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

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

metadata_backend/api/handlers/submission.py

@@ -390,3 +390,35 @@ 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"]
+        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)
+
+        data: List[str] = await req.json()
+
+        if isinstance(data, list):
+            for accession_id in data:
+                await file_operator.remove_file_submission(accession_id, "accessionId", submission_id)
+                LOG.info("Removing file: %r from submission with ID: %r was successful.", accession_id, submission_id)
+                return web.HTTPNoContent()
+
+        reason = "Request does not contain a list of files identified by `accessionId`"
+        LOG.error(reason)
+        raise web.HTTPBadRequest(reason=reason)

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", _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."""