Fix combine CLI producing empty output with invalid data

[nebfield]

When processing a single file, if the combine CLI encountered an invalid variant it would quietly fail to write out any variants (quiet except for a misleading log statement). Some investigation notes:

• The invalid data wasn't invalid (some variants failed harmonisation and were missing mandatory fields)
  • Update the pydantic models to support this case properly
• The CLI wasn't re-raising exceptions correctly because I had a return statement inside a finally block 😬
  • Add tests to make sure badly harmonised variants do create an output file and invalid variants do throw a ValidationError exception
  • Add a check to the CLI that an output file actually exists
• Re-test this branch on the entire Catalog and check for exceptions

Closes #55

Test results

22 (older) scoring files contain invalid rsIDs:

pgscatalog.core.cli.combine_cli: 2024-10-18 14:43:12 CRITICAL PGS000019 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 14:52:23 CRITICAL PGS000042 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 15:09:03 CRITICAL PGS000212 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 15:09:03 CRITICAL PGS000213 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 15:09:03 CRITICAL PGS000214 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 15:09:03 CRITICAL PGS000215 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 15:09:03 CRITICAL PGS000216 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:26:04 CRITICAL PGS000310 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:26:04 CRITICAL PGS000311 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:26:06 CRITICAL PGS000317 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:36:01 CRITICAL PGS000330 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:46:39 CRITICAL PGS000332 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:46:39 CRITICAL PGS000333 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:48:31 CRITICAL PGS000344 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:48:31 CRITICAL PGS000345 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:48:31 CRITICAL PGS000346 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 16:48:31 CRITICAL PGS000347 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 19:14:11 CRITICAL PGS000727 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 19:15:24 CRITICAL PGS000728 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 19:15:24 CRITICAL PGS000729 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 19:22:39 CRITICAL PGS000754 contains invalid data, stopping and exploding
pgscatalog.core.cli.combine_cli: 2024-10-18 19:33:12 CRITICAL PGS000867 contains invalid data, stopping and exploding

Fix is to relax the rsID check when harmonisation goes wrong. No other ValidationErrors get thrown.

[codecov]

Codecov Report

Attention: Patch coverage is 98.30508% with 1 line in your changes missing coverage. Please review.

Project coverage is 89.61%. Comparing base (15f7095) to head (1566a89).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
pgscatalog.core/src/pgscatalog/core/lib/models.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #56      +/-   ##
==========================================
+ Coverage   89.37%   89.61%   +0.24%     
==========================================
  Files          54       54              
  Lines        3434     3475      +41     
==========================================
+ Hits         3069     3114      +45     
+ Misses        365      361       -4     

Flag	Coverage Δ
pgscatalog.core	92.57% <98.30%> (+0.45%)	⬆️

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[smlmbrt]

If it passes on all existing harmonized files it should be good to go.