Author: clopes
Date: 2012-08-03 12:03:39 -0700 (Fri, 03 Aug 2012)
New Revision: 30084
Modified:
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
Log:
Groups now takes advantage of the ".SUID" column name convention to always get
the new SUIDs of external edges on session loading. IO impl changed to
transparently send the new SUIDs when loading Cy2 sessions, as well.
Modified:
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
===================================================================
---
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
2012-08-03 18:27:28 UTC (rev 30083)
+++
core3/impl/trunk/group-session-restore-shim/src/main/java/org/cytoscape/group/session/restore/shim/internal/SessionEventsListener.java
2012-08-03 19:03:39 UTC (rev 30084)
@@ -34,7 +34,7 @@
private final CyGroupManager groupMgr;
private final CyNetworkManager netMgr;
private final CyRootNetworkManager rootNetMgr;
- private final String EXTERNAL_EDGE_ATTRIBUTE="__externalEdges";
+ private final String EXTERNAL_EDGE_ATTRIBUTE="__externalEdges.SUID";
private final String GROUP_COLLAPSED_ATTRIBUTE="__groupCollapsed";
// 2.x group attributes
private final String GROUP_STATE_ATTRIBUTE="__groupState";
@@ -126,17 +126,10 @@
// Add in the missing external edges if we're collapsed
// CyRow groupNodeRow = net.getRow(n,
CyNetwork.HIDDEN_ATTRS);
if (rnRow.isSet(EXTERNAL_EDGE_ATTRIBUTE)) {
- Class<?> listType =
rnRow.getTable().getColumn(EXTERNAL_EDGE_ATTRIBUTE).getListElementType();
- List<?> externalIDs =
rnRow.getList(EXTERNAL_EDGE_ATTRIBUTE, listType);
+ List<Long> externalIDs =
rnRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
List<CyEdge> externalEdges = new
ArrayList<CyEdge>();
- for (Object oldId: externalIDs) {
- CyEdge newEdge = null;
-
- if (oldId instanceof Long) // Cy3 old
edge IDs are SUIDs
- newEdge =
sess.getObject((Long)oldId, CyEdge.class);
- else // Cy2 uses edge labels as IDs
- newEdge =
sess.getObject(oldId.toString(), CyEdge.class);
-
+ for (Long suid: externalIDs) {
+ CyEdge newEdge = rootNet.getEdge(suid);
if (newEdge != null)
externalEdges.add(newEdge);
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-08-03 18:27:28 UTC (rev 30083)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-08-03 19:03:39 UTC (rev 30084)
@@ -61,6 +61,9 @@
public class ReadDataManager {
+ public final static String GROUP_STATE_ATTRIBUTE="__groupState";
+ public final static String
EXTERNAL_EDGE_ATTRIBUTE="__externalEdges.SUID";
+
protected final static String XLINK = "http://www.w3.org/1999/xlink";;
/* RDF Data */
@@ -470,7 +473,7 @@
CyNode actualSrc = net.getNode(source.getSUID());
CyNode actualTgt = net.getNode(target.getSUID());
- List<String> extEdgeIds = null; // For 2.x groups
+ List<Long> extEdgeIds = null; // For 2.x groups
if ( (getDocumentVersion() < 3.0 || !isSessionFormat()) &&
(actualSrc == null || actualTgt == null) ) {
// The nodes might have been added to other
sub-networks, but not to the current one.
@@ -497,18 +500,18 @@
// Check for the group's metadata attribute
final CyRow grhRow = grNet.getRow(grNode,
CyNetwork.HIDDEN_ATTRS);
- if (grhRow.isSet("__groupState")) { // It's a
group!
+ if (grhRow.isSet(GROUP_STATE_ATTRIBUTE)) { //
It's a group!
// Add extra metadata for external
edges, so that the information is not lost
final CyRow rnRow =
getRootNetwork().getRow(grNode, CyNetwork.HIDDEN_ATTRS);
- if
(rnRow.getTable().getColumn("__externalEdges") == null)
-
rnRow.getTable().createListColumn("__externalEdges", String.class, false);
+ if
(rnRow.getTable().getColumn(EXTERNAL_EDGE_ATTRIBUTE) == null)
+
rnRow.getTable().createListColumn(EXTERNAL_EDGE_ATTRIBUTE, Long.class, false);
- extEdgeIds =
rnRow.getList("__externalEdges", String.class);
+ extEdgeIds =
rnRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
if (extEdgeIds == null) {
- extEdgeIds = new
ArrayList<String>();
- rnRow.set("__externalEdges",
extEdgeIds);
+ extEdgeIds = new
ArrayList<Long>();
+
rnRow.set(EXTERNAL_EDGE_ATTRIBUTE, extEdgeIds);
}
}
}
@@ -517,7 +520,7 @@
edge = net.addEdge(actualSrc, actualTgt, directed);
if (extEdgeIds != null)
- extEdgeIds.add(id.toString());
+ extEdgeIds.add(edge.getSUID());
mapSUIDs(id, edge.getSUID());
}
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
2012-08-03 18:27:28 UTC (rev 30083)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReaderTest.java
2012-08-03 19:03:39 UTC (rev 30084)
@@ -310,7 +310,7 @@
int npCount = 0;
for (CyNode n : net.getNodeList()) {
- if (net.getRow(n,
CyNetwork.HIDDEN_ATTRS).isSet("__groupState")) {
+ if (net.getRow(n,
CyNetwork.HIDDEN_ATTRS).isSet(ReadDataManager.GROUP_STATE_ATTRIBUTE)) {
gn = n;
if (++npCount > 1) fail("There should be only
one group node!");
} else { // The other nodes have no network pointer!
@@ -331,11 +331,11 @@
// Check external edges metadata (must be added by the reader!)
CyRootNetwork rootNet = rootNetworkMgr.getRootNetwork(np);
CyRow rnRow = rootNet.getRow(gn, HIDDEN_ATTRS);
- List<String> extEdgeIds = rnRow.getList("__externalEdges",
String.class);
+ List<Long> extEdgeIds =
rnRow.getList(ReadDataManager.EXTERNAL_EDGE_ATTRIBUTE, Long.class);
assertNotNull(extEdgeIds);
assertEquals(1, extEdgeIds.size());
- assertEquals("node1 (DirectedEdge) node2", extEdgeIds.get(0));
+ assertNotNull(rootNet.getEdge(extEdgeIds.get(0)));
return gn;
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
