Author: kono
Date: 2012-06-08 11:57:35 -0700 (Fri, 08 Jun 2012)
New Revision: 29508
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
Log:
refs #1041 Custom graphics are now restored to the CGManager from 2.x session
file.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2012-06-08 17:46:40 UTC (rev 29507)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2012-06-08 18:57:35 UTC (rev 29508)
@@ -36,11 +36,14 @@
import static org.cytoscape.model.CyNetwork.DEFAULT_ATTRS;
import static org.cytoscape.model.CyNetwork.SELECTED;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
@@ -99,6 +102,11 @@
*/
public class Cy2SessionReaderImpl extends AbstractSessionReader {
+ private static final String TEMP_DIR = "java.io.tmpdir";
+
+ // In 3, CG Manager is treated as a regular app. This is a unique name
for it.
+ private static final String DING_CG_MANAGER_NAME =
"org.cytoscape.ding.customgraphicsmgr";
+
public static final String CY2_PARENT_NETWORK_COLUMN = "Cytoscape2
Parent Network";
public static final String CY_PROPS_FILE = "session_cytoscape.props";
@@ -152,7 +160,7 @@
}
@Override
- protected void handleEntry(InputStream is, String entryName) throws
Exception {
+ protected void handleEntry(InputStream is, String entryName) throws
Exception {
if (entryName.contains("/" + PLUGINS_FOLDER)) {
extractPluginEntry(is, entryName);
} else if (entryName.endsWith(CYSESSION_FILE)) {
@@ -173,7 +181,9 @@
}
} else if (entryName.endsWith(BOOKMARKS_FILE)) {
extractBookmarks(is, entryName);
- } else if (!entryName.contains("/" + IMAGES_FOLDER)) {
+ } else if (entryName.contains("/" + IMAGES_FOLDER)) {
+ extractImages(is, entryName);
+ } else {
logger.warn("Unknown entry found in session zip
file!\n" + entryName);
}
}
@@ -424,7 +434,44 @@
CyProperty.SavePolicy.SESSION_FILE);
properties.add(cyProps);
}
+
+ private void extractImages(final InputStream is, final String
entryName) {
+ final String[] items = entryName.split("/");
+ if (items.length < 3) {
+ // It's a directory name, not a file name
+ return;
+ }
+
+ final String fileName = items[items.length - 1];
+ final String tmpDir = System.getProperty(TEMP_DIR);
+ final File theFile = new File(tmpDir, fileName);
+
+ try {
+ // Write input stream into temp file (Use binary
streams to support images/movies/etc.)
+ final BufferedInputStream bin = new
BufferedInputStream(is);
+ final BufferedOutputStream output = new
BufferedOutputStream(new FileOutputStream(theFile));
+ final byte buf[] = new byte[256];
+
+ int len;
+ while ((len = bin.read(buf)) != -1)
+ output.write(buf, 0, len);
+
+ output.flush();
+ output.close();
+ bin.close();
+
+ } catch (IOException e) {
+ logger.error("Error: read from zip: " + entryName, e);
+ return;
+ }
+
+ // Put the file into appFileListMap
+ if (!appFileListMap.containsKey(DING_CG_MANAGER_NAME))
appFileListMap.put(DING_CG_MANAGER_NAME, new ArrayList<File>());
+ List<File> fileList = appFileListMap.get(DING_CG_MANAGER_NAME);
+ fileList.add(theFile);
+ }
+
private void extractSessionState(InputStream is, String entryName)
throws Exception {
CyPropertyReader reader = propertyReaderMgr.getReader(is,
entryName);
reader.run(taskMonitor);
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