Fix skydDataId on TargetedMSRun (#1033)

- Added method to update skydDataId on a TargetedMSRun

Author: vagisha

api-src/org/labkey/api/targetedms/TargetedMSService.java

@@ -22,6 +22,7 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.ExperimentRunType;
 import org.labkey.api.exp.XarFormatException;
+import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
@@ -72,6 +73,9 @@ enum FolderType
     ITargetedMSRun getRunByFileName(String fileName, Container container);
     List<ITargetedMSRun> getRuns(Container container);
     ITargetedMSRun getRunByLsid(String lsid, Container container);
+
+    boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, User user);
+
     List<? extends SkylineAnnotation> getReplicateAnnotations(Container container);
     void registerSkylineDocumentImportListener(SkylineDocumentImportListener skyLineDocumentImportListener);
     List<SkylineDocumentImportListener> getSkylineDocumentImportListener();

src/org/labkey/targetedms/TargetedMSManager.java

@@ -73,6 +73,7 @@
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.DeletePermission;
+import org.labkey.api.targetedms.ITargetedMSRun;
 import org.labkey.api.targetedms.RepresentativeDataState;
 import org.labkey.api.targetedms.RunRepresentativeDataState;
 import org.labkey.api.targetedms.TargetedMSService;
@@ -123,6 +124,7 @@
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.TreeMap;
 import java.util.TreeSet;
@@ -861,6 +863,30 @@ public static TargetedMSRun getRunByLsid(String lsid, Container c)
         throw new IllegalArgumentException("More than one TargetedMS runs found for LSID "+lsid);
     }
 
+    public static boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, User user)
+    {
+        if (!(run instanceof TargetedMSRun))
+        {
+            throw new IllegalArgumentException("Invalid run type. Expected TargetedMSRun but received " +
+                    (run != null ? run.getClass().getName() : "null"));
+        }
+        if (newSkydData == null)
+        {
+            throw new IllegalArgumentException("Cannot update with null newSkydData. A valid ExpData object is required");
+        }
+
+        TargetedMSRun targetedRun = (TargetedMSRun) run;
+
+        ExpRun expRun = ExperimentService.get().getExpRun(targetedRun.getExperimentRunLSID());
+        if (expRun == null) return false;
+
+        if (!Objects.equals(newSkydData.getRunId(), expRun.getRowId())) return false;
+
+        targetedRun.setSkydDataId(newSkydData.getRowId());
+        TargetedMSManager.updateRun(targetedRun, user);
+        return true;
+    }
+
     public static List<Long> getRunIdsByInstrument(String serialNumber)
     {
         SQLFragment sql = new SQLFragment("SELECT DISTINCT r.Id FROM ");

src/org/labkey/targetedms/TargetedMSServiceImpl.java

@@ -22,6 +22,7 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.ExperimentRunType;
 import org.labkey.api.exp.XarFormatException;
+import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
@@ -275,6 +276,11 @@ public ITargetedMSRun getRunByLsid(String lsid, Container container)
         return TargetedMSManager.getRunByLsid(lsid, container);
     }
 
+    public boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, User user)
+    {
+        return TargetedMSManager.updateSkydDataId(run, newSkydData, user);
+    }
+
     @Override
     public ExperimentRunType getExperimentRunType()
     {