Author: noelr
Date: 2009-08-13 03:01:38 -0700 (Thu, 13 Aug 2009)
New Revision: 17805
Added:
cytoscape/trunk/tests/cytoscape/data/readers/CytoscapeSessionReaderTest.java
Modified:
cytoscape/trunk/src/cytoscape/data/ImportHandler.java
cytoscape/trunk/src/cytoscape/data/servers/BioDataServer.java
cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
cytoscape/trunk/src/cytoscape/plugin/InstallablePlugin.java
cytoscape/trunk/src/cytoscape/plugin/PluginManager.java
cytoscape/trunk/src/cytoscape/util/URLUtil.java
cytoscape/trunk/src/cytoscape/util/ZipUtil.java
cytoscape/trunk/src/cytoscape/visual/CalculatorIO.java
Log:
Third batch of fixes for Bug 1988
These are the files that required both trivial and non-trivial alteration
Modified: cytoscape/trunk/src/cytoscape/data/ImportHandler.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/ImportHandler.java 2009-08-13
04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/data/ImportHandler.java 2009-08-13
10:01:38 UTC (rev 17805)
@@ -475,42 +475,51 @@
BufferedReader in = null;
out = new BufferedWriter(new FileWriter(tmpFile));
- in = new BufferedReader(new
InputStreamReader(conn.getInputStream()));
+ try {
+ in = new BufferedReader(new
InputStreamReader(conn.getInputStream()));
+ try {
+ String inputLine = null;
+ double percent = 0.0d;
- String inputLine = null;
- double percent = 0.0d;
+ while ((inputLine = in.readLine()) != null) {
+ progressCount += inputLine.length();
- while ((inputLine = in.readLine()) != null) {
- progressCount += inputLine.length();
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount / maxCount) * 100.0;
- // Report on Progress
- if (taskMonitor != null) {
- percent = ((double) progressCount / maxCount) *
100.0;
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
- if (maxCount == -1) { // file size unknown
- percent = -1;
- }
+ JTask jTask = (JTask) taskMonitor;
- JTask jTask = (JTask) taskMonitor;
+ if (jTask.haltRequested()) { //abort
+ tmpFile = null;
+ taskMonitor.setStatus("Canceling the download task
...");
+ taskMonitor.setPercentCompleted(100);
- if (jTask.haltRequested()) { //abort
- tmpFile = null;
- taskMonitor.setStatus("Canceling the
download task ...");
- taskMonitor.setPercentCompleted(100);
+ break;
+ }
- break;
- }
-
- taskMonitor.setPercentCompleted((int) percent);
- }
-
- out.write(inputLine);
- out.newLine();
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ out.write(inputLine);
+ out.newLine();
+ }
+ }
+ finally {
+ if (in != null) {
+ in.close();
+ }
+ }
}
+ finally {
+ if (out != null) {
+ out.close();
+ }
+ }
- in.close();
- out.close();
-
return tmpFile;
} // End of downloadFromURL()
}
Modified: cytoscape/trunk/src/cytoscape/data/servers/BioDataServer.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/servers/BioDataServer.java
2009-08-13 04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/data/servers/BioDataServer.java
2009-08-13 10:01:38 UTC (rev 17805)
@@ -219,18 +219,21 @@
//
protected boolean checkFileType(final BufferedReader br) throws
IOException {
String curLine = null;
+ boolean rv;
- while (null != (curLine = br.readLine())) {
- if (curLine.startsWith(OBO_FILE) ||
curLine.startsWith(GENE_ASSOCIATION_FILE)) {
