more file submission ops

[blankdots]

Description

Related issues

related to: #148
continuation of #627

Type of change

• New feature (non-breaking change which adds functionality)

Changes Made

• check files have the status ready when being read from the submission
• 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) - in future version we can also check if the submission actually has files
• missing docs about raise exception in files
• update status of a file
  • /submission/<submission_id>/files receives a list of files

  [
      {
        "accessionId": 1,
        "version": 1,
        "status": "ready".
        "objectId": {
           "accessionId": 4,
           "schema": "study"
        }
      },
      {
        "accessionId": 2,
        "version": 1,
        "status": "ready"
      },
      {
        "accessionId": 3,
        "version": 1,
        "status": "ready"
      }
    ]
  

and transforms it to mongodb query for each file in update_file_submission e.g.:

{
    "files.$.status": "ready",
    "files.$.version": 1,
    "files.$.objectId": {
      "accessionId": 4,
      "schema": "study"
    }

• remove file from submission when flagged as deleted, via remove_file_submission which is called when a file is flagged for deletion but can also be called whenever we want to remove all files with a specific accessionId or file path from one or multiple submissions
• operation to assign metadata object to file, also marking a file as ready, done via /submission/<submission_id>/files as one or multiple files can be marked as ready - will be used also MQ integration.
• small bug fixes and typo fixes

Testing

• Needs testing (start an issue or do a follow up PR about it)

Mentions

this is dependent on #642

[csc-felipe]

Looking good

[blankdots]

changed base so that mypy fixes are included

[csc-jm]

Found a few things to nitpick but otherwise looks good to me

[csc-felipe]

LGTM

Need to create an issue for tests.

[blankdots]

Need to create an issue for tests.

I thought this was it: #629