Author: noelr
Date: 2009-08-13 03:05:23 -0700 (Thu, 13 Aug 2009)
New Revision: 17806
Modified:
cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
Log:
Third batch of fixes for Bug 1988
These are the files that required both trivial and non-trivial alteration
Also fixed Bug 1929
Modified: cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2009-08-13 10:01:38 UTC (rev 17805)
+++ cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2009-08-13 10:05:23 UTC (rev 17806)
@@ -87,6 +87,7 @@
import cytoscape.util.URLUtil;
import cytoscape.view.CyNetworkView;
import cytoscape.logger.CyLogger;
+import java.net.URLEncoder;
/**
* Reader to load CYtoscape Session file (.cys).<br>
@@ -253,40 +254,55 @@
ZipInputStream zis = new ZipInputStream(juc.getInputStream());
- networkURLs = new HashMap();
+ try {
+ networkURLs = new HashMap();
- // Extract list of entries
- ZipEntry zen = null;
- String entryName = null;
+ // Extract list of entries
+ ZipEntry zen = null;
+ String entryName = null;
- while ((zen = zis.getNextEntry()) != null) {
- entryName = zen.getName();
+ while ((zen = zis.getNextEntry()) != null) {
+ entryName = zen.getName();
- if (entryName.contains("/plugins/")) {
- extractPluginEntry(entryName);
- } else if (entryName.endsWith(CYSESSION)) {
- cysessionFileURL = new URL("jar:" +
sourceURL.toString() + "!/" + entryName);
- } else if (entryName.endsWith(VIZMAP_PROPS)) {
- vizmapFileURL = new URL("jar:" +
sourceURL.toString() + "!/" + entryName);
- } else if (entryName.endsWith(CY_PROPS)) {
- cytoscapePropsURL = new URL("jar:" +
sourceURL.toString() + "!/" + entryName);
- } else if (entryName.endsWith(XGMML_EXT)) {
- URL networkURL = new URL("jar:" +
sourceURL.toString() + "!/" + entryName);
- networkURLs.put(entryName, networkURL);
- networkCounter++;
- } else if (entryName.endsWith(BOOKMARKS_FILE)) {
- bookmarksFileURL = new URL("jar:" +
sourceURL.toString() + "!/" + entryName);
- } else {
- logger.warn("Unknown entry found in session zip
file: " + entryName);
- }
- } // while loop
+ if (entryName.contains("/plugins/")) {
+ extractPluginEntry(entryName);
+ } else if (entryName.endsWith(CYSESSION)) {
+ cysessionFileURL = new URL("jar:" + sourceURL.toString() +
"!/" + entryName);
+ } else if (entryName.endsWith(VIZMAP_PROPS)) {
+ vizmapFileURL = new URL("jar:" + sourceURL.toString() +
"!/" + entryName);
+ } else if (entryName.endsWith(CY_PROPS)) {
+ cytoscapePropsURL = new URL("jar:" + sourceURL.toString()
+ "!/" + entryName);
+ } else if (entryName.endsWith(XGMML_EXT)) {
+ // entryName should only contain one "/" character
seperating the session directory from the file name
+ // All other "/" are eliminated by
CytoscapeSessionWriter.getValidFileName
+ // URLEncoding the remainder of entryName makes sure the
URL is valid
+ // without the need to eliminate additional characters
when creating the filename.
