[bot] Merge 26.3 to develop (Conflicts)#1216
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* flat protein/molecule list for a Skyline document
* match columns with Skyline file
* code review comment
* update text
* More direct Panorama links
* Self-review
* Fix build
* Remove extra import
* Fix test failures
* Comments
* Switch to centralized method
* Code review followup
* Another test fix
* Protein vs peptide group
* Missing files
* Better comments
* Self-review improvements
* Simplify after refactor
* Extract TargetedMSHelper and add upgrade test for 26.3 schema migration
Extracts setupFolder(), selectFolderType(), and importData() from TargetedMSTest
into a new TargetedMSHelper class so the logic can be shared without subclassing.
Adds TargetedMSUpgradeTest to verify the targetedms-26.006-26.007 migration correctly
populates PeptideGroupCount, MoleculeGroupCount, and ProteinCount on existing runs.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Protein group, not peptide group
* Protein group, not peptide group
* Split upgrade test into pre- and post-upgrade count checks; fix upgrade script and run summary labels
testPreUpgradeCounts queries columns available in 25.11 (Peptides, SmallMolecules,
Replicates) and runs on both setup and verify phases. testPostUpgradeCounts is
gated with @EarliestVersion("26.3") and Assume.assumeFalse(isUpgradeSetupPhase)
so it only runs after the 26.006-26.007 migration.
Also adds missing PeptideGroupCount NOT NULL constraint to the upgrade script and
renames 'peptide group' labels to 'protein group' in verifyRunSummaryCounts.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Fix field names
* Fix annotations
---------
Co-authored-by: labkey-jeckels <jeckels@labkey.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
…on (#1211) * Extract TargetedMSHelper and add upgrade test for 26.3 schema migration Extracts setupFolder(), selectFolderType(), and importData() from TargetedMSTest into a new TargetedMSHelper class so the logic can be shared without subclassing. Adds TargetedMSUpgradeTest to verify the targetedms-26.006-26.007 migration correctly populates PeptideGroupCount, MoleculeGroupCount, and ProteinCount on existing runs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Split upgrade test into pre- and post-upgrade count checks testPreUpgradeCounts queries columns available in 25.11 (Peptides, SmallMolecules, Replicates) and runs on both setup and verify phases. testPostUpgradeCounts is gated with @EarliestVersion("26.3") and Assume.assumeFalse(isUpgradeSetupPhase) so it only runs on the new server after the 26.006-26.007 migration. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Fix field names * Not ready for Java 25 yet * Fix annotations --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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May 27, 2026
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