HTTP Delete file from submission & changelog

- add changelog for file operation update and remove
- add delete endpoint to remove a list of files identified by accession id
- add endpoints in specification.yml

CHANGELOG.md

@@ -42,6 +42,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - add message broker publishing to workflow
   - add rabbitmq + default config to integration tests
 - File operator that does database operations for files #148
+  - introduced `/v1/submissions/{submissionId}/files` to update and remove files in a submission #633
+  - file flagged for deletion also removed from submission and check files have the status ready when being read from the submission #633
+  - prevent publish if files have in submission have status added (added but no metadata object) or failed (failed in ingestion, completion, or for any other reason) #633
 - Mongo indexes for `file` schema #148
 - `/files` endpoint to retrieve files attached to a project #148 #627
 - option to add additional members to `application/problem+json` #642

docs/specification.yml

@@ -1410,6 +1410,90 @@ paths:
               schema:
                 $ref: "#/components/schemas/405MethodNotAllowed"
   /v1/submissions/{submissionId}/files:
+    post:
+      tags:
+        - Submission
+      summary: Add new files to a submission.
+      parameters:
+        - name: submissionId
+          in: path
+          description: ID of the object submission.
+          schema:
+            type: string
+          required: true
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: array
+              items:
+                type: object
+                properties:
+                  accessionId:
+                    type: string
+                    title: Accession Id for file
+                  version:
+                    type: integer
+                    title: Version of the file
+      responses:
+        204:
+          description: No Content
+        400:
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/400BadRequest"
+        401:
+          description: Unauthorized
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/401Unauthorized"
+        403:
+          description: Forbidden
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/403Forbidden"
+    get:
+      tags:
+        - Query
+      summary: Retrieve all files with detailed info specific to a submission.
+      parameters:
+        - name: submissionId
+          in: path
+          description: ID of the object submission.
+          schema:
+            type: string
+          required: true
+      responses:
+        200:
+          description: OK
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/File"
+        400:
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/400BadRequest"
+        401:
+          description: Unauthorized
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/401Unauthorized"
+        403:
+          description: Forbidden
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/403Forbidden"
     put:
       tags:
         - Manage
@@ -1459,6 +1543,45 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/405MethodNotAllowed"
+  /v1/submissions/{submissionId}/files/{fileId}:
+    delete:
+      tags:
+        - Manage
+      summary: Remove file from a submission.
+      parameters:
+        - name: submissionId
+          in: path
+          description: ID of the object submission.
+          schema:
+            type: string
+          required: true
+        - name: fileId
+          in: path
+          description: ID of the object submission.
+          schema:
+            type: string
+          required: true
+      responses:
+        204:
+          description: No Content
+        400:
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/400BadRequest"
+        401:
+          description: Unauthorized
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/401Unauthorized"
+        403:
+          description: Forbidden
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/403Forbidden"
   /v1/publish/{submissionId}:
     patch:
       tags:
@@ -3010,7 +3133,7 @@ components:
       type: object
       description: Describes a submission file information that can be attached to a submission
       properties:
-        accesionId:
+        accessionId:
           type: string
           title: Accession Id for file
         version:
@@ -3032,5 +3155,5 @@ components:
                 description: type of schema this Accession ID relates to and was added in submit
         error:
           type: string
-          title: Accession Id for file
+          title: Error for file if status is failed
           description: required only if status is failed

metadata_backend/api/handlers/submission.py

@@ -390,3 +390,28 @@ async def add_submission_files(self, req: Request) -> Response:
         reason = "Request does not contain a list of Objects each with `accessionId` and `version`"
         LOG.error(reason)
         raise web.HTTPBadRequest(reason=reason)
+
+    async def delete_submission_files(self, req: Request) -> Response:
+        """Remove files from a submission.
+
+        Body needs to contain a list of accessionId for files.
+
+        :param req: POST request with metadata schema in the body
+        :returns: HTTP No Content response
+        """
+        submission_id = req.match_info["submissionId"]
+        file_accession_id = req.match_info["fileId"]
+        db_client = req.app["db_client"]
+        submission_operator = SubmissionOperator(db_client)
+
+        # Check submission exists and is not already published
+        await submission_operator.check_submission_exists(submission_id)
+        await submission_operator.check_submission_published(submission_id, req.method)
+
+        await self._handle_check_ownership(req, "submission", submission_id)
+
+        file_operator = FileOperator(db_client)
+
+        await file_operator.remove_file_submission(file_accession_id, "accessionId", submission_id)
+        LOG.info("Removing file: %r from submission with ID: %r was successful.", file_accession_id, submission_id)
+        return web.HTTPNoContent()

metadata_backend/server.py

@@ -143,6 +143,7 @@ async def on_prepare(_: web.Request, response: web.StreamResponse) -> None:
         web.put("/submissions/{submissionId}/files", _submission.put_submission_path),
         web.patch("/submissions/{submissionId}", _submission.patch_submission),
         web.delete("/submissions/{submissionId}", _submission.delete_submission),
+        web.delete("/submissions/{submissionId}/files/{fileId}", _submission.delete_submission_files),
         # publish submissions
         web.patch("/publish/{submissionId}", _publish_submission.publish_submission),
         # users operations

tests/unit/test_server.py

@@ -51,7 +51,7 @@ async def test_api_routes_are_set(self):
 
         """
         server = await self.get_application()
-        self.assertIs(len(server.router.routes()), 60)
+        self.assertIs(len(server.router.routes()), 61)
 
     async def test_frontend_routes_are_set(self):
         """Test correct routes are set when frontend folder exists."""