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Microarray container scope
1 parent b539e28 commit 8616ebf

3 files changed

Lines changed: 200 additions & 54 deletions

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‎microarray/src/org/labkey/microarray/MicroarrayManager.java‎

Lines changed: 77 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -21,11 +21,15 @@
2121
import org.jetbrains.annotations.NotNull;
2222
import org.jetbrains.annotations.Nullable;
2323
import org.labkey.api.collections.CaseInsensitiveHashMap;
24+
import org.labkey.api.data.CompareType;
2425
import org.labkey.api.data.Container;
2526
import org.labkey.api.data.ContainerFilter;
27+
import org.labkey.api.data.ContainerManager;
2628
import org.labkey.api.data.DbSchema;
2729
import org.labkey.api.data.DbScope;
2830
import org.labkey.api.data.JdbcType;
31+
import org.labkey.api.data.Results;
32+
import org.labkey.api.data.RuntimeSQLException;
2933
import org.labkey.api.data.SQLFragment;
3034
import org.labkey.api.data.SimpleFilter;
3135
import org.labkey.api.data.SqlExecutor;
@@ -50,20 +54,27 @@
5054
import org.labkey.api.reader.DataLoader;
5155
import org.labkey.api.reader.TabLoader;
5256
import org.labkey.api.security.User;
57+
import org.labkey.api.security.permissions.Permission;
5358
import org.labkey.api.util.ContainerUtil;
5459
import org.labkey.api.util.FileUtil;
5560
import org.labkey.api.util.PageFlowUtil;
61+
import org.labkey.api.view.UnauthorizedException;
5662
import org.labkey.microarray.controllers.FeatureAnnotationSetController;
5763
import org.labkey.microarray.matrix.ExpressionMatrixProtocolSchema;
5864
import org.labkey.microarray.query.MicroarrayUserSchema;
5965

6066
import java.io.File;
6167
import java.sql.SQLException;
68+
import java.util.ArrayList;
6269
import java.util.Arrays;
6370
import java.util.Collection;
6471
import java.util.Collections;
72+
import java.util.HashSet;
6573
import java.util.List;
6674
import java.util.Map;
75+
import java.util.Set;
76+
77+
import static org.labkey.api.data.DataRegion.MessagePart.filter;
6778

6879
public class MicroarrayManager
6980
{
@@ -87,7 +98,7 @@ private static TableInfo getAnnotationQueryTableInfo(User user, Container contai
8798
return schema.getTable(MicroarrayUserSchema.TABLE_FEATURE_ANNOTATION, false);
8899
}
89100

90-
private static TableInfo getAnnotationSetSchemaTableInfo()
101+
public static TableInfo getAnnotationSetSchemaTableInfo()
91102
{
92103
DbSchema schema = MicroarrayUserSchema.getSchema();
93104
return schema.getTable(MicroarrayUserSchema.TABLE_FEATURE_ANNOTATION_SET);
@@ -105,32 +116,22 @@ public long featureAnnotationSetCount(Container c)
105116
return selector.getRowCount();
106117
}
107118

108-
public int deleteFeatureAnnotationSet(int... rowId)
119+
public int deleteFeatureAnnotationSet(Collection<Integer> ids)
109120
{
110-
DbScope scope = MicroarrayUserSchema.getSchema().getScope();
111-
112-
Integer[] ids = ArrayUtils.toObject(rowId);
113-
114-
try (DbScope.Transaction tx = scope.ensureTransaction())
121+
try (DbScope.Transaction tx = MicroarrayUserSchema.getSchema().getScope().ensureTransaction())
115122
{
116123
// Delete all annotations first.
117-
TableInfo annotationSchemaTableInfo = getAnnotationSchemaTableInfo();
118-
SimpleFilter filter = new SimpleFilter();
119-
filter.addInClause(FieldKey.fromParts("FeatureAnnotationSetId"), Arrays.asList(ids));
120-
int rowsDeleted = Table.delete(annotationSchemaTableInfo, filter);
124+
int rowsDeleted = Table.delete(getAnnotationSchemaTableInfo(), new SimpleFilter(FieldKey.fromParts("FeatureAnnotationSetId"), ids, CompareType.IN));
121125

