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Remove Mascot test infrastructure - #3231

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labkey-jeckels merged 1 commit into
developfrom
fb_remove_mascot
Oct 8, 2026
Merged

labkey-jeckels merged 1 commit into
developfrom
fb_remove_mascot

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Rationale

Remove test infrastructure for Mascot, whose support is being removed from the MS2 module.

Related Pull Requests

Changes

  • Remove the mock Mascot server and the Mascot test category
  • Drop the Mascot server link from the admin console link expectations

@labkey-jeckels
labkey-jeckels marked this pull request as ready for review October 6, 2026 04:21
@labkey-jeckels labkey-jeckels self-assigned this Oct 6, 2026
@labkey-jeckels
labkey-jeckels requested review from a team and DariaBod and removed request for a team October 6, 2026 04:21
@labkey-jeckels
labkey-jeckels merged commit 8a513a3 into develop Oct 8, 2026
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@labkey-jeckels
labkey-jeckels deleted the fb_remove_mascot branch October 8, 2026 03:55
labkey-jeckels added a commit to LabKey/commonAssays that referenced this pull request Oct 8, 2026
## Rationale
Remove Mascot support from the MS2 module, which has gone unused for
years.

## Related Pull Requests
- LabKey/testAutomation#3231

## Changes
- Remove the Mascot search pipeline, the Mascot server configuration and
connection test, and native `.dat` result import, viewing, and search
indexing
- Remove the Mascot run type, so Mascot-exported pepXML now imports as
an unknown search engine
- Upgrade script permanently drops the Mascot-only file columns from
`ms2.Runs` and deletes the stored Mascot server settings
- Existing Mascot runs stay in the database but display as an unknown
run type, without their peptide grid, Mascot scores, MS2 search listing,
experiment-run link for pipeline searches, or spectra for native `.dat`
imports
- Saved views, reports, and queries that reference the removed Mascot
tables or columns will no longer resolve
- Remove the Mascot test and sample data
- Drop the unused opencsv and Lombok dependencies

## Tasks
- [x] Claude Code Review
- [x] Manual Testing - N/A
- [x] Test Automation - N/A
- [x] User Education @labkey-hannah  @labkey-keith - not needed
  - I (Josh) don't think that anyone will care 
  - But we can drop anything in the docs
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