+ int sp;
+ String entryDir;
+ String entryRest;
- if (zis != null) {
- try {
+ entryDir = "";
+ entryRest = entryName;
+ sp = entryName.indexOf("/");
+ if (sp != -1) {
+ entryDir = entryRest.substring(0, sp + 1);
+ entryRest = entryRest.substring(sp + 1);
+ }
+
+ URL networkURL = new URL("jar:" + sourceURL.toString() +
"!/" + entryDir + URLEncoder.encode(entryRest, "UTF-8"));
+ networkURLs.put(entryName, networkURL);
+ networkCounter++;
+ } else if (entryName.endsWith(BOOKMARKS_FILE)) {
+ bookmarksFileURL = new URL("jar:" + sourceURL.toString() +
"!/" + entryName);
+ } else {
+ logger.warn("Unknown entry found in session zip file: " +
entryName);
+ }
+ } // while loop
+ }
+ finally {
+ if (zis != null) {
zis.close();
- } finally {
- zis = null;
- }
+ }
}
}
@@ -473,22 +489,33 @@
InputStream is =
URLUtil.getBasicInputStream(theURL);
// Write input stream into tmp file
+ BufferedReader in = null;
BufferedWriter out = null;
- BufferedReader in = null;
in = new BufferedReader(new
InputStreamReader(is));
- out = new BufferedWriter(new
FileWriter(theFile));
+ try {
+ out = new BufferedWriter(new FileWriter(theFile));
- // Write to tmp file
- String inputLine;
+ try {
+ // Write to tmp file
+ String inputLine;
- while ((inputLine = in.readLine()) !=
null) {
- out.write(inputLine);
- out.newLine();
- }
-
- in.close();
- out.close();
+ while ((inputLine = in.readLine()) != null) {
+ out.write(inputLine);
+ out.newLine();
+ }
+ }
+ finally {
+ if (out != null) {
+ out.close();
+ }
+ }
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
} catch (IOException e) {
theFile = null;
logger.error("Error: reading from zip:
" + URLstr, e);
@@ -517,17 +544,20 @@
// InputStream is = pBookmarksFileURL.openStream();
// Use URLUtil to get the InputStream since we might be
using a proxy server
// and because pages may be cached:
- InputStream is =
URLUtil.getBasicInputStream(pBookmarksFileURL);
-
final JAXBContext jaxbContext =
JAXBContext.newInstance(BOOKMARK_PACKAGE_NAME,
this.getClass().getClassLoader());
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
- theBookmark = (Bookmarks) unmarshaller.unmarshal(is);
+ InputStream is =
URLUtil.getBasicInputStream(pBookmarksFileURL);
- if (is != null) {
- is.close();
- }
+ try {
+ theBookmark = (Bookmarks) unmarshaller.unmarshal(is);
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
} catch (FileNotFoundException e1) {
logger.warn("Can not find bookmark file in
"+pBookmarksFileURL.toString(), e1);
} catch (IOException e2) {
@@ -544,19 +574,18 @@
// Even though cytoscapeFileURL is probably a local URL, error
on the
// side of caution and use URLUtil to get the input stream
(which
// handles proxy servers and cached pages):
- InputStream is = URLUtil.getBasicInputStream(cysessionFileURL);
final JAXBContext jaxbContext =
JAXBContext.newInstance(PACKAGE_NAME,
this.getClass().getClassLoader());
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
+ InputStream is = URLUtil.getBasicInputStream(cysessionFileURL);
- session = (Cysession) unmarshaller.unmarshal(is);
-
- if (is != null) {
- try {
+ try {
+ session = (Cysession) unmarshaller.unmarshal(is);
+ }
+ finally {
+ if (is != null) {
is.close();
- } finally {
- is = null;
- }
+ }
}
/*
@@ -641,50 +670,50 @@
continue;
}
+ XGMMLReader reader = null;
jarConnection = (JarURLConnection)
targetNetworkURL.openConnection();
networkStream = (InputStream)
jarConnection.getContent();
- // Get the current state of the vsbSwitch
- Properties prop = CytoscapeInit.getProperties();
- String vsbSwitch =
prop.getProperty("visualStyleBuilder");
- // Since we're reading a session (which already has
visual
- // styles defined) force the vsbSwitch off
- prop.setProperty("visualStyleBuilder", "off");
+ try {
+ // Get the current state of the vsbSwitch
+ Properties prop = CytoscapeInit.getProperties();
+ String vsbSwitch = prop.getProperty("visualStyleBuilder");
+ // Since we're reading a session (which already has visual
+ // styles defined) force the vsbSwitch off
+ prop.setProperty("visualStyleBuilder", "off");
- final XGMMLReader reader = new
