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Merged
labkey-nicka merged 3 commits into from
Nov 25, 2025
Merged

Expand registry relationships represented by lineage #7210

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aab88a8
Reconcile protein sequences, vectors
labkey-nicka Nov 14, 2025
b37388d
Recreate exp.dataancestors table upon upgrade
labkey-nicka Nov 14, 2025
f031df2
repopulateAncestors
labkey-nicka Nov 15, 2025
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6 changes: 5 additions & 1 deletion api/src/org/labkey/api/exp/api/ExperimentService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,6 @@
import org.labkey.api.util.Pair;
import org.labkey.api.util.StringUtilsLabKey;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.NotFoundException;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.api.view.ViewContext;
import org.labkey.vfs.FileLike;
Expand Down Expand Up @@ -1183,6 +1182,11 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(

Map<String, Map<String, Object>> getDomainMetrics();

void clearAncestors(ExpRunItem runItem);
void clearDataAncestors(Collection<Long> dataRowIds);
void clearMaterialAncestors(Collection<Long> materialRowIds);
void repopulateAncestors();

class XarExportOptions
{
String _lsidRelativizer = LSID_OPTION_FOLDER_RELATIVE;
Expand Down
37 changes: 16 additions & 21 deletions experiment/src/org/labkey/experiment/api/ClosureQueryHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import org.labkey.api.data.MutableColumnInfo;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SqlExecutor;
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TempTableTracker;
import org.labkey.api.data.VirtualTable;
Expand Down Expand Up @@ -349,26 +350,26 @@ private static void incrementalRecomputeFromTempTable(SQLFragment familyTempTabl
}
}

public static void clearAncestorsForMaterial(long rowId)
public static void clearAncestorsForMaterials(Collection<Long> materialRowIds)
{
var tx = getScope().getCurrentTransaction();
if (null != tx)
{
tx.addCommitTask(() -> clearAncestorsForMaterial(rowId), DbScope.CommitTaskOption.POSTCOMMIT);
tx.addCommitTask(() -> clearAncestorsForMaterials(materialRowIds), DbScope.CommitTaskOption.POSTCOMMIT);
return;
}
recomputeMaterialAncestors(rowId);
recomputeMaterialAncestors(materialRowIds);
}

public static void clearAncestorsForDataObject(long rowId)
public static void clearAncestorsForDataObjects(Collection<Long> dataRowIds)
{
var tx = getScope().getCurrentTransaction();
if (null != tx)
{
tx.addCommitTask(() -> clearAncestorsForDataObject(rowId), DbScope.CommitTaskOption.POSTCOMMIT);
tx.addCommitTask(() -> clearAncestorsForDataObjects(dataRowIds), DbScope.CommitTaskOption.POSTCOMMIT);
return;
}
recomputeDataObjectAncestors(rowId);
recomputeDataObjectAncestors(dataRowIds);
}

public static void populateMaterialAncestors(Logger logger)
Expand Down Expand Up @@ -425,14 +426,12 @@ public static void truncateAndRecreate()

public static void truncateAndRecreate(Logger logger)
{
try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction())
{
TableInfo tInfo = ExperimentServiceImpl.get().getTinfoMaterialAncestors();
new SqlExecutor(tInfo.getSchema()).execute("TRUNCATE TABLE " + tInfo);
Table.truncate(ExperimentServiceImpl.get().getTinfoMaterialAncestors());
ClosureQueryHelper.populateMaterialAncestors(logger);

tInfo = ExperimentServiceImpl.get().getTinfoDataAncestors();
new SqlExecutor(tInfo.getSchema()).execute("TRUNCATE TABLE " + tInfo);
Table.truncate(ExperimentServiceImpl.get().getTinfoDataAncestors());
ClosureQueryHelper.populateDataAncestors(logger);

transaction.commit();
Expand Down Expand Up @@ -485,11 +484,11 @@ public static void recomputeFromSeeds(SQLFragment selectSeedsSql, boolean isSamp
}
}

private static void recomputeMaterialAncestors(long rowId)
private static void recomputeMaterialAncestors(Collection<Long> rowIds)
{
SQLFragment selectSeedsSql = new SQLFragment()
.append("SELECT m.RowId, m.ObjectId, 'm' AS ObjectType FROM exp.material m\n")
.append("WHERE m.RowId = ").appendValue(rowId);
.append("WHERE m.RowId ").appendInClause(rowIds, getScope().getSqlDialect());
recomputeFromSeeds(selectSeedsSql, true);
}

