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Fix skydDataId on TargetedMSRun #1033

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Merged
vagisha merged 3 commits into from
Mar 22, 2025
Merged

Fix skydDataId on TargetedMSRun #1033

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16f4c79
Add method to update skydDataId on a TargetedMSRun
vagisha Mar 16, 2025
0802d89
Added null check for newSkydData
vagisha Mar 19, 2025
75c3783
CR feedback - throw an IllegalArgumentException on null or unexpected…
vagisha Mar 21, 2025
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4 changes: 4 additions & 0 deletions api-src/org/labkey/api/targetedms/TargetedMSService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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();
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26 changes: 26 additions & 0 deletions src/org/labkey/targetedms/TargetedMSManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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 ");
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6 changes: 6 additions & 0 deletions src/org/labkey/targetedms/TargetedMSServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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()
{
Expand Down