From 2fdda269cb3aefc188693ddd95fdab29f62c8417 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Thu, 28 May 2026 15:28:24 -0700 Subject: [PATCH 1/2] Update copyrights and licenses --- .../labkey/api/targetedms/IModification.java | 15 +++++++++++++++ .../org/labkey/api/targetedms/ISampleFile.java | 15 +++++++++++++++ .../labkey/api/targetedms/ISpectrumLibrary.java | 15 +++++++++++++++ .../labkey/api/targetedms/ITargetedMSRun.java | 2 +- .../api/targetedms/RepresentativeDataState.java | 2 +- .../targetedms/RunRepresentativeDataState.java | 15 +++++++++++++++ .../api/targetedms/SkylineAnnotation.java | 2 +- .../SkylineDocumentImportListener.java | 15 +++++++++++++++ .../TargetedMSFolderTypeListener.java | 15 +++++++++++++++ .../api/targetedms/TargetedMSService.java | 2 +- .../labkey/api/targetedms/TargetedMSUrls.java | 15 +++++++++++++++ .../api/targetedms/model/OutlierCounts.java | 15 +++++++++++++++ .../targetedms/model/QCMetricConfiguration.java | 2 +- .../api/targetedms/model/QCMetricStatus.java | 15 +++++++++++++++ .../api/targetedms/model/SampleFileInfo.java | 15 +++++++++++++++ .../api/targetedms/model/SampleFilePath.java | 15 +++++++++++++++ build.gradle | 15 +++++++++++++++ .../CalibrationCurveMoleculePrecursors.sql | 2 +- .../targetedms/CalibrationCurvePrecursors.sql | 2 +- .../queries/targetedms/DefaultGuideSet.sql | 5 +++++ .../queries/targetedms/GuideSetForOutliers.sql | 5 +++++ .../queries/targetedms/InstrumentBilling.sql | 2 +- .../targetedms/InstrumentBillingByMonth.sql | 2 +- .../targetedms/InstrumentSummaryByFolder.sql | 5 +++++ resources/queries/targetedms/PTMPercents.sql | 5 +++++ .../queries/targetedms/PTMPercentsGrouped.sql | 5 +++++ .../targetedms/PTMPercentsGroupedPrepivot.sql | 5 +++++ .../queries/targetedms/PTMPercentsPrepivot.sql | 5 +++++ resources/queries/targetedms/PassportMxN.sql | 5 +++++ .../targetedms/Passport_TotalPrecursorArea.sql | 5 +++++ .../queries/targetedms/Passport_proteins.sql | 5 +++++ resources/queries/targetedms/PeptideIds.sql | 5 +++++ resources/queries/targetedms/QCAnnotation.js | 5 +++++ .../targetedms/QCGroupingPrecursorMolecules.sql | 5 +++++ .../targetedms/QCGroupingPrecursorPeptides.sql | 5 +++++ .../queries/targetedms/QCInstrumentSummary.sql | 5 +++++ .../QCMetricEnabled_precursorArea.sql | 2 +- .../QCMetricEnabled_transitionArea.sql | 2 +- .../QCMetric_IsotopologuePrecursorAccuracy.sql | 5 +++++ .../QCMetric_IsotopologuePrecursorLOD.sql | 5 +++++ .../QCMetric_IsotopologuePrecursorLOQ.sql | 5 +++++ .../QCMetric_IsotopologuePrecursorRSquared.sql | 5 +++++ resources/queries/targetedms/QCMetric_fwb.sql | 2 +- resources/queries/targetedms/QCMetric_fwhm.sql | 2 +- .../queries/targetedms/QCMetric_isotopeDotp.sql | 2 +- .../queries/targetedms/QCMetric_lhRatio.sql | 2 +- .../queries/targetedms/QCMetric_libraryDotp.sql | 2 +- .../targetedms/QCMetric_massErrorPrecursor.sql | 2 +- .../targetedms/QCMetric_massErrorTransition.sql | 2 +- .../queries/targetedms/QCMetric_peakArea.sql | 2 +- .../targetedms/QCMetric_precursorArea.sql | 2 +- .../targetedms/QCMetric_retentionTime.sql | 2 +- .../targetedms/QCMetric_transitionArea.sql | 2 +- .../QCMetric_transitionPrecursorRatio.sql | 2 +- .../targetedms/QCRunMetric_iRTCorrelation.sql | 2 +- .../targetedms/QCRunMetric_iRTIntercept.sql | 2 +- .../queries/targetedms/QCRunMetric_iRTSlope.sql | 2 +- .../queries/targetedms/QCRunMetric_ticArea.sql | 2 +- .../targetedms/SampleFileAssayResults.sql | 5 +++++ .../queries/targetedms/SampleFileForQC.sql | 5 +++++ .../queries/targetedms/msProjectDetails.sql | 5 +++++ .../queries/targetedms/qcMetricsConfig.sql | 2 +- .../postgresql/targetedms-0.000-25.000.sql | 2 +- .../postgresql/targetedms-25.000-25.001.sql | 5 +++++ .../postgresql/targetedms-25.001-25.002.sql | 5 +++++ .../postgresql/targetedms-25.002-25.003.sql | 5 +++++ .../postgresql/targetedms-25.003-25.004.sql | 5 +++++ .../postgresql/targetedms-25.004-25.005.sql | 5 +++++ .../postgresql/targetedms-25.005-25.006.sql | 5 +++++ .../postgresql/targetedms-25.006-25.007.sql | 5 +++++ .../postgresql/targetedms-26.000-26.001.sql | 5 +++++ .../postgresql/targetedms-26.001-26.002.sql | 5 +++++ .../postgresql/targetedms-26.002-26.003.sql | 5 +++++ .../postgresql/targetedms-26.003-26.004.sql | 5 +++++ .../postgresql/targetedms-26.004-26.005.sql | 5 +++++ .../postgresql/targetedms-26.005-26.006.sql | 5 +++++ .../postgresql/targetedms-26.006-26.007.sql | 5 +++++ .../postgresql/targetedms-26.007-26.008.sql | 5 +++++ .../dbscripts/postgresql/targetedms-create.sql | 5 +++++ .../dbscripts/postgresql/targetedms-drop.sql | 5 +++++ resources/schemas/targetedms.xml | 2 +- .../window/AddNewAnnotationMetricWindow.js | 5 +++-- .../window/AddNewMetricWindow.js | 5 +++-- .../window/AddNewTraceMetricWindow.js | 5 +++-- .../PanoramaPremiumController.java | 15 +++++++++++++-- .../panoramapremium/QCNotificationSender.java | 15 +++++++++++++++ .../View/QCSummaryMenuCustomizer.java | 15 +++++++++++++++ .../panoramapremium/model/UserSubscription.java | 15 +++++++++++++++ .../query/QCEmailNotificationsTable.java | 15 +++++++++++++++ src/org/labkey/targetedms/IrtPeptide.java | 2 +- .../targetedms/PanoramaBadDataException.java | 2 +- .../targetedms/SkylineAuditLogManager.java | 2 +- .../targetedms/SkylineBinaryDataHandler.java | 2 +- .../labkey/targetedms/SkylineDocImporter.java | 4 ++-- src/org/labkey/targetedms/SkylineFileUtils.java | 2 +- .../labkey/targetedms/TargetedMSController.java | 2 +- .../targetedms/TargetedMSDataHandler.java | 2 +- .../targetedms/TargetedMSExperimentRunType.java | 2 +- .../labkey/targetedms/TargetedMSFolderType.java | 2 +- .../labkey/targetedms/TargetedMSListener.java | 2 +- .../labkey/targetedms/TargetedMSManager.java | 2 +- src/org/labkey/targetedms/TargetedMSModule.java | 2 +- src/org/labkey/targetedms/TargetedMSRun.java | 2 +- src/org/labkey/targetedms/TargetedMSSchema.java | 2 +- .../targetedms/TargetedMSServiceImpl.java | 2 +- .../targetedms/TargetedMSUpgradeCode.java | 2 +- ...getedMsRepresentativeStateAuditProvider.java | 2 +- .../GeneralMoleculeResultDataSet.java | 2 +- .../calculations/NormalizationMethodAreas.java | 2 +- .../calculations/ReplicateDataSet.java | 2 +- .../targetedms/calculations/RunQuantifier.java | 2 +- .../quantification/CalibrationCurveDataSet.java | 2 +- .../quantification/DesignMatrix.java | 2 +- .../quantification/FoldChangeDataSet.java | 2 +- .../quantification/GroupComparisonDataSet.java | 2 +- .../quantification/LinearModel.java | 2 +- .../quantification/NameValueCollection.java | 2 +- .../quantification/NormalizationMethod.java | 2 +- .../quantification/RegressionFit.java | 2 +- .../quantification/RegressionWeighting.java | 2 +- .../calculations/quantification/SampleType.java | 2 +- .../quantification/TransitionAreas.java | 2 +- .../quantification/TransitionKeys.java | 2 +- .../labkey/targetedms/chart/ChartColors.java | 2 +- .../chart/ChromatogramChartMaker.java | 2 +- .../chart/ChromatogramChartMakerFactory.java | 2 +- .../targetedms/chart/ChromatogramDataset.java | 2 +- .../labkey/targetedms/chart/ColorGenerator.java | 15 +++++++++++++++ .../labkey/targetedms/chart/ComparisonAxis.java | 2 +- .../targetedms/chart/ComparisonCategory.java | 2 +- .../chart/ComparisonChartInputMaker.java | 2 +- .../targetedms/chart/ComparisonChartMaker.java | 2 +- .../targetedms/chart/ComparisonDataset.java | 2 +- .../labkey/targetedms/chart/LabelFactory.java | 2 +- .../chart/MoleculePrecursorColorIndexer.java | 2 +- .../chart/MultiLineXYPointerAnnotation.java | 2 +- .../targetedms/chart/PrecursorColorIndexer.java | 2 +- .../chart/ReplicateLabelMinimizer.java | 2 +- .../RetentionTimeBoxAndWhiskerRenderer.java | 2 +- .../targetedms/chromlib/AbstractLibEntity.java | 15 +++++++++++++++ .../labkey/targetedms/chromlib/BaseDaoImpl.java | 2 +- .../chromlib/ChromLibSqliteSchemaCreator.java | 2 +- .../chromlib/ChromatogramLibraryUtils.java | 2 +- .../chromlib/ChromatogramLibraryWriter.java | 2 +- .../targetedms/chromlib/ConnectionSource.java | 2 +- .../labkey/targetedms/chromlib/Constants.java | 2 +- .../ContainerChromatogramLibraryWriter.java | 2 +- src/org/labkey/targetedms/chromlib/Dao.java | 2 +- src/org/labkey/targetedms/chromlib/LibInfo.java | 2 +- .../labkey/targetedms/chromlib/LibInfoDao.java | 2 +- .../targetedms/chromlib/LibIrtLibrary.java | 2 +- .../chromlib/LibIsotopeModification.java | 2 +- .../chromlib/LibIsotopeModificationDao.java | 2 +- .../labkey/targetedms/chromlib/LibPeptide.java | 2 +- .../targetedms/chromlib/LibPeptideDao.java | 2 +- .../chromlib/LibPeptideStructuralModDao.java | 2 +- .../LibPeptideStructuralModification.java | 2 +- .../targetedms/chromlib/LibPrecursor.java | 2 +- .../targetedms/chromlib/LibPrecursorDao.java | 2 +- .../LibPrecursorIsotopeModification.java | 2 +- .../LibPrecursorIsotopeModificationDao.java | 2 +- .../chromlib/LibPrecursorRetentionTime.java | 2 +- .../chromlib/LibPrecursorRetentionTimeDao.java | 2 +- .../targetedms/chromlib/LibPredictor.java | 15 +++++++++++++++ .../targetedms/chromlib/LibPredictorDao.java | 15 +++++++++++++++ .../labkey/targetedms/chromlib/LibProtein.java | 2 +- .../targetedms/chromlib/LibProteinDao.java | 2 +- .../targetedms/chromlib/LibSampleFile.java | 2 +- .../targetedms/chromlib/LibSampleFileDao.java | 2 +- .../chromlib/LibStructuralModLoss.java | 2 +- .../chromlib/LibStructuralModLossDao.java | 2 +- .../chromlib/LibStructuralModification.java | 2 +- .../chromlib/LibStructuralModificationDao.java | 2 +- .../targetedms/chromlib/LibTransition.java | 2 +- .../targetedms/chromlib/LibTransitionDao.java | 2 +- .../chromlib/LibTransitionOptimization.java | 15 +++++++++++++++ .../chromlib/LibTransitionOptimizationDao.java | 15 +++++++++++++++ .../clustergrammer/ClustergrammerClient.java | 2 +- .../clustergrammer/ClustergrammerHeatMap.java | 2 +- .../targetedms/conflict/ConflictPrecursor.java | 2 +- .../targetedms/conflict/ConflictTransition.java | 2 +- .../targetedms/datasource/MsDataDirSource.java | 15 +++++++++++++++ .../targetedms/datasource/MsDataFileSource.java | 15 +++++++++++++++ .../targetedms/datasource/MsDataSource.java | 15 +++++++++++++++ .../datasource/MsDataSourceTypes.java | 15 +++++++++++++++ .../targetedms/datasource/MsDataSourceUtil.java | 15 +++++++++++++++ .../datasource/MsMultiDataSource.java | 15 +++++++++++++++ .../targetedms/datasource/PsiInstruments.java | 2 +- .../folderImport/PanoramaQCSettings.java | 15 +++++++++++++++ .../folderImport/QCFolderConstants.java | 15 +++++++++++++++ .../folderImport/QCFolderImporter.java | 15 +++++++++++++++ .../folderImport/QCFolderWriterFactory.java | 15 +++++++++++++++ .../labkey/targetedms/model/AutoQCPingData.java | 15 +++++++++++++++ src/org/labkey/targetedms/model/GuideSet.java | 2 +- .../labkey/targetedms/model/GuideSetKey.java | 15 +++++++++++++++ .../labkey/targetedms/model/GuideSetStats.java | 2 +- .../targetedms/model/InstrumentNickname.java | 15 +++++++++++++++ .../targetedms/model/PeptideOutliers.java | 15 +++++++++++++++ .../model/PrecursorChromInfoLitePlus.java | 2 +- .../model/PrecursorChromInfoPlus.java | 2 +- .../targetedms/model/QCMetricExclusion.java | 2 +- .../labkey/targetedms/model/QCPlotFragment.java | 15 +++++++++++++++ .../targetedms/model/QCTraceMetricValues.java | 15 +++++++++++++++ .../targetedms/model/RawMetricDataSet.java | 2 +- .../targetedms/model/SampleFileQCMetadata.java | 15 +++++++++++++++ .../labkey/targetedms/model/passport/IFile.java | 15 +++++++++++++++ .../targetedms/model/passport/IKeyword.java | 15 +++++++++++++++ .../targetedms/model/passport/IPeptide.java | 15 +++++++++++++++ .../targetedms/model/passport/IProtein.java | 15 +++++++++++++++ .../targetedms/outliers/OutlierGenerator.java | 2 +- .../targetedms/parser/AbstractAnnotation.java | 2 +- .../targetedms/parser/AbstractChromInfo.java | 2 +- .../targetedms/parser/AnnotatedEntity.java | 2 +- .../targetedms/parser/AnnotationSetting.java | 2 +- src/org/labkey/targetedms/parser/AreaRatio.java | 2 +- .../parser/CalibrationCurveEntity.java | 2 +- src/org/labkey/targetedms/parser/ChromInfo.java | 2 +- .../labkey/targetedms/parser/Chromatogram.java | 2 +- .../parser/ChromatogramBinaryFormat.java | 2 +- .../targetedms/parser/ChromatogramGroupId.java | 2 +- .../parser/ComplexFragmentIonName.java | 2 +- src/org/labkey/targetedms/parser/CustomIon.java | 2 +- .../labkey/targetedms/parser/DataSettings.java | 2 +- .../labkey/targetedms/parser/FoldChange.java | 2 +- .../targetedms/parser/GeneralMolecule.java | 2 +- .../parser/GeneralMoleculeAnnotation.java | 2 +- .../parser/GeneralMoleculeChromInfo.java | 2 +- .../targetedms/parser/GeneralPrecursor.java | 2 +- .../targetedms/parser/GeneralTransition.java | 2 +- .../parser/GroupComparisonSettings.java | 2 +- .../labkey/targetedms/parser/Instrument.java | 2 +- src/org/labkey/targetedms/parser/Molecule.java | 2 +- .../targetedms/parser/MoleculePrecursor.java | 2 +- .../targetedms/parser/MoleculeTransition.java | 2 +- .../targetedms/parser/OptimizationDBRow.java | 15 +++++++++++++++ .../parser/PeakAreaRatioCalculator.java | 2 +- src/org/labkey/targetedms/parser/Peptide.java | 2 +- .../targetedms/parser/PeptideAreaRatio.java | 2 +- .../labkey/targetedms/parser/PeptideGroup.java | 2 +- .../parser/PeptideGroupAnnotation.java | 2 +- .../targetedms/parser/PeptideSettings.java | 2 +- .../parser/PeptideSettingsParser.java | 2 +- src/org/labkey/targetedms/parser/Precursor.java | 2 +- .../targetedms/parser/PrecursorAnnotation.java | 2 +- .../targetedms/parser/PrecursorAreaRatio.java | 2 +- .../targetedms/parser/PrecursorChromInfo.java | 2 +- .../parser/PrecursorChromInfoAnnotation.java | 2 +- src/org/labkey/targetedms/parser/Protein.java | 15 +++++++++++++++ .../targetedms/parser/ProteinAnnotation.java | 2 +- .../parser/QuantificationSettings.java | 2 +- src/org/labkey/targetedms/parser/Replicate.java | 2 +- .../targetedms/parser/ReplicateAnnotation.java | 2 +- .../labkey/targetedms/parser/SampleFile.java | 2 +- .../targetedms/parser/SampleFileChromInfo.java | 2 +- src/org/labkey/targetedms/parser/SignedMz.java | 2 +- .../targetedms/parser/SkylineBinaryParser.java | 2 +- .../parser/SkylineDocumentParser.java | 2 +- .../labkey/targetedms/parser/SkylineEntity.java | 2 +- .../targetedms/parser/SkylineReplicate.java | 2 +- .../targetedms/parser/SpectrumFilter.java | 2 +- src/org/labkey/targetedms/parser/Target.java | 2 +- .../targetedms/parser/TimeIntensities.java | 2 +- .../labkey/targetedms/parser/Transition.java | 2 +- .../targetedms/parser/TransitionAnnotation.java | 2 +- .../targetedms/parser/TransitionAreaRatio.java | 2 +- .../targetedms/parser/TransitionChromInfo.java | 2 +- .../TransitionChromInfoAndPrecursorTally.java | 15 +++++++++++++++ .../parser/TransitionChromInfoAnnotation.java | 2 +- .../targetedms/parser/TransitionLoss.java | 2 +- .../parser/TransitionOptimization.java | 2 +- .../targetedms/parser/TransitionSettings.java | 2 +- src/org/labkey/targetedms/parser/XmlUtil.java | 2 +- .../targetedms/parser/list/ListColumn.java | 2 +- .../labkey/targetedms/parser/list/ListData.java | 2 +- .../targetedms/parser/list/ListDefinition.java | 2 +- .../labkey/targetedms/parser/list/ListItem.java | 2 +- .../targetedms/parser/list/ListItemValue.java | 2 +- .../proto/ChromatogramGroupDataOuterClass.java | 15 +++++++++++++++ .../parser/proto/SkylineDocument.java | 15 +++++++++++++++ .../parser/skyaudit/AuditLogEntry.java | 2 +- .../parser/skyaudit/AuditLogMessage.java | 2 +- .../parser/skyaudit/AuditLogTree.java | 2 +- .../parser/skyaudit/DatabaseUtil.java | 15 +++++++++++++++ .../parser/skyaudit/SkylineAuditLogParser.java | 2 +- .../SkylineAuditLogSecurityManager.java | 2 +- .../parser/skyaudit/UnitTestUtil.java | 2 +- .../targetedms/parser/skyd/CacheFormat.java | 2 +- .../parser/skyd/CacheFormatVersion.java | 2 +- .../parser/skyd/CacheHeaderStruct.java | 2 +- .../parser/skyd/CachedFileHeaderStruct.java | 2 +- .../parser/skyd/ChromGroupHeaderInfo.java | 2 +- .../targetedms/parser/skyd/ChromPeak.java | 2 +- .../targetedms/parser/skyd/ChromTransition.java | 2 +- .../targetedms/parser/speclib/BlibSpectrum.java | 2 +- .../parser/speclib/BlibSpectrumReader.java | 2 +- .../targetedms/parser/speclib/ElibSpectrum.java | 2 +- .../parser/speclib/ElibSpectrumReader.java | 2 +- .../targetedms/parser/speclib/LibSpectrum.java | 2 +- .../parser/speclib/LibSpectrumReader.java | 2 +- .../parser/speclib/SpeclibReaderException.java | 2 +- .../targetedms/passport/PassportController.java | 2 +- .../pipeline/TargetedMSImportPipelineJob.java | 2 +- .../pipeline/TargetedMSImportTask.java | 2 +- .../pipeline/TargetedMSPipelineProvider.java | 2 +- .../query/AbstractGeneralMoleculeTableInfo.java | 2 +- .../AbstractGeneralPrecursorTableInfo.java | 2 +- .../AbstractGeneralTransitionTableInfo.java | 2 +- .../targetedms/query/AdminSchedulingTable.java | 15 +++++++++++++++ .../query/AnnotatedTargetedMSTable.java | 2 +- ...nditionalFormattingDisplayColumnFactory.java | 15 +++++++++++++++ .../query/CDRDisplayColumnFactory.java | 15 +++++++++++++++ .../targetedms/query/CalibrationCurveTable.java | 2 +- .../query/ChromatogramDisplayColumnFactory.java | 2 +- .../query/ChromatogramGridQuerySettings.java | 2 +- .../query/ConflictResultsManager.java | 2 +- .../query/CrossLinkedPeptideDisplayColumn.java | 15 +++++++++++++++ .../query/DocTransitionsTableInfo.java | 2 +- .../GeneralMoleculeAnnotationTableInfo.java | 2 +- .../GeneralMoleculeChromInfoTableInfo.java | 2 +- ...MoleculePrecursorChromatogramsTableInfo.java | 2 +- .../query/GroupChromatogramsTableInfo.java | 2 +- .../labkey/targetedms/query/GuideSetTable.java | 2 +- src/org/labkey/targetedms/query/IconColumn.java | 2 +- .../targetedms/query/InstrumentManager.java | 2 +- .../query/InstrumentScheduleOverlapTrigger.java | 15 +++++++++++++++ .../query/InstrumentScheduleTable.java | 15 +++++++++++++++ .../query/InstrumentUsagePaymentTrigger.java | 15 +++++++++++++++ .../targetedms/query/IsotopeLabelManager.java | 2 +- .../targetedms/query/JoinedTargetedMSTable.java | 2 +- .../labkey/targetedms/query/LibraryManager.java | 2 +- .../targetedms/query/ModificationManager.java | 2 +- .../query/ModifiedSequenceDisplayColumn.java | 2 +- .../targetedms/query/MoleculeManager.java | 2 +- .../query/MoleculePrecursorManager.java | 2 +- .../query/MoleculePrecursorTableInfo.java | 2 +- .../targetedms/query/MoleculeTableInfo.java | 2 +- .../query/MoleculeTransitionManager.java | 2 +- .../query/MoleculeTransitionsTableInfo.java | 2 +- .../query/OwnProjectSchedulingTable.java | 15 +++++++++++++++ .../targetedms/query/PTMPercentsCustomizer.java | 15 +++++++++++++++ .../query/PTMPercentsGroupedCustomizer.java | 15 +++++++++++++++ .../query/PTMRiskDisplayColumnFactory.java | 15 +++++++++++++++ .../query/PeptideChromatogramsTableInfo.java | 2 +- .../targetedms/query/PeptideGroupManager.java | 2 +- .../PeptideIsotopeModificationTableInfo.java | 2 +- .../labkey/targetedms/query/PeptideManager.java | 2 +- .../PeptideStructuralModificationTableInfo.java | 2 +- .../targetedms/query/PeptideTableInfo.java | 2 +- .../query/PrecursorChromInfoTable.java | 2 +- .../query/PrecursorChromatogramsTableInfo.java | 2 +- .../targetedms/query/PrecursorManager.java | 2 +- .../targetedms/query/PrecursorTableInfo.java | 2 +- .../targetedms/query/ProjectAddUserTrigger.java | 15 +++++++++++++++ .../targetedms/query/QCAnnotationTable.java | 2 +- .../targetedms/query/QCAnnotationTypeTable.java | 2 +- .../targetedms/query/QCEnabledMetricsTable.java | 2 +- .../query/QCFolderDisplayColumnFactory.java | 15 +++++++++++++++ .../query/QCMetricConfigurationTable.java | 4 ++-- .../query/QCMetricExclusionTable.java | 2 +- .../QCMetricStatusDisplayColumnFactory.java | 15 +++++++++++++++ .../query/QCTraceMetricValuesTable.java | 15 +++++++++++++++ .../targetedms/query/ReplicateManager.java | 2 +- .../query/RepresentativeStateDisplayColumn.java | 2 +- .../query/RepresentativeStateManager.java | 2 +- .../targetedms/query/SampleFileTable.java | 2 +- .../targetedms/query/SamplePivotCustomizer.java | 15 +++++++++++++++ .../targetedms/query/SimpleTargetedMSTable.java | 15 +++++++++++++++ .../query/SiteLocationDisplayColumnFactory.java | 15 +++++++++++++++ .../targetedms/query/SkylineAuditTable.java | 15 +++++++++++++++ .../targetedms/query/SkylineListManager.java | 2 +- .../targetedms/query/SkylineListSchema.java | 15 +++++++++++++++ .../targetedms/query/SkylineListTable.java | 2 +- .../targetedms/query/SkylineListUnionTable.java | 15 +++++++++++++++ .../query/TargetedMSCrosstabView.java | 15 +++++++++++++++ .../targetedms/query/TargetedMSForeignKey.java | 2 +- .../targetedms/query/TargetedMSQueryView.java | 15 +++++++++++++++ .../targetedms/query/TargetedMSTable.java | 2 +- .../targetedms/query/TransitionManager.java | 2 +- .../search/ModificationSearchBean.java | 2 +- .../search/ModificationSearchWebPart.java | 2 +- .../targetedms/search/ProteinSearchWebPart.java | 2 +- .../targetedms/search/modificationSearch.jsp | 2 +- .../labkey/targetedms/search/peptideSearch.jsp | 2 +- .../view/AnnotationUIDisplayColumn.java | 2 +- .../targetedms/view/CalibrationCurveChart.java | 2 +- .../targetedms/view/CalibrationCurveView.java | 15 +++++++++++++++ .../targetedms/view/CalibrationCurvesView.java | 2 +- .../targetedms/view/ChromatogramGridView.java | 15 +++++++++++++++ .../view/ChromatogramsDataRegion.java | 2 +- .../targetedms/view/CrossLinkedPeptideInfo.java | 15 +++++++++++++++ .../view/DocumentGeneralMoleculesView.java | 2 +- .../view/DocumentPeptideGroupView.java | 2 +- .../targetedms/view/DocumentPrecursorsView.java | 2 +- .../targetedms/view/DocumentProteinView.java | 2 +- .../view/DocumentTransitionsView.java | 2 +- .../labkey/targetedms/view/DocumentView.java | 2 +- .../targetedms/view/FiguresOfMeritView.java | 15 +++++++++++++++ .../targetedms/view/FontAwesomeLinkColumn.java | 15 +++++++++++++++ .../targetedms/view/GroupComparisonView.java | 2 +- src/org/labkey/targetedms/view/IconFactory.java | 2 +- .../view/InstrumentSummaryWebPart.java | 15 +++++++++++++++ .../view/LibraryQueryViewWebPart.java | 2 +- .../view/ModifiedPeptideHtmlMaker.java | 2 +- .../MoleculePrecursorChromatogramsView.java | 2 +- .../view/PeptidePrecursorChromatogramsView.java | 2 +- .../targetedms/view/PeptidePrecursorsView.java | 2 +- .../targetedms/view/PeptideTransitionsView.java | 2 +- .../targetedms/view/PrecursorHtmlMaker.java | 2 +- .../targetedms/view/QuantificationView.java | 2 +- .../view/ReplicateSummaryWebPart.java | 2 +- ...ditLogExtraInfoAJAXDisplayColumnFactory.java | 15 +++++++++++++++ .../view/SmallMoleculePrecursorsView.java | 2 +- .../view/SmallMoleculeTransitionsView.java | 2 +- .../view/TargetedMSRunsWebPartView.java | 2 +- .../targetedms/view/TargetedMsRunListView.java | 2 +- .../TransitionPeptideSearchViewProvider.java | 2 +- .../TransitionProteinSearchViewProvider.java | 2 +- .../view/archivedRevisionsDownload.jsp | 2 +- .../labkey/targetedms/view/calibrationCurve.jsp | 2 +- .../view/chromatogramLibraryDownload.jsp | 2 +- .../targetedms/view/chromatogramsForm.jsp | 2 +- .../labkey/targetedms/view/confirmImport.jsp | 2 +- .../labkey/targetedms/view/conflictSummary.jsp | 2 +- .../labkey/targetedms/view/figuresOfMerit.jsp | 2 +- src/org/labkey/targetedms/view/folderSetup.jsp | 2 +- .../targetedms/view/instrumentCalendar.jsp | 2 +- .../labkey/targetedms/view/moleculeListView.jsp | 2 +- .../view/moleculePrecursorChromatogramsView.jsp | 2 +- .../targetedms/view/moleculeSummaryView.jsp | 2 +- src/org/labkey/targetedms/view/nickname.jsp | 2 +- src/org/labkey/targetedms/view/paretoPlot.jsp | 2 +- .../targetedms/view/passport/MxNReport.jsp | 17 +++++++++++++++++ .../view/passport/ProteinListView.java | 15 +++++++++++++++ .../view/passport/beforeAfterReport.jsp | 17 +++++++++++++++++ .../targetedms/view/passport/chromatograms.jsp | 17 +++++++++++++++++ .../view/passport/webPartPlaceholder.jsp | 17 +++++++++++++++++ .../targetedms/view/peptideSummaryView.jsp | 2 +- .../labkey/targetedms/view/pharmacokinetics.jsp | 2 +- .../view/precursorChromatogramsView.jsp | 2 +- .../view/precursorConflictResolutionView.jsp | 2 +- .../view/proteinConflictResolutionView.jsp | 2 +- .../labkey/targetedms/view/proteinSearch.jsp | 2 +- src/org/labkey/targetedms/view/qcSummary.jsp | 2 +- .../targetedms/view/qcTrendPlotReport.jsp | 2 +- src/org/labkey/targetedms/view/renameRun.jsp | 2 +- .../labkey/targetedms/view/runMethodChain.jsp | 2 +- .../labkey/targetedms/view/runSummaryView.jsp | 2 +- .../view/skylineAuditLogExtraInfoView.jsp | 17 +++++++++++++++++ .../view/spectrum/LibrarySpectrumMatch.java | 2 +- .../spectrum/LibrarySpectrumMatchGetter.java | 2 +- .../view/spectrum/PeptideSpectrumView.java | 2 +- .../targetedms/view/spectrum/spectrumView.jsp | 2 +- .../targetedms/view/summaryChartsView.jsp | 2 +- .../targetedms/CalibrationCurveWebpart.java | 2 +- .../targetedms/ClustergrammerDialog.java | 2 +- .../test/components/targetedms/GuideSet.java | 2 +- .../components/targetedms/GuideSetStats.java | 2 +- .../components/targetedms/GuideSetWebPart.java | 2 +- .../components/targetedms/LinkVersionsGrid.java | 2 +- .../targetedms/ParetoPlotsWebPart.java | 2 +- .../targetedms/PeptideSummaryWebPart.java | 15 +++++++++++++++ .../targetedms/PrecursorsWebPart.java | 15 +++++++++++++++ .../targetedms/QCAnnotationTypeWebPart.java | 2 +- .../targetedms/QCAnnotationWebPart.java | 2 +- .../test/components/targetedms/QCPlot.java | 2 +- .../components/targetedms/QCPlotsWebPart.java | 2 +- .../components/targetedms/QCSummaryWebPart.java | 2 +- .../targetedms/SequenceCoverageWebPart.java | 15 +++++++++++++++ .../targetedms/TargetedMSRunsTable.java | 2 +- .../targetedms/UtilizationCalendarWebPart.java | 15 +++++++++++++++ .../panoramapremium/ConfigureMetricsUIPage.java | 15 +++++++++++++++ .../pages/targetedms/AnnotationInsertPage.java | 2 +- .../targetedms/AnnotationTypeInsertPage.java | 2 +- .../test/pages/targetedms/GuideSetPage.java | 2 +- .../test/pages/targetedms/PKReportPage.java | 2 +- .../pages/targetedms/PanoramaAnnotations.java | 2 +- .../pages/targetedms/PanoramaDashboard.java | 2 +- .../test/pages/targetedms/ParetoPlotPage.java | 2 +- .../TargetedMSHidePeptidesAndMolecules.java | 15 +++++++++++++++ .../TargetedMSIsotopologueTest.java | 15 +++++++++++++++ .../panoramapremium/TargetedMSPremiumTest.java | 15 +++++++++++++++ .../TargetedMSQCFolderImportExport.java | 15 +++++++++++++++ .../TargetedMSQCPremiumTest.java | 15 +++++++++++++-- .../TargetedMSSampleManagerIntegrationTest.java | 15 +++++++++++++++ .../TargetedMSiRTMetricsTest.java | 15 +++++++++++++++ .../targetedms/AbstractQuantificationTest.java | 2 +- .../tests/targetedms/ClustergrammerTest.java | 2 +- .../test/tests/targetedms/GetDataAPITest.java | 2 +- .../targetedms/InstrumentSchedulingTest.java | 2 +- .../targetedms/TargetedMSAuditLogTest.java | 15 +++++++++++++++ .../TargetedMSCalibrationCurveTest.java | 2 +- .../TargetedMSChromatogramOptimizationTest.java | 15 +++++++++++++++ .../TargetedMSDocumentFormatsTest.java | 2 +- .../TargetedMSEarlyStagePTMReportTest.java | 15 +++++++++++++++ .../targetedms/TargetedMSExperimentIrtTest.java | 2 +- .../targetedms/TargetedMSExperimentTest.java | 2 +- .../TargetedMSExperimentalQCLinkTest.java | 15 +++++++++++++++ .../TargetedMSGroupComparisonTest.java | 2 +- .../TargetedMSInstrumentNicknameTest.java | 2 +- .../tests/targetedms/TargetedMSIrtTest.java | 2 +- .../targetedms/TargetedMSLibraryIrtTest.java | 2 +- .../tests/targetedms/TargetedMSLibraryTest.java | 2 +- .../TargetedMSLightHeavyRatioTest.java | 15 +++++++++++++++ .../targetedms/TargetedMSLinkVersionsTest.java | 2 +- .../tests/targetedms/TargetedMSListTest.java | 2 +- .../tests/targetedms/TargetedMSMAMTest.java | 2 +- ...TargetedMSMovingSKYDocAcrossFoldersTest.java | 15 +++++++++++++++ .../TargetedMSMultiplePeptidePlotTest.java | 15 +++++++++++++++ .../TargetedMSMxNReproducibilityReportTest.java | 15 +++++++++++++++ .../TargetedMSPeptideLibraryTest.java | 2 +- .../TargetedMSPeptideSummaryHeatmapTest.java | 15 +++++++++++++++ .../TargetedMSPrecursorLevelDataTest.java | 2 +- .../TargetedMSProteinGroupingTest.java | 15 +++++++++++++++ .../TargetedMSProteinSequenceViewTest.java | 15 +++++++++++++++ .../TargetedMSQCConfigureMetricTest.java | 15 +++++++++++++++ .../targetedms/TargetedMSQCGuideSetTest.java | 2 +- .../targetedms/TargetedMSQCSummaryTest.java | 2 +- .../test/tests/targetedms/TargetedMSQCTest.java | 2 +- .../TargetedMSSampleFileChromInfoTest.java | 2 +- .../targetedms/TargetedMSSkydTextIdTest.java | 2 +- .../TargetedMSSmallMoleculeLibraryTest.java | 2 +- ...getedMSSmallMoleculeLightHeavyRatioTest.java | 15 +++++++++++++++ .../test/tests/targetedms/TargetedMSTest.java | 2 +- .../TargetedMSTrailingMeanAndCVTest.java | 15 +++++++++++++++ .../TargetedMSTransitionChromInfoLimitTest.java | 15 +++++++++++++++ .../TargetedMSUtilizationCalendarTest.java | 15 +++++++++++++++ .../tests/targetedms/passport/PassportTest.java | 2 +- .../targetedms/passport/PassportTestPart.java | 2 +- .../upgrade/TargetedMSUpgradeTest.java | 15 +++++++++++++++ .../test/util/targetedms/ConnectionSource.java | 15 +++++++++++++++ .../labkey/test/util/targetedms/QCHelper.java | 2 +- .../test/util/targetedms/TargetedMSHelper.java | 15 +++++++++++++++ webapp/TargetedMS/js/BaseQCPlotPanel.js | 2 +- webapp/TargetedMS/js/CUSUMPlotHelper.js | 2 +- webapp/TargetedMS/js/CalibrationCurve.js | 2 +- webapp/TargetedMS/js/LeveyJenningsPlotHelper.js | 2 +- webapp/TargetedMS/js/LinkVersionsDialog.js | 2 +- webapp/TargetedMS/js/MovingRangePlotHelper.js | 2 +- webapp/TargetedMS/js/ParetoPlotPanel.js | 2 +- webapp/TargetedMS/js/PlotTypeCheckCombo.js | 5 +++++ webapp/TargetedMS/js/QCMetricConfigLoader.js | 5 +++++ webapp/TargetedMS/js/QCPlotHelperBase.js | 2 +- webapp/TargetedMS/js/QCPlotHelperWrapper.js | 2 +- webapp/TargetedMS/js/QCPlotHoverPanel.js | 2 +- webapp/TargetedMS/js/QCPlotLegendHelper.js | 2 +- webapp/TargetedMS/js/QCSummaryPanel.js | 2 +- webapp/TargetedMS/js/QCTrendPlotPanel.js | 2 +- webapp/TargetedMS/js/TrailingCVPlotHelper.js | 2 +- webapp/TargetedMS/js/TrailingMeanPlotHelper.js | 2 +- webapp/TargetedMS/js/clipboardHelper.js | 5 +++++ webapp/TargetedMS/js/fullcalendar.js | 5 +++++ webapp/TargetedMS/js/js-year-calendar.js | 5 +++++ webapp/TargetedMS/js/misc.js | 5 +++++ webapp/TargetedMS/js/scheduleUtils.js | 5 +++++ webapp/TargetedMS/js/scheduler.js | 5 +++++ webapp/TargetedMS/js/svgChart.js | 5 +++++ webapp/passport/js/MxN/protein.js | 5 +++++ webapp/passport/js/beforeAfter/protein.js | 5 +++++ webapp/passport/js/peakareachart.js | 5 +++++ webapp/passport/js/proteinbar.js | 5 +++++ webapp/passport/js/settings.js | 5 +++++ webapp/passport/js/util.js | 5 +++++ 562 files changed, 2430 insertions(+), 400 deletions(-) diff --git a/api-src/org/labkey/api/targetedms/IModification.java b/api-src/org/labkey/api/targetedms/IModification.java index 5d4e39da5..9befe42a7 100644 --- a/api-src/org/labkey/api/targetedms/IModification.java +++ b/api-src/org/labkey/api/targetedms/IModification.