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Avoid loading full result sets for run input roles and the classic Lineage panel #8157

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Merged
labkey-jeckels merged 2 commits into from
Oct 19, 2026
Merged

Avoid loading full result sets for run input roles and the classic Lineage panel #8157

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149e26f
Select distinct input roles instead of loading every input row
labkey-jeckels Oct 11, 2026
bc1db85
Build the classic Lineage panel from lineage ids instead of loading e…
labkey-jeckels Oct 11, 2026
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128 changes: 54 additions & 74 deletions experiment/src/org/labkey/experiment/ParentChildView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,18 +15,21 @@
*/
package org.labkey.experiment;

import org.jetbrains.annotations.Nullable;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.DataRegion;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.data.TableInfo;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExpDataClass;
import org.labkey.api.exp.api.ExpLineageOptions;
import org.labkey.api.exp.api.ExpMaterial;
import org.labkey.api.exp.api.ExpRunItem;
import org.labkey.api.exp.api.ExpSampleType;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.api.SampleTypeService;
import org.labkey.api.exp.query.ExpDataTable;
import org.labkey.api.exp.query.ExpMaterialTable;
Expand All @@ -39,15 +42,15 @@
import org.labkey.api.query.UserSchema;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.util.Pair;
import org.labkey.api.view.HBox;
import org.labkey.api.view.VBox;
import org.labkey.api.view.ViewContext;
import org.labkey.experiment.api.ExpDataImpl;
import org.labkey.experiment.api.ExperimentServiceImpl;
import org.labkey.experiment.lineage.ExpLineageServiceImpl;
import org.labkey.experiment.lineage.ExpLineageServiceImpl.LineageResult;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

Expand All @@ -64,29 +67,50 @@ public ParentChildView(ExpRunItem output, ViewContext context)
addView(parentsHBox);
addView(childrenHBox);

Pair<Set<ExpData>, Set<ExpMaterial>> parents = ExperimentService.get().getParents(context.getContainer(), context.getUser(), output);
Set<ExpData> parentDatas = parents.first;
ExpLineageOptions parentOptions = new ExpLineageOptions();
parentOptions.setChildren(false);
LineageResult parents = ExpLineageServiceImpl.get().getLineageResult(getContainer(), getUser(), Set.of(output), parentOptions);
parentsHBox.addView(createDataView(parents.dataIds(), "parentData", "Parent Data"));
parentsHBox.addView(createMaterialsView(parents.materialIds(), "parentMaterials", "Precursor Samples"));

ExpLineageOptions childOptions = new ExpLineageOptions();
childOptions.setParents(false);
LineageResult children = ExpLineageServiceImpl.get().getLineageResult(getContainer(), getUser(), Set.of(output), childOptions);
childrenHBox.addView(createDataView(children.dataIds(), "childData", "Child Data"));
childrenHBox.addView(createMaterialsView(children.materialIds(), "childMaterials", "Child Samples"));
}

QueryView parentDatasView = createDataView(parentDatas, "parentData", "Parent Data");
parentsHBox.addView(parentDatasView);
private Container getContainer() { return getViewContext().getContainer(); }
private User getUser() { return getViewContext().getUser(); }

Set<ExpMaterial> parentMaterials = parents.second;
QueryView parentSamplesView = createMaterialsView(parentMaterials, "parentMaterials", "Precursor Samples");
parentsHBox.addView(parentSamplesView);
/**
* @param singleType the type shared by every readable row, or null if they differ
* @param containerFilter readable folders holding the rows; lineage crosses folders (Issue 38018)
*/
private record LineageRows(@Nullable Object singleType, ContainerFilter containerFilter) {}

Pair<Set<ExpData>, Set<ExpMaterial>> children = ExperimentService.get().getChildren(context.getContainer(), context.getUser(), output);
Set<ExpData> childData = children.first;
QueryView childDataView = createDataView(childData, "childData", "Child Data");
childrenHBox.addView(childDataView);
private LineageRows getLineageRows(TableInfo table, String typeColumn, Set<Long> rowIds)
{
Set<Container> containers = new HashSet<>();
Set<Object> types = new HashSet<>();
if (!rowIds.isEmpty())
{
SQLFragment sql = new SQLFragment("SELECT DISTINCT Container, " + typeColumn + " FROM ").append(table, "t").append(" WHERE RowId ");
table.getSqlDialect().appendInClauseSql(sql, rowIds);
new SqlSelector(table.getSchema(), sql).forEach(rs -> {
Container c = ContainerManager.getForId(rs.getString(1));
if (c != null && c.hasPermission(getUser(), ReadPermission.class))
{
containers.add(c);
types.add(rs.getObject(2));
}
});
}

