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Container scope #1023

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8616ebf
Microarray container scope
labkey-nicka Jun 12, 2026
9a8b204
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labkey-nicka Jun 12, 2026
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121 changes: 77 additions & 44 deletions microarray/src/org/labkey/microarray/MicroarrayManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,15 @@
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.CaseInsensitiveHashMap;
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.DbSchema;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.JdbcType;
import org.labkey.api.data.Results;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.SqlExecutor;
Expand All @@ -50,20 +54,25 @@
import org.labkey.api.reader.DataLoader;
import org.labkey.api.reader.TabLoader;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.Permission;
import org.labkey.api.util.ContainerUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.microarray.controllers.FeatureAnnotationSetController;
import org.labkey.microarray.matrix.ExpressionMatrixProtocolSchema;
import org.labkey.microarray.query.MicroarrayUserSchema;

import java.io.File;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

public class MicroarrayManager
{
Expand All @@ -87,7 +96,7 @@ private static TableInfo getAnnotationQueryTableInfo(User user, Container contai
return schema.getTable(MicroarrayUserSchema.TABLE_FEATURE_ANNOTATION, false);
}

private static TableInfo getAnnotationSetSchemaTableInfo()
public static TableInfo getAnnotationSetSchemaTableInfo()
{
DbSchema schema = MicroarrayUserSchema.getSchema();
return schema.getTable(MicroarrayUserSchema.TABLE_FEATURE_ANNOTATION_SET);
Expand All @@ -105,32 +114,22 @@ public long featureAnnotationSetCount(Container c)
return selector.getRowCount();
}

public int deleteFeatureAnnotationSet(int... rowId)
public int deleteFeatureAnnotationSet(Collection<Integer> ids)
{
DbScope scope = MicroarrayUserSchema.getSchema().getScope();

Integer[] ids = ArrayUtils.toObject(rowId);

try (DbScope.Transaction tx = scope.ensureTransaction())
try (DbScope.Transaction tx = MicroarrayUserSchema.getSchema().getScope().ensureTransaction())
{
// Delete all annotations first.
TableInfo annotationSchemaTableInfo = getAnnotationSchemaTableInfo();
SimpleFilter filter = new SimpleFilter();
filter.addInClause(FieldKey.fromParts("FeatureAnnotationSetId"), Arrays.asList(ids));
int rowsDeleted = Table.delete(annotationSchemaTableInfo, filter);
int rowsDeleted = Table.delete(getAnnotationSchemaTableInfo(), new SimpleFilter(FieldKey.fromParts("FeatureAnnotationSetId"), ids, CompareType.IN));

// Then delete annotation set.
TableInfo annotationSetSchemaTableInfo = getAnnotationSetSchemaTableInfo();
filter = new SimpleFilter();
filter.addInClause(FieldKey.fromParts("RowId"), Arrays.asList(ids));
Table.delete(annotationSetSchemaTableInfo, filter);
Table.delete(getAnnotationSetSchemaTableInfo(), new SimpleFilter(FieldKey.fromParts("RowId"), ids, CompareType.IN));

tx.commit();
return rowsDeleted;
}
}

private Integer insertFeatureAnnotationSet(User user, Container container, String name, String vendor, String description, String comment, BatchValidationException errors)
public Integer insertFeatureAnnotationSet(User user, Container container, String name, String vendor, String description, String comment, BatchValidationException errors)
throws SQLException, BatchValidationException, QueryUpdateServiceException, DuplicateKeyException
{
MicroarrayUserSchema schema = new MicroarrayUserSchema(user, container);
Expand Down Expand Up @@ -175,7 +174,7 @@ private Integer insertFeatureAnnotations(User user, Container container, Integer
return -1;
}

/** Creates feature annotation set AND inserts all feature annotations from TSV */
/** Creates a feature annotation set AND inserts all feature annotations from TSV */
public Integer createFeatureAnnotationSet(User user, Container c, FeatureAnnotationSetController.FeatureAnnotationSetForm form, DataLoader loader, BatchValidationException errors)
throws SQLException, BatchValidationException, QueryUpdateServiceException, DuplicateKeyException
{
Expand All @@ -187,48 +186,82 @@ public Integer createFeatureAnnotationSet(User user, Container c, FeatureAnnotat
return -1;
}

/**
* Get feature annotation set by name if it is in scope (current, project, and shared container).
*/
@Nullable
public Integer getFeatureAnnotationSet(Container c, User user, String featureSetName)
private void applyContainerFilter(Container c, User user, SimpleFilter filter)
{
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromParts("Name"), featureSetName);

