Merge pull request #73 from datasci4health/development

Development Deploy 07-08-2020

.gitignore

@@ -62,3 +62,8 @@ typings/
 
 .idea/
 .chglog/
+
+src/adonisjs/public/artifacts/cases/
+
+# vscode configuration file
+.vscode/

CHANGELOG.md

@@ -0,0 +1,94 @@
+<a name="unreleased"></a>
+## [Unreleased]
+
+### Features
+- 🎸 Auth mechanism with `refresh token`: From now on, `POST auth/login/` responds with a pair of `<<token, refresh token>>`. `refresh_token` must be used to re-signin the user
+whose `token` was revoked by `harena-manager` server.
+
+     ✅ Closes issue #70
+
+- 🎸 Enable `logout` through endpoint `POST auth/logout`
+- 🎸 Newly created REST endpoint `POST /admin/institution` for create a new institution
+- 🎸 Newly created REST endpoints: `GET auth/quest/cases` and `GET play/quest/cases`
+
+	 ✅ Closes: #71
+
+- 🎸 Migrate database - Related issue: [#62](https://github.com/datasci4health/harena-manager/issues/23)
+- 🎸 Share cases: Allows the author associate more contributors to her case
+- 🎸 Auth: Implement adonis ACL to control roles and permissions - Closes issue: #40
+- 🎸 Provide quest services 
+     ✅ Closes issue #37
+
+### Fix
+- Error on delete case. Related issue: [#23](https://github.com/datasci4health/harena-manager/issues/23)
+- Enable upload of .jpeg files
+
+### Chore
+- 🤖 dependency update: Apply suggestions made by dependabot alerts
+- 🤖 docker: Provide a develop environment to be  used by collaborators team.
+Thecontainer orchastrate the whole environment (harenamanager, database,
+and database-ui).
+
+### Docs
+- ✏️ Add auth sequence diagram
+- ✏️ Add a schema versioning mechanism. It keeps the track of 3 such files: schema.dia,
+schema.pdf, schema.png. They are representations of the schema defined
+on database/migrations. Schemas are located at https://github.com/datasci4health/harena-manager/tree/development/src/adonisjs/database/schema_design)
+- ✏️ Added a CHANGELOG in the project.
+
+
+<!-- ### Performance Improvements
+- ⚡️ improvement on auth mechanism: Enable `logout` through the endpoint `POST auth/logout`
+ -->
+### Refactor
+<!-- - 💡 improvements on REST endpoints: Refactoring code related to REST endpoints -->
+- 💡 Implements hooks through `file.method`
+
+### BREAKING CHANGE
+
+`POST /case/list` was replaced by two new endpoints: `GET /cases` and
+`GET /user/:id/cases`
+
+<a name="v1.0.8"></a>
+## [v1.0.8] - 2020-03-22
+
+### Error
+- There was an error connecting to http://localhost:10020/api/v1/quest.
+
+### Feat
+- 🎸 Provide quest services
+
+<a name="v1.0.7"></a>
+## [v1.0.7] - 2019-08-05
+### Build
+- **docker:** A docker image of develop environment avaivable
+
+### Fix
+- **artifact:** Enable upload of .jpeg files
+- **artifact:** Fix error at artifact upload
+
+<a name="v1.0.5"></a>
+## [v1.0.5] - 2019-07-07
+### Bug
+- Error on delete case - [#23](https://github.com/datasci4health/harena-manager/issues/23)
+
+### Docs
+-  ✏️ Add a CHANGELOG.
+
+<a name="v0.0.1"></a>
+## v0.0.1 - 2019-04-15
+
+[Unreleased]: https://github.com/datasci4health/harena-manager/compare/v1.0.11...HEAD
+[v1.0.11]: https://github.com/datasci4health/harena-manager/compare/v1.0.10...v1.0.11
+[v1.0.10]: https://github.com/datasci4health/harena-manager/compare/v1.0.9...v1.0.10
+[v1.0.9]: https://github.com/datasci4health/harena-manager/compare/v1.0.8...v1.0.9
+[v1.0.8]: https://github.com/datasci4health/harena-manager/compare/v1.0.7...v1.0.8
+[v1.0.7]: https://github.com/datasci4health/harena-manager/compare/v1.0.6...v1.0.7
+[v1.0.6]: https://github.com/datasci4health/harena-manager/compare/v1.0.5...v1.0.6
+[v1.0.5]: https://github.com/datasci4health/harena-manager/compare/v1.0.4...v1.0.5
+[v1.0.4]: https://github.com/datasci4health/harena-manager/compare/v1.0.3...v1.0.4
+[v1.0.3]: https://github.com/datasci4health/harena-manager/compare/v1.0.1...v1.0.3
+[v1.0.1]: https://github.com/datasci4health/harena-manager/compare/v1.0.2...v1.0.1
+[v1.0.2]: https://github.com/datasci4health/harena-manager/compare/v1.0.0...v1.0.2
+[v1.0.0]: https://github.com/datasci4health/harena-manager/compare/v0.1.0...v1.0.0
+[v0.1.0]: https://github.com/datasci4health/harena-manager/compare/v0.0.1...v0.1.0