- br.close();
+ rv = false;
+ try {
+ while (!rv && (null != (curLine = br.readLine()))) {
+ if (curLine.startsWith(OBO_FILE) ||
curLine.startsWith(GENE_ASSOCIATION_FILE)) {
+ rv = true;
+ }
+ }
+ }
+ finally {
+ br.close();
+ }
- return true;
- }
- }
-
- br.close();
-
- return false;
+ return rv;
}
//
----------------------------------------------------------------------------------------
@@ -390,30 +393,37 @@
// Reader for the ".obo" file
BufferedReader oboReader = new BufferedReader(new
OboOntologyReader(new FileReader(filename)));
- OntologyFlatFileReader reader = new
OntologyFlatFileReader(oboReader);
- list.add(reader.getOntology());
- oboReader.close();
+ try {
+ OntologyFlatFileReader reader = new
OntologyFlatFileReader(oboReader);
+ list.add(reader.getOntology());
+ }
+ finally {
+ oboReader.close();
+ }
BufferedReader oboReader2 = new BufferedReader(new
OboOntologyReader2(new FileReader(filename)));
- String line;
- String[] parts = null;
+ try {
+ String line;
+ String[] parts = null;
- while ((line = oboReader2.readLine()) != null) {
- parts = line.split("=");
+ while ((line = oboReader2.readLine()) != null) {
+ parts = line.split("=");
- if (parts.length == 2) {
- //logger.info("ID = " + parts[0] + ", "
+ parts[1]);
- if
(parts[1].equals("biological_process")) {
- ontologyTypeMap.put(parts[0],
"P");
- } else if
(parts[1].equals("molecular_function")) {
- ontologyTypeMap.put(parts[0],
"F");
- } else if
(parts[1].equals("cellular_component")) {
- ontologyTypeMap.put(parts[0],
"C");
- }
- }
- }
-
- oboReader2.close();
+ if (parts.length == 2) {
+ //logger.info("ID = " + parts[0] + ", " + parts[1]);
+ if (parts[1].equals("biological_process")) {
+ ontologyTypeMap.put(parts[0], "P");
+ } else if (parts[1].equals("molecular_function")) {
+ ontologyTypeMap.put(parts[0], "F");
+ } else if (parts[1].equals("cellular_component")) {
+ ontologyTypeMap.put(parts[0], "C");
+ }
+ }
+ }
+ }
+ finally {
+ oboReader2.close();
+ }
}
return (Ontology[]) list.toArray(new Ontology[0]);
@@ -488,33 +498,43 @@
ontologyTypeMap,
new FileReader(filename)));
- BufferedReader ccRd = new BufferedReader(new
CellularComponentAnnotationReader(taxonName,
-
ontologyTypeMap,
-
new FileReader(filename)));
+ try {
+ BufferedReader ccRd = new BufferedReader(new
CellularComponentAnnotationReader(taxonName,
+
ontologyTypeMap,
+
new FileReader(filename)));
+ try {
+ BufferedReader mfRd = new BufferedReader(new
MolecularFunctionAnnotationReader(taxonName,
+
ontologyTypeMap,
+
new FileReader(filename)));
- BufferedReader mfRd = new BufferedReader(new
MolecularFunctionAnnotationReader(taxonName,
-
ontologyTypeMap,
-
new FileReader(filename)));
+ try {
+ AnnotationFlatFileReader bpReader = new
AnnotationFlatFileReader(bpRd, thesaurus, flip);
+ AnnotationFlatFileReader ccReader = new
AnnotationFlatFileReader(ccRd, thesaurus, flip);
+ AnnotationFlatFileReader mfReader = new
AnnotationFlatFileReader(mfRd, thesaurus, flip);
- AnnotationFlatFileReader bpReader = new
AnnotationFlatFileReader(bpRd, thesaurus, flip);
- AnnotationFlatFileReader ccReader = new
AnnotationFlatFileReader(ccRd, thesaurus, flip);
- AnnotationFlatFileReader mfReader = new
AnnotationFlatFileReader(mfRd, thesaurus, flip);
