d9558f3d6f813f02ff3a6dc6698 \ + --hash=sha256:ecaac27da855b8d73f92123e5f03612b04c5632fd0a476e469dfc47cd37d6b2e \ + --hash=sha256:ecdbde46235f3d560b18be0cb706c8e8ad1b965e5c13bbba7450c86064e96561 \ + --hash=sha256:ed550ed05540c03f0e69e6d74ad58d026de61b9eaebebbaaf8873e585cbb18de \ + --hash=sha256:eeb3d3d6b399ffe55f9a04e09e635554012f1980696d6b0aca3e6cf42a17a03b \ + --hash=sha256:ef337945bbd76cce390d1b2496ccf9f90b1c1242a3a7bc242ca4a9fc5993427a \ + --hash=sha256:f1365e032a477c1430cfe0cf2856679529a2331426f8081172c4a74186f1d595 \ + --hash=sha256:f23b55eb5464468f9e0e9a9935ce3ed2a870608d5f534025cd5536bca25b1402 \ + --hash=sha256:f2e9072d71c1f6cfc79a36d4484c82823c560e6f5599c43c1ca6b5cdbd54f881 \ + --hash=sha256:f323306d0556351735b54acbf82904fe30a27b6a7147153cbe6e19aaaa2aa429 \ + --hash=sha256:f36a3489d9e28fe4b67be9992a23029c3cec0babc3bd9afb39f49844a8c721c5 \ + --hash=sha256:f64f82cc3443149292b32387086d02a6c7fb39b8781563e0ca7b8d7d9cf72bd7 \ + --hash=sha256:f6defd966ca3b187ec6c366604e9296f585021d922e666b99c47e78738b5666c \ + --hash=sha256:f7c2b8eb9fc872e68b46eeaf835e86bccc3a58ba57d0eedc109cbb14177be531 \ + --hash=sha256:fa7db7558607afeccb33c0e4bf1c9a9a835e26599e76af6fe2fcea45904083a6 \ + --hash=sha256:fcb83175cc4936a5425dde3356f079ae03c0802bbdf8ff82c035f8a54b333521 + # via pydantic +pydantic-settings==2.0.3 \ + --hash=sha256:962dc3672495aad6ae96a4390fac7e593591e144625e5112d359f8f67fb75945 \ + --hash=sha256:ddd907b066622bd67603b75e2ff791875540dc485b7307c4fffc015719da8625 + # via hexkit pyjsg==0.11.10 \ --hash=sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d \ --hash=sha256:4bd6e3ff2833fa2b395bbe803a2d72a5f0bab5b7285bccd0da1a1bc0aee88bfa @@ -1100,7 +1189,9 @@ python-dateutil==2.8.2 \ python-dotenv==1.0.0 \ --hash=sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba \ --hash=sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a - # via uvicorn + # via + # pydantic-settings + # uvicorn pytrie==0.4.0 \ --hash=sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379 # via curies @@ -1201,7 +1292,9 @@ rfc3339-validator==0.1.4 \ rfc3986[idna2008]==1.5.0 \ --hash=sha256:270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835 \ --hash=sha256:a86d6e1f5b1dc238b218b012df0aa79409667bb209e58da56d0b94704e712a97 - # via httpx + # via + # httpx + # rfc3986 rfc3987==1.3.8 \ --hash=sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53 \ --hash=sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733 @@ -1456,9 +1549,11 @@ stringcase==1.2.0 \ # via # -r /workspace/requirements-dev-common.in # linkml-validator -testcontainers[mongo]==3.4.1 \ - --hash=sha256:7626f2899f869b929c14b8eb4996b1e70a4b4bd1934de500be193db89b18f7cc - # via hexkit +testcontainers[kafka,mongo]==3.7.1 \ + --hash=sha256:7f48cef4bf0ccd78f1a4534d4b701a003a3bace851f24eae58a32f9e3f0aeba0 + # via + # hexkit + # testcontainers tomli==2.0.1 \ --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \ --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f @@ -1503,9 +1598,11 @@ typing-extensions==4.8.0 \ --hash=sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef # via # black + # fastapi # mypy # prefixmaps # pydantic + # pydantic-core # sqlalchemy # starlette # typer @@ -1524,7 +1621,9 @@ urllib3==2.0.6 \ uvicorn[standard]==0.20.0 \ --hash=sha256:a4e12017b940247f836bc90b72e725d7dfd0c8ed1c51eb365f5ba30d9f5127d8 \ --hash=sha256:c3ed1598a5668208723f2bb49336f4509424ad198d6ab2615b7783db58d919fd - # via ghga-service-commons + # via + # ghga-service-commons + # uvicorn uvloop==0.17.0 \ --hash=sha256:0949caf774b9fcefc7c5756bacbbbd3fc4c05a6b7eebc7c7ad6f825b23998d6d \ --hash=sha256:0ddf6baf9cf11a1a22c71487f39f15b2cf78eb5bde7e5b45fbb99e8a9d91b9e1 \ diff --git a/requirements.txt b/requirements.txt index a1eaca8e..75461ba8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ # This file is autogenerated by pip-compile with Python 3.9 # by the following command: # -# pip-compile --constraint=/workspace/requirements-dev.txt --generate-hashes --output-file=/workspace/requirements.txt /tmp/tmpu62427re/pyproject.toml +# pip-compile --constraint=/workspace/requirements-dev.txt --generate-hashes --output-file=/workspace/requirements.txt /tmp/tmph8bxvet7/pyproject.toml # aiokafka==0.8.0 \ --hash=sha256:021e9f0027ca63c6c04daccfdd0e985f7a56d51bd0d43f482f674a58fada52f5 \ @@ -39,6 +39,12 @@ aiokafka==0.8.0 \ # via # -c /workspace/requirements-dev.txt # hexkit +annotated-types==0.6.0 \ + --hash=sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43 \ + --hash=sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d + # via + # -c /workspace/requirements-dev.txt + # pydantic antlr4-python3-runtime==4.9.3 \ --hash=sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b # via @@ -46,11 +52,12 @@ antlr4-python3-runtime==4.9.3 \ # linkml # pyjsg # pyshexc -anyio==4.0.0 \ - --hash=sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f \ - --hash=sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a +anyio==3.7.1 \ + --hash=sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780 \ + --hash=sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5 # via # -c /workspace/requirements-dev.txt + # fastapi # httpcore # starlette # watchfiles @@ -376,7 +383,6 @@ dnspython==2.3.0 \ # via # -c /workspace/requirements-dev.txt # email-validator - # ghga-event-schemas # pymongo email-validator==2.0.0.post2 \ --hash=sha256:1ff6e86044200c56ae23595695c54e9614f4a9551e0e393614f764860b3d7900 \ @@ -397,9 +403,9 @@ exceptiongroup==1.1.3 \ # -c /workspace/requirements-dev.txt # anyio # pytest -fastapi==0.96.1 \ - --hash=sha256:22d773ce95f14f04f8f37a0c8998fc163e67af83b65510d2879de6cbaaa10215 \ - --hash=sha256:5c1d243030e63089ccfc0aec69c2da6d619943917727e8e82ee502358d5119bf +fastapi==0.103.2 \ + --hash=sha256:3270de872f0fe9ec809d4bd3d4d890c6d5cc7b9611d721d6438f9dacc8c4ef2e \ + --hash=sha256:75a11f6bfb8fc4d2bec0bd710c2d5f2829659c0e8c0afd5560fdda6ce25ec653 # via # -c /workspace/requirements-dev.txt # ghga-service-commons @@ -409,17 +415,18 @@ fqdn==1.5.1 \ # via # -c /workspace/requirements-dev.txt # jsonschema -ghga-event-schemas==0.13.5 \ - --hash=sha256:1ce129c7c969fe2b263483d55c500a3d7f75b6c97e0acb6f49ddd84eca1e1974 \ - --hash=sha256:c5fb0abab7d06512b2470bb84247473528051d109200ba69a87b6701e3384d6c +ghga-event-schemas==1.0.0 \ + --hash=sha256:34e3dcfc97025dcf9c05de73f3d40cf3c1cb361ba74f4cb2ef621de16bc158c2 \ + --hash=sha256:9f006151bb19064eb135313967e8ca6c07382ecfe0a273884e96236ffd01f3ea # via # -c /workspace/requirements-dev.txt # metldata (pyproject.toml) -ghga-service-commons[api,auth]==0.7.1 \ - --hash=sha256:70a6bc39d3ab8309524dfbcd4c29e5f37de118c41107fb42054834e5dcf8decc \ - --hash=sha256:888a789cbea86bcd7433e0b848c137928eea87bd9194de3504a3c25a36ac983c +ghga-service-commons[api,auth]==1.1.0 \ + --hash=sha256:2502ac05e429f988d066303b53147691b86c9915455c375c79a4c73d65060e8a \ + --hash=sha256:a198195e731c0239e2c248e8f40c3918ebb6087f1d0fb8f55eef91479c7ea287 # via # -c /workspace/requirements-dev.txt + # ghga-service-commons # metldata (pyproject.toml) graphviz==0.20.1 \ --hash=sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977 \ @@ -507,11 +514,12 @@ hbreader==0.9.1 \ # jsonasobj2 # linkml # linkml-runtime -hexkit[akafka,mongodb]==0.10.2 \ - --hash=sha256:1495f2bc6ae7423874bc20367dd28555cd15a74ccf5cb4997e0fb8307757987e \ - --hash=sha256:436ea50e706ab616803eb85a9a9f5e7bec727379b750b966650d6e64d4ea5ef0 +hexkit[akafka,mongodb]==1.0.0 \ + --hash=sha256:767e9cda5433f8e0c74e8f0b0376dccbfee8db1efecd2dc75e3f2b841dc99c60 \ + --hash=sha256:a88afb9d8ff9c1672fe81a233501b2ae369e155b72aae46ff5ae83f7bb252b6b # via # -c /workspace/requirements-dev.txt + # hexkit # metldata (pyproject.toml) httpcore==0.16.3 \ --hash=sha256:c5d6f04e2fc530f39e0c077e6a30caa53f1451096120f1f38b954afd0b17c0cb \ @@ -652,6 +660,7 @@ jsonschema[format]==4.19.1 \ # -c /workspace/requirements-dev.txt # ghga-event-schemas # hexkit + # jsonschema # linkml # linkml-runtime jsonschema-specifications==2023.7.1 \ @@ -820,43 +829,9 @@ pycparser==2.21 \ # via # -c /workspace/requirements-dev.txt # cffi -pydantic[email]==1.10.6 \ - --hash=sha256:012c99a9c0d18cfde7469aa1ebff922e24b0c706d03ead96940f5465f2c9cf62 \ - --hash=sha256:0abd9c60eee6201b853b6c4be104edfba4f8f6c5f3623f8e1dba90634d63eb35 \ - --hash=sha256:12e837fd320dd30bd625be1b101e3b62edc096a49835392dcf418f1a5ac2b832 \ - --hash=sha256:163e79386c3547c49366e959d01e37fc30252285a70619ffc1b10ede4758250a \ - --hash=sha256:189318051c3d57821f7233ecc94708767dd67687a614a4e8f92b4a020d4ffd06 \ - --hash=sha256:1c84583b9df62522829cbc46e2b22e0ec11445625b5acd70c5681ce09c9b11c4 \ - --hash=sha256:3091d2eaeda25391405e36c2fc2ed102b48bac4b384d42b2267310abae350ca6 \ - --hash=sha256:32937835e525d92c98a1512218db4eed9ddc8f4ee2a78382d77f54341972c0e7 \ - --hash=sha256:3a2be0a0f32c83265fd71a45027201e1278beaa82ea88ea5b345eea6afa9ac7f \ - --hash=sha256:3ac1cd4deed871dfe0c5f63721e29debf03e2deefa41b3ed5eb5f5df287c7b70 \ - --hash=sha256:3ce13a558b484c9ae48a6a7c184b1ba0e5588c5525482681db418268e5f86186 \ - --hash=sha256:415a3f719ce518e95a92effc7ee30118a25c3d032455d13e121e3840985f2efd \ - --hash=sha256:43cdeca8d30de9a897440e3fb8866f827c4c31f6c73838e3a01a14b03b067b1d \ - --hash=sha256:476f6674303ae7965730a382a8e8d7fae18b8004b7b69a56c3d8fa93968aa21c \ - --hash=sha256:4c19eb5163167489cb1e0161ae9220dadd4fc609a42649e7e84a8fa8fff7a80f \ - --hash=sha256:4ca83739c1263a044ec8b79df4eefc34bbac87191f0a513d00dd47d46e307a65 \ - --hash=sha256:528dcf7ec49fb5a84bf6fe346c1cc3c55b0e7603c2123881996ca3ad79db5bfc \ - --hash=sha256:53de12b4608290992a943801d7756f18a37b7aee284b9ffa794ee8ea8153f8e2 \ - --hash=sha256:587d92831d0115874d766b1f5fddcdde0c5b6c60f8c6111a394078ec227fca6d \ - --hash=sha256:60184e80aac3b56933c71c48d6181e630b0fbc61ae455a63322a66a23c14731a \ - --hash=sha256:6195ca908045054dd2d57eb9c39a5fe86409968b8040de8c2240186da0769da7 \ - --hash=sha256:61f1f08adfaa9cc02e0cbc94f478140385cbd52d5b3c5a657c2fceb15de8d1fb \ - --hash=sha256:72cb30894a34d3a7ab6d959b45a70abac8a2a93b6480fc5a7bfbd9c935bdc4fb \ - --hash=sha256:751f008cd2afe812a781fd6aa2fb66c620ca2e1a13b6a2152b1ad51553cb4b77 \ - --hash=sha256:89f15277d720aa57e173954d237628a8d304896364b9de745dcb722f584812c7 \ - --hash=sha256:8c32b6bba301490d9bb2bf5f631907803135e8085b6aa3e5fe5a770d46dd0160 \ - --hash=sha256:acc6783751ac9c9bc4680379edd6d286468a1dc8d7d9906cd6f1186ed682b2b0 \ - --hash=sha256:b1eb6610330a1dfba9ce142ada792f26bbef1255b75f538196a39e9e90388bf4 \ - --hash=sha256:b243b564cea2576725e77aeeda54e3e0229a168bc587d536cd69941e6797543d \ - --hash=sha256:b41822064585fea56d0116aa431fbd5137ce69dfe837b599e310034171996084 \ - --hash=sha256:bbd5c531b22928e63d0cb1868dee76123456e1de2f1cb45879e9e7a3f3f1779b \ - --hash=sha256:cf95adb0d1671fc38d8c43dd921ad5814a735e7d9b4d9e437c088002863854fd \ - --hash=sha256:e277bd18339177daa62a294256869bbe84df1fb592be2716ec62627bb8d7c81d \ - --hash=sha256:ea4e2a7cb409951988e79a469f609bba998a576e6d7b9791ae5d1e0619e1c0f2 \ - --hash=sha256:f9289065611c48147c1dd1fd344e9d57ab45f1d99b0fb26c51f1cf72cd9bcd31 \ - --hash=sha256:fd9b9e98068fa1068edfc9eabde70a7132017bdd4f362f8b4fd0abed79c33083 +pydantic[email]==2.4.2 \ + --hash=sha256:94f336138093a5d7f426aac732dcfe7ab4eb4da243c88f891d65deb4a2556ee7 \ + --hash=sha256:bc3ddf669d234f4220e6e1c4d96b061abe0998185a8d7855c0126782b7abc8c1 # via # -c /workspace/requirements-dev.txt # curies @@ -867,6 +842,123 @@ pydantic[email]==1.10.6 \ # linkml # linkml-runtime # linkml-validator + # pydantic-settings +pydantic-core==2.10.1 \ + --hash=sha256:042462d8d6ba707fd3ce9649e7bf268633a41018d6a998fb5fbacb7e928a183e \ + --hash=sha256:0523aeb76e03f753b58be33b26540880bac5aa54422e4462404c432230543f33 \ + --hash=sha256:05560ab976012bf40f25d5225a58bfa649bb897b87192a36c6fef1ab132540d7 \ + --hash=sha256:0675ba5d22de54d07bccde38997e780044dcfa9a71aac9fd7d4d7a1d2e3e65f7 \ + --hash=sha256:073d4a470b195d2b2245d0343569aac7e979d3a0dcce6c7d2af6d8a920ad0bea \ + --hash=sha256:07ec6d7d929ae9c68f716195ce15e745b3e8fa122fc67698ac6498d802ed0fa4 \ + --hash=sha256:0880e239827b4b5b3e2ce05e6b766a7414e5f5aedc4523be6b68cfbc7f61c5d0 \ + --hash=sha256:0c27f38dc4fbf07b358b2bc90edf35e82d1703e22ff2efa4af4ad5de1b3833e7 \ + --hash=sha256:0d8a8adef23d86d8eceed3e32e9cca8879c7481c183f84ed1a8edc7df073af94 \ + --hash=sha256:0e2a35baa428181cb2270a15864ec6286822d3576f2ed0f4cd7f0c1708472aff \ + --hash=sha256:0f8682dbdd2f67f8e1edddcbffcc29f60a6182b4901c367fc8c1c40d30bb0a82 \ + --hash=sha256:0fa467fd300a6f046bdb248d40cd015b21b7576c168a6bb20aa22e595c8ffcdd \ + --hash=sha256:128552af70a64660f21cb0eb4876cbdadf1a1f9d5de820fed6421fa8de07c893 \ + --hash=sha256:1396e81b83516b9d5c9e26a924fa69164156c148c717131f54f586485ac3c15e \ + --hash=sha256:149b8a07712f45b332faee1a2258d8ef1fb4a36f88c0c17cb687f205c5dc6e7d \ + --hash=sha256:14ac492c686defc8e6133e3a2d9eaf5261b3df26b8ae97450c1647286750b901 \ + --hash=sha256:14cfbb00959259e15d684505263d5a21732b31248a5dd4941f73a3be233865b9 \ + --hash=sha256:14e09ff0b8fe6e46b93d36a878f6e4a3a98ba5303c76bb8e716f4878a3bee92c \ + --hash=sha256:154ea7c52e32dce13065dbb20a4a6f0cc012b4f667ac90d648d36b12007fa9f7 \ + --hash=sha256:15d6bca84ffc966cc9976b09a18cf9543ed4d4ecbd97e7086f9ce9327ea48891 \ + --hash=sha256:1d40f55222b233e98e3921df7811c27567f0e1a4411b93d4c5c0f4ce131bc42f \ + --hash=sha256:25bd966103890ccfa028841a8f30cebcf5875eeac8c4bde4fe221364c92f0c9a \ + --hash=sha256:2cf5bb4dd67f20f3bbc1209ef572a259027c49e5ff694fa56bed62959b41e1f9 \ + --hash=sha256:2e0e2959ef5d5b8dc9ef21e1a305a21a36e254e6a34432d00c72a92fdc5ecda5 \ + --hash=sha256:320f14bd4542a04ab23747ff2c8a778bde727158b606e2661349557f0770711e \ + --hash=sha256:3625578b6010c65964d177626fde80cf60d7f2e297d56b925cb5cdeda6e9925a \ + --hash=sha256:39215d809470f4c8d1881758575b2abfb80174a9e8daf8f33b1d4379357e417c \ + --hash=sha256:3f0ac9fb8608dbc6eaf17956bf623c9119b4db7dbb511650910a82e261e6600f \ + --hash=sha256:417243bf599ba1f1fef2bb8c543ceb918676954734e2dcb82bf162ae9d7bd514 \ + --hash=sha256:420a692b547736a8d8703c39ea935ab5d8f0d2573f8f123b0a294e49a73f214b \ + --hash=sha256:443fed67d33aa85357464f297e3d26e570267d1af6fef1c21ca50921d2976302 \ + --hash=sha256:48525933fea744a3e7464c19bfede85df4aba79ce90c60b94d8b6e1eddd67096 \ + --hash=sha256:485a91abe3a07c3a8d1e082ba29254eea3e2bb13cbbd4351ea4e5a21912cc9b0 \ + --hash=sha256:4a5be350f922430997f240d25f8219f93b0c81e15f7b30b868b2fddfc2d05f27 \ + --hash=sha256:4d966c47f9dd73c2d32a809d2be529112d509321c5310ebf54076812e6ecd884 \ + --hash=sha256:524ff0ca3baea164d6d93a32c58ac79eca9f6cf713586fdc0adb66a8cdeab96a \ + --hash=sha256:53df009d1e1ba40f696f8995683e067e3967101d4bb4ea6f667931b7d4a01357 \ + --hash=sha256:5994985da903d0b8a08e4935c46ed8daf5be1cf217489e673910951dc533d430 \ + --hash=sha256:5cabb9710f09d5d2e9e2748c3e3e20d991a4c5f96ed8f1132518f54ab2967221 \ + --hash=sha256:5fdb39f67c779b183b0c853cd6b45f7db84b84e0571b3ef1c89cdb1dfc367325 \ + --hash=sha256:600d04a7b342363058b9190d4e929a8e2e715c5682a70cc37d5ded1e0dd370b4 \ + --hash=sha256:631cb7415225954fdcc2a024119101946793e5923f6c4d73a5914d27eb3d3a05 \ + --hash=sha256:63974d168b6233b4ed6a0046296803cb13c56637a7b8106564ab575926572a55 \ + --hash=sha256:64322bfa13e44c6c30c518729ef08fda6026b96d5c0be724b3c4ae4da939f875 \ + --hash=sha256:655f8f4c8d6a5963c9a0687793da37b9b681d9ad06f29438a3b2326d4e6b7970 \ + --hash=sha256:6835451b57c1b467b95ffb03a38bb75b52fb4dc2762bb1d9dbed8de31ea7d0fc \ + --hash=sha256:6db2eb9654a85ada248afa5a6db5ff1cf0f7b16043a6b070adc4a5be68c716d6 \ + --hash=sha256:7c4d1894fe112b0864c1fa75dffa045720a194b227bed12f4be7f6045b25209f \ + --hash=sha256:7eb037106f5c6b3b0b864ad226b0b7ab58157124161d48e4b30c4a43fef8bc4b \ + --hash=sha256:8282bab177a9a3081fd3d0a0175a07a1e2bfb7fcbbd949519ea0980f8a07144d \ + --hash=sha256:82f55187a5bebae7d81d35b1e9aaea5e169d44819789837cdd4720d768c55d15 \ + --hash=sha256:8572cadbf4cfa95fb4187775b5ade2eaa93511f07947b38f4cd67cf10783b118 \ + --hash=sha256:8cdbbd92154db2fec4ec973d45c565e767ddc20aa6dbaf50142676484cbff8ee \ + --hash=sha256:8f6e6aed5818c264412ac0598b581a002a9f050cb2637a84979859e70197aa9e \ + 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--hash=sha256:d6495008733c7521a89422d7a68efa0a0122c99a5861f06020ef5b1f51f9ba7c \ + --hash=sha256:d8f1ebca515a03e5654f88411420fea6380fc841d1bea08effb28184e3d4899f \ + --hash=sha256:d99277877daf2efe074eae6338453a4ed54a2d93fb4678ddfe1209a0c93a2468 \ + --hash=sha256:da01bec0a26befab4898ed83b362993c844b9a607a86add78604186297eb047e \ + --hash=sha256:db9a28c063c7c00844ae42a80203eb6d2d6bbb97070cfa00194dff40e6f545ab \ + --hash=sha256:dda81e5ec82485155a19d9624cfcca9be88a405e2857354e5b089c2a982144b2 \ + --hash=sha256:e357571bb0efd65fd55f18db0a2fb0ed89d0bb1d41d906b138f088933ae618bb \ + --hash=sha256:e544246b859f17373bed915182ab841b80849ed9cf23f1f07b73b7c58baee5fb \ + --hash=sha256:e562617a45b5a9da5be4abe72b971d4f00bf8555eb29bb91ec2ef2be348cd132 \ + --hash=sha256:e570ffeb2170e116a5b17e83f19911020ac79d19c96f320cbfa1fa96b470185b \ + --hash=sha256:e6f31a17acede6a8cd1ae2d123ce04d8cca74056c9d456075f4f6f85de055607 \ + --hash=sha256:e9121b4009339b0f751955baf4543a0bfd6bc3f8188f8056b1a25a2d45099934 \ + --hash=sha256:ebedb45b9feb7258fac0a268a3f6bec0a2ea4d9558f3d6f813f02ff3a6dc6698 \ + --hash=sha256:ecaac27da855b8d73f92123e5f03612b04c5632fd0a476e469dfc47cd37d6b2e \ + --hash=sha256:ecdbde46235f3d560b18be0cb706c8e8ad1b965e5c13bbba7450c86064e96561 \ + --hash=sha256:ed550ed05540c03f0e69e6d74ad58d026de61b9eaebebbaaf8873e585cbb18de \ + --hash=sha256:eeb3d3d6b399ffe55f9a04e09e635554012f1980696d6b0aca3e6cf42a17a03b \ + --hash=sha256:ef337945bbd76cce390d1b2496ccf9f90b1c1242a3a7bc242ca4a9fc5993427a \ + --hash=sha256:f1365e032a477c1430cfe0cf2856679529a2331426f8081172c4a74186f1d595 \ + --hash=sha256:f23b55eb5464468f9e0e9a9935ce3ed2a870608d5f534025cd5536bca25b1402 \ + --hash=sha256:f2e9072d71c1f6cfc79a36d4484c82823c560e6f5599c43c1ca6b5cdbd54f881 \ + --hash=sha256:f323306d0556351735b54acbf82904fe30a27b6a7147153cbe6e19aaaa2aa429 \ + --hash=sha256:f36a3489d9e28fe4b67be9992a23029c3cec0babc3bd9afb39f49844a8c721c5 \ + --hash=sha256:f64f82cc3443149292b32387086d02a6c7fb39b8781563e0ca7b8d7d9cf72bd7 \ + --hash=sha256:f6defd966ca3b187ec6c366604e9296f585021d922e666b99c47e78738b5666c \ + --hash=sha256:f7c2b8eb9fc872e68b46eeaf835e86bccc3a58ba57d0eedc109cbb14177be531 \ + --hash=sha256:fa7db7558607afeccb33c0e4bf1c9a9a835e26599e76af6fe2fcea45904083a6 \ + --hash=sha256:fcb83175cc4936a5425dde3356f079ae03c0802bbdf8ff82c035f8a54b333521 + # via + # -c /workspace/requirements-dev.txt + # pydantic +pydantic-settings==2.0.3 \ + --hash=sha256:962dc3672495aad6ae96a4390fac7e593591e144625e5112d359f8f67fb75945 \ + --hash=sha256:ddd907b066622bd67603b75e2ff791875540dc485b7307c4fffc015719da8625 + # via + # -c /workspace/requirements-dev.txt + # hexkit pyjsg==0.11.10 \ --hash=sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d \ --hash=sha256:4bd6e3ff2833fa2b395bbe803a2d72a5f0bab5b7285bccd0da1a1bc0aee88bfa @@ -1002,6 +1094,7 @@ python-dotenv==1.0.0 \ --hash=sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a # via # -c /workspace/requirements-dev.txt + # pydantic-settings # uvicorn pytrie==0.4.0 \ --hash=sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379 @@ -1113,6 +1206,7 @@ rfc3986[idna2008]==1.5.0 \ # via # -c /workspace/requirements-dev.txt # httpx + # rfc3986 rfc3987==1.3.8 \ --hash=sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53 \ --hash=sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733 @@ -1385,8 +1479,10 @@ typing-extensions==4.8.0 \ --hash=sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef # via # -c /workspace/requirements-dev.txt + # fastapi # prefixmaps # pydantic + # pydantic-core # sqlalchemy # starlette # typer @@ -1409,6 +1505,7 @@ uvicorn[standard]==0.20.0 \ # via # -c /workspace/requirements-dev.txt # ghga-service-commons + # uvicorn uvloop==0.17.0 \ --hash=sha256:0949caf774b9fcefc7c5756bacbbbd3fc4c05a6b7eebc7c7ad6f825b23998d6d \ --hash=sha256:0ddf6baf9cf11a1a22c71487f39f15b2cf78eb5bde7e5b45fbb99e8a9d91b9e1 \ diff --git a/scripts/license_checker.py b/scripts/license_checker.py index 0ddc7861..5d8be069 100755 --- a/scripts/license_checker.py +++ b/scripts/license_checker.py @@ -88,6 +88,9 @@ "xml", "yaml", "yml", + "tsv", + "fastq", + "gz", ] # exclude any files with names that match any of the following regex: diff --git a/scripts/update_config_docs.py b/scripts/update_config_docs.py index b1be57a0..90c12081 100755 --- a/scripts/update_config_docs.py +++ b/scripts/update_config_docs.py @@ -28,7 +28,6 @@ from typing import Any import yaml -from pydantic import BaseSettings from script_utils.cli import echo_failure, echo_success, run @@ -44,7 +43,7 @@ class ValidationError(RuntimeError): """Raised when validation of config documentation fails.""" -def get_config_class() -> type[BaseSettings]: +def get_config_class(): """ Dynamically imports and returns the Config class from the current service. This makes the script service repo agnostic. @@ -77,14 +76,16 @@ def get_schema() -> str: """Returns a JSON schema generated from a Config class.""" config = get_dev_config() - return config.schema_json(indent=2) + return config.schema_json(indent=2) # change eventually to .model_json_schema(...) def get_example() -> str: """Returns an example config YAML.""" config = get_dev_config() - normalized_config_dict = json.loads(config.json()) + normalized_config_dict = json.loads( + config.json() # change eventually to .model_dump_json() + ) return yaml.dump(normalized_config_dict) # pyright: ignore diff --git a/src/metldata/accession_registry/accession_registry.py b/src/metldata/accession_registry/accession_registry.py index bc310009..24701d88 100644 --- a/src/metldata/accession_registry/accession_registry.py +++ b/src/metldata/accession_registry/accession_registry.py @@ -19,7 +19,8 @@ import secrets from collections.abc import Iterable -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings from metldata.accession_registry.accession_store import AccessionStore @@ -30,12 +31,14 @@ class AccessionRegistryConfig(BaseSettings): prefix_mapping: dict[str, str] = Field( ..., description="Specifies the ID prefix (values) per resource type (keys).", - example={ - "file": "GHGAF", - "experiment": "GHGAE", - "sample": "GHGAS", - "dataset": "GHGAD", - }, + examples=[ + { + "file": "GHGAF", + "experiment": "GHGAE", + "sample": "GHGAS", + "dataset": "GHGAD", + } + ], ) suffix_length: int = Field(8, description="Length of the numeric ID suffix.") diff --git a/src/metldata/accession_registry/accession_store.py b/src/metldata/accession_registry/accession_store.py index d190cb9c..4501ce63 100644 --- a/src/metldata/accession_registry/accession_store.py +++ b/src/metldata/accession_registry/accession_store.py @@ -18,7 +18,8 @@ from pathlib import Path -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings class AccessionStoreConfig(BaseSettings): diff --git a/src/metldata/artifacts_rest/config.py b/src/metldata/artifacts_rest/config.py index 4cdac9f6..6b85f7c1 100644 --- a/src/metldata/artifacts_rest/config.py +++ b/src/metldata/artifacts_rest/config.py @@ -16,7 +16,8 @@ """Config parameters and their defaults.""" -from pydantic import BaseSettings, Field, validator +from pydantic import Field, field_validator +from pydantic_settings import BaseSettings from metldata.artifacts_rest.models import ArtifactInfo @@ -30,7 +31,7 @@ class ArtifactsRestConfig(BaseSettings): ) # pylint: disable=no-self-argument - @validator("artifact_infos") + @field_validator("artifact_infos") def validate_artifact_info_names( cls, value: list[ArtifactInfo] ) -> list[ArtifactInfo]: diff --git a/src/metldata/artifacts_rest/models.py b/src/metldata/artifacts_rest/models.py index 250aa17c..66b7c156 100644 --- a/src/metldata/artifacts_rest/models.py +++ b/src/metldata/artifacts_rest/models.py @@ -16,10 +16,11 @@ """Data models.""" -from typing import Optional, TypedDict +from typing import Optional from ghga_service_commons.utils.utc_dates import DateTimeUTC -from pydantic import BaseModel, Field, validator +from pydantic import BaseModel, Field, field_validator +from typing_extensions import TypedDict from metldata.custom_types import Json from metldata.model_utils.anchors import AnchorPoint @@ -74,7 +75,7 @@ class ArtifactInfo(BaseModel): ) # pylint: disable=no-self-argument - @validator("resource_classes") + @field_validator("resource_classes") def check_resource_class_names( cls, value: dict[str, ArtifactResourceClass] ) -> dict[str, ArtifactResourceClass]: diff --git a/src/metldata/builtin_transformations/add_accessions/config.py b/src/metldata/builtin_transformations/add_accessions/config.py index 74b0befe..1ec2f0e5 100644 --- a/src/metldata/builtin_transformations/add_accessions/config.py +++ b/src/metldata/builtin_transformations/add_accessions/config.py @@ -16,7 +16,8 @@ """Config parameters and their defaults.""" -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings class AccessionAdditionConfig(BaseSettings): diff --git a/src/metldata/builtin_transformations/aggregate/config.py b/src/metldata/builtin_transformations/aggregate/config.py index 66ad3308..431268c5 100644 --- a/src/metldata/builtin_transformations/aggregate/config.py +++ b/src/metldata/builtin_transformations/aggregate/config.py @@ -18,7 +18,8 @@ from typing import Optional -from pydantic import BaseModel, BaseSettings, root_validator +from pydantic import BaseModel, model_validator +from pydantic_settings import BaseSettings from metldata.builtin_transformations.aggregate.func import ( AggregationFunction, @@ -37,7 +38,7 @@ class AggregationOperation(BaseModel): function: type[AggregationFunction] # pylint: disable=no-self-argument - @root_validator(pre=True) + @model_validator(mode="before") def lookup_operation(cls, values: dict) -> dict: """Replaces operation strings with operation types.""" if "function" in values: diff --git