122126
// Then delete annotation set.
123-
TableInfo annotationSetSchemaTableInfo = getAnnotationSetSchemaTableInfo();
124-
filter = new SimpleFilter();
125-
filter.addInClause(FieldKey.fromParts("RowId"), Arrays.asList(ids));
126-
Table.delete(annotationSetSchemaTableInfo, filter);
127+
Table.delete(getAnnotationSetSchemaTableInfo(), new SimpleFilter(FieldKey.fromParts("RowId"), ids, CompareType.IN));
127128

128129
tx.commit();
129130
return rowsDeleted;
130131
}
131132
}
132133

133-
private Integer insertFeatureAnnotationSet(User user, Container container, String name, String vendor, String description, String comment, BatchValidationException errors)
134+
public Integer insertFeatureAnnotationSet(User user, Container container, String name, String vendor, String description, String comment, BatchValidationException errors)
134135
throws SQLException, BatchValidationException, QueryUpdateServiceException, DuplicateKeyException
135136
{
136137
MicroarrayUserSchema schema = new MicroarrayUserSchema(user, container);
@@ -175,7 +176,7 @@ private Integer insertFeatureAnnotations(User user, Container container, Integer
175176
return -1;
176177
}
177178

178-
/** Creates feature annotation set AND inserts all feature annotations from TSV */
179+
/** Creates a feature annotation set AND inserts all feature annotations from TSV */
179180
public Integer createFeatureAnnotationSet(User user, Container c, FeatureAnnotationSetController.FeatureAnnotationSetForm form, DataLoader loader, BatchValidationException errors)
180181
throws SQLException, BatchValidationException, QueryUpdateServiceException, DuplicateKeyException
181182
{
@@ -187,48 +188,80 @@ public Integer createFeatureAnnotationSet(User user, Container c, FeatureAnnotat
187188
return -1;
188189
}
189190

190-
/**
191-
* Get feature annotation set by name if it is in scope (current, project, and shared container).
192-
*/
193-
@Nullable
194-
public Integer getFeatureAnnotationSet(Container c, User user, String featureSetName)
191+
private void applyContainerFilter(Container c, User user, SimpleFilter filter)
195192
{
196-
SimpleFilter filter = new SimpleFilter();
197-
filter.addCondition(FieldKey.fromParts("Name"), featureSetName);
198-
199193
// The container filter matches the assay's featureSet run property lookup
200194
ContainerFilter cf = new ContainerFilter.CurrentPlusProjectAndShared(c, user);
201195
filter.addClause(cf.createFilterClause(MicroarrayUserSchema.getSchema(), FieldKey.fromParts("container")));
196+
}
197+
198+
/**
199+
* Get a feature annotation set by name if it is in scope (current, project, and shared container).
200+
*/
201+
public @Nullable Integer getFeatureAnnotationSet(Container c, User user, String featureSetName)
202+
{
203+
return getFeatureAnnotationSet(c, user, new SimpleFilter(FieldKey.fromParts("Name"), featureSetName));
204+
}
205+
206+
/**
207+
* Get a feature annotation set by id if it is in scope (current, project, and shared container).
208+
*/
209+
public @Nullable Integer getFeatureAnnotationSet(Container c, User user, int id)
210+
{
211+
return getFeatureAnnotationSet(c, user, new SimpleFilter(FieldKey.fromParts("RowId"), id));
212+
}
213+
214+
private @Nullable Integer getFeatureAnnotationSet(Container c, User user, SimpleFilter filter)
215+
{
216+
applyContainerFilter(c, user, filter);
217+
List<Integer> rowIds = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null).getArrayList(Integer.class);
202218

