[bot] Fast-forward for 26.3.2

resources/queries/targetedms/qcannotation/.qview.xml

@@ -4,6 +4,8 @@
         <column name="Date" />
         <column name="EndDate" />
         <column name="QCAnnotationTypeId" />
+        <column name="instrumentModel" />
+        <column name="instrumentSerialNumber" />
         <column name="Container" />
         <column name="Created" />
         <column name="Modified" />

resources/queries/targetedms/qcannotationtype/.qview.xml

@@ -4,6 +4,7 @@
         <column name="Description" />
         <column name="Color" />
         <column name="Container" />
+        <column name="Shareable"/>
         <column name="Created" />
         <column name="Modified" />
     </columns>

resources/schemas/dbscripts/postgresql/targetedms-26.002-26.003.sql

@@ -0,0 +1,5 @@
+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);
+
+UPDATE targetedms.QCAnnotationType SET Shareable = TRUE WHERE Name = 'Instrumentation Change';

resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql

@@ -0,0 +1,15 @@
+SELECT core.executeJavaUpgradeCode('reparentOrphanedTargetedMSData');
+
+-- Adding missing foreign keys to core.Containers(EntityId)
+ALTER TABLE targetedms.Runs ADD CONSTRAINT FK_Runs_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.QCAnnotation ADD CONSTRAINT FK_QCAnnotation_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.GuideSet ADD CONSTRAINT FK_GuideSet_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.AutoQCPing ADD CONSTRAINT FK_AutoQCPing_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.PrecursorChromInfo ADD CONSTRAINT FK_PrecursorChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.SampleFileChromInfo ADD CONSTRAINT FK_SampleFileChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+
+-- Adding missing indices on Container
+CREATE INDEX IX_QCAnnotationType_Container ON targetedms.QCAnnotationType(Container);
+CREATE INDEX IX_QCAnnotation_Container ON targetedms.QCAnnotation(Container);
+CREATE INDEX IX_GuideSet_Container ON targetedms.GuideSet(Container);
+CREATE INDEX IX_QCMetricConfiguration_Container ON targetedms.QCMetricConfiguration(Container);

resources/schemas/targetedms.xml

@@ -1262,6 +1262,7 @@
             <column columnName="Name"/>
             <column columnName="Description"/>
             <column columnName="Color"/>
+            <column columnName="Shareable"/>
         </columns>
     </table>
 
@@ -1307,6 +1308,8 @@
                 <columnTitle>Annotation Type</columnTitle>
                 <description>The category of the event</description>
             </column>
+            <column columnName="instrumentModel"/>
+            <column columnName="instrumentSerialNumber"/>
         </columns>
     </table>
     <table tableName="QCMetricConfiguration" tableDbType="TABLE">

src/org/labkey/targetedms/TargetedMSController.java

@@ -505,6 +505,9 @@ else if (FolderType.QC.toString().equals(folderSetupForm.getFolderType()))
             addDataPipelineTab(c);
             addRawFilesPipelineTab(c);
 
+            // We may have toggled into or out of QC folder type, so clear out the cache
+            TargetedMSManager.get().clearQCMetricCache(c, true);
+
             // Inform listeners so that any additional folder configuration can be done.
             TargetedMSService.get().getTargetedMSFolderTypeListeners().forEach(listener -> listener.folderCreated(c, getUser()));
 

src/org/labkey/targetedms/TargetedMSManager.java

@@ -17,6 +17,8 @@
 package org.labkey.targetedms;
 
 import com.google.common.base.Joiner;
+import lombok.Getter;
+import lombok.Setter;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
@@ -165,9 +167,18 @@ private TargetedMSManager()
     private static final Cache<Container, List<QCMetricConfiguration>> _metricCache = CacheManager.getBlockingCache(1000, TimeUnit.HOURS.toMillis(1), "Enabled QC metric configs",
             (c, argument) ->
             {
+                if (!(argument instanceof TargetedMSSchema schema))
+                {
+                    throw new IllegalArgumentException("Argument must be a TargetedMSSchema but was " + argument);
+                }
+
+                if (getFolderType(schema.getContainer()) != TargetedMSService.FolderType.QC)
+                {
+                    return Collections.emptyList();
+                }
+
                 try
                 {
-                    TargetedMSSchema schema = (TargetedMSSchema) argument;
                     TableInfo metricsTable = schema.getTableOrThrow("qcMetricsConfig", null);
                     List<QCMetricConfiguration> metrics = new TableSelector(metricsTable, null, new Sort(FieldKey.fromParts("Name"))).getArrayList(QCMetricConfiguration.class);
 
