Author: Christian Lopes
Date: 2011-06-01 15:23:05 -0700 (Wed, 01 Jun 2011)
New Revision: 25618
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
Log:
Updated the Session Reader implementation to read Cysession's NetworkTree
correctly, since Cytoscape 3.0 does not have a "Network Root" anymore.
Added the id of the Cysession when writing it to the cys file.
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-06-01 22:18:01 UTC (rev 25617)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-06-01 22:23:05 UTC (rev 25618)
@@ -65,7 +65,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
-import org.cytoscape.property.session.Child;
import org.cytoscape.property.session.Cysession;
import org.cytoscape.property.session.Edge;
import org.cytoscape.property.session.Network;
@@ -88,16 +87,15 @@
public static final String VIZMAP_XML = "vizmap.xml";
public static final String CY_PROPS = "cytoscape.props";
public static final String XGMML_EXT = ".xgmml";
- public static final String BOOKMARKS_FILE = "session_bookmarks.xml";
- public static final String NETWORK_ROOT = "Network Root";
+ public static final String BOOKMARKS_FILE = "session_bookmarks.xml";
+ public static final String NETWORK_ROOT = "Network Root";
+ public static final int MAJOR_DOC_VERSION = 3;
-
private static final Logger logger =
LoggerFactory.getLogger(SessionReaderImpl.class);
private final Map<String, List<File>> pluginFileListMap = new
HashMap<String, List<File>>();
private final Map<String,CyNetworkView[]> networkViews = new
HashMap<String,CyNetworkView[]>();
private final Map<CyNetworkView,String> visualStyleMap = new
HashMap<CyNetworkView,String>();
- private final Map<String, Network> netMap = new HashMap<String,
Network>();
private final InputStream sourceInputStream;
private final CyNetworkReaderManager netviewReaderMgr;
@@ -329,58 +327,59 @@
}
private void processNetworks() throws Exception {
-
if (cysession.getNetworkTree() == null){
return;
}
- for (Network curNet : cysession.getNetworkTree().getNetwork())
- netMap.put(curNet.getId(), curNet);
-
- walkTree(netMap.get(NETWORK_ROOT), null);
- }
-
- /**
- * Load the root network and then create its children.<br>
- *
- * @param currentNetwork
- * @param parent
- * @throws IOException
- */
- private void walkTree(final Network currentNetwork, final CyNetwork
parent) throws Exception {
-
- for (Child child : currentNetwork.getChild() ) {
-
- Network childNet = netMap.get(child.getId());
-
- CyNetworkView view =
getNetworkView(childNet.getFilename());
- if ( view == null ) {
- logger.warn("failed to find network in session:
" + childNet.getFilename());
- return;
+ boolean isOldFormat = false;
+ String docVersion = cysession.getDocumentVersion();
+
+ if (docVersion != null) {
+ String[] tokens = docVersion.split(".");
+
+ if (tokens.length > 0) {
+ String t0 = tokens[0];
+
+ try {
+ int majorVersion = Integer.parseInt(t0);
+ isOldFormat = majorVersion <
MAJOR_DOC_VERSION;
+ } catch (NumberFormatException nfe) {
+ logger.warn("The Cysession document
version is invalid!");
+ }
}
-
- String vsName = childNet.getVisualStyle();
- if (vsName == null)
- vsName = "default";
-
- visualStyleMap.put( view, vsName );
-
- CyNetwork new_network = view.getModel();
-
- if ( childNet.getHiddenNodes() != null )
- setBooleanNodeAttr(new_network,
childNet.getHiddenNodes().getNode().iterator(), "hidden");
- if ( childNet.getHiddenEdges() != null )
- setBooleanEdgeAttr(new_network,
childNet.getHiddenEdges().getEdge().iterator(), "hidden");
- if ( childNet.getSelectedNodes() != null )
- setBooleanNodeAttr(new_network,
childNet.getSelectedNodes().getNode().iterator(), "selected");
- if ( childNet.getSelectedEdges() != null )
- setBooleanEdgeAttr(new_network,
childNet.getSelectedEdges().getEdge().iterator(), "selected");
-
- // Load child networks
- if (childNet.getChild().size() != 0)
- // child 2
- walkTree(childNet, new_network);
+ } else {
+ logger.warn("The Cysession has no document version!");
}
+
+ for (Network net : cysession.getNetworkTree().getNetwork()) {
+ // We no longer have the concept of a top-level network
root,
+ // so let's ignore a network with that name, but only
if the Cysession doc version is old.
