flat protein/molecule list for a Skyline document#1208
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labkey-jeckels
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I made flat lists for other links too. Please review my changes before merging.
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I also split out proteins from peptide groups, which was a more involved change. I updated automated tests but this deserves some testing |
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>
ankurjuneja
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May 18, 2026
…de 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>
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Rationale
https://github.com/LabKey/internal-issues/issues/1045
Related Pull Requests
Changes
ProteinCount, redefinePeptideGroupCount(peptide-bearing groups only), and addMoleculeGroupCounttotargetedms.Runs; populate during import and via upgrade scripttargetedms-26.006-26.007.sqlProteinCountimport: the parser's count missed single-protein groups (the common case); replaced with_importedProteinCountinSkylineDocImporter.insertProtein()ShowPeptideGroupListAction(peptide-bearing groups) andShowMoleculeGroupListAction(small-molecule groups)ShowProteinListActionbacked byDocumentProteinView— queriestargetedms.Proteinrather thanPeptideGroupShowPeptideListActionandShowMoleculeListAction— dedicated flat-list pages for peptides and small molecules in a runrunSummaryView.jspto show separate conditional links for peptide groups, molecule lists, proteins, peptides, and small molecules, each navigating to its own actionPeptideGroups,MoleculeLists, andProteinsas conditionally visible columns in the runs grid; addcontainerHasMoleculeGroups()andcontainerHasProteins()toTargetedMSManager; fixTargetedMSSchema.hasPeptides()bug (was callingcontainerHasSmallMolecules())targetedms.xmlcolumn URLs and add column metadata forMoleculeGroupCountandProteinCountTargetedMSSchema.createGroupTable()and addPeptideCount/MoleculeCountcomputed columns to the group tables; new list views filter by these to show only non-empty groupsAnnotatedTargetedMSTable.NOTE_ANNOTATIONS_COLUMN_NAMEconstant; updatePrecursorTableInfoandMoleculePrecursorTableInfoto use itverifyRunDetailLinks()integration test and refactorverifyRunSummaryCountshelpers to cover peptide groups, molecule lists, and proteins separately