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; public interface IModification diff --git a/api-src/org/labkey/api/targetedms/ISampleFile.java b/api-src/org/labkey/api/targetedms/ISampleFile.java index 3fbbe6a18..a1a3241a2 100644 --- a/api-src/org/labkey/api/targetedms/ISampleFile.java +++ b/api-src/org/labkey/api/targetedms/ISampleFile.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; import java.util.Date; diff --git a/api-src/org/labkey/api/targetedms/ISpectrumLibrary.java b/api-src/org/labkey/api/targetedms/ISpectrumLibrary.java index 6c7fd4810..41ea2bad9 100644 --- a/api-src/org/labkey/api/targetedms/ISpectrumLibrary.java +++ b/api-src/org/labkey/api/targetedms/ISpectrumLibrary.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; public interface ISpectrumLibrary diff --git a/api-src/org/labkey/api/targetedms/ITargetedMSRun.java b/api-src/org/labkey/api/targetedms/ITargetedMSRun.java index a0566c173..3c01553d4 100644 --- a/api-src/org/labkey/api/targetedms/ITargetedMSRun.java +++ b/api-src/org/labkey/api/targetedms/ITargetedMSRun.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2015-2019 LabKey Corporation + * Copyright (c) 2015-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/api-src/org/labkey/api/targetedms/RepresentativeDataState.java b/api-src/org/labkey/api/targetedms/RepresentativeDataState.java index 3a4b1773c..a077f9f25 100644 --- a/api-src/org/labkey/api/targetedms/RepresentativeDataState.java +++ b/api-src/org/labkey/api/targetedms/RepresentativeDataState.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2012-2019 LabKey Corporation + * Copyright (c) 2012-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/api-src/org/labkey/api/targetedms/RunRepresentativeDataState.java b/api-src/org/labkey/api/targetedms/RunRepresentativeDataState.java index e83a887c6..5a2b81b28 100644 --- a/api-src/org/labkey/api/targetedms/RunRepresentativeDataState.java +++ b/api-src/org/labkey/api/targetedms/RunRepresentativeDataState.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; public enum RunRepresentativeDataState diff --git a/api-src/org/labkey/api/targetedms/SkylineAnnotation.java b/api-src/org/labkey/api/targetedms/SkylineAnnotation.java index a0471c3c4..8a774faa6 100644 --- a/api-src/org/labkey/api/targetedms/SkylineAnnotation.java +++ b/api-src/org/labkey/api/targetedms/SkylineAnnotation.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2015-2019 LabKey Corporation + * Copyright (c) 2015-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/api-src/org/labkey/api/targetedms/SkylineDocumentImportListener.java b/api-src/org/labkey/api/targetedms/SkylineDocumentImportListener.java index b110829c0..ddfc27f31 100644 --- a/api-src/org/labkey/api/targetedms/SkylineDocumentImportListener.java +++ b/api-src/org/labkey/api/targetedms/SkylineDocumentImportListener.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; import org.labkey.api.data.Container; diff --git a/api-src/org/labkey/api/targetedms/TargetedMSFolderTypeListener.java b/api-src/org/labkey/api/targetedms/TargetedMSFolderTypeListener.java index a59b4fb7d..906cde612 100644 --- a/api-src/org/labkey/api/targetedms/TargetedMSFolderTypeListener.java +++ b/api-src/org/labkey/api/targetedms/TargetedMSFolderTypeListener.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; import org.labkey.api.data.Container; diff --git a/api-src/org/labkey/api/targetedms/TargetedMSService.java b/api-src/org/labkey/api/targetedms/TargetedMSService.java index 19dee383a..da12b2847 100644 --- a/api-src/org/labkey/api/targetedms/TargetedMSService.java +++ b/api-src/org/labkey/api/targetedms/TargetedMSService.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2015-2019 LabKey Corporation + * Copyright (c) 2015-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/api-src/org/labkey/api/targetedms/TargetedMSUrls.java b/api-src/org/labkey/api/targetedms/TargetedMSUrls.java index f00fe68a3..e7ce6a08e 100644 --- a/api-src/org/labkey/api/targetedms/TargetedMSUrls.java +++ b/api-src/org/labkey/api/targetedms/TargetedMSUrls.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms; import org.labkey.api.action.UrlProvider; diff --git a/api-src/org/labkey/api/targetedms/model/OutlierCounts.java b/api-src/org/labkey/api/targetedms/model/OutlierCounts.java index 10ca81354..891b5fc0d 100644 --- a/api-src/org/labkey/api/targetedms/model/OutlierCounts.java +++ b/api-src/org/labkey/api/targetedms/model/OutlierCounts.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms.model; import org.jetbrains.annotations.NotNull; diff --git a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java index e96fae1df..82c830cb0 100644 --- a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java +++ b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/api-src/org/labkey/api/targetedms/model/QCMetricStatus.java b/api-src/org/labkey/api/targetedms/model/QCMetricStatus.java index 4b89eb8cb..e95c3c4aa 100644 --- a/api-src/org/labkey/api/targetedms/model/QCMetricStatus.java +++ b/api-src/org/labkey/api/targetedms/model/QCMetricStatus.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms.model; public enum QCMetricStatus diff --git a/api-src/org/labkey/api/targetedms/model/SampleFileInfo.java b/api-src/org/labkey/api/targetedms/model/SampleFileInfo.java index 0e97b96e2..8f290cfe5 100644 --- a/api-src/org/labkey/api/targetedms/model/SampleFileInfo.java +++ b/api-src/org/labkey/api/targetedms/model/SampleFileInfo.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms.model; import org.jetbrains.annotations.NotNull; diff --git a/api-src/org/labkey/api/targetedms/model/SampleFilePath.java b/api-src/org/labkey/api/targetedms/model/SampleFilePath.java index bb734ada5..0500d772f 100644 --- a/api-src/org/labkey/api/targetedms/model/SampleFilePath.java +++ b/api-src/org/labkey/api/targetedms/model/SampleFilePath.java @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.targetedms.model; import org.jetbrains.annotations.Nullable; diff --git a/build.gradle b/build.gradle index e250321d2..d41b7bbb6 100644 --- a/build.gradle +++ b/build.gradle @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2016-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import org.labkey.gradle.util.BuildUtils import org.labkey.gradle.util.ExternalDependency diff --git a/resources/queries/targetedms/CalibrationCurveMoleculePrecursors.sql b/resources/queries/targetedms/CalibrationCurveMoleculePrecursors.sql index 9354ca079..1e49dd699 100644 --- a/resources/queries/targetedms/CalibrationCurveMoleculePrecursors.sql +++ b/resources/queries/targetedms/CalibrationCurveMoleculePrecursors.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2017-2019 LabKey Corporation + * Copyright (c) 2017-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/CalibrationCurvePrecursors.sql b/resources/queries/targetedms/CalibrationCurvePrecursors.sql index 12e0d784e..8107739a9 100644 --- a/resources/queries/targetedms/CalibrationCurvePrecursors.sql +++ b/resources/queries/targetedms/CalibrationCurvePrecursors.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2017-2019 LabKey Corporation + * Copyright (c) 2017-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/DefaultGuideSet.sql b/resources/queries/targetedms/DefaultGuideSet.sql index f9d590e1d..747f784f6 100644 --- a/resources/queries/targetedms/DefaultGuideSet.sql +++ b/resources/queries/targetedms/DefaultGuideSet.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT 0 AS RowId, diff --git a/resources/queries/targetedms/GuideSetForOutliers.sql b/resources/queries/targetedms/GuideSetForOutliers.sql index 5b99b29b2..80fb128a5 100644 --- a/resources/queries/targetedms/GuideSetForOutliers.sql +++ b/resources/queries/targetedms/GuideSetForOutliers.