@@ -207,7 +218,8 @@ public static TargetedMSManager get()
 
     public static List<SampleFileChromInfo> getSampleFileChromInfos(SampleFile sampleFile)
     {
-        return new TableSelector(getTableInfoSampleFileChromInfo(), new SimpleFilter(FieldKey.fromParts("SampleFileId"), sampleFile.getId()), new Sort("TextId")).getArrayList(SampleFileChromInfo.class);    }
+        return new TableSelector(getTableInfoSampleFileChromInfo(), new SimpleFilter(FieldKey.fromParts("SampleFileId"), sampleFile.getId()), new Sort("TextId")).getArrayList(SampleFileChromInfo.class);
+    }
 
     public static SampleFileChromInfo getSampleFileChromInfo(int id, Container c)
     {
@@ -548,7 +560,8 @@ public static TableInfo getTableInfoQuantificationSettings()
         return getSchema().getTable(TargetedMSSchema.TABLE_QUANTIIFICATION_SETTINGS);
     }
 
-    public static TableInfo getTableInfoCalibrationCurve() {
+    public static TableInfo getTableInfoCalibrationCurve()
+    {
         return getSchema().getTable(TargetedMSSchema.TABLE_CALIBRATION_CURVE);
     }
 
@@ -628,19 +641,23 @@ public static TableInfo getTableInfoSkylineAuditLogMessage()
         return getSchema().getTable(TargetedMSSchema.TABLE_SKYLINE_AUDITLOG_MESSAGE);
     }
 
-    public static TableInfo getTableInfoListDefinition() {
+    public static TableInfo getTableInfoListDefinition()
+    {
         return getSchema().getTable(TargetedMSSchema.TABLE_LIST_DEFINITION);
     }
 
-    public static TableInfo getTableInfoListColumnDefinition() {
+    public static TableInfo getTableInfoListColumnDefinition()
+    {
         return getSchema().getTable(TargetedMSSchema.TABLE_LIST_COLUMN_DEFINITION);
     }
 
-    public static TableInfo getTableInfoListItem() {
+    public static TableInfo getTableInfoListItem()
+    {
         return getSchema().getTable(TargetedMSSchema.TABLE_LIST_ITEM);
     }
 
-    public static TableInfo getTableInfoListItemValue() {
+    public static TableInfo getTableInfoListItemValue()
+    {
         return getSchema().getTable(TargetedMSSchema.TABLE_LIST_ITEM_VALUE);
     }
 
@@ -1246,7 +1263,7 @@ public List<InstrumentNickname> getNickname(String name, TargetedMSSchema schema
         }
 
         List<InstrumentNickname> result = new ArrayList<>(dedupeAcrossContainers.values());
-        
+
         if (matches.isEmpty())
         {
             String sql = "SELECT DISTINCT InstrumentNickname, " +
@@ -2516,6 +2533,17 @@ public void moveRun(TargetedMSRun run, Container newContainer, String newRunLSID
 
         new SqlExecutor(getSchema()).execute(updatePrecChromInfoSql);
 