a/src/metldata/builtin_transformations/custom_embeddings/config.py b/src/metldata/builtin_transformations/custom_embeddings/config.py index ce4a27d8..135c104f 100644 --- a/src/metldata/builtin_transformations/custom_embeddings/config.py +++ b/src/metldata/builtin_transformations/custom_embeddings/config.py @@ -16,7 +16,8 @@ """Models used to describe embedding profiles.""" -from pydantic import BaseSettings, Field, validator +from pydantic import Field, field_validator +from pydantic_settings import BaseSettings from metldata.builtin_transformations.custom_embeddings.embedding_profile import ( EmbeddingProfile, @@ -50,7 +51,7 @@ class CustomEmbeddingConfig(BaseSettings): ) # pylint: disable=no-self-argument - @validator("embedding_profiles") + @field_validator("embedding_profiles") def check_embedding_profiles_unique( cls, value: list[EmbeddingProfile], diff --git a/src/metldata/builtin_transformations/delete_slots/config.py b/src/metldata/builtin_transformations/delete_slots/config.py index 41e7e0a3..0c97f04e 100644 --- a/src/metldata/builtin_transformations/delete_slots/config.py +++ b/src/metldata/builtin_transformations/delete_slots/config.py @@ -16,7 +16,8 @@ """Config parameters and their defaults.""" -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings class SlotDeletionConfig(BaseSettings): @@ -29,11 +30,13 @@ class SlotDeletionConfig(BaseSettings): + " The keys refer to classes, the values to the slots that should be" + " deleted from the respective class." ), - example={ - "class_a": ["some_slot", "another_slot"], - "class_b": ["some_slot"], - "class_c": ["some_slot", "yet_another_slot"], - }, + examples=[ + { + "class_a": ["some_slot", "another_slot"], + "class_b": ["some_slot"], + "class_c": ["some_slot", "yet_another_slot"], + } + ], ) class Config: diff --git a/src/metldata/builtin_transformations/infer_references/config.py b/src/metldata/builtin_transformations/infer_references/config.py index 4c0ba2aa..06bd85fa 100644 --- a/src/metldata/builtin_transformations/infer_references/config.py +++ b/src/metldata/builtin_transformations/infer_references/config.py @@ -16,7 +16,8 @@ """Models used to describe all inferred references based on existing references.""" -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings from metldata.builtin_transformations.infer_references.reference import ( InferredReference, @@ -39,24 +40,26 @@ class ReferenceInferenceConfig(BaseSettings): + " refer to the names of the new slots of classes that hold the inferred" + " references. The values refer to the actual references details." ), - example={ - "class_a": { - "class_d": { - "path": "class_a(class_b)>class_b(class_d)>class_d", - "multivalued": False, + examples=[ + { + "class_a": { + "class_d": { + "path": "class_a(class_b)>class_b(class_d)>class_d", + "multivalued": False, + }, + "class_c": { + "path": "class_a(class_b)>class_b<(class_c)class_c", + "multivalued": True, + }, }, - "class_c": { - "path": "class_a(class_b)>class_b<(class_c)class_c", - "multivalued": True, + "class_b": { + "class_c": { + "path": "class_b<(class_c)class_c", + "multivalued": True, + } }, - }, - "class_b": { - "class_c": { - "path": "class_b<(class_c)class_c", - "multivalued": True, - } - }, - }, + } + ], ) @property diff --git a/src/metldata/builtin_transformations/infer_references/path/path.py b/src/metldata/builtin_transformations/infer_references/path/path.py index 06b9a381..1f2e567a 100644 --- a/src/metldata/builtin_transformations/infer_references/path/path.py +++ b/src/metldata/builtin_transformations/infer_references/path/path.py @@ -16,6 +16,8 @@ """Logic for handling reference paths.""" +from pydantic import GetJsonSchemaHandler, ValidationInfo + from metldata.builtin_transformations.infer_references.path.path_str import ( PATH_PATTERN, ValidationError, @@ -72,7 +74,7 @@ def __init__(self, *, path_str: str): self.target = self.elements[-1].target @classmethod - def validate(cls, value) -> "ReferencePath": + def validate(cls, value, info: ValidationInfo) -> "ReferencePath": """A validator for pydantic.""" if isinstance(value, cls): return value @@ -91,7 +93,9 @@ def __get_validators__(cls): yield cls.validate @classmethod - def __modify_schema__(cls, field_schema: dict): + def __get_pydantic_json_schema__( + cls, field_schema: dict, handler: GetJsonSchemaHandler + ): """Modify the field schema for pydantic.""" field_schema.update(type="string", pattern=PATH_PATTERN) diff --git a/src/metldata/builtin_transformations/infer_references/reference.py b/src/metldata/builtin_transformations/infer_references/reference.py index 4f821eb1..62cc94c4 100644 --- a/src/metldata/builtin_transformations/infer_references/reference.py +++ b/src/metldata/builtin_transformations/infer_references/reference.py @@ -16,7 +16,7 @@ """Reference models.""" -from pydantic import BaseModel, Field, root_validator +from pydantic import BaseModel, Field, model_validator from metldata.builtin_transformations.infer_references.path.path import ReferencePath @@ -49,18 +49,18 @@ class InferredReference(ReferenceDetails): description="The name of the new slot in the source to store the inferred reference.", ) - @root_validator(pre=False) + @model_validator(mode="after") @classmethod def validate_source_and_target(cls, values): """Validate that the source and target attributes are identical with the source and target specified in the path. """ - if values.get("source") != values.get("path").source: + if values.source != values.path.source: raise ValueError( "The source is not identical with the source of the specified path." ) - if values.get("target") != values.get("path").target: + if values.target != values.path.target: raise ValueError( "The target is not identical with the target of the specified path." ) diff --git a/src/metldata/builtin_transformations/merge_slots/config.py b/src/metldata/builtin_transformations/merge_slots/config.py index 3497b831..96598cfe 100644 --- a/src/metldata/builtin_transformations/merge_slots/config.py +++ b/src/metldata/builtin_transformations/merge_slots/config.py @@ -16,7 +16,8 @@ """Config parameters and their defaults.""" -from pydantic import BaseSettings, Field, validator +from pydantic import Field, field_validator +from pydantic_settings import BaseSettings from metldata.builtin_transformations.merge_slots.models import SlotMergeInstruction @@ -34,7 +35,7 @@ class SlotMergingConfig(BaseSettings): + " a source slot in another merge instruction." + " The source slots will not be deleted." ), - example=[ + examples=[ { "class_name": "class_a", "source_slots": ["some_slot", "another_slot"], @@ -44,7 +45,7 @@ class SlotMergingConfig(BaseSettings): ) # pylint: disable=no-self-argument - @validator("merge_instructions") + @field_validator("merge_instructions") def validate_merge_instructions( cls, filtered_merge_instructions: list[SlotMergeInstruction] ) -> list[SlotMergeInstruction]: diff --git a/src/metldata/builtin_transformations/merge_slots/models.py b/src/metldata/builtin_transformations/merge_slots/models.py index 5340c938..c3781fc2 100644 --- a/src/metldata/builtin_transformations/merge_slots/models.py +++ b/src/metldata/builtin_transformations/merge_slots/models.py @@ -18,7 +18,7 @@ from typing import Optional -from pydantic import BaseModel, Field, root_validator +from pydantic import BaseModel, Field, model_validator class SlotMergeInstruction(BaseModel): @@ -28,7 +28,7 @@ class SlotMergeInstruction(BaseModel): source_slots: list[str] = Field( ..., description="The slots that should be merged into the target slot.", - min_items=2, + min_length=2, ) target_slot: str = Field( ..., description="The slot into which the source slots should be merged." @@ -38,9 +38,8 @@ class SlotMergeInstruction(BaseModel): description="A description of the target slot.", ) - # pylint: disable=no-self-argument - @root_validator() - def validate_overlapping_slots(cls, values: dict) -> dict: + @model_validator(mode="before") + def validate_overlapping_slots(cls, values) -> dict: """Validate that source and target slots do not overlap.""" source_slots = set(values["source_slots"]) target_slot = values["target_slot"] diff --git a/src/metldata/event_handling/artifact_events.py b/src/metldata/event_handling/artifact_events.py index 55ebf987..0559ebf2 100644 --- a/src/metldata/event_handling/artifact_events.py +++ b/src/metldata/event_handling/artifact_events.py @@ -16,7 +16,7 @@ """Logic for handling artifact events.""" -from pydantic import BaseModel, Field, validator +from pydantic import BaseModel, Field, field_validator class ArtifactEventConfig(BaseModel): @@ -32,7 +32,7 @@ class ArtifactEventConfig(BaseModel): ) # pylint: disable=no-self-argument - @validator("artifact_topic_prefix") + @field_validator("artifact_topic_prefix") def artifact_topic_prefix_must_not_contain_dots(cls, value: str): """Validate that artifact topic prefix does not contain dots.""" if "." in value: diff --git a/src/metldata/event_handling/event_handling.py b/src/metldata/event_handling/event_handling.py index 5ef22d84..9b56f235 100644 --- a/src/metldata/event_handling/event_handling.py +++ b/src/metldata/event_handling/event_handling.py @@ -25,7 +25,8 @@ from hexkit.custom_types import Ascii, JsonObject from hexkit.protocols.eventpub import EventPublisherProtocol from hexkit.protocols.eventsub import EventSubscriberProtocol -from pydantic import BaseModel, BaseSettings, Field +from pydantic import BaseModel, Field +from pydantic_settings import BaseSettings class FileSystemEventConfig(BaseSettings): diff --git a/src/metldata/event_handling/submission_events.py b/src/metldata/event_handling/submission_events.py index a1ed9552..2f5e86c2 100644 --- a/src/metldata/event_handling/submission_events.py +++ b/src/metldata/event_handling/submission_events.py @@ -19,7 +19,8 @@ """ -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings class SourceEventConfig(BaseSettings): diff --git a/src/metldata/load/collect.py b/src/metldata/load/collect.py index 4a26f264..29d9cfb3 100644 --- a/src/metldata/load/collect.py +++ b/src/metldata/load/collect.py @@ -18,7 +18,7 @@ from collections import defaultdict -from pydantic import Field, validator +from pydantic import Field, field_validator from metldata.event_handling.artifact_events import ( ArtifactEventConfig, @@ -41,7 +41,7 @@ class ArtifactCollectorConfig(ArtifactEventConfig): ) # pylint: disable=no-self-argument - @validator("artifact_types") + @field_validator("artifact_types") def artifact_types_must_not_contain_dots(cls, value: list[str]): """Validate that artifact types do not contain dots.""" for artifact_type in value: diff --git a/src/metldata/load/event_publisher.py b/src/metldata/load/event_publisher.py index f2a4281c..dfa5c2c7 100644 --- a/src/metldata/load/event_publisher.py +++ b/src/metldata/load/event_publisher.py @@ -26,7 +26,8 @@ SearchableResourceInfo, ) from hexkit.protocols.eventpub import EventPublisherProtocol -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings class EventPubTranslatorConfig(BaseSettings): @@ -36,47 +37,47 @@ class EventPubTranslatorConfig(BaseSettings): ..., description="Name of the artifact from which the information for outgoing" + " change events is derived.", - example="embedded_public", + examples=["embedded_public"], ) primary_dataset_name: str = Field( ..., description="Name of the resource class corresponding to the embedded_dataset slot.", - example="EmbeddedDataset", + examples=["EmbeddedDataset"], ) resource_change_event_topic: str = Field( ..., description="Name of the topic used for events informing other services about" + " resource changes, i.e. deletion or insertion.", - example="searchable_resources", + examples=["searchable_resources"], ) resource_deletion_event_type: str = Field( ..., description="Type used for events indicating the deletion of a previously" + " existing resource.", - example="searchable_resource_deleted", + examples=["searchable_resource_deleted"], ) resource_upsertion_type: str = Field( ..., description="Type used for events indicating the upsert of a resource.", - example="searchable_resource_upserted", + examples=["searchable_resource_upserted"], ) dataset_change_event_topic: str = Field( ..., description="Name of the topic announcing, among other things, the list of" + " files included in a new dataset.", - example="metadata_datasets", + examples=["metadata_datasets"], ) dataset_deletion_type: str = Field( ..., description="Type used for events announcing a new dataset overview.", - example="dataset_deleted", + examples=["dataset_deleted"], ) dataset_upsertion_type: str = Field( ..., description="Type used for events announcing a new dataset overview.", - example="dataset_created", + examples=["dataset_created"], ) diff --git a/src/metldata/model_utils/config.py b/src/metldata/model_utils/config.py index b9f2a1a2..19f72620 100644 --- a/src/metldata/model_utils/config.py +++ b/src/metldata/model_utils/config.py @@ -17,7 +17,8 @@ from pathlib import Path -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings from metldata.model_utils.assumptions import check_basic_model_assumption from metldata.model_utils.essentials import MetadataModel diff --git a/src/metldata/submission_registry/models.py b/src/metldata/submission_registry/models.py index 4a21debe..962a9a55 100644 --- a/src/metldata/submission_registry/models.py +++ b/src/metldata/submission_registry/models.py @@ -21,7 +21,7 @@ from typing import Optional from ghga_service_commons.utils.utc_dates import DateTimeUTC, now_as_utc -from pydantic import BaseModel, Field, validator +from pydantic import BaseModel, Field, field_validator from typing_extensions import TypeAlias from metldata.custom_types import SubmissionContent @@ -106,7 +106,7 @@ def current_status(self) -> SubmissionStatus: return sorted_history[-1].new_status # pylint: disable=no-self-argument - @validator("accession_map") + @field_validator("accession_map") def check_accession_uniqueness(cls, value: AccessionMap) -> AccessionMap: """Check that no accessions are re-used accross classes.""" total_resources = 0 diff --git a/src/metldata/submission_registry/submission_store.py b/src/metldata/submission_registry/submission_store.py index e80cd0c9..f23a838a 100644 --- a/src/metldata/submission_registry/submission_store.py +++ b/src/metldata/submission_registry/submission_store.py @@ -19,7 +19,8 @@ import json from pathlib import Path -from pydantic import BaseSettings, Field +from pydantic import Field +from pydantic_settings import BaseSettings from metldata.submission_registry import models @@ -67,7 +68,7 @@ def _save(self, *, submission: models.Submission) -> None: """Save a submission to a JSON file.""" json_path = self._get_submission_json_path(submission_id=submission.id) with open(json_path, "w", encoding="utf-8") as file: - file.write(submission.json(indent=4)) + file.write(submission.model_dump_json(indent=4)) def exists(self, *, submission_id: str) -> bool: """Check whether a submission with the specified ID exists.""" diff --git a/src/metldata/transform/base.py b/src/metldata/transform/base.py index 567e8db2..d8a62092 100644 --- a/src/metldata/transform/base.py +++ b/src/metldata/transform/base.py @@ -22,7 +22,7 @@ from graphlib import CycleError, TopologicalSorter from typing import Callable, Generic, Optional, TypeVar -from pydantic import BaseModel, Field, create_model, root_validator, validator +from pydantic import BaseModel, Field, create_model, field_validator, model_validator from metldata.custom_types import Json from metldata.event_handling.models import SubmissionAnnotation @@ -97,7 +97,8 @@ class TransformationDefinition(Generic[Config]): + " MetadataModelTransformationError if the transformation fails." ), ) - metadata_transformer_factory: type[MetadataTransformer[Config]] = Field( + # FIXME type[MetadataTransformer[Config]] + metadata_transformer_factory: type[MetadataTransformer] = Field( ..., description=( "A class for transforming metadata. Raises a MetadataTransformationError" @@ -158,7 +159,7 @@ class WorkflowDefinition(BaseModel): ) # pylint: disable=no-self-argument - @validator("steps", pre=False) + @field_validator("steps", mode="after") def validate_step_references( cls, steps: dict[str, WorkflowStep] ) -> dict[str, WorkflowStep]: @@ -188,13 +189,13 @@ def validate_step_references( return steps - @root_validator(pre=False) + @model_validator(mode="after") def validate_artifact_references(cls, values): """Validate that artifacts reference existing workflow steps.""" - steps = values.get("steps") + steps = values.steps if steps is None: raise ValueError("Steps are undefined.") - artifacts = values.get("artifacts") + artifacts = values.artifacts if artifacts is None: raise ValueError("Artifacts are undefined.") diff --git a/src/metldata/transform/handling.py b/src/metldata/transform/handling.py index e59d4013..b2f81150 100644 --- a/src/metldata/transform/handling.py +++ b/src/metldata/transform/handling.py @@ -139,7 +139,7 @@ def check_workflow_config( Raises: WorkflowConfigMismatchError: """ - if workflow_config.schema_json() == workflow_definition.schema_json(): + if workflow_config.model_json_schema() == workflow_definition.model_json_schema(): raise WorkflowConfigMismatchError( workflow_definition=workflow_definition, workflow_config=workflow_config ) diff --git a/tests/artifact_rest/test_api_factory.py b/tests/artifact_rest/test_api_factory.py index 361de5f6..45f20f32 100644 --- a/tests/artifact_rest/test_api_factory.py +++ b/tests/artifact_rest/test_api_factory.py @@ -166,7 +166,11 @@ async def test_get_stats_endpoint( observed_stats = response.json() assert isinstance(observed_stats, dict) - observed_created = DateTimeUTC.fromisoformat(observed_stats.pop("created")) + raw_observed_created = observed_stats.pop("created") + if isinstance(raw_observed_created, str) and raw_observed_created.endswith("Z"): + raw_observed_created = raw_observed_created.replace("Z", "+00:00") + + observed_created = DateTimeUTC.fromisoformat(raw_observed_created) assert abs((now_as_utc() - observed_created).seconds) < 5 expected_stats = { diff --git a/tests/fixtures/load/config.py b/tests/fixtures/load/config.py index cef7ea88..cc84b331 100644 --- a/tests/fixtures/load/config.py +++ b/tests/fixtures/load/config.py @@ -18,7 +18,7 @@ from typing import Optional, Union import yaml -from pydantic.env_settings import BaseSettings +from pydantic_settings import BaseSettings from metldata.load.config import ArtifactLoaderAPIConfig from tests.fixtures.load.utils import BASE_DIR diff --git a/tests/transform/test_base.py b/tests/transform/test_base.py index d835d62f..a3612c96 100644 --- a/tests/transform/test_base.py +++ b/tests/transform/test_base.py @@ -104,16 +104,17 @@ def test_workflow_definition_config_cls(): """Test that the config_cls of the WorkflowDefinition generates a concatenated config class correctly.""" - config_fields = EXAMPLE_WORKFLOW_DEFINITION.config_cls.__fields__ + config_fields = EXAMPLE_WORKFLOW_DEFINITION.config_cls.model_fields assert "infer_references" in config_fields assert "delete_slots" in config_fields assert ( - config_fields["infer_references"].type_ + config_fields["infer_references"].annotation == REFERENCE_INFERENCE_TRANSFORMATION.config_cls ) assert ( - config_fields["delete_slots"].type_ == SLOT_DELETION_TRANSFORMATION.config_cls + config_fields["delete_slots"].annotation + == SLOT_DELETION_TRANSFORMATION.config_cls ) From 8e19e374178da75978d175df3053226c401ffac2 Mon Sep 17 00:00:00 2001 From: Seyit Zor Date: Thu, 16 Nov 2023 13:16:05 +0000 Subject: [PATCH 02/10] readme update --- README.md | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 430cab48..ffbac9af 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -[![tests](https://github.com/ghga-de/metldata/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/metldata/actions/workflows/unit_and_int_tests.yaml) +[![tests](https://github.com/ghga-de/metldata/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/metldata/actions/workflows/tests.yaml) [![Coverage Status](https://coveralls.io/repos/github/ghga-de/metldata/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/metldata?branch=main) # Metldata @@ -58,6 +58,7 @@ accessions are not violated, however, data might become unavailable. ## Installation + We recommend using the provided Docker container. A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/metldata): @@ -89,6 +90,7 @@ metldata --help ``` ## Configuration + ### Parameters The service requires the following configuration parameters: @@ -383,19 +385,20 @@ that is applied to the source events as explained above. ## Development + For setting up the development environment, we rely on the -[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode +[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of VS Code in combination with Docker Compose. -To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers" +To use it, you have to have Docker Compose as well as VS Code with its "Remote - Containers" extension (`ms-vscode-remote.remote-containers`) installed. -Then open this repository in vscode and run the command -`Remote-Containers: Reopen in Container` from the vscode "Command Palette". +Then open this repository in VS Code and run the command +`Remote-Containers: Reopen in Container` from the VS Code "Command Palette". This will give you a full-fledged, pre-configured development environment including: - infrastructural dependencies of the service (databases, etc.) -- all relevant vscode extensions pre-installed -- pre-configured linting and auto-formating +- all relevant VS Code extensions pre-installed +- pre-configured linting and auto-formatting - a pre-configured debugger - automatic license-header insertion @@ -407,9 +410,11 @@ if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the [`./requirements-dev.txt`](./requirements-dev.txt), please run it again. ## License + This repository is free to use and modify according to the [Apache 2.0 License](./LICENSE). -## Readme Generation -This readme is autogenerate, please see [`readme_generation.md`](./readme_generation.md) +## README Generation + +This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md) for details. From 6eaf148a6eb1fc40351e554fc7246ad4c97e755d Mon Sep 17 00:00:00 2001 From: Seyit Zor Date: Thu, 16 Nov 2023 13:23:17 +0000 Subject: [PATCH 03/10] update fixme context --- src/metldata/transform/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/metldata/transform/base.py b/src/metldata/transform/base.py index d8a62092..2516d18c 100644 --- a/src/metldata/transform/base.py +++ b/src/metldata/transform/base.py @@ -97,7 +97,7 @@ class TransformationDefinition(Generic[Config]): + " MetadataModelTransformationError if the transformation fails." ), ) - # FIXME type[MetadataTransformer[Config]] + # FIXME type[MetadataTransformer[Config]]: TypeError: '_GenericAlias' object cannot be converted to 'PyType' metadata_transformer_factory: type[MetadataTransformer] = Field( ..., description=( From 0375983e27187e9e2721c9fe0df2acb0ea804cc3 Mon Sep 17 00:00:00 2001 From: TheByronHimes Date: Thu, 16 Nov 2023 14:17:44 +0000 Subject: [PATCH 04/10] Update deprecated pydantic methods --- scripts/update_readme.py | 4 ++-- src/metldata/load/event_publisher.py | 8 ++++---- src/metldata/submission_registry/event_publisher.py | 2 +- src/metldata/submission_registry/submission_registry.py | 6 +++--- src/metldata/transform/artifact_publisher.py | 2 +- src/metldata/transform/main.py | 2 +- tests/fixtures/event_handling.py | 4 ++-- tests/fixtures/load/config.py | 2 +- tests/load/test_client.py | 2 +- tests/submission_registry/test_event_publisher.py | 2 +- tests/submission_registry/test_submission_store.py | 4 ++-- tests/transform/test_main.py | 6 +++--- 12 files changed, 22 insertions(+), 22 deletions(-) diff --git a/scripts/update_readme.py b/scripts/update_readme.py index 244d0ba3..765e4d46 100755 --- a/scripts/update_readme.py +++ b/scripts/update_readme.py @@ -180,8 +180,8 @@ def get_package_details() -> PackageDetails: description = read_package_description() config_description = generate_config_docs() return PackageDetails( - **header.dict(), - **name.dict(), + **header.model_dump(), + **name.model_dump(), description=description, config_description=config_description, design_description=read_design_description(), diff --git a/src/metldata/load/event_publisher.py b/src/metldata/load/event_publisher.py index dfa5c2c7..ee309d67 100644 --- a/src/metldata/load/event_publisher.py +++ b/src/metldata/load/event_publisher.py @@ -130,7 +130,7 @@ async def process_dataset_deletion(self, *, accession: str): """ dataset_id = MetadataDatasetID(accession=accession) - payload = json.loads(dataset_id.json()) + payload = json.loads(dataset_id.model_dump_json()) await self._provider.publish( payload=payload, type_=self._config.dataset_deletion_type, @@ -147,7 +147,7 @@ async def process_resource_deletion(self, *, accession: str, class_name: str): accession=accession, class_name=class_name ) - payload = json.loads(resource_info.json()) + payload = json.loads(resource_info.model_dump_json()) await self._provider.publish( payload=payload, type_=self._config.resource_deletion_event_type, @@ -162,7 +162,7 @@ async def process_dataset_upsert( Fires an event that should be processed by the WPS """ - payload = json.loads(dataset_overview.json()) + payload = json.loads(dataset_overview.model_dump_json()) await self._provider.publish( payload=payload, type_=self._config.dataset_upsertion_type, @@ -175,7 +175,7 @@ async def process_resource_upsert(self, *, resource: SearchableResource): Fires an event that should be processed by MASS """ - payload = json.loads(resource.json()) + payload = json.loads(resource.model_dump_json()) await self._provider.publish( payload=payload, type_=self._config.resource_upsertion_type, diff --git a/src/metldata/submission_registry/event_publisher.py b/src/metldata/submission_registry/event_publisher.py index 1feca5c6..e3554b5e 100644 --- a/src/metldata/submission_registry/event_publisher.py +++ b/src/metldata/submission_registry/event_publisher.py @@ -56,6 +56,6 @@ def publish_submission(self, submission: models.Submission): topic=self._config.source_event_topic, type_=self._config.source_event_type, key=submission.id, - payload=json.loads(payload.json()), + payload=json.loads(payload.model_dump_json()), ) ) diff --git a/src/metldata/submission_registry/submission_registry.py b/src/metldata/submission_registry/submission_registry.py index 957b4a89..283daafe 100644 --- a/src/metldata/submission_registry/submission_registry.py +++ b/src/metldata/submission_registry/submission_registry.py @@ -112,7 +112,7 @@ def init_submission(self, *, header: models.SubmissionHeader) -> str: submission content is still empty. """ id_ = generate_submission_id() - submission_creation = models.Submission(id=id_, **header.dict()) + submission_creation = models.Submission(id=id_, **header.model_dump()) self._submission_store.insert_new(submission=submission_creation) return id_ @@ -156,7 +156,7 @@ def upsert_submission_content( anchor_points_by_target=self._anchor_points_by_target, ) - updated_submission = submission.copy( + updated_submission = submission.model_copy( update={"content": content, "accession_map": updated_accession_map} ) self._submission_store.update_existing(submission=updated_submission) @@ -186,7 +186,7 @@ def complete_submission(self, *, id_: str) -> None: status_change = models.StatusChange( timestamp=now_as_utc(), new_status=models.SubmissionStatus.COMPLETED ) - updated_submission = submission.copy( + updated_submission = submission.model_copy( update={ "status_history": submission.status_history # noqa: RUF005 + (status_change,) diff --git a/src/metldata/transform/artifact_publisher.py b/src/metldata/transform/artifact_publisher.py index 39a198d5..073afa31 100644 --- a/src/metldata/transform/artifact_publisher.py +++ b/src/metldata/transform/artifact_publisher.py @@ -52,7 +52,7 @@ def __init__( async def publish_artifact(self, artifact_event: ArtifactEvent): """Publish an artifact as submission event""" - payload = json.loads(artifact_event.payload.json()) + payload = json.loads(artifact_event.payload.model_dump_json()) topic = get_artifact_topic( artifact_topic_prefix=self._config.artifact_topic_prefix, artifact_type=artifact_event.artifact_type, diff --git a/src/metldata/transform/main.py b/src/metldata/transform/main.py index 31ab5d7d..1495d8d8 100644 --- a/src/metldata/transform/main.py +++ b/src/metldata/transform/main.py @@ -56,7 +56,7 @@ async def run_workflow_on_source_event( for artifact_type, artifact_content in artifacts.items(): artifact_event = ArtifactEvent( artifact_type=artifact_type, - payload=source_event.copy(update={"content": artifact_content}), + payload=source_event.model_copy(update={"content": artifact_content}), ) await publish_artifact_func(artifact_event) diff --git a/tests/fixtures/event_handling.py b/tests/fixtures/event_handling.py index a6500c8f..bfc7be48 100644 --- a/tests/fixtures/event_handling.py +++ b/tests/fixtures/event_handling.py @@ -62,8 +62,8 @@ def expect_events(self, expected_events: list[Event]) -> None: ) # hashable versions for comparison: - observed_event_jsons = {event.json() for event in observed_events} - expected_event_jsons = {event.json() for event in expected_events} + observed_event_jsons = {event.model_dump_json() for event in observed_events} + expected_event_jsons = {event.model_dump_json() for event in expected_events} if expected_event_jsons != observed_event_jsons: raise EventExpectationMismatch( diff --git a/tests/fixtures/load/config.py b/tests/fixtures/load/config.py index cc84b331..68e6a373 100644 --- a/tests/fixtures/load/config.py +++ b/tests/fixtures/load/config.py @@ -37,7 +37,7 @@ def get_config( if sources is not None: for source in sources: if isinstance(source, BaseSettings): - sources_dict.update(**source.dict()) + sources_dict.update(**source.model_dump()) else: sources_dict.update(**source) diff --git a/tests/load/test_client.py b/tests/load/test_client.py index 9ea88af2..cfbd1c33 100644 --- a/tests/load/test_client.py +++ b/tests/load/test_client.py @@ -51,7 +51,7 @@ async def test_upload_artifacts_via_http_api( artifact_types=list(EXAMPLE_ARTIFACTS.keys()), artifact_topic_prefix="artifact", loader_api_root="http://localhost:8000", - **file_system_event_fixture.config.dict(), + **file_system_event_fixture.config.model_dump(), ) # publish artifacts: diff --git a/tests/submission_registry/test_event_publisher.py b/tests/submission_registry/test_event_publisher.py index 8ad42b3c..00604327 100644 --- a/tests/submission_registry/test_event_publisher.py +++ b/tests/submission_registry/test_event_publisher.py @@ -58,7 +58,7 @@ def check_source_events( annotation=SubmissionAnnotation( accession_map=expected_submission.accession_map ), - ).json() + ).model_dump_json() ), ) for expected_submission in expected_submissions diff --git a/tests/submission_registry/test_submission_store.py b/tests/submission_registry/test_submission_store.py index 920ba966..23968e37 100644 --- a/tests/submission_registry/test_submission_store.py +++ b/tests/submission_registry/test_submission_store.py @@ -62,7 +62,7 @@ def test_happy(config_sub_fixture: SubmissionConfig): # noqa: F811 assert EXAMPLE_SUBMISSION == submission_queried # update the submision: - submission_updated = EXAMPLE_SUBMISSION.copy( + submission_updated = EXAMPLE_SUBMISSION.model_copy( update={"title": "updated test submission"} ) submission_store.update_existing(submission=submission_updated) @@ -74,7 +74,7 @@ def test_happy(config_sub_fixture: SubmissionConfig): # noqa: F811 assert submission_updated_queried == submission_updated # test getting all existing submission IDs - submission_2 = EXAMPLE_SUBMISSION.copy(update={"id": "testsubmission002"}) + submission_2 = EXAMPLE_SUBMISSION.model_copy(update={"id": "testsubmission002"}) submission_store.insert_new(submission=submission_2) assert submission_store.get_all_submission_ids() == [ diff --git a/tests/transform/test_main.py b/tests/transform/test_main.py index fc70a79a..d04ad5d2 100644 --- a/tests/transform/test_main.py +++ b/tests/transform/test_main.py @@ -47,7 +47,7 @@ async def test_run_workflow_on_all_source_events( artifact_topic_prefix="artifacts", source_event_topic="source-events", source_event_type="source-event", - **file_system_event_fixture.config.dict(), + **file_system_event_fixture.config.model_dump(), ) submission_id = "some-submission-id" @@ -60,7 +60,7 @@ async def test_run_workflow_on_all_source_events( submission_id=submission_id, content=EXAMPLE_WORKFLOW_TEST_CASE.original_metadata, annotation=EXAMPLE_WORKFLOW_TEST_CASE.submission_annotation, - ).json() + ).model_dump_json() ), ) await file_system_event_fixture.publish_events(events=[source_event]) @@ -78,7 +78,7 @@ async def test_run_workflow_on_all_source_events( submission_id=submission_id, content=artifact, annotation=EXAMPLE_WORKFLOW_TEST_CASE.submission_annotation, - ).json() + ).model_dump_json() ), ) for artifact_type, artifact in EXAMPLE_WORKFLOW_TEST_CASE.artifact_metadata.items() From 5e4e66d7721dc379ba8b6e6e5d2673923fd3fb69 Mon Sep 17 00:00:00 2001 From: TheByronHimes Date: Thu, 16 Nov 2023 14:18:23 +0000 Subject: [PATCH 05/10] Use model_config instead of class Config --- .../add_accessions/config.py | 9 +++----- .../custom_embeddings/config.py | 9 +++----- .../delete_slots/config.py | 9 +++----- .../infer_references/config.py | 9 +++----- .../infer_references/reference.py | 9 +++----- .../merge_slots/config.py | 9 +++----- src/metldata/model_utils/anchors.py | 9 +++----- src/metldata/transform/base.py | 21 +++++++++---------- src/metldata/transform/handling.py | 8 ++----- tests/test_event_handling.py | 8 ++----- 10 files changed, 35 insertions(+), 65 deletions(-) diff --git a/src/metldata/builtin_transformations/add_accessions/config.py b/src/metldata/builtin_transformations/add_accessions/config.py index 1ec2f0e5..38ca599e 100644 --- a/src/metldata/builtin_transformations/add_accessions/config.py +++ b/src/metldata/builtin_transformations/add_accessions/config.py @@ -17,12 +17,14 @@ """Config parameters and their defaults.""" from pydantic import Field -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict class AccessionAdditionConfig(BaseSettings): """Config to add accessions to a model and associated metadata.""" + model_config = SettingsConfigDict(extra="forbid") + accession_slot_name: str = Field( "accession", description="The name of the slot to contain the accessions to." ) @@ -30,8 +32,3 @@ class AccessionAdditionConfig(BaseSettings): "The accession for an entity.", description="The description of the slot to contain the accessions to.", ) - - class Config: - """Pydantic config.""" - - extra = "forbid" diff --git a/src/metldata/builtin_transformations/custom_embeddings/config.py b/src/metldata/builtin_transformations/custom_embeddings/config.py index 135c104f..c527ad8b 100644 --- a/src/metldata/builtin_transformations/custom_embeddings/config.py +++ b/src/metldata/builtin_transformations/custom_embeddings/config.py @@ -17,7 +17,7 @@ """Models used to describe embedding profiles.""" from pydantic import Field, field_validator -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict from metldata.builtin_transformations.custom_embeddings.embedding_profile import ( EmbeddingProfile, @@ -43,6 +43,8 @@ class CustomEmbeddingConfig(BaseSettings): model. """ + model_config = SettingsConfigDict(extra="forbid") + embedding_profiles: list[EmbeddingProfile] = Field( ..., description=( @@ -67,8 +69,3 @@ def check_embedding_profiles_unique( raise ValueError("Names for embedded classes must be unique.") return value - - class Config: - """Pydantic config.""" - - extra = "forbid" diff --git a/src/metldata/builtin_transformations/delete_slots/config.py b/src/metldata/builtin_transformations/delete_slots/config.py index 0c97f04e..09679b6a 100644 --- a/src/metldata/builtin_transformations/delete_slots/config.py +++ b/src/metldata/builtin_transformations/delete_slots/config.py @@ -17,12 +17,14 @@ """Config parameters and their defaults.""" from pydantic import Field -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict class SlotDeletionConfig(BaseSettings): """Config containing slots to be deleted from models and associated metadata.""" + model_config = SettingsConfigDict(extra="forbid") + slots_to_delete: dict[str, list[str]] = Field( ..., description=( @@ -38,8 +40,3 @@ class SlotDeletionConfig(BaseSettings): } ], ) - - class Config: - """Pydantic config.""" - - extra = "forbid" diff --git a/src/metldata/builtin_transformations/infer_references/config.py b/src/metldata/builtin_transformations/infer_references/config.py index 06bd85fa..9362b17a 100644 --- a/src/metldata/builtin_transformations/infer_references/config.py +++ b/src/metldata/builtin_transformations/infer_references/config.py @@ -17,7 +17,7 @@ """Models used to describe all inferred references based on existing references.""" from pydantic import Field -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict from metldata.builtin_transformations.infer_references.reference import ( InferredReference, @@ -31,6 +31,8 @@ class ReferenceInferenceConfig(BaseSettings): a list of InferredReferences. """ + model_config = SettingsConfigDict(extra="forbid") + inferred_ref_map: dict[str, dict[str, ReferenceDetails]] = Field( ..., description=( @@ -81,8 +83,3 @@ def inferred_references(self) -> list[InferredReference]: ) return inferred_refs - - class Config: - """Pydantic config.""" - - extra = "forbid" diff --git a/src/metldata/builtin_transformations/infer_references/reference.py b/src/metldata/builtin_transformations/infer_references/reference.py index 62cc94c4..f1b15858 100644 --- a/src/metldata/builtin_transformations/infer_references/reference.py +++ b/src/metldata/builtin_transformations/infer_references/reference.py @@ -16,7 +16,7 @@ """Reference models.""" -from pydantic import BaseModel, Field, model_validator +from pydantic import BaseModel, ConfigDict, Field, model_validator from metldata.builtin_transformations.infer_references.path.path import ReferencePath @@ -40,6 +40,8 @@ class InferredReference(ReferenceDetails): references. """ + model_config = ConfigDict(frozen=True) + source: str = Field( ..., description="The source class to which this reference should be added." ) @@ -66,8 +68,3 @@ def validate_source_and_target(cls, values): ) return values - - class Config: - """Config for this model.""" - - frozen = True diff --git