XGMMLReader(networkStream);
- try {
- new_network = Cytoscape.createNetwork(reader,
false, parent);
- } catch (Exception e) {
- String message = "Unable to read XGMML file:
"+childNet.getFilename()+". "+e.getMessage();
- logger.error(message, e);
- Cytoscape.destroyNetwork(new_network);
- if (taskMonitor != null)
- taskMonitor.setException(e, message);
- // Load child networks, even if this network is
bad
- if (childNet.getChild().size() != 0)
- walkTree(childNet, new_network,
sessionSource);
- continue;
- }
- logger.info("XGMMLReader " +
new_network.getIdentifier() + ": "
- + (System.currentTimeMillis() -
start) + " msec.");
+ reader = new XGMMLReader(networkStream);
+ try {
+ new_network = Cytoscape.createNetwork(reader, false,
parent);
+ } catch (Exception e) {
+ String message = "Unable to read XGMML file:
"+childNet.getFilename()+". "+e.getMessage();
+ logger.error(message, e);
+ Cytoscape.destroyNetwork(new_network);
+ if (taskMonitor != null)
+ taskMonitor.setException(e, message);
+ // Load child networks, even if this network is bad
+ if (childNet.getChild().size() != 0)
+ walkTree(childNet, new_network, sessionSource);
+ continue;
+ }
+ logger.info("XGMMLReader " + new_network.getIdentifier() + ": "
+ + (System.currentTimeMillis() - start) + "
msec.");
- // Restore the original state of the vsbSwitch
- if (vsbSwitch != null)
- prop.setProperty("visualStyleBuilder",
vsbSwitch);
- else
- prop.remove("visualStyleBuilder");
+ // Restore the original state of the vsbSwitch
+ if (vsbSwitch != null)
+ prop.setProperty("visualStyleBuilder", vsbSwitch);
+ else
+ prop.remove("visualStyleBuilder");
- if ((taskMonitor != null) && (networkCounter >= 20)) {
- netIndex++;
- taskMonitor.setPercentCompleted(((Number)
((netIndex / networkCounter) * 100))
-
.intValue());
- }
-
- if (networkStream != null) {
- try {
- networkStream.close();
- } finally {
- networkStream = null;
+ if ((taskMonitor != null) && (networkCounter >= 20)) {
+ netIndex++;
+ taskMonitor.setPercentCompleted(((Number) ((netIndex /
networkCounter) * 100))
+ .intValue());
+ }
+ }
+ finally {
+ if (networkStream != null) {
+ networkStream.close();
}
}
@@ -863,12 +892,10 @@
newMap.put(server.getName(), new URL(server.getHref()));
targetCyNetworkID =
getNetworkIdFromTitle(server.getName());
- cytoscape.data.ontology.Ontology onto = new
cytoscape.data.ontology.Ontology(server
-
.getName(),
+ cytoscape.data.ontology.Ontology onto = new
cytoscape.data.ontology.Ontology(server.getName(),
curator,
description,
-
Cytoscape
-
.getNetwork(targetCyNetworkID));
+
Cytoscape.getNetwork(targetCyNetworkID));
Cytoscape.getOntologyServer().addOntology(onto);
}
@@ -914,22 +941,30 @@
byte[] buffer = new byte[100000];
java.io.OutputStream localContent = new
java.io.FileOutputStream(tempFile);
- // java.io.InputStream remoteContent =
remoteURL.openStream();
- // Use URLUtil to get the InputStream since we might be
using a proxy server
- // and because pages may be cached:
- java.io.InputStream remoteContent =
URLUtil.getBasicInputStream(remoteURL);
+ try {
+ // java.io.InputStream remoteContent =
remoteURL.openStream();
+ // Use URLUtil to get the InputStream since we might be using
a proxy server
+ // and because pages may be cached:
+ java.io.InputStream remoteContent =
URLUtil.getBasicInputStream(remoteURL);
- for (int nBytes = remoteContent.read(buffer); nBytes >
0;
- nBytes = remoteContent.read(buffer)) {
- localContent.write(buffer, 0, nBytes);
- }
+ try {
+ for (int nBytes = remoteContent.read(buffer); nBytes > 0;
+ nBytes = remoteContent.read(buffer)) {
+ localContent.write(buffer, 0, nBytes);
+ }
+ }
+ finally {
+ if (remoteContent != null) {
+ remoteContent.close();
+ }
+ }
+ }
+ finally {
+ if (localContent != null) {
+ localContent.close();
+ }
+ }
- remoteContent.close();
- localContent.close();
- remoteContent = null;
- localContent = null;
- buffer = null;
-
return tempFile.toURL();
} catch (FileNotFoundException e) {
// This could happen if the OS' temp directory doesn't
exist
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