+        SQLFragment updateSampleFileChromInfoSql = new SQLFragment("UPDATE ");
+        updateSampleFileChromInfoSql.append(getTableInfoSampleFileChromInfo(), "");
+        updateSampleFileChromInfoSql.append(" SET container = ?").add(newContainer);
+        updateSampleFileChromInfoSql.append(" WHERE sampleFileId IN (");
+        updateSampleFileChromInfoSql.append(" SELECT sf.Id FROM ").append(getTableInfoSampleFile(), "sf");
+        updateSampleFileChromInfoSql.append(" INNER JOIN ").append(getTableInfoReplicate(), "rep").append(" ON rep.Id = sf.ReplicateId");
+        updateSampleFileChromInfoSql.append(" WHERE rep.runId = ?").add(run.getId());
+        updateSampleFileChromInfoSql.append(" )");
+
+        new SqlExecutor(getSchema()).execute(updateSampleFileChromInfoSql);
+
         run.setExperimentRunLSID(newRunLSID);
         run.setDataId(newDataRowId);
         run.setContainer(newContainer);
@@ -3046,6 +3074,39 @@ private QueryUpdateService getNicknameUpdateService(User user, Container contain
         return Objects.requireNonNull(table.getUpdateService());
     }
 
+    public static class InstrumentDetails
+    {
+        @Getter @Setter
+        private String instrumentSerialNumber;
+        @Getter @Setter
+        private String model;
+
+        public InstrumentDetails()
+        {
+        }
+    }
+
+    public static List<InstrumentDetails> getInstrumentDetails(Container container)
+    {
+        SQLFragment sql = new SQLFragment("SELECT DISTINCT sf.InstrumentSerialNumber, i.Model FROM ");
+        sql.append(getTableInfoSampleFile(), "sf");
+        sql.append(" INNER JOIN ");
+        sql.append(getTableInfoInstrument(), "i");
+        sql.append(" ON sf.InstrumentId = i.Id ");
+        sql.append(" INNER JOIN ");
+        sql.append(getTableInfoReplicate(), "rep");
+        sql.append(" ON sf.ReplicateId = rep.Id ");
+        sql.append(" INNER JOIN ");
+        sql.append(getTableInfoRuns(), "r");
+        sql.append(" ON rep.RunId = r.Id ");
+        sql.append(" WHERE r.Container = ?");
+        sql.add(container);
+
+        return new SqlSelector(getSchema(), sql).getArrayList(InstrumentDetails.class);
+
+    }
+
+
     public void deleteNickname(InstrumentNickname name, User user) throws SQLException, BatchValidationException, QueryUpdateServiceException, InvalidKeyException
     {
         getNicknameUpdateService(user, name.getContainer()).
@@ -3071,4 +3132,15 @@ public void saveNickname(InstrumentNickname name, User user) throws SQLException
                     insertRows(user, name.getContainer(), Arrays.asList(row), errors, null, null);
         }
     }
+
+    public static boolean isQCAnnotationTypeShareable(int qcAnnotationTypeId)
+    {
+        SQLFragment sql = new SQLFragment("SELECT Shareable FROM ");
+        sql.append(getTableInfoQCAnnotationType());
+        sql.append(" WHERE Id = ?");
+        sql.add(qcAnnotationTypeId);
+
+        Boolean isShareable = new SqlSelector(getSchema(), sql).getObject(Boolean.class);
+        return isShareable != null && isShareable;
+    }
 }

src/org/labkey/targetedms/TargetedMSModule.java

@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.002;
+        return 26.004;
     }
 
     @Override

src/org/labkey/targetedms/TargetedMSUpgradeCode.java

@@ -108,4 +108,42 @@ public void populatePTMPercentsGroupedPrepivotCache(final ModuleContext moduleCo
 