a/src/metldata/builtin_transformations/merge_slots/config.py b/src/metldata/builtin_transformations/merge_slots/config.py index 96598cfe..b54eaebd 100644 --- a/src/metldata/builtin_transformations/merge_slots/config.py +++ b/src/metldata/builtin_transformations/merge_slots/config.py @@ -17,7 +17,7 @@ """Config parameters and their defaults.""" from pydantic import Field, field_validator -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict from metldata.builtin_transformations.merge_slots.models import SlotMergeInstruction @@ -25,6 +25,8 @@ class SlotMergingConfig(BaseSettings): """Config containing slots to be deleted from models and associated metadata.""" + model_config = SettingsConfigDict(extra="forbid") + merge_instructions: list[SlotMergeInstruction] = Field( ..., description=( @@ -83,8 +85,3 @@ def validate_merge_instructions( ) return filtered_merge_instructions - - class Config: - """Pydantic config.""" - - extra = "forbid" diff --git a/src/metldata/model_utils/anchors.py b/src/metldata/model_utils/anchors.py index 10ab524a..3834ae12 100644 --- a/src/metldata/model_utils/anchors.py +++ b/src/metldata/model_utils/anchors.py @@ -21,7 +21,7 @@ from linkml_runtime import SchemaView from linkml_runtime.linkml_model import SlotDefinition -from pydantic import BaseModel, Field +from pydantic import BaseModel, ConfigDict, Field from metldata.model_utils.essentials import ROOT_CLASS, MetadataModel from metldata.model_utils.identifiers import get_class_identifiers @@ -42,6 +42,8 @@ class ClassNotAnchoredError(RuntimeError): class AnchorPoint(BaseModel): """A model for describing an anchor point for the specified target class.""" + model_config = ConfigDict(frozen=True) + target_class: str = Field(..., description="The name of the class to be targeted.") identifier_slot: str = Field( ..., @@ -56,11 +58,6 @@ class AnchorPoint(BaseModel): ), ) - class Config: - """Pydantic Configs.""" - - frozen = True - def check_root_slot(slot: SlotDefinition): """Make sure that the given root slot is a valid anchor point. Validates that the diff --git a/src/metldata/transform/base.py b/src/metldata/transform/base.py index d8a62092..a91a5bf8 100644 --- a/src/metldata/transform/base.py +++ b/src/metldata/transform/base.py @@ -22,7 +22,14 @@ from graphlib import CycleError, TopologicalSorter from typing import Callable, Generic, Optional, TypeVar -from pydantic import BaseModel, Field, create_model, field_validator, model_validator +from pydantic import ( + BaseModel, + ConfigDict, + Field, + create_model, + field_validator, + model_validator, +) from metldata.custom_types import Json from metldata.event_handling.models import SubmissionAnnotation @@ -114,6 +121,7 @@ class WorkflowConfig(BaseModel, ABC): class WorkflowStepBase(BaseModel, ABC): """A base class for workflow steps.""" + model_config = ConfigDict(frozen=True) description: str = Field(..., description="A description of the step.") input: Optional[str] = Field( ..., @@ -123,11 +131,6 @@ class WorkflowStepBase(BaseModel, ABC): ), ) - class Config: - """Config for the workflow step.""" - - frozen = True - class WorkflowStep(WorkflowStepBase): """A single step in a transformation workflow.""" @@ -141,6 +144,7 @@ class WorkflowStep(WorkflowStepBase): class WorkflowDefinition(BaseModel): """A definition of a transformation workflow.""" + model_config = ConfigDict(frozen=True) description: str = Field(..., description="A description of the workflow.") steps: dict[str, WorkflowStep] = Field( ..., @@ -240,8 +244,3 @@ def step_order(self) -> list[str]: return list(topological_sorter.static_order()) except CycleError as exc: raise RuntimeError("Step definitions imply a circular dependency.") from exc - - class Config: - """Config for the workflow step.""" - - frozen = True diff --git a/src/metldata/transform/handling.py b/src/metldata/transform/handling.py index b2f81150..cf4dda9d 100644 --- a/src/metldata/transform/handling.py +++ b/src/metldata/transform/handling.py @@ -16,7 +16,7 @@ """Logic for handling Transformation.""" -from pydantic import BaseModel +from pydantic import BaseModel, ConfigDict from metldata.custom_types import Json from metldata.event_handling.models import SubmissionAnnotation @@ -115,13 +115,9 @@ def transform_metadata( class ResolvedWorkflowStep(WorkflowStepBase): """A resolved workflow step contains a transformation handler.""" + model_config = ConfigDict(arbitrary_types_allowed=True) transformation_handler: TransformationHandler - class Config: - """Config for ResolvedWorkflowStep.""" - - arbitrary_types_allowed = True - class ResolvedWorkflow(WorkflowDefinition): """A resolved workflow contains a list of resolved workflow steps.""" diff --git a/tests/test_event_handling.py b/tests/test_event_handling.py index 5499dfb0..4548613d 100644 --- a/tests/test_event_handling.py +++ b/tests/test_event_handling.py @@ -21,7 +21,7 @@ import pytest from hexkit.custom_types import Ascii, JsonObject from hexkit.protocols.eventsub import EventSubscriberProtocol -from pydantic import BaseModel, Field +from pydantic import BaseModel, ConfigDict, Field from metldata.event_handling.event_handling import FileSystemEventSubscriber from tests.fixtures.event_handling import ( @@ -44,15 +44,11 @@ class ConsumedEvent(BaseModel): """Consumed event without the key.""" + model_config = ConfigDict(frozen=True) topic: str type_: str payload: str = Field(..., description="JSON string of the event payload.") - class Config: - """Pydantic model configuration.""" - - frozen = True - @pytest.mark.asyncio async def test_pub_sub_workflow( From 9162a4ce808e377c8809a841903ec8373c03fb9a Mon Sep 17 00:00:00 2001 From: TheByronHimes Date: Fri, 17 Nov 2023 09:28:29 +0000 Subject: [PATCH 06/10] Don't use model_json_schema on WorkflowDefinition --- src/metldata/transform/handling.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/metldata/transform/handling.py b/src/metldata/transform/handling.py index cf4dda9d..8a542a72 100644 --- a/src/metldata/transform/handling.py +++ b/src/metldata/transform/handling.py @@ -135,7 +135,7 @@ def check_workflow_config( Raises: WorkflowConfigMismatchError: """ - if workflow_config.model_json_schema() == workflow_definition.model_json_schema(): + if isinstance(workflow_config, workflow_definition.config_cls): raise WorkflowConfigMismatchError( workflow_definition=workflow_definition, workflow_config=workflow_config ) From f942c4a6ecb575a80ab2a17eeba49a8cdc50ec58 Mon Sep 17 00:00:00 2001 From: TheByronHimes Date: Fri, 17 Nov 2023 09:39:09 +0000 Subject: [PATCH 07/10] Replace deprecated .parse_obj methods --- tests/builtin_tranformations/aggregate/conftest.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/builtin_tranformations/aggregate/conftest.py b/tests/builtin_tranformations/aggregate/conftest.py index 1bcfd0c1..cc4999c5 100644 --- a/tests/builtin_tranformations/aggregate/conftest.py +++ b/tests/builtin_tranformations/aggregate/conftest.py @@ -54,7 +54,7 @@ def data_complete_1_resolved_public() -> Json: @fixture def config() -> AggregateConfig: """A working config""" - return AggregateConfig.parse_obj( + return AggregateConfig.model_validate( load_yaml(Path("transformations/aggregate/default/config.yaml")) ) @@ -62,6 +62,6 @@ def config() -> AggregateConfig: @fixture def invalid_config() -> AggregateConfig: """An invalid config with conflicting output paths.""" - return AggregateConfig.parse_obj( + return AggregateConfig.model_validate( load_yaml(Path("transformations/aggregate/config_invalid.yaml")) ) From 46c14eb2a1546bead096d3ad78201c394d0ce363 Mon Sep 17 00:00:00 2001 From: TheByronHimes Date: Fri, 17 Nov 2023 09:44:57 +0000 Subject: [PATCH 08/10] Update template files, config, and readme --- .devcontainer/.dev_config.yaml | 2 +- README.md | 197 +++++++++++-- config_schema.json | 524 +++++++++++++++++---------------- example_config.yaml | 7 +- scripts/update_readme.py | 4 +- 5 files changed, 449 insertions(+), 285 deletions(-) diff --git a/.devcontainer/.dev_config.yaml b/.devcontainer/.dev_config.yaml index eb79728d..fda99703 100644 --- a/.devcontainer/.dev_config.yaml +++ b/.devcontainer/.dev_config.yaml @@ -302,7 +302,7 @@ loader_token_hashes: log_level: trace service_name: metldata -service_instance_id: 001 +service_instance_id: "001" kafka_servers: ["kafka:9092"] primary_artifact_name: embedded_public diff --git a/README.md b/README.md index ffbac9af..bd21b2f2 100644 --- a/README.md +++ b/README.md @@ -94,38 +94,142 @@ metldata --help ### Parameters The service requires the following configuration parameters: -- **`artifact_infos`** *(array)*: Information for artifacts to be queryable via the Artifacts REST API. +- **`db_connection_str`** *(string, format: password)*: MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/. - - **Items**: Refer to *[#/definitions/ArtifactInfo](#definitions/ArtifactInfo)*. -- **`db_connection_str`** *(string, format: password)*: MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/. + Examples: + + ```json + "mongodb://localhost:27017" + ``` + - **`db_name`** *(string)*: Name of the database located on the MongoDB server. + + Examples: + + ```json + "my-database" + ``` + + - **`service_name`** *(string)*: Default: `"metldata"`. - **`service_instance_id`** *(string)*: A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id. + + Examples: + + ```json + "germany-bw-instance-001" + ``` + + - **`kafka_servers`** *(array)*: A list of connection strings to connect to Kafka bootstrap servers. - **Items** *(string)* + + Examples: + + ```json + [ + "localhost:9092" + ] + ``` + + +- **`kafka_security_protocol`** *(string)*: Protocol used to communicate with brokers. Valid values are: PLAINTEXT, SSL. Must be one of: `["PLAINTEXT", "SSL"]`. Default: `"PLAINTEXT"`. + +- **`kafka_ssl_cafile`** *(string)*: Certificate Authority file path containing certificates used to sign broker certificates. If a CA not specified, the default system CA will be used if found by OpenSSL. Default: `""`. + +- **`kafka_ssl_certfile`** *(string)*: Optional filename of client certificate, as well as any CA certificates needed to establish the certificate's authenticity. Default: `""`. + +- **`kafka_ssl_keyfile`** *(string)*: Optional filename containing the client private key. Default: `""`. + +- **`kafka_ssl_password`** *(string)*: Optional password to be used for the client private key. Default: `""`. + - **`primary_artifact_name`** *(string)*: Name of the artifact from which the information for outgoing change events is derived. + + Examples: + + ```json + "embedded_public" + ``` + + - **`primary_dataset_name`** *(string)*: Name of the resource class corresponding to the embedded_dataset slot. + + Examples: + + ```json + "EmbeddedDataset" + ``` + + - **`resource_change_event_topic`** *(string)*: Name of the topic used for events informing other services about resource changes, i.e. deletion or insertion. + + Examples: + + ```json + "searchable_resources" + ``` + + - **`resource_deletion_event_type`** *(string)*: Type used for events indicating the deletion of a previously existing resource. + + Examples: + + ```json + "searchable_resource_deleted" + ``` + + - **`resource_upsertion_type`** *(string)*: Type used for events indicating the upsert of a resource. + + Examples: + + ```json + "searchable_resource_upserted" + ``` + + - **`dataset_change_event_topic`** *(string)*: Name of the topic announcing, among other things, the list of files included in a new dataset. + + Examples: + + ```json + "metadata_datasets" + ``` + + - **`dataset_deletion_type`** *(string)*: Type used for events announcing a new dataset overview. + + Examples: + + ```json + "dataset_deleted" + ``` + + - **`dataset_upsertion_type`** *(string)*: Type used for events announcing a new dataset overview. + + Examples: + + ```json + "dataset_created" + ``` + + - **`host`** *(string)*: IP of the host. Default: `"127.0.0.1"`. - **`port`** *(integer)*: Port to expose the server on the specified host. Default: `8080`. @@ -142,60 +246,91 @@ The service requires the following configuration parameters: - **`docs_url`** *(string)*: Path to host the swagger documentation. This is relative to the specified host and port. Default: `"/docs"`. -- **`cors_allowed_origins`** *(array)*: A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin. +- **`cors_allowed_origins`**: A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin. Default: `null`. - - **Items** *(string)* + - **Any of** -- **`cors_allow_credentials`** *(boolean)*: Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified. + - *array* -- **`cors_allowed_methods`** *(array)*: A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods. + - **Items** *(string)* - - **Items** *(string)* + - *null* -- **`cors_allowed_headers`** *(array)*: A list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all headers. The