+ if (isOldFormat && net.getId().equals(NETWORK_ROOT))
continue;
+
+ CyNetworkView view = getNetworkView(net.getFilename());
+
+ if (view == null) {
+ logger.warn("Failed to find network in session:
" + net.getFilename());
+ } else {
+ String vsName = net.getVisualStyle();
+ if (vsName != null) visualStyleMap.put(view, vsName);
+
+ CyNetwork cyNet = view.getModel();
+
+ if (net.getHiddenNodes() != null)
+ setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode().iterator(), "hidden");
+ if (net.getHiddenEdges() != null)
+ setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge().iterator(), "hidden");
+
+ if (isOldFormat) {
+ // From Cytoscape 3.0, the selection info is
stored inside CyTables
+ if (net.getSelectedNodes() != null)
+ setBooleanNodeAttr(cyNet,
net.getSelectedNodes().getNode().iterator(), CyNetwork.SELECTED);
+ if (net.getSelectedEdges() != null)
+ setBooleanEdgeAttr(cyNet,
net.getSelectedEdges().getEdge().iterator(), CyNetwork.SELECTED);
+ }
+ }
+ }
}
private CyNetworkView getNetworkView(String name) {
@@ -393,12 +392,12 @@
return null;
}
- private void setBooleanNodeAttr(final CyNetwork net, Iterator it, final
String attrName) {
- if (it == null)
- return;
+ private void setBooleanNodeAttr(final CyNetwork net, Iterator<?> it,
final String attrName) {
+ if (it == null) return;
// create an id map
Map<String,CyNode> nodeMap = new HashMap<String,CyNode>();
+
for ( CyNode n : net.getNodeList() )
nodeMap.put(n.getCyRow().get("name",String.class), n);
@@ -410,9 +409,8 @@
}
}
- private void setBooleanEdgeAttr(final CyNetwork net, final Iterator it,
final String attrName) {
- if (it == null)
- return;
+ private void setBooleanEdgeAttr(final CyNetwork net, final Iterator<?>
it, final String attrName) {
+ if (it == null) return;
// create an id map
Map<String,CyEdge> edgeMap = new HashMap<String,CyEdge>();
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-06-01 22:18:01 UTC (rev 25617)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-06-01 22:23:05 UTC (rev 25618)
@@ -97,9 +97,6 @@
// These values will be replaced.
private static final char[] INVALID_CHAR = {'[', '\\', '/', ':', '*',
'?',
'"', '<', '>', '|', ']'};
-
- // cysession.xml document version
- private static final String cysessionVersion = "0.9";
// Enumerate types (node & edge)
public static final int NODE = 1;
@@ -299,9 +296,12 @@
* @throws Exception
*/
private void zipCySession() throws Exception {
+ Cysession cysess = session.getCysession();
+ cysess.setId(sessionDirName);
+
zos.putNextEntry(new ZipEntry(sessionDir + CYSESSION_FILE_NAME)
);
- CyWriter cysessionWriter =
propertyWriterMgr.getWriter(session.getCysession(), cysessionFilter, zos );
+ CyWriter cysessionWriter = propertyWriterMgr.getWriter(cysess,
cysessionFilter, zos );
cysessionWriter.run(taskMonitor);
zos.closeEntry();
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