203-
TableSelector featureAnnotationSelector = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null);
204-
List<Integer> rowIds = featureAnnotationSelector.getArrayList(Integer.class);
205219
// TODO: Order results by container depth
206-
if (!rowIds.isEmpty())
207-
return rowIds.get(0);
220+
if (rowIds.isEmpty())
221+
return null;
208222

209-
return null;
223+
return rowIds.get(0);
210224
}
211225

212226
/**
213-
* Get feature annotation set by id if it is in scope (current, project, and shared container).
227+
* Gets feature annotation sets by id that are in folder scope (current, project, and shared container). The user
228+
* must have the provided permissions in all containers that the feature annotation sets are declared in.
214229
*/
215-
@Nullable
216-
public Integer getFeatureAnnotationSet(Container c, User user, int id)
230+
public @NotNull List<Integer> getFeatureAnnotationSets(Container c, User user, Collection<Integer> rowIds, Class<? extends Permission> permission)
217231
{
218-
SimpleFilter filter = new SimpleFilter();
219-
filter.addCondition(FieldKey.fromParts("RowId"), id);
232+
if (rowIds == null || rowIds.isEmpty())
233+
return Collections.emptyList();
220234

221-
// The container filter matches the assay's featureSet run property lookup
222-
ContainerFilter cf = new ContainerFilter.CurrentPlusProjectAndShared(c, user);
223-
filter.addClause(cf.createFilterClause(MicroarrayUserSchema.getSchema(), FieldKey.fromParts("container")));
235+
SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("RowId"), rowIds, CompareType.IN);
236+
applyContainerFilter(c, user, filter);
224237

225-
TableSelector featureAnnotationSelector = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId"), filter, null);
226-
List<Integer> rowIds = featureAnnotationSelector.getArrayList(Integer.class);
227-
// TODO: Order results by container depth
228-
if (!rowIds.isEmpty())
229-
return rowIds.get(0);
238+
List<Integer> setRowIds = new ArrayList<>();
239+
Set<String> processed = new HashSet<>();
240+
try (Results results = new TableSelector(getAnnotationSetSchemaTableInfo(), PageFlowUtil.set("RowId", "Container"), filter, null).getResults())
241+
{
242+
while (results.next())
243+
{
244+
Integer rowId = results.getInt(FieldKey.fromParts("RowId"));
245+
String containerId = results.getString(FieldKey.fromParts("Container"));
230246

231-
return null;
247+
if (!processed.contains(containerId))
248+
{
249+
Container container = ContainerManager.getForId(containerId);
250+
if (!container.hasPermission(user, permission))
251+
throw new UnauthorizedException("You do not have sufficient permission in " + container.getPath() + " for feature annotation set (" + rowId + ").");
252+
253+
processed.add(containerId);
254+
}
255+
256+
setRowIds.add(rowId);
257+
}
258+
}
259+
catch (SQLException e)
260+
{
261+
throw new RuntimeSQLException(e);
262+
}
263+
264+
return Collections.unmodifiableList(setRowIds);
232265
}
233266

234267
/**

‎microarray/src/org/labkey/microarray/MicroarrayModule.java‎

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -44,15 +44,14 @@
4444
public class MicroarrayModule extends SpringModule
4545
{
4646
private static final String WEBPART_FEATURE_ANNOTATION_SET = "Feature Annotation Sets";
47-
4847
private static final String FEATURE_ANNOTATION_SET_CONTROLLER_NAME = "feature-annotationset";
49-
5048
public static final String DB_SCHEMA_NAME = "microarray";
49+
public static final String NAME = "Microarray";
5150

5251
@Override
5352
public String getName()
5453
{
55-
return "Microarray";
54+
return NAME;
5655
}
5756

5857
@Override
@@ -121,4 +120,12 @@ public Set<String> getSchemaNames()
121120
{
122121
return Collections.singleton(DB_SCHEMA_NAME);
123122
}
123+
124+
@Override
125+
public @NotNull Set<Class> getIntegrationTests()
126+
{
127+
return Set.of(
128+
FeatureAnnotationSetController.ContainerScopingTestCase.class
129+
);
130+
}
124131
}

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