README.md

@@ -7,34 +7,16 @@
 
 # Harena Manager
 
-Harena's Database Access API.
+Harena's database management module
+> It provides an api for data access
 
-## Table of contents
+## Available end points
 
-<!-- MarkdownTOC autolink=true -->
-
-- [Change log](#change-log)
-- [Getting Started](#getting-started)
-    - [Access harena-manager service](#running-locally---linux)
-    - [Running as Docker containers - Linux](#running-as-docker-containers---linux)
-- [Contributing](#contributing)
-    - [Branch organization](#branch-organization)
-
-<!-- /MarkdownTOC -->
-
-## Change log
-
-The change log can be found in the CHANGELOG.md file.
+Check https://documenter.getpostman.com/view/7243662/T1Ds8ag7?version=latest to discover available endpoints provided by `harena manager api`.
 
 ## Getting Started
 
-### Access `harena-manager` service
-
-`<URL_HARENA_MANAGER>`
-
-### Running locally within docker containers
-
-We provide a docker container to run `harena-manager` code. Containers usage guarantees the minimal configuration required to run the code. Read [docker](https://docs.docker.com/install/) e [docker-compose](https://docs.docker.com/compose/install/) documentations to install docker and learn further about containers.
+We provide a `docker container` to locally run `harena-manager` code. Containers guarantee the required minimal configuration to run the code. Read [docker](https://docs.docker.com/install/) e [docker-compose](https://docs.docker.com/compose/install/) documentations to install docker and learn further about containers.
 
 #### Instructions (for Linux users)
 
@@ -49,13 +31,13 @@ docker build . -t manager
 cd ..
 ```
 
-Then, up the docker container:
+Start up the docker container:
 