Accept, Accept-Language, Content-Language and Content-Type headers are always allowed for CORS requests. - - **Items** *(string)* + Examples: -- **`loader_token_hashes`** *(array)*: Hashes of tokens used to authenticate for loading artifact. + ```json + [ + "https://example.org", + "https://www.example.org" + ] + ``` - - **Items** *(string)* -## Definitions +- **`cors_allow_credentials`**: Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified. Default: `null`. + + - **Any of** + + - *boolean* + + - *null* + + + Examples: + + ```json + [ + "https://example.org", + "https://www.example.org" + ] + ``` -- **`AnchorPoint`** *(object)*: A model for describing an anchor point for the specified target class. +- **`cors_allowed_methods`**: A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods. Default: `null`. - - **`target_class`** *(string, required)*: The name of the class to be targeted. + - **Any of** - - **`identifier_slot`** *(string, required)*: The name of the slot in the target class that is used as identifier. + - *array* - - **`root_slot`** *(string, required)*: The name of the slot in the root class used to link to the target class. + - **Items** *(string)* -- **`ArtifactResourceClass`** *(object)*: Model to describe a resource class of an artifact. + - *null* - - **`name`** *(string, required)*: The name of the metadata class. - - **`description`** *(string)*: A description of the metadata class. + Examples: - - **`anchor_point`**: The anchor point for this metadata class. + ```json + [ + "*" + ] + ``` - - **All of** - - : Refer to *[#/definitions/AnchorPoint](#definitions/AnchorPoint)*. +- **`cors_allowed_headers`**: A list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all headers. The Accept, Accept-Language, Content-Language and Content-Type headers are always allowed for CORS requests. Default: `null`. - - **`json_schema`** *(object, required)*: The JSON schema for this metadata class. + - **Any of** -- **`ArtifactInfo`** *(object)*: Model to describe general information on an artifact. -Please note, it does not contain actual artifact instances derived from specific -metadata. + - *array* - - **`name`** *(string, required)*: The name of the artifact. + - **Items** *(string)* - - **`description`** *(string, required)*: A description of the artifact. + - *null* - - **`resource_classes`** *(object, required)*: A dictionary of resource classes for this artifact. The keys are the names of the classes. The values are the corresponding class models. Can contain additional properties. - - **Additional Properties**: Refer to *[#/definitions/ArtifactResourceClass](#definitions/ArtifactResourceClass)*. + Examples: + + ```json + [] + ``` + + +- **`artifact_infos`** *(array)*: Information for artifacts to be queryable via the Artifacts REST API. + + - **Items**: Refer to *[#/$defs/ArtifactInfo](#$defs/ArtifactInfo)*. + +- **`loader_token_hashes`** *(array)*: Hashes of tokens used to authenticate for loading artifact. + + - **Items** *(string)* ### Usage: diff --git a/config_schema.json b/config_schema.json index e3f55882..216d19cb 100644 --- a/config_schema.json +++ b/config_schema.json @@ -1,167 +1,266 @@ { - "title": "ModSettings", - "description": "Modifies the orginal Settings class provided by the user", - "type": "object", - "properties": { - "artifact_infos": { - "title": "Artifact Infos", - "description": "Information for artifacts to be queryable via the Artifacts REST API.", - "env_names": [ - "metldata_artifact_infos" + "$defs": { + "AnchorPoint": { + "description": "A model for describing an anchor point for the specified target class.", + "properties": { + "target_class": { + "description": "The name of the class to be targeted.", + "title": "Target Class", + "type": "string" + }, + "identifier_slot": { + "description": "The name of the slot in the target class that is used as identifier.", + "title": "Identifier Slot", + "type": "string" + }, + "root_slot": { + "description": "The name of the slot in the root class used to link to the target class.", + "title": "Root Slot", + "type": "string" + } + }, + "required": [ + "target_class", + "identifier_slot", + "root_slot" ], - "type": "array", - "items": { - "$ref": "#/definitions/ArtifactInfo" - } + "title": "AnchorPoint", + "type": "object" }, + "ArtifactInfo": { + "description": "Model to describe general information on an artifact.\nPlease note, it does not contain actual artifact instances derived from specific\nmetadata.", + "properties": { + "name": { + "description": "The name of the artifact.", + "title": "Name", + "type": "string" + }, + "description": { + "description": "A description of the artifact.", + "title": "Description", + "type": "string" + }, + "resource_classes": { + "additionalProperties": { + "$ref": "#/$defs/ArtifactResourceClass" + }, + "description": "A dictionary of resource classes for this artifact. The keys are the names of the classes. The values are the corresponding class models.", + "title": "Resource Classes", + "type": "object" + } + }, + "required": [ + "name", + "description", + "resource_classes" + ], + "title": "ArtifactInfo", + "type": "object" + }, + "ArtifactResourceClass": { + "description": "Model to describe a resource class of an artifact.", + "properties": { + "name": { + "description": "The name of the metadata class.", + "title": "Name", + "type": "string" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "A description of the metadata class.", + "title": "Description" + }, + "anchor_point": { + "allOf": [ + { + "$ref": "#/$defs/AnchorPoint" + } + ], + "description": "The anchor point for this metadata class." + }, + "json_schema": { + "description": "The JSON schema for this metadata class.", + "title": "Json Schema", + "type": "object" + } + }, + "required": [ + "name", + "anchor_point", + "json_schema" + ], + "title": "ArtifactResourceClass", + "type": "object" + } + }, + "additionalProperties": false, + "description": "Modifies the orginal Settings class provided by the user", + "properties": { "db_connection_str": { - "title": "Db Connection Str", "description": "MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/", - "example": "mongodb://localhost:27017", - "env_names": [ - "metldata_db_connection_str" + "examples": [ + "mongodb://localhost:27017" ], + "format": "password", + "title": "Db Connection Str", "type": "string", - "writeOnly": true, - "format": "password" + "writeOnly": true }, "db_name": { - "title": "Db Name", "description": "Name of the database located on the MongoDB server.", - "example": "my-database", - "env_names": [ - "metldata_db_name" + "examples": [ + "my-database" ], + "title": "Db Name", "type": "string" }, "service_name": { - "title": "Service Name", "default": "metldata", - "env_names": [ - "metldata_service_name" - ], + "title": "Service Name", "type": "string" }, "service_instance_id": { - "title": "Service Instance Id", "description": "A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.", - "example": "germany-bw-instance-001", - "env_names": [ - "metldata_service_instance_id" + "examples": [ + "germany-bw-instance-001" ], + "title": "Service Instance Id", "type": "string" }, "kafka_servers": { - "title": "Kafka Servers", "description": "A list of connection strings to connect to Kafka bootstrap servers.", - "example": [ - "localhost:9092" - ], - "env_names": [ - "metldata_kafka_servers" + "examples": [ + [ + "localhost:9092" + ] ], - "type": "array", "items": { "type": "string" - } + }, + "title": "Kafka Servers", + "type": "array" + }, + "kafka_security_protocol": { + "default": "PLAINTEXT", + "description": "Protocol used to communicate with brokers. Valid values are: PLAINTEXT, SSL.", + "enum": [ + "PLAINTEXT", + "SSL" + ], + "title": "Kafka Security Protocol", + "type": "string" + }, + "kafka_ssl_cafile": { + "default": "", + "description": "Certificate Authority file path containing certificates used to sign broker certificates. If a CA not specified, the default system CA will be used if found by OpenSSL.", + "title": "Kafka Ssl Cafile", + "type": "string" + }, + "kafka_ssl_certfile": { + "default": "", + "description": "Optional filename of client certificate, as well as any CA certificates needed to establish the certificate's authenticity.", + "title": "Kafka Ssl Certfile", + "type": "string" + }, + "kafka_ssl_keyfile": { + "default": "", + "description": "Optional filename containing the client private key.", + "title": "Kafka Ssl Keyfile", + "type": "string" + }, + "kafka_ssl_password": { + "default": "", + "description": "Optional password to be used for the client private key.", + "title": "Kafka Ssl Password", + "type": "string" }, "primary_artifact_name": { - "title": "Primary Artifact Name", "description": "Name of the artifact from which the information for outgoing change events is derived.", - "example": "embedded_public", - "env_names": [ - "metldata_primary_artifact_name" + "examples": [ + "embedded_public" ], + "title": "Primary Artifact Name", "type": "string" }, "primary_dataset_name": { - "title": "Primary Dataset Name", "description": "Name of the resource class corresponding to the embedded_dataset slot.", - "example": "EmbeddedDataset", - "env_names": [ - "metldata_primary_dataset_name" + "examples": [ + "EmbeddedDataset" ], + "title": "Primary Dataset Name", "type": "string" }, "resource_change_event_topic": { - "title": "Resource Change Event Topic", "description": "Name of the topic used for events informing other services about resource changes, i.e. deletion or insertion.", - "example": "searchable_resources", - "env_names": [ - "metldata_resource_change_event_topic" + "examples": [ + "searchable_resources" ], + "title": "Resource Change Event Topic", "type": "string" }, "resource_deletion_event_type": { - "title": "Resource Deletion Event Type", "description": "Type used for events indicating the deletion of a previously existing resource.", - "example": "searchable_resource_deleted", - "env_names": [ - "metldata_resource_deletion_event_type" + "examples": [ + "searchable_resource_deleted" ], + "title": "Resource Deletion Event Type", "type": "string" }, "resource_upsertion_type": { - "title": "Resource Upsertion Type", "description": "Type used for events indicating the upsert of a resource.", - "example": "searchable_resource_upserted", - "env_names": [ - "metldata_resource_upsertion_type" + "examples": [ + "searchable_resource_upserted" ], + "title": "Resource Upsertion Type", "type": "string" }, "dataset_change_event_topic": { - "title": "Dataset Change Event Topic", "description": "Name of the topic announcing, among other things, the list of files included in a new dataset.", - "example": "metadata_datasets", - "env_names": [ - "metldata_dataset_change_event_topic" + "examples": [ + "metadata_datasets" ], + "title": "Dataset Change Event Topic", "type": "string" }, "dataset_deletion_type": { - "title": "Dataset Deletion Type", "description": "Type used for events announcing a new dataset overview.", - "example": "dataset_deleted", - "env_names": [ - "metldata_dataset_deletion_type" + "examples": [ + "dataset_deleted" ], + "title": "Dataset Deletion Type", "type": "string" }, "dataset_upsertion_type": { - "title": "Dataset Upsertion Type", "description": "Type used for events announcing a new dataset overview.", - "example": "dataset_created", - "env_names": [ - "metldata_dataset_upsertion_type" + "examples": [ + "dataset_created" ], + "title": "Dataset Upsertion Type", "type": "string" }, "host": { - "title": "Host", - "description": "IP of the host.", "default": "127.0.0.1", - "env_names": [ - "metldata_host" - ], + "description": "IP of the host.", + "title": "Host", "type": "string" }, "port": { - "title": "Port", - "description": "Port to expose the server on the specified host", "default": 8080, - "env_names": [ - "metldata_port" - ], + "description": "Port to expose the server on the specified host", + "title": "Port", "type": "integer" }, "log_level": { - "title": "Log Level", - "description": "Controls the verbosity of the log.", "default": "info", - "env_names": [ - "metldata_log_level" - ], + "description": "Controls the verbosity of the log.", "enum": [ "critical", "error", @@ -170,120 +269,138 @@ "debug", "trace" ], + "title": "Log Level", "type": "string" }, "auto_reload": { - "title": "Auto Reload", - "description": "A development feature. Set to `True` to automatically reload the server upon code changes", "default": false, - "env_names": [ - "metldata_auto_reload" - ], + "description": "A development feature. Set to `True` to automatically reload the server upon code changes", + "title": "Auto Reload", "type": "boolean" }, "workers": { - "title": "Workers", - "description": "Number of workers processes to run.", "default": 1, - "env_names": [ - "metldata_workers" - ], + "description": "Number