[ORCA-253] Return Failure Reasons to suites.json and Failed Tests to output.csv

[BWMac]

Problem:

Currently, the results provided by DCQC to users in the output file are limited to the dcqc_status for each file in the original manifest. Additionally, there is no status indicating that a test was unable to be performed on a file due to an error encountered during the execution of an external test.

Scope:

This PR adds functionality to capture failure reasons for both internal and external tests, but errors and error reasons for external tests only. I also encountered a complication with external tests where many of them will return the same exit_code whether they have failed or errored out. This will be addressed in future work by adding some more complex/specific logic to assess a "true" failure vs. an error. For now, these errors show up as failures, and the error_reason is captured instead as failure_reason.

Solution:

To surface more information about DCQC runs to users, the following changes were made:

• Implemented logic for capturing failure reasons for both external and internal tests.
  • For external tests, this involved updates to the ExternalTestMixin and each individual external test class to capture information about how each test should be interpreted.
  • For internal tests, this involved adding failure reason strings at each place in the test logic where a test failure would be determined.
  • As mentioned above, errors and error reasons were also captured for external tests only.
  • Implemented logic to surface which tests were required, skipped, failed, and errored for each file in the final DCQC output file.

Testing:

• All necessary tests and test files were updated in the repository to accommodate these changes.
• New testing conditions were added for capturing the internal test failure reasons where needed.
• The changes above were tested on Nextflow Tower.
  • This run was used to test a set of files to determine if the overall logic was working.
  • This run was used to test the suite error by intentionally providing a bad file path to the TiffTag306DateTimeTest
  • Both test runs used a new test_full configuration that I created to test all file types that we support. The files used are housed here on Synapse.

Notes:

• Bumped fs-synapse to 2.0 (synapseclient version 4.1.1).
• Updated CONTRIBUTING.md.
• Added DPE as code owners.

[swarmia]

✅  Linked to Story ORCA-253 · DCQC: Return reasons for individual tests not passing QC
➡️  Part of Epic ORCA-250 · DCQC Failure Reasons
➡️  Part of IBCDPE-502 · DCQC

[BryanFauble]

Logic looks great to me, just a few comments.

[BWMac]

Thanks for the suggestions @BryanFauble! I made those changes in ba4d83f and ab39fcf.

[thomasyu888]

🔥 LGTM! Excellent work and review!

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
120 Accepted issues

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

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