Expand Down Expand Up @@ -525,18 +524,16 @@ private static void recomputeMaterialAncestorsForRuns(Collection<Long> runIds)
.append("SELECT m.RowId, m.ObjectId, 'm' AS ObjectType FROM exp.material m\n")
.append("INNER JOIN exp.MaterialInput mi ON m.rowId = mi.materialId\n")
.append("INNER JOIN exp.ProtocolApplication pa ON mi.TargetApplicationId = pa.RowId\n")
.append("WHERE pa.RunId ");
getScope().getSqlDialect().appendInClauseSql(selectSeedsSql, runIds);
selectSeedsSql
.append("WHERE pa.RunId ").appendInClause(runIds, getScope().getSqlDialect())
.append(" AND pa.CpasType = ").appendValue(ExperimentRunOutput);
recomputeFromSeeds(selectSeedsSql, true);
}

private static void recomputeDataObjectAncestors(long rowId)
private static void recomputeDataObjectAncestors(Collection<Long> rowIds)
{
SQLFragment selectSeedsSql = new SQLFragment()
.append("SELECT d.RowId, d.ObjectId, 'd' AS ObjectType FROM exp.data d\n")
.append("WHERE d.RowId = ").appendValue(rowId);
.append("WHERE d.RowId ").appendInClause(rowIds, getScope().getSqlDialect());
recomputeFromSeeds(selectSeedsSql, false);
}

Expand Down Expand Up @@ -572,9 +569,7 @@ private static void recomputeDataAncestorsForRuns(Collection<Long> runIds)
.append("SELECT d.RowId, d.ObjectId, 'd' AS ObjectType FROM exp.data d\n")
.append("INNER JOIN exp.DataInput di ON d.rowId = di.dataId\n")
.append("INNER JOIN exp.ProtocolApplication pa ON di.TargetApplicationId = pa.RowId\n")
.append("WHERE pa.RunId ");
getScope().getSqlDialect().appendInClauseSql(selectSeedsSql, runIds);
selectSeedsSql
.append("WHERE pa.RunId ").appendInClause(runIds, getScope().getSqlDialect())
.append(" AND pa.CpasType = ").appendValue(ExperimentRunOutput);
recomputeFromSeeds(selectSeedsSql, false);
}
Expand Down
23 changes: 17 additions & 6 deletions experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -236,15 +236,13 @@
import org.labkey.api.view.HttpView;
import org.labkey.api.view.JspTemplate;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NotFoundException;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.api.view.ViewContext;
import org.labkey.experiment.ExperimentAuditProvider;
import org.labkey.experiment.FileLinkFileListener;
import org.labkey.experiment.MissingFilesCheckInfo;
import org.labkey.experiment.XarExportType;
import org.labkey.experiment.XarExporter;
import org.labkey.experiment.XarReader;
import org.labkey.experiment.api.property.DomainPropertyManager;
import org.labkey.experiment.controllers.exp.ExperimentController;
Expand All @@ -253,13 +251,11 @@
import org.labkey.experiment.pipeline.ExperimentPipelineJob;
import org.labkey.experiment.pipeline.MoveRunsPipelineJob;
import org.labkey.experiment.xar.AutoFileLSIDReplacer;
import org.labkey.experiment.xar.XarExportSelection;
import org.labkey.vfs.FileLike;
import org.springframework.dao.DataIntegrityViolationException;
import org.springframework.dao.PessimisticLockingFailureException;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UncheckedIOException;
import java.net.MalformedURLException;
Expand Down Expand Up @@ -3615,9 +3611,24 @@ public void clearAncestors(ExpRunItem runItem)
{
boolean isSample = runItem instanceof ExpMaterial;
if (isSample)
ClosureQueryHelper.clearAncestorsForMaterial(runItem.getRowId());
clearMaterialAncestors(List.of(runItem.getRowId()));
else
ClosureQueryHelper.clearAncestorsForDataObject(runItem.getRowId());
clearDataAncestors(List.of(runItem.getRowId()));
}

public void repopulateAncestors()
{
ClosureQueryHelper.truncateAndRecreate();
}

public void clearDataAncestors(Collection<Long> dataRowIds)
{
ClosureQueryHelper.clearAncestorsForDataObjects(dataRowIds);
}

public void clearMaterialAncestors(Collection<Long> materialRowIds)
{
ClosureQueryHelper.clearAncestorsForMaterials(materialRowIds);
}

public List<ProtocolApplication> getProtocolApplicationsForRun(long runId)
Expand Down