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT RowId, TrainingStart, diff --git a/resources/queries/targetedms/InstrumentBilling.sql b/resources/queries/targetedms/InstrumentBilling.sql index fba7ba8ee..3552fe07a 100644 --- a/resources/queries/targetedms/InstrumentBilling.sql +++ b/resources/queries/targetedms/InstrumentBilling.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2025-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/InstrumentBillingByMonth.sql b/resources/queries/targetedms/InstrumentBillingByMonth.sql index eda019381..3018290cf 100644 --- a/resources/queries/targetedms/InstrumentBillingByMonth.sql +++ b/resources/queries/targetedms/InstrumentBillingByMonth.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2025-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/InstrumentSummaryByFolder.sql b/resources/queries/targetedms/InstrumentSummaryByFolder.sql index 183c11336..557fc2e56 100644 --- a/resources/queries/targetedms/InstrumentSummaryByFolder.sql +++ b/resources/queries/targetedms/InstrumentSummaryByFolder.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT COUNT(DISTINCT ReplicateId.RunId) AS SkylineDocumentCount, COUNT(DISTINCT ReplicateId) AS ReplicateCount, diff --git a/resources/queries/targetedms/PTMPercents.sql b/resources/queries/targetedms/PTMPercents.sql index aa525a65c..1dcc47e53 100644 --- a/resources/queries/targetedms/PTMPercents.sql +++ b/resources/queries/targetedms/PTMPercents.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT StructuralModId AS Modification, diff --git a/resources/queries/targetedms/PTMPercentsGrouped.sql b/resources/queries/targetedms/PTMPercentsGrouped.sql index 42402a76e..cc99f6ee4 100644 --- a/resources/queries/targetedms/PTMPercentsGrouped.sql +++ b/resources/queries/targetedms/PTMPercentsGrouped.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT PeptideGroupId, SiteLocation, diff --git a/resources/queries/targetedms/PTMPercentsGroupedPrepivot.sql b/resources/queries/targetedms/PTMPercentsGroupedPrepivot.sql index cc8fce3c4..6e9f75e9f 100644 --- a/resources/queries/targetedms/PTMPercentsGroupedPrepivot.sql +++ b/resources/queries/targetedms/PTMPercentsGroupedPrepivot.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ --Calculate the percentage for each individual modification WITH InitialGrouping AS ( (SELECT StructuralModId AS Modification, diff --git a/resources/queries/targetedms/PTMPercentsPrepivot.sql b/resources/queries/targetedms/PTMPercentsPrepivot.sql index 3b4edf2f5..c3f29f52d 100644 --- a/resources/queries/targetedms/PTMPercentsPrepivot.sql +++ b/resources/queries/targetedms/PTMPercentsPrepivot.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT ci.ModifiedAreaProportion, ci.PeptideId AS Id, ci.PeptideId.PeptideModifiedSequence, diff --git a/resources/queries/targetedms/PassportMxN.sql b/resources/queries/targetedms/PassportMxN.sql index 2170bb7f8..5cd279fa4 100644 --- a/resources/queries/targetedms/PassportMxN.sql +++ b/resources/queries/targetedms/PassportMxN.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT * FROM ( SELECT diff --git a/resources/queries/targetedms/Passport_TotalPrecursorArea.sql b/resources/queries/targetedms/Passport_TotalPrecursorArea.sql index dad1adc51..8c9715721 100644 --- a/resources/queries/targetedms/Passport_TotalPrecursorArea.sql +++ b/resources/queries/targetedms/Passport_TotalPrecursorArea.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT PrecursorId.Id, SampleFileId.ReplicateId.Name AS Replicate, SampleFileId.AcquiredTime AS AcquiredTime, diff --git a/resources/queries/targetedms/Passport_proteins.sql b/resources/queries/targetedms/Passport_proteins.sql index f53b76dae..be006926a 100644 --- a/resources/queries/targetedms/Passport_proteins.sql +++ b/resources/queries/targetedms/Passport_proteins.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT sequenceid, min(sequenceid.description) AS name, diff --git a/resources/queries/targetedms/PeptideIds.sql b/resources/queries/targetedms/PeptideIds.sql index e0b47b4bc..92b872470 100644 --- a/resources/queries/targetedms/PeptideIds.sql +++ b/resources/queries/targetedms/PeptideIds.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT PrecursorId.PeptideId.PeptideGroupId @hidden, ROUND(AVG(BestRetentionTime), 1) AS RetentionTime, diff --git a/resources/queries/targetedms/QCAnnotation.js b/resources/queries/targetedms/QCAnnotation.js index 56378343e..a712bd3e9 100644 --- a/resources/queries/targetedms/QCAnnotation.js +++ b/resources/queries/targetedms/QCAnnotation.js @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ function beforeInsert(row, errors) { if (row.date && row.date.getTime && row.enddate && row.enddate.getTime) { if (row.enddate.getTime() < row.date.getTime()) { diff --git a/resources/queries/targetedms/QCGroupingPrecursorMolecules.sql b/resources/queries/targetedms/QCGroupingPrecursorMolecules.sql index d0df7b367..126dd7df8 100644 --- a/resources/queries/targetedms/QCGroupingPrecursorMolecules.sql +++ b/resources/queries/targetedms/QCGroupingPrecursorMolecules.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- This query for Molecules displays under QC Summary menu 'Include or Exclude Peptides/Molecules' SELECT diff --git a/resources/queries/targetedms/QCGroupingPrecursorPeptides.sql b/resources/queries/targetedms/QCGroupingPrecursorPeptides.sql index f4bd03430..d244fb669 100644 --- a/resources/queries/targetedms/QCGroupingPrecursorPeptides.sql +++ b/resources/queries/targetedms/QCGroupingPrecursorPeptides.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- This query for Precursor Peptides displays under QC Summary menu 'Include or Exclude Peptides/Molecules' SELECT diff --git a/resources/queries/targetedms/QCInstrumentSummary.sql b/resources/queries/targetedms/QCInstrumentSummary.sql index 6490bc7a6..244563ce1 100644 --- a/resources/queries/targetedms/QCInstrumentSummary.sql +++ b/resources/queries/targetedms/QCInstrumentSummary.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT sf.InstrumentNickname AS Nickname, sf.InstrumentId.model AS InstrumentName, diff --git a/resources/queries/targetedms/QCMetricEnabled_precursorArea.sql b/resources/queries/targetedms/QCMetricEnabled_precursorArea.sql index 13474dae1..a74420fca 100644 --- a/resources/queries/targetedms/QCMetricEnabled_precursorArea.sql +++ b/resources/queries/targetedms/QCMetricEnabled_precursorArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2023-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetricEnabled_transitionArea.sql b/resources/queries/targetedms/QCMetricEnabled_transitionArea.sql index 34805d959..fda94d0b2 100644 --- a/resources/queries/targetedms/QCMetricEnabled_transitionArea.sql +++ b/resources/queries/targetedms/QCMetricEnabled_transitionArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2021-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorAccuracy.sql b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorAccuracy.sql index f81c77f74..5965d8e87 100644 --- a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorAccuracy.sql +++ b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorAccuracy.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT PrecursorChromInfoId, x.SampleFileId AS SampleFileId, diff --git a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOD.sql b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOD.sql index 99e462043..aab155586 100644 --- a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOD.sql +++ b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOD.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT precursorchrominfoid AS PrecursorChromInfoId, precursorchrominfoid.SampleFileId AS SampleFileId, diff --git a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOQ.sql b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOQ.sql index 317c662d9..1f40b3108 100644 --- a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOQ.sql +++ b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorLOQ.