[GEN-1027] Store failed annotations error report

[rxu17]

Purpose: This PR is intended to allow the concatenation and storage to Synapse of the failed annotations per center. This is currently a draft PR - there's some points of discussion needed in some areas.

Changes: Old functions:

• Split annotation_mutation into create_annotation_paths and revised annotation_mutation to improve testability, and ease of access to the filepaths used in the annotation

New functions: These functions are created primarily for the concatenation and storage to synapse of the annotation reports. We also have a check function that just makes sure our narrow maf failed annotations count match the error report rows.

• concat_annotation_error_reports
• check_annotation_error_reports
• store_annotation_error_reports

Testing:

• Unit and integration tests added to, to account for the new and revised functions above
• Ran on docker image built on this branch
• Ran processing on just mutation data and files show up here in the Errors folders for each center: https://www.synapse.org/#!Synapse:syn11601248/tables/

Depends on #544

[dpulls[bot]]

:tada: All dependencies have been resolved !

[sonarcloud[bot]]

Quality Gate passed

The SonarCloud Quality Gate passed, but some issues were introduced.

39 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[rxu17]

Note that this PR introduces a new variable genomic_location_explanation to the full maf file during mutation processing that leads an issue with the store_maf_files function in genie/database_to_staging.py that will be resolved with #548. See that PR for more details.