PeakAnnotationsLoader 2 - MSRunsLoader updates

[hepcat72]

Summary Change Description

The MSRunsLoader was updated to add a method for the PeakAnnotationsLoader to retrieve the MSRunSample records associated with samples gotten from peak annotations files. The ability to skip samples was added, and updates were made to the associated MSRunSequence loader.

Exceptions were also improved to take advantage of the new summarizable errors, so that missing samples and MSRunSample records could be summarized without custom code needed in the loaders. This included various sample errors and researcher wanrings.

Details:

• MSRunsLoader (TableLoader)
  • Data files where I added a "Skip" column (looks to be none??)
  • MSRunSequencesLoader
  • Researcher (could_be_variant_researcher & get_researchers)
  • Exceptions:
  • MzxmlSampleHeaderMismatch
  • RecordDoesNotExist
  • MissingRecords
  • MissingSamples
  • NewResearcher/NewResearchers

A few other changes were pulled in due to the complexity of the patch.

Affected Issues/Pull Requests

• Partially addresses #825
• Merges into #992
• Next PR: #994

Review Notes

See comments in-line.

Checklist

This pull request will be merged once the following requirements are met. The author and/or reviewers should uncheck any unmet requirements:

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• Associated issue/pull request requirements:
  • [x] All requirements in affected issues marked "resolved" are satisfied
  • [x] All required pull requests are merged (or none)
• Basic requirements
  • [x] All linters pass
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• Overhead requirements
  • [x] New/changed method tests implemented/updated (or no change)
  • [ ] Updated Unreleased section of changelog.md (or no change)
  • [x] Migrations created & committed (or no change)