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT precursorchrominfoid AS PrecursorChromInfoId, precursorchrominfoid.SampleFileId AS SampleFileId, diff --git a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorRSquared.sql b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorRSquared.sql index ba2dd8ca7..e79e88f69 100644 --- a/resources/queries/targetedms/QCMetric_IsotopologuePrecursorRSquared.sql +++ b/resources/queries/targetedms/QCMetric_IsotopologuePrecursorRSquared.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2019-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT precursorchrominfoid AS PrecursorChromInfoId, precursorchrominfoid.SampleFileId AS SampleFileId, diff --git a/resources/queries/targetedms/QCMetric_fwb.sql b/resources/queries/targetedms/QCMetric_fwb.sql index f474ac118..d05028d23 100644 --- a/resources/queries/targetedms/QCMetric_fwb.sql +++ b/resources/queries/targetedms/QCMetric_fwb.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_fwhm.sql b/resources/queries/targetedms/QCMetric_fwhm.sql index dcd6043d5..388297036 100644 --- a/resources/queries/targetedms/QCMetric_fwhm.sql +++ b/resources/queries/targetedms/QCMetric_fwhm.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_isotopeDotp.sql b/resources/queries/targetedms/QCMetric_isotopeDotp.sql index 6609f8721..7ef04acb7 100644 --- a/resources/queries/targetedms/QCMetric_isotopeDotp.sql +++ b/resources/queries/targetedms/QCMetric_isotopeDotp.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2022-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_lhRatio.sql b/resources/queries/targetedms/QCMetric_lhRatio.sql index 8f5f0a6cc..c40f1eaf7 100644 --- a/resources/queries/targetedms/QCMetric_lhRatio.sql +++ b/resources/queries/targetedms/QCMetric_lhRatio.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_libraryDotp.sql b/resources/queries/targetedms/QCMetric_libraryDotp.sql index d27f9a179..46c10f313 100644 --- a/resources/queries/targetedms/QCMetric_libraryDotp.sql +++ b/resources/queries/targetedms/QCMetric_libraryDotp.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2022-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_massErrorPrecursor.sql b/resources/queries/targetedms/QCMetric_massErrorPrecursor.sql index 0ce0c2c75..926e7dd27 100644 --- a/resources/queries/targetedms/QCMetric_massErrorPrecursor.sql +++ b/resources/queries/targetedms/QCMetric_massErrorPrecursor.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_massErrorTransition.sql b/resources/queries/targetedms/QCMetric_massErrorTransition.sql index 20127dc67..ec4f40222 100644 --- a/resources/queries/targetedms/QCMetric_massErrorTransition.sql +++ b/resources/queries/targetedms/QCMetric_massErrorTransition.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2024-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_peakArea.sql b/resources/queries/targetedms/QCMetric_peakArea.sql index 0244e9302..7151b5a7b 100644 --- a/resources/queries/targetedms/QCMetric_peakArea.sql +++ b/resources/queries/targetedms/QCMetric_peakArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_precursorArea.sql b/resources/queries/targetedms/QCMetric_precursorArea.sql index 38b866020..648d043b0 100644 --- a/resources/queries/targetedms/QCMetric_precursorArea.sql +++ b/resources/queries/targetedms/QCMetric_precursorArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_retentionTime.sql b/resources/queries/targetedms/QCMetric_retentionTime.sql index b1a32857b..26b91e4d4 100644 --- a/resources/queries/targetedms/QCMetric_retentionTime.sql +++ b/resources/queries/targetedms/QCMetric_retentionTime.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_transitionArea.sql b/resources/queries/targetedms/QCMetric_transitionArea.sql index 9eb7d8d70..7504bf58e 100644 --- a/resources/queries/targetedms/QCMetric_transitionArea.sql +++ b/resources/queries/targetedms/QCMetric_transitionArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCMetric_transitionPrecursorRatio.sql b/resources/queries/targetedms/QCMetric_transitionPrecursorRatio.sql index e74b6dbe8..f176310fb 100644 --- a/resources/queries/targetedms/QCMetric_transitionPrecursorRatio.sql +++ b/resources/queries/targetedms/QCMetric_transitionPrecursorRatio.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2016-2019 LabKey Corporation + * Copyright (c) 2016-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCRunMetric_iRTCorrelation.sql b/resources/queries/targetedms/QCRunMetric_iRTCorrelation.sql index d7d4061f2..edd62613e 100644 --- a/resources/queries/targetedms/QCRunMetric_iRTCorrelation.sql +++ b/resources/queries/targetedms/QCRunMetric_iRTCorrelation.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2021-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCRunMetric_iRTIntercept.sql b/resources/queries/targetedms/QCRunMetric_iRTIntercept.sql index e44aed068..7430e7761 100644 --- a/resources/queries/targetedms/QCRunMetric_iRTIntercept.sql +++ b/resources/queries/targetedms/QCRunMetric_iRTIntercept.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2021-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCRunMetric_iRTSlope.sql b/resources/queries/targetedms/QCRunMetric_iRTSlope.sql index 96215be26..63595b7ab 100644 --- a/resources/queries/targetedms/QCRunMetric_iRTSlope.sql +++ b/resources/queries/targetedms/QCRunMetric_iRTSlope.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2021-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/QCRunMetric_ticArea.sql b/resources/queries/targetedms/QCRunMetric_ticArea.sql index a2a8881d4..480f43a11 100644 --- a/resources/queries/targetedms/QCRunMetric_ticArea.sql +++ b/resources/queries/targetedms/QCRunMetric_ticArea.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2019-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/queries/targetedms/SampleFileAssayResults.sql b/resources/queries/targetedms/SampleFileAssayResults.sql index 91d150e18..68d55f8d1 100644 --- a/resources/queries/targetedms/SampleFileAssayResults.sql +++ b/resources/queries/targetedms/SampleFileAssayResults.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT SampleIdentifier AS SampleName, ReplicateId.RunId.FileName, diff --git a/resources/queries/targetedms/SampleFileForQC.sql b/resources/queries/targetedms/SampleFileForQC.sql index b2a39e209..78e8a57e3 100644 --- a/resources/queries/targetedms/SampleFileForQC.sql +++ b/resources/queries/targetedms/SampleFileForQC.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT sf.*, sf.ReplicateId.Name AS ReplicateName, diff --git a/resources/queries/targetedms/msProjectDetails.sql b/resources/queries/targetedms/msProjectDetails.sql index 0db9f4989..f32b6e094 100644 --- a/resources/queries/targetedms/msProjectDetails.sql +++ b/resources/queries/targetedms/msProjectDetails.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT p.Id, p.affiliation, diff --git a/resources/queries/targetedms/qcMetricsConfig.sql b/resources/queries/targetedms/qcMetricsConfig.sql index bb5d5082d..990fe9317 100644 --- a/resources/queries/targetedms/qcMetricsConfig.sql +++ b/resources/queries/targetedms/qcMetricsConfig.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2019-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/schemas/dbscripts/postgresql/targetedms-0.000-25.000.sql b/resources/schemas/dbscripts/postgresql/targetedms-0.000-25.000.sql index 8f3f6bd6f..165fa555b 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-0.000-25.000.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-0.000-25.000.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2019 LabKey Corporation + * Copyright (c) 2022-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.000-25.001.