Author: clopes
Date: 2012-07-20 10:32:09 -0700 (Fri, 20 Jul 2012)
New Revision: 29940
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
Log:
Added unit tests to make sure 2.x custom attributes are imported as mutable
CyColumns.
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-07-20 15:41:35 UTC (rev 29939)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-07-20 17:32:09 UTC (rev 29940)
@@ -16,6 +16,7 @@
import org.cytoscape.io.internal.util.ReadCache;
import org.cytoscape.io.internal.util.UnrecognizedVisualPropertyManager;
import org.cytoscape.io.internal.util.session.SessionUtil;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
@@ -84,6 +85,7 @@
List<CyNetworkView> views = getViews("galFiltered.xgmml");
CyNetwork net = checkSingleNetwork(views, 331, 362);
findInteraction(net, "YGR136W", "YGR058W", "pp", 1);
+ testCustomColumnsAreMutable(net);
}
@Test
@@ -108,6 +110,8 @@
assertNotNull(defEdgeTbl.getColumn("name"));
CyTable hiddenEdgeTbl = net.getRow(net.getEdgeList().get(0),
CyNetwork.HIDDEN_ATTRS).getTable();
assertNotNull(hiddenEdgeTbl.getColumn("_private_real"));
+
+ testCustomColumnsAreMutable(net);
}
@Test
@@ -125,7 +129,15 @@
// The group network should not be registered, so the network
list must contain only the base network
assertEquals(1, reader.getNetworks().length);
CyNetwork net = checkSingleNetwork(views, 2, 1);
- check2xGroupMetadata(net);
+ CyNode grNode = check2xGroupMetadata(net);
+ // Check group network data
+ CyNetwork grNet = grNode.getNetworkPointer();
+ for (CyNode n : grNet.getNodeList()) {
+ assertNotNull(grNet.getRow(n,
CyNetwork.HIDDEN_ATTRS).get("__metanodeHintX", Double.class));
+ assertNotNull(grNet.getRow(n,
CyNetwork.HIDDEN_ATTRS).get("__metanodeHintY", Double.class));
+ }
+ testCustomColumnsAreMutable(net);
+ testCustomColumnsAreMutable(grNet);
}
@Test
@@ -200,7 +212,29 @@
assertEquals("SansSerif,bold,12",
GenericXGMMLReader.convertOldFontValue("SansSerif,bold,12"));
}
- private void check2xGroupMetadata(final CyNetwork net) {
+ private void testCustomColumnsAreMutable(CyNetwork net) {
+ // User or non-default columns should be immutable
+ CyTable[] tables = new CyTable[] {
+ net.getTable(CyNetwork.class, CyNetwork.DEFAULT_ATTRS),
+ net.getTable(CyNetwork.class, CyNetwork.HIDDEN_ATTRS),
+ net.getTable(CyNode.class, CyNetwork.DEFAULT_ATTRS),
+ net.getTable(CyNode.class, CyNetwork.HIDDEN_ATTRS),
+ net.getTable(CyEdge.class, CyNetwork.DEFAULT_ATTRS),
+ net.getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS)
+ };
+ for (CyTable t : tables) {
+ for (CyColumn c : t.getColumns()) {
+ String name = c.getName();
+ if (!name.equals(CyNetwork.SUID) &&
!name.equals(CyNetwork.NAME) &&
+ !name.equals(CyNetwork.SELECTED) &&
!name.equals(CyEdge.INTERACTION) &&
+ !c.getVirtualColumnInfo().isVirtual()) {
+ assertFalse("Column " + c.getName() + "
should NOT be immutable", c.isImmutable());
+ }
+ }
+ }
+ }
+
+ private CyNode check2xGroupMetadata(final CyNetwork net) {
// Test 2.x group parsed as network pointer
CyNode gn = null;
int npCount = 0;
@@ -232,6 +266,8 @@
assertNotNull(extEdgeIds);
assertEquals(1, extEdgeIds.size());
assertEquals("node1 (DirectedEdge) node2", extEdgeIds.get(0));
+
+ return gn;
}
private List<CyNetworkView> getViews(String file) throws Exception {
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