// The container filter matches the assay's featureSet run property lookup
ContainerFilter cf = new ContainerFilter.CurrentPlusProjectAndShared(c, user);
filter.addClause(cf.createFilterClause(MicroarrayUserSchema.getSchema(), FieldKey.fromParts("container")));
}

/**
* Get a feature annotation set by name if it is in scope (current, project, and shared container).
*/
public @Nullable Integer getFeatureAnnotationSet(Container c, User user, String featureSetName)
{
return getFeatureAnnotationSet(c, user, new SimpleFilter(FieldKey.fromParts("Name"), featureSetName));
}

/**
* Get a feature annotation set by id if it is in scope (current, project, and shared container).
*/
public @Nullable Integer getFeatureAnnotationSet(Container c, User user, int id)
{
return getFeatureAnnotationSet(c, user, new SimpleFilter(FieldKey.fromParts("RowId"), id));
}

private @Nullable Integer getFeatureAnnotationSet(Container c, User user, SimpleFilter filter)
{
applyContainerFilter(c, user, filter);
List<Integer> rowIds = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null).getArrayList(Integer.class);

TableSelector featureAnnotationSelector = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null);
List<Integer> rowIds = featureAnnotationSelector.getArrayList(Integer.class);
// TODO: Order results by container depth
if (!rowIds.isEmpty())
return rowIds.get(0);
if (rowIds.isEmpty())
return null;

return null;
return rowIds.get(0);
}

/**
* Get feature annotation set by id if it is in scope (current, project, and shared container).
* Gets feature annotation sets by id that are in folder scope (current, project, and shared container). The user
* must have the provided permissions in all containers that the feature annotation sets are declared in.
*/
@Nullable
public Integer getFeatureAnnotationSet(Container c, User user, int id)
public @NotNull List<Integer> getFeatureAnnotationSets(Container c, User user, Collection<Integer> rowIds, Class<? extends Permission> permission)
{
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromParts("RowId"), id);
if (rowIds == null || rowIds.isEmpty())
return Collections.emptyList();

// The container filter matches the assay's featureSet run property lookup
ContainerFilter cf = new ContainerFilter.CurrentPlusProjectAndShared(c, user);
filter.addClause(cf.createFilterClause(MicroarrayUserSchema.getSchema(), FieldKey.fromParts("container")));
SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("RowId"), rowIds, CompareType.IN);
applyContainerFilter(c, user, filter);

TableSelector featureAnnotationSelector = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null);
List<Integer> rowIds = featureAnnotationSelector.getArrayList(Integer.class);
// TODO: Order results by container depth
if (!rowIds.isEmpty())
return rowIds.get(0);
List<Integer> setRowIds = new ArrayList<>();
Set<String> processed = new HashSet<>();
try (Results results = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId", "Container"), filter, null).getResults())
{
while (results.next())
{
Integer rowId = results.getInt(FieldKey.fromParts("RowId"));
String containerId = results.getString(FieldKey.fromParts("Container"));

return null;
if (!processed.contains(containerId))
{
Container container = ContainerManager.getForId(containerId);
if (container == null)
throw new UnauthorizedException("Unable to determine container for feature annotation set (" + rowId + ")");
if (!container.hasPermission(user, permission))
throw new UnauthorizedException("You do not have sufficient permission in " + container.getPath() + " for feature annotation set (" + rowId + ")");

processed.add(containerId);
}

setRowIds.add(rowId);
}
}
catch (SQLException e)
{
throw new RuntimeSQLException(e);
}

return Collections.unmodifiableList(setRowIds);
}

/**
Expand Down
13 changes: 10 additions & 3 deletions microarray/src/org/labkey/microarray/MicroarrayModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,15 +44,14 @@
public class MicroarrayModule extends SpringModule
{
private static final String WEBPART_FEATURE_ANNOTATION_SET = "Feature Annotation Sets";

private static final String FEATURE_ANNOTATION_SET_CONTROLLER_NAME = "feature-annotationset";

public static final String DB_SCHEMA_NAME = "microarray";
public static final String NAME = "Microarray";

@Override
public String getName()
{
return "Microarray";
return NAME;
}

@Override
Expand Down Expand Up @@ -121,4 +120,12 @@ public Set<String> getSchemaNames()
{
return Collections.singleton(DB_SCHEMA_NAME);
}

@Override
public @NotNull Set<Class> getIntegrationTests()
{
return Set.of(
FeatureAnnotationSetController.ContainerScopingTestCase.class
);
}
}
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