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.000-25.001.sql index f438b2e1c..6080dbbb7 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.000-25.001.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.000-25.001.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE TABLE targetedms.msProject ( Id SERIAL NOT NULL , diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.001-25.002.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.001-25.002.sql index fb9840542..6984aea87 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.001-25.002.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.001-25.002.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- script from 24.11 CREATE FUNCTION targetedms.ensureColumns() RETURNS void AS $$ diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.002-25.003.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.002-25.003.sql index 0ffd34850..0d89e22ce 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.002-25.003.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.002-25.003.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE TABLE targetedms.rateType ( Id SERIAL NOT NULL , diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.003-25.004.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.003-25.004.sql index 7fdd571dd..44383f37e 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.003-25.004.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.003-25.004.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE TABLE targetedms.InstrumentNickname ( Id BIGSERIAL NOT NULL, diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.004-25.005.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.004-25.005.sql index f7fbe1fbd..dee149ae5 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.004-25.005.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.004-25.005.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ DELETE FROM targetedms.QCMetricExclusion WHERE MetricId IN (SELECT Id FROM targetedms.QCMetricConfiguration WHERE Series2QueryName IS NOT NULL); diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql index 4e7d0a41d..fab4ba8a3 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE TABLE targetedms.QCMetricCache ( Container entityid NOT NULL, diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.006-25.007.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.006-25.007.sql index 16d453688..a4a229481 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-25.006-25.007.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-25.006-25.007.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- Don't allow duplicate project/researcher mapping rows DELETE FROM targetedms.projectresearcher WHERE Id NOT IN (SELECT MIN(Id) FROM targetedms.projectresearcher GROUP BY project, researcher); diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.000-26.001.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.000-26.001.sql index 307cb822b..a79913f4e 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.000-26.001.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.000-26.001.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- Add FKs to Containers and delete orphaned rows DELETE FROM targetedms.instrumentUsagePayment WHERE Container NOT IN (SELECT EntityId FROM core.Containers); DELETE FROM targetedms.instrumentSchedule WHERE Container NOT IN (SELECT EntityId FROM core.Containers); diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.001-26.002.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.001-26.002.sql index 59d26d370..ffec27429 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.001-26.002.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.001-26.002.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE TABLE targetedms.PTMPercentsGroupedPrepivotCache ( Id BIGINT NOT NULL, -- PeptideId lookup, not a primary key diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.002-26.003.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.002-26.003.sql index 9c49a31f7..6b7d43011 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.002-26.003.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.002-26.003.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE targetedms.QCAnnotationType ADD COLUMN Shareable BOOLEAN DEFAULT FALSE; ALTER TABLE targetedms.QCAnnotation ADD COLUMN instrumentModel VARCHAR(300); ALTER TABLE targetedms.QCAnnotation ADD COLUMN instrumentSerialNumber VARCHAR(200); diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql index 2238063f4..7c71d2d2d 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT core.executeJavaUpgradeCode('reparentOrphanedTargetedMSData'); -- Adding missing foreign keys to core.Containers(EntityId) diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.004-26.005.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.004-26.005.sql index 14e1c1165..06d4532f6 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.004-26.005.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.004-26.005.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- Dropping idx_instrumentusagepayment_instrumentscheduleid [instrumentScheduleId] because it overlaps with pk_instrumentusagepayment [instrumentScheduleId, paymentMethod] DROP INDEX targetedms.idx_instrumentusagepayment_instrumentscheduleid; -- Dropping ix_qcannotationtype_container [Container] because it overlaps with uq_qcannotationtype_containername [Container, Name] diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.005-26.006.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.005-26.006.sql index 9327670a0..039048298 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.005-26.006.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.005-26.006.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- When reparenting the QCEmailNotifications table from PanoramaPremium schema to targetedms, an attempt was made to -- drop this index, but the attempt failed because it targeted the old schema. This index is redundant with -- IX_qcEmailNotifications_Container. diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.006-26.007.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.006-26.007.sql index 3ee9b11ed..a8d0e4f56 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.006-26.007.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.006-26.007.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE targetedms.Runs ADD COLUMN ProteinCount INT; UPDATE targetedms.Runs r diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql index 17c40a29a..8398ace0c 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql @@ -1 +1,6 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN AnnotationName VARCHAR(255); diff --git a/resources/schemas/dbscripts/postgresql/targetedms-create.sql b/resources/schemas/dbscripts/postgresql/targetedms-create.sql index 05a2653ce..6bcb29647 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-create.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-create.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ CREATE VIEW targetedms.AuditLog AS ( diff --git a/resources/schemas/dbscripts/postgresql/targetedms-drop.sql b/resources/schemas/dbscripts/postgresql/targetedms-drop.sql index ce7449561..082c02d76 100644 --- a/resources/schemas/dbscripts/postgresql/targetedms-drop.sql +++ b/resources/schemas/dbscripts/postgresql/targetedms-drop.sql @@ -1 +1,6 @@ +/* + * Copyright (c) 2020-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT core.fn_dropifexists('AuditLog', 'targetedms', 'VIEW', NULL); diff --git a/resources/schemas/targetedms.xml b/resources/schemas/targetedms.xml index 1ba2d107b..aabdf5017 100644 --- a/resources/schemas/targetedms.xml +++ b/resources/schemas/targetedms.xml @@ -1,7 +1,7 @@