 ```bash
 docker-compose -f docker-compose-dev.yml up
 ```
 
-After starting the container, access http://localhost:10020/ to check if the system is up.
+Once the start up process is done, access http://localhost:10020/ to check if the system is working.
 
 If you want to get the command line of the container, then run the command:
 
@@ -109,3 +91,7 @@ docker exec -it harena-manager_harena-manager_1 bash
     * new bugs registered on the issue list https://github.com/datasci4health/harena-manager/issues.
 * `tags`:
     * Are used for creating Dockerhub image versions at https://cloud.docker.com/u/datasci4health/repository/docker/datasci4health/harena-manager .    
+
+## Change log
+
+Release updates can be found at [CHANGELOG.md](https://github.com/datasci4health/harena-manager/blob/development/CHANGELOG.md) file.

src/adonisjs/app/Controllers/Http/AuthController.js

@@ -0,0 +1,80 @@
+'use strict'
+
+const User = use('App/Models/v1/User');
+const Token = use('App/Models/v1/Token');
+
+class AuthController {
+
+	async login({ request, auth, response }) {
+        console.log(request.all())
+        let { email, password, refresh_token } = request.all();
+        let user = ""
+        let token = ""
+
+        try{
+            await auth.check()
+            return response.json('user is signed already')
+        } catch(e) {
+            console.log(e)
+            // token expired
+            if (e.code == 'E_JWT_TOKEN_EXPIRED'){
+                token = await auth.generateForRefreshToken(refresh_token)
+
+                Object.entries(token).forEach(entry => {
+                    if (entry[0] == 'refreshToken'){
+                        refresh_token = entry[1]
+                    }
+                }); 
+            }
+
+            // unloged user
+            if (e.code == 'E_INVALID_JWT_TOKEN'){
+                console.log(7)
+                try{
+                   token = await auth.withRefreshToken().attempt(email, password)
+                } catch(e){
+                    console.log('erro aqui')
+                    console.log(e)
+                }
+            }
+
+            // generic error
+            if (token == "")
+                return response.status(e.status).json(e.message)
+
+            user = await User.findBy('email', email)
+            Object.assign(user, token)
+
+            return response.json(user)
+        }
+    }
+
+    async login2({ request, auth, response }) {
+        try{
+            let refresh_token  = request.input('access_code');
+
+            let token = await auth.generateForRefreshToken(refresh_token)
+            return response.json(token)
+        }catch(e){
+            console.log(e)
+            return response.status(500).json(e.message)
+        }
+
+    }
+
+    async logout({ auth, response }) {
+        try{
+
+            const refreshToken = auth.getAuthHeader()
+            await auth.revokeTokens(refreshToken)
+
+            return response.json('successfull logout')
+        }catch(e){
+            console.log(e)
+            return response.status(500).json(e.message)
+        }
+
+    }
+}
+
+module.exports = AuthController

src/adonisjs/app/Controllers/Http/v1/AdminController.js

@@ -4,6 +4,8 @@
 /** @typedef {import('@adonisjs/framework/src/Response')} Response */
 /** @typedef {import('@adonisjs/framework/src/View')} View */
 
+const Database = use('Database')
+
 const Role = use('Adonis/Acl/Role');
 const Permission = use('Adonis/Acl/Permission');
 const User = use('App/Models/v1/User');
@@ -93,7 +95,6 @@ class AdminController {
 
     async list_roles({ response }) {
         try{
-            console.log('chegou')
             let roles = await Role.all()
             return response.json(roles)
         } catch(e){
@@ -121,7 +122,7 @@ class AdminController {
         }
     }
 
-    async list_permissions_by_user({ params, response }) {
+    async list_permissions_by_role({ params, response }) {
         try{
             let role = await Role.find(params.id)
 
@@ -131,6 +132,38 @@ class AdminController {
             return response.status(500).json({ message: e.message })
         }
     }
+
+    async list_permissions_by_user({ params, response }) {
+        try{
+
+            let user = await User.find(params.id)
+
+            // let role = await Role.find(params.id)
+
+            return response.json(await user.getPermissions())
+        } catch(e){
+            console.log(e)
+            return response.status(500).json({ message: e.message })
+        }
+    }
+
+    async revoke_tokens({ auth, params, response }) {
+        try{
+            // await user.tokens().update({ is_revoked: true })
+// console.log('antes')
+// console.log(await auth.listTokens())
+// //         const affectedRows = await Database
+// //             .table('tokens').update('is_revoked', true)
+// // console.log(affectedRows)
+// console.log('depois')
+// console.log(await auth.listTokens())
+await auth.revokeTokens()
+            return response.json('tokens revoked')
+        } catch(e){
+            console.log(e)
+            return response.status(500).json({ message: e.message })
+        }
+    }
 }
 
 module.exports = AdminController

src/adonisjs/app/Controllers/Http/v1/ArtifactController.js

@@ -16,7 +16,7 @@ class ArtifactController {
 			  						extnames: ['png', 'jpg', 'jpeg', 'gif','mp4','avi', '.wmv']
 								  }
 
-		this.relativePath     = '/artifacts/' 
+		this.relativePath     = '/resources/artifacts/' 
 
 
 	}
@@ -25,38 +25,38 @@ class ArtifactController {
 		try{
 
 			const file             = request.file('file', this.validationOptions)
-			const caseID           = request.input('case_uuid', null)
+			const case_id           = request.input('case_id', null)
 
-			var linkedCase = await Case.find(caseID)
+			var c = await Case.find(case_id)
 
-			if (caseID != null && linkedCase == null){
+			console.log(c)
+			if (case_id != null && c == null){
 				return response.json({ message: "Case id not found" })
 			} 
 
-			let fsPath = Helpers.publicPath(this.relativePath)
-			let caseRelativePath = this.relativePath
-			if (caseID != null){
-				fsPath += 'cases/' + caseID + '/'
-				caseRelativePath += 'cases/' + caseID + '/'
+			let fs_path = Helpers.publicPath(this.relativePath)
+			let case_relative_path = this.relativePath
+			if (case_id != null){
+				fs_path += 'cases/' + case_id + '/'
+				case_relative_path += 'cases/' + case_id + '/'
 			}
 
-			const artifactID       = await uuid4() 
-			const artifactFileName = artifactID + "." + file.extname
+			const artifact_id       = await uuid4() 
+			const artifact_file_name = artifact_id + "." + file.extname
 
-			await file.move(fsPath, {name: artifactFileName, overwrite: false})
+			await file.move(fs_path, {name: artifact_file_name, overwrite: false})
 
 			const artifact = new Artifact()
-			artifact.id       = artifactID
-			artifact.fs_path       = fsPath + artifactFileName
-			artifact.relative_path = caseRelativePath + artifactFileName
-			artifact.case_id       = linkedCase != null ? linkedCase.uuid : linkedCase;
-			await auth.user.artifacts().save(artifact)
+			artifact.id       = artifact_id
+			artifact.fs_path       = fs_path + artifact_file_name
+			artifact.relative_path = case_relative_path + artifact_file_name
+			artifact.case_id       = c != null ? c.id : c;
 
 			const base_url = Env.getOrFail('APP_URL')
 
 			let bodyMessage = { message:       "Artifact successfully stored",
-								filename:      artifactFileName,
-								case:          linkedCase,										   
+								filename:      artifact_file_name,
+								case:          c,										   
 								size_in_bytes: file.size,
 								type:          file.type,
 								subtype:       file.subtype,
@@ -66,6 +66,8 @@ class ArtifactController {
 								url:           base_url+artifact.relative_path 
 			}
 
+			await auth.user.artifacts().save(artifact)
+
 			return response.status(200).json(bodyMessage)
 		} catch(e){
 			console.log(e)