Author: kono
Date: 2011-07-06 17:06:57 -0700 (Wed, 06 Jul 2011)
New Revision: 26093
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
Log:
fixes #311 URL decorder had been added to session reader to extract correct
file name String.
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
2011-07-06 23:55:29 UTC (rev 26092)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-07-07 00:06:57 UTC (rev 26093)
@@ -35,6 +35,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Collections;
@@ -145,6 +146,7 @@
this.csvCyReaderFactory = csvCyReaderFactory;
}
+
/**
* Read a session file.
*/
@@ -535,13 +537,13 @@
logger.warn("The Cysession has no document version!");
}
- for (Network net : cysession.getNetworkTree().getNetwork()) {
+ for (final 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;
+ final String fileName = net.getFilename();
+ final CyNetworkView view = getNetworkView(fileName);
- CyNetworkView view = getNetworkView(net.getFilename());
-
if (view == null) {
logger.warn("Failed to find network in session:
" + net.getFilename());
} else {
@@ -566,9 +568,17 @@
}
}
- private CyNetworkView getNetworkView(String name) {
- for (String s : networkViews.keySet()) {
- if (s.endsWith("/" + name)) {
+ private CyNetworkView getNetworkView(final String name) {
+ for(String s : networkViews.keySet()) {
+ String decode = s;
+ try {
+ decode = URLDecoder.decode(s, "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ return null;
+ }
+
+ if (decode.endsWith("/" + name)) {
// this is OK since XGMML only ever reads one
network
return networkViews.get(s)[0];
}
Modified:
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
===================================================================
---
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2011-07-06 23:55:29 UTC (rev 26092)
+++
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2011-07-07 00:06:57 UTC (rev 26093)
@@ -171,10 +171,8 @@
}
// Restore visual styles
- logger.debug("Restoring visual styles...");
- Set<VisualStyle> styles = sess.getVisualStyles();
- Map<String, VisualStyle> stylesMap = new
HashMap<String, VisualStyle>();
-
+ final Set<VisualStyle> styles = sess.getVisualStyles();
+ final Map<String, VisualStyle> stylesMap = new
HashMap<String, VisualStyle>();
if (styles != null) {
for (VisualStyle vs : styles) {
vmMgr.addVisualStyle(vs);
@@ -184,23 +182,23 @@
}
// Get network frames info
- Cysession cysess = sess.getCysession();
+ final Cysession cysess = sess.getCysession();
if
(cysess.getSessionState().getDesktop().getNetworkFrames() != null) {
List<NetworkFrame> frames =
cysess.getSessionState().getDesktop().getNetworkFrames().getNetworkFrame();
Map<String, NetworkFrame> framesLookup = new
Hashtable<String, NetworkFrame>();
- for (NetworkFrame nf : frames) {
+ for (NetworkFrame nf : frames)
framesLookup.put(nf.getFrameID(), nf);
- }
// Set visual styles to network views
- Map<CyNetworkView, String> netStyleMap =
sess.getViewVisualStyleMap();
-
+
+ // This is a map from network view to Visual
Style TITLE (may not be unique. TODO: use ID?)
+ final Map<CyNetworkView, String> netStyleMap =
sess.getViewVisualStyleMap();
for (Entry<CyNetworkView, String> entry :
netStyleMap.entrySet()) {
- CyNetworkView netView = entry.getKey();
- String stName = entry.getValue();
- VisualStyle vs = stylesMap.get(stName);
+ final CyNetworkView netView =
entry.getKey();
+ final String stName = entry.getValue();
+ final VisualStyle vs =
stylesMap.get(stName);
if (vs != null) {
vmMgr.setVisualStyle(vs,
netView);
--
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