Set<ExpMaterial> childMaterials = children.second;
QueryView childSamplesView = createMaterialsView(childMaterials, "childMaterials", "Child Samples");
childrenHBox.addView(childSamplesView);
Object singleType = types.size() == 1 ? types.iterator().next() : null;
return new LineageRows(singleType, new ContainerFilter.SimpleContainerFilterWithUser(getUser(), containers));
}

private Container getContainer() { return getViewContext().getContainer(); }
private User getUser() { return getViewContext().getUser(); }

private QueryView configureView(QueryView view, String title)
{
view.disableContainerFilterSelection();
Expand All @@ -104,26 +128,10 @@ private QueryView configureView(QueryView view, String title)
return view;
}

private QueryView createDataView(Set<ExpData> data, String dataRegionName, String title)
private QueryView createDataView(Set<Long> rowIds, String dataRegionName, String title)
{
Long classId = null;
data.removeIf(d -> !d.getContainer().hasPermission(getUser(), ReadPermission.class));
for (ExpData d : data)
{
Long id = ((ExpDataImpl)d).getDataObject().getClassId();
if (classId == null)
{
classId = id;
}
else if (!classId.equals(id))
{
classId = null;
break;
}
}

final List<Long> rowIds = data.stream().map(ExpData::getRowId).toList();
final ExpDataClass dataClass = classId == null ? null : ExperimentServiceImpl.get().getDataClass(classId);
LineageRows rows = getLineageRows(ExperimentServiceImpl.get().getTinfoData(), "ClassId", rowIds);
final ExpDataClass dataClass = rows.singleType() instanceof Number classId ? ExperimentServiceImpl.get().getDataClass(classId.longValue()) : null;

UserSchema schema = new ExpSchema(getUser(), getContainer());
QuerySettings settings;
Expand All @@ -140,9 +148,7 @@ else if (!classId.equals(id))
}

QueryView queryView = new QueryView(schema, settings, null);
// Issue 38018: Sample Type: Multiple data inputs from different containers are not shown in the Parent Data grid
// Use ContainerFilter.EVERYTHING - We've already set an IN clause that restricts us to showing just data that we have permission to view
queryView.setContainerFilter(ContainerFilter.getUnsafeEverythingFilter());
queryView.setContainerFilter(rows.containerFilter());
TableInfo table = queryView.getTable();

CustomView v = queryView.getCustomView();
Expand Down Expand Up @@ -170,35 +176,11 @@ else if (!classId.equals(id))
return configureView(queryView, title);
}

private QueryView createMaterialsView(final Set<ExpMaterial> materials, String dataRegionName, String title)
private QueryView createMaterialsView(Set<Long> rowIds, String dataRegionName, String title)
{
// Strip out materials in folders that the user can't see - this lets us avoid a container filter that
// enforces the permissions when we do the query
String typeName = null;
boolean sameType = true;
for (Iterator<ExpMaterial> iter = materials.iterator(); iter.hasNext(); )
{
ExpMaterial material = iter.next();
if (!material.getContainer().hasPermission(getUser(), ReadPermission.class))
{
iter.remove();
}

String type = material.getCpasType();
if (sameType)
{
if (typeName == null)
typeName = type;
else if (!typeName.equals(type))
{
typeName = null;
sameType = false;
}
}
}

LineageRows rows = getLineageRows(ExperimentServiceImpl.get().getTinfoMaterial(), "CpasType", rowIds);
final ExpSampleType st;
if (sameType && typeName != null && !ExpMaterial.DEFAULT_CPAS_TYPE.equals(typeName) && !"Sample".equals(typeName))
if (rows.singleType() instanceof String typeName && !ExpMaterial.DEFAULT_CPAS_TYPE.equals(typeName) && !"Sample".equals(typeName))
st = SampleTypeService.get().getSampleType(typeName);
else
st = null;
Expand All @@ -216,16 +198,14 @@ else if (!typeName.equals(type))
settings = schema.getSettings(getViewContext(), dataRegionName, st.getName());
}

final List<Long> rowIds = materials.stream().map(ExpMaterial::getRowId).toList();
settings.getBaseFilter().addInClause(FieldKey.fromParts(ExpMaterialTable.Column.RowId), rowIds);

QueryView queryView = new QueryView(schema, settings, null)
{
@Override
protected TableInfo createTable()
{
// Use ContainerFilter.EVERYTHING - We've already set an IN clause that restricts us to showing just data that we have permission to view
ExpMaterialTable table = ExperimentServiceImpl.get().createMaterialTable(getSchema(), ContainerFilter.getUnsafeEverythingFilter(), st);
ExpMaterialTable table = ExperimentServiceImpl.get().createMaterialTable(getSchema(), rows.containerFilter(), st);
table.populate();

List<FieldKey> defaultVisibleColumns = new ArrayList<>();
Expand Down
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2287,7 +2287,7 @@ public Set<String> getMaterialInputRoles(Container container, User user, ExpProt

private Set<String> getInputRoles(Container ignoredContainer, ContainerFilter filter, TableInfo table, ExpProtocol.ApplicationType... types)
{
SQLFragment sql = new SQLFragment("SELECT role FROM ");
SQLFragment sql = new SQLFragment("SELECT DISTINCT role FROM ");
sql.append(table, "t");
sql.append(" WHERE targetapplicationid IN (SELECT pa.rowid FROM ");
sql.append(getTinfoProtocolApplication(), "pa");
Expand Down
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