         LOG.info("Finished populating PTMPercentsGroupedPrepivotCache for existing ExperimentMAM folders");
     }
+
+    @SuppressWarnings("UnusedDeclaration")
+    public void reparentOrphanedTargetedMSData(final ModuleContext moduleContext)
+    {
+        if (moduleContext.isNewInstall())
+        {
+            return;
+        }
+
+        Container sharedContainer = ContainerManager.getSharedContainer();
+
+        SqlExecutor executor = new SqlExecutor(TargetedMSManager.getSchema());
+
+        String[] tablesToDeleteOrphans = {"QCAnnotation", "GuideSet", "AutoQCPing"};
+        for (String tableName : tablesToDeleteOrphans)
+        {
+            SQLFragment deleteSql = new SQLFragment("DELETE FROM targetedms.").append(tableName)
+                    .append(" WHERE Container NOT IN (SELECT EntityId FROM core.Containers)");
+            int deletedCount = executor.execute(deleteSql);
+            if (deletedCount > 0)
+            {
+                LOG.info("Deleted " + deletedCount + " orphaned rows from targetedms." + tableName);
+            }
+        }
+
+        String[] tablesToReparentOrphans = {"Runs", "PrecursorChromInfo", "SampleFileChromInfo"};
+        for (String tableName : tablesToReparentOrphans)
+        {
+            SQLFragment updateSql = new SQLFragment("UPDATE targetedms.").append(tableName)
+                    .append(" SET Container = ? WHERE Container NOT IN (SELECT EntityId FROM core.Containers)")
+                    .add(sharedContainer.getEntityId());
+            int updatedCount = executor.execute(updateSql);
+            if (updatedCount > 0)
+            {
+                LOG.info("Reparented " + updatedCount + " orphaned rows from targetedms." + tableName + " to /Shared");
+            }
+        }
+    }
 }

src/org/labkey/targetedms/query/QCAnnotationTable.java

@@ -15,13 +15,27 @@
  */
 package org.labkey.targetedms.query;
 
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.gwt.client.AuditBehaviorType;
+import org.labkey.api.query.BatchValidationException;
+import org.labkey.api.query.DefaultQueryUpdateService;
+import org.labkey.api.query.DuplicateKeyException;
 import org.labkey.api.query.QueryForeignKey;
+import org.labkey.api.query.QueryUpdateService;
+import org.labkey.api.query.QueryUpdateServiceException;
 import org.labkey.api.query.SimpleUserSchema;
+import org.labkey.api.query.ValidationException;
+import org.labkey.api.security.User;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
 
+import java.sql.SQLException;
+import java.util.List;
+import java.util.Map;
+
 import static org.labkey.targetedms.query.GuideSetTable.appendFormatLabel;
 
 /**
@@ -44,4 +58,54 @@ public QCAnnotationTable(TargetedMSSchema schema, ContainerFilter cf)
         appendFormatLabel(getMutableColumn("EndDate"));
         setAuditBehavior(AuditBehaviorType.DETAILED);
     }
+
+    @Override
+    public QueryUpdateService getUpdateService()
+    {
+        TableInfo table = getRealTable();
+        if (table != null)
+        {
+            return new DefaultQueryUpdateService(this, getRealTable())
+            {
+                @Override
+                public List<Map<String, Object>> insertRows(User user, Container container, List<Map<String, Object>> rows, BatchValidationException errors, @Nullable Map<Enum, Object> configParameters, @Nullable Map<String, Object> extraScriptContext) throws SQLException, QueryUpdateServiceException, DuplicateKeyException
+                {
+                    List<Map<String, Object>> resultRows = new java.util.ArrayList<>();
+                    for (Map<String, Object> row : rows)
+                    {
+                        // Check if the QCAnnotationType is shareable
+                        int qcAnnotationTypeId = (Integer) row.get("QCAnnotationTypeId");
+                        boolean isShareable = TargetedMSManager.isQCAnnotationTypeShareable(qcAnnotationTypeId);
+
+                        if (isShareable)
+                        {
+                            List<TargetedMSManager.InstrumentDetails> instruments = TargetedMSManager.getInstrumentDetails(getContainer());
+                            if (instruments.isEmpty())
+                            {
+                                resultRows.add(row);
+                            }
+                            else
+                            {
+                                for (TargetedMSManager.InstrumentDetails instrument : instruments)
+                                {
+                                    Map<String, Object> newRow = new java.util.HashMap<>(row);
+                                    newRow.put("instrumentModel", instrument.getModel());
+                                    newRow.put("instrumentSerialNumber", instrument.getInstrumentSerialNumber());
+                                    newRow.put("Container", getContainer().getId());
+                                    resultRows.add(newRow);
+                                }
+                            }
+                        }
+                        else
+                        {
+                            resultRows.add(row);
+                        }
+                    }
+
+                    return super.insertRows(user, container, resultRows, errors, configParameters, extraScriptContext);
+                }
+            };
+        }
+        return null;
+    }
 }