of workers processes to run.", + "title": "Workers", "type": "integer" }, "api_root_path": { - "title": "Api Root Path", - "description": "Root path at which the API is reachable. This is relative to the specified host and port.", "default": "/", - "env_names": [ - "metldata_api_root_path" - ], + "description": "Root path at which the API is reachable. This is relative to the specified host and port.", + "title": "Api Root Path", "type": "string" }, "openapi_url": { - "title": "Openapi Url", - "description": "Path to get the openapi specification in JSON format. This is relative to the specified host and port.", "default": "/openapi.json", - "env_names": [ - "metldata_openapi_url" - ], + "description": "Path to get the openapi specification in JSON format. This is relative to the specified host and port.", + "title": "Openapi Url", "type": "string" }, "docs_url": { - "title": "Docs Url", - "description": "Path to host the swagger documentation. This is relative to the specified host and port.", "default": "/docs", - "env_names": [ - "metldata_docs_url" - ], + "description": "Path to host the swagger documentation. This is relative to the specified host and port.", + "title": "Docs Url", "type": "string" }, "cors_allowed_origins": { - "title": "Cors Allowed Origins", - "description": "A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin.", - "example": [ - "https://example.org", - "https://www.example.org" + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } ], - "env_names": [ - "metldata_cors_allowed_origins" + "default": null, + "description": "A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin.", + "examples": [ + [ + "https://example.org", + "https://www.example.org" + ] ], - "type": "array", - "items": { - "type": "string" - } + "title": "Cors Allowed Origins" }, "cors_allow_credentials": { - "title": "Cors Allow Credentials", - "description": "Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified.", - "example": [ - "https://example.org", - "https://www.example.org" + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } ], - "env_names": [ - "metldata_cors_allow_credentials" + "default": null, + "description": "Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified.", + "examples": [ + [ + "https://example.org", + "https://www.example.org" + ] ], - "type": "boolean" + "title": "Cors Allow Credentials" }, "cors_allowed_methods": { - "title": "Cors Allowed Methods", - "description": "A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods.", - "example": [ - "*" + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } ], - "env_names": [ - "metldata_cors_allowed_methods" + "default": null, + "description": "A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods.", + "examples": [ + [ + "*" + ] ], - "type": "array", - "items": { - "type": "string" - } + "title": "Cors Allowed Methods" }, "cors_allowed_headers": { - "title": "Cors Allowed Headers", + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "default": null, "description": "A list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all headers. The Accept, Accept-Language, Content-Language and Content-Type headers are always allowed for CORS requests.", - "example": [], - "env_names": [ - "metldata_cors_allowed_headers" + "examples": [ + [] ], - "type": "array", + "title": "Cors Allowed Headers" + }, + "artifact_infos": { + "description": "Information for artifacts to be queryable via the Artifacts REST API.", "items": { - "type": "string" - } + "$ref": "#/$defs/ArtifactInfo" + }, + "title": "Artifact Infos", + "type": "array" }, "loader_token_hashes": { - "title": "Loader Token Hashes", "description": "Hashes of tokens used to authenticate for loading artifact.", - "env_names": [ - "metldata_loader_token_hashes" - ], - "type": "array", "items": { "type": "string" - } + }, + "title": "Loader Token Hashes", + "type": "array" } }, "required": [ - "artifact_infos", "db_connection_str", "db_name", "service_instance_id", @@ -296,102 +413,9 @@ "dataset_change_event_topic", "dataset_deletion_type", "dataset_upsertion_type", + "artifact_infos", "loader_token_hashes" ], - "additionalProperties": false, - "definitions": { - "AnchorPoint": { - "title": "AnchorPoint", - "description": "A model for describing an anchor point for the specified target class.", - "type": "object", - "properties": { - "target_class": { - "title": "Target Class", - "description": "The name of the class to be targeted.", - "type": "string" - }, - "identifier_slot": { - "title": "Identifier Slot", - "description": "The name of the slot in the target class that is used as identifier.", - "type": "string" - }, - "root_slot": { - "title": "Root Slot", - "description": "The name of the slot in the root class used to link to the target class.", - "type": "string" - } - }, - "required": [ - "target_class", - "identifier_slot", - "root_slot" - ] - }, - "ArtifactResourceClass": { - "title": "ArtifactResourceClass", - "description": "Model to describe a resource class of an artifact.", - "type": "object", - "properties": { - "name": { - "title": "Name", - "description": "The name of the metadata class.", - "type": "string" - }, - "description": { - "title": "Description", - "description": "A description of the metadata class.", - "type": "string" - }, - "anchor_point": { - "title": "Anchor Point", - "description": "The anchor point for this metadata class.", - "allOf": [ - { - "$ref": "#/definitions/AnchorPoint" - } - ] - }, - "json_schema": { - "title": "Json Schema", - "description": "The JSON schema for this metadata class.", - "type": "object" - } - }, - "required": [ - "name", - "anchor_point", - "json_schema" - ] - }, - "ArtifactInfo": { - "title": "ArtifactInfo", - "description": "Model to describe general information on an artifact.\nPlease note, it does not contain actual artifact instances derived from specific\nmetadata.", - "type": "object", - "properties": { - "name": { - "title": "Name", - "description": "The name of the artifact.", - "type": "string" - }, - "description": { - "title": "Description", - "description": "A description of the artifact.", - "type": "string" - }, - "resource_classes": { - "title": "Resource Classes", - "description": "A dictionary of resource classes for this artifact. The keys are the names of the classes. The values are the corresponding class models.", - "type": "object", - "additionalProperties": { - "$ref": "#/definitions/ArtifactResourceClass" - } - } - }, - "required": [ - "name", - "description", - "resource_classes" - ] - } - } + "title": "ModSettings", + "type": "object" } \ No newline at end of file diff --git a/example_config.yaml b/example_config.yaml index 3bb158e5..2aa32e0d 100644 --- a/example_config.yaml +++ b/example_config.yaml @@ -204,8 +204,13 @@ db_connection_str: '**********' db_name: dev_db docs_url: /docs host: 127.0.0.1 +kafka_security_protocol: PLAINTEXT kafka_servers: - kafka:9092 +kafka_ssl_cafile: '' +kafka_ssl_certfile: '' +kafka_ssl_keyfile: '' +kafka_ssl_password: '' loader_token_hashes: - 09e5724dab34b50fe2db5ebae7ac5eac4ef2904d105f8f2b3d5a4cb2c7f43da4 log_level: trace @@ -216,6 +221,6 @@ primary_dataset_name: EmbeddedDataset resource_change_event_topic: searchable_resources resource_deletion_event_type: searchable_resource_deleted resource_upsertion_type: searchable_resource_upserted -service_instance_id: '1' +service_instance_id: '001' service_name: metldata workers: 1 diff --git a/scripts/update_readme.py b/scripts/update_readme.py index 765e4d46..244d0ba3 100755 --- a/scripts/update_readme.py +++ b/scripts/update_readme.py @@ -180,8 +180,8 @@ def get_package_details() -> PackageDetails: description = read_package_description() config_description = generate_config_docs() return PackageDetails( - **header.model_dump(), - **name.model_dump(), + **header.dict(), + **name.dict(), description=description, config_description=config_description, design_description=read_design_description(), From 1a046519609b17e357c522be6d498912f585fefe Mon Sep 17 00:00:00 2001 From: Seyit Zor Date: Mon, 20 Nov 2023 10:36:08 +0000 Subject: [PATCH 09/10] delete fixme --- src/metldata/transform/base.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/metldata/transform/base.py b/src/metldata/transform/base.py index d6ef0bfb..e2d37a4c 100644 --- a/src/metldata/transform/base.py +++ b/src/metldata/transform/base.py @@ -104,7 +104,6 @@ class TransformationDefinition(Generic[Config]): + " MetadataModelTransformationError if the transformation fails." ), ) - # FIXME type[MetadataTransformer[Config]]: TypeError: '_GenericAlias' object cannot be converted to 'PyType' metadata_transformer_factory: type[MetadataTransformer] = Field( ..., description=( From 4e424ddee68c8a0b173b9f98d9ed4378047842dd Mon Sep 17 00:00:00 2001 From: Seyit Zor Date: Tue, 21 Nov 2023 10:31:15 +0100 Subject: [PATCH 10/10] Delete pylint ignore lines Co-authored-by: Byron Himes --- src/metldata/artifacts_rest/config.py | 1 - src/metldata/artifacts_rest/models.py | 1 - src/metldata/builtin_transformations/aggregate/config.py | 1 - src/metldata/builtin_transformations/merge_slots/config.py | 1 - src/metldata/event_handling/artifact_events.py | 1 - src/metldata/load/collect.py | 1 - src/metldata/submission_registry/models.py | 1 - 7 files changed, 7 deletions(-) diff --git a/src/metldata/artifacts_rest/config.py b/src/metldata/artifacts_rest/config.py index 6b85f7c1..814c000e 100644 --- a/src/metldata/artifacts_rest/config.py +++ b/src/metldata/artifacts_rest/config.py @@ -30,7 +30,6 @@ class ArtifactsRestConfig(BaseSettings): description="Information for artifacts to be queryable via the Artifacts REST API.", ) - # pylint: disable=no-self-argument @field_validator("artifact_infos") def validate_artifact_info_names( cls, value: list[ArtifactInfo] diff --git a/src/metldata/artifacts_rest/models.py b/src/metldata/artifacts_rest/models.py index 66b7c156..d82eeec3 100644 --- a/src/metldata/artifacts_rest/models.py +++ b/src/metldata/artifacts_rest/models.py @@ -74,7 +74,6 @@ class ArtifactInfo(BaseModel): ), ) - # pylint: disable=no-self-argument @field_validator("resource_classes") def check_resource_class_names( cls, value: dict[str, ArtifactResourceClass] diff --git a/src/metldata/builtin_transformations/aggregate/config.py b/src/metldata/builtin_transformations/aggregate/config.py index 431268c5..e25d6335 100644 --- a/src/metldata/builtin_transformations/aggregate/config.py +++ b/src/metldata/builtin_transformations/aggregate/config.py @@ -37,7 +37,6 @@ class AggregationOperation(BaseModel): visit_only_once: Optional[list[str]] = None function: type[AggregationFunction] - # pylint: disable=no-self-argument @model_validator(mode="before") def lookup_operation(cls, values: dict) -> dict: """Replaces operation strings with operation types.""" diff --git a/src/metldata/builtin_transformations/merge_slots/config.py b/src/metldata/builtin_transformations/merge_slots/config.py index b54eaebd..93c2b81e 100644 --- a/src/metldata/builtin_transformations/merge_slots/config.py +++ b/src/metldata/builtin_transformations/merge_slots/config.py @@ -46,7 +46,6 @@ class SlotMergingConfig(BaseSettings): ], ) - # pylint: disable=no-self-argument @field_validator("merge_instructions") def validate_merge_instructions( cls, filtered_merge_instructions: list[SlotMergeInstruction] diff --git a/src/metldata/event_handling/artifact_events.py b/src/metldata/event_handling/artifact_events.py index 0559ebf2..422f5f3f 100644 --- a/src/metldata/event_handling/artifact_events.py +++ b/src/metldata/event_handling/artifact_events.py @@ -31,7 +31,6 @@ class ArtifactEventConfig(BaseModel): ), ) - # pylint: disable=no-self-argument @field_validator("artifact_topic_prefix") def artifact_topic_prefix_must_not_contain_dots(cls, value: str): """Validate that artifact topic prefix does not contain dots.""" diff --git a/src/metldata/load/collect.py b/src/metldata/load/collect.py index 29d9cfb3..3b5c5abc 100644 --- a/src/metldata/load/collect.py +++ b/src/metldata/load/collect.py @@ -40,7 +40,6 @@ class ArtifactCollectorConfig(ArtifactEventConfig): ), ) - # pylint: disable=no-self-argument @field_validator("artifact_types") def artifact_types_must_not_contain_dots(cls, value: list[str]): """Validate that artifact types do not contain dots.""" diff --git a/src/metldata/submission_registry/models.py b/src/metldata/submission_registry/models.py index 962a9a55..65322d61 100644 --- a/src/metldata/submission_registry/models.py +++ b/src/metldata/submission_registry/models.py @@ -105,7 +105,6 @@ def current_status(self) -> SubmissionStatus: return sorted_history[-1].new_status - # pylint: disable=no-self-argument @field_validator("accession_map") def check_accession_uniqueness(cls, value: AccessionMap) -> AccessionMap: """Check that no accessions are re-used accross classes."""