+ bpAnnotation = bpReader.getAnnotation();
+ ccAnnotation = ccReader.getAnnotation();
+ mfAnnotation = mfReader.getAnnotation();
- bpAnnotation = bpReader.getAnnotation();
- ccAnnotation = ccReader.getAnnotation();
- mfAnnotation = mfReader.getAnnotation();
+ bpAnnotation.setOntology(pickOntology(ontologies,
bpAnnotation));
+ ccAnnotation.setOntology(pickOntology(ontologies,
ccAnnotation));
+ mfAnnotation.setOntology(pickOntology(ontologies,
mfAnnotation));
- bpAnnotation.setOntology(pickOntology(ontologies,
bpAnnotation));
- ccAnnotation.setOntology(pickOntology(ontologies,
ccAnnotation));
- mfAnnotation.setOntology(pickOntology(ontologies,
mfAnnotation));
-
- server.addAnnotation(bpAnnotation);
- server.addAnnotation(ccAnnotation);
- server.addAnnotation(mfAnnotation);
-
- bpRd.close();
- ccRd.close();
- mfRd.close();
+ server.addAnnotation(bpAnnotation);
+ server.addAnnotation(ccAnnotation);
+ server.addAnnotation(mfAnnotation);
+ }
+ finally {
+ mfRd.close();
+ }
+ }
+ finally {
+ ccRd.close();
+ }
+ }
+ finally {
+ bpRd.close();
+ }
}
} // loadAnnotationFiles2
@@ -587,12 +607,16 @@
BufferedReader thRd = new BufferedReader(new
SynonymReader(taxonName,
new FileReader(filename)));
- ThesaurusFlatFileReader reader = new
ThesaurusFlatFileReader(thRd, flip);
- thesaurus = reader.getThesaurus();
+ try {
+ ThesaurusFlatFileReader reader = new
ThesaurusFlatFileReader(thRd, flip);
+ thesaurus = reader.getThesaurus();
- //thesaurus.dump();
- server.addThesaurus(thesaurus.getSpecies(), thesaurus);
- thRd.close();
+ //thesaurus.dump();
+ server.addThesaurus(thesaurus.getSpecies(), thesaurus);
+ }
+ finally {
+ thRd.close();
+ }
}
} // loadThesaurusFiles
Modified: cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
2009-08-13 04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
2009-08-13 10:01:38 UTC (rev 17805)
@@ -244,16 +244,21 @@
zos = new ZipOutputStream(new
FileOutputStream(sessionFileName));
- for (CyNetwork network : networks)
- zipNetwork(network);
- zipCySession();
- zipVizmapProps();
- zipCytoscapeProps();
- zipBookmarks();
- zipFileListMap();
+ try {
+ for (CyNetwork network : networks)
+ zipNetwork(network);
+ zipCySession();
+ zipVizmapProps();
+ zipCytoscapeProps();
+ zipBookmarks();
+ zipFileListMap();
+ }
+ finally {
+ if (zos != null) {
+ zos.close();
+ }
+ }
- zos.close();
-
Cytoscape.firePropertyChange(Cytoscape.SESSION_SAVED, null,
null);
}
@@ -336,10 +341,15 @@
zos.putNextEntry(new ZipEntry(sessionDir + VIZMAP_FILE) );
- Writer writer = new OutputStreamWriter( zos );
- CalculatorIO.storeCatalog(catalog, writer);
-
- zos.closeEntry();
+ try {
+ Writer writer = new OutputStreamWriter( zos );
+ CalculatorIO.storeCatalog(catalog, writer);
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
}
/**
@@ -349,9 +359,14 @@
zos.putNextEntry(new ZipEntry(sessionDir + CYPROP_FILE) );
- CytoscapeInit.getProperties().store(zos, "Cytoscape Property
File");
-
- zos.closeEntry();
+ try {
+ CytoscapeInit.getProperties().store(zos, "Cytoscape Property
File");
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
}
/**
@@ -361,10 +376,15 @@
zos.putNextEntry(new ZipEntry(sessionDir + BOOKMARKS_FILE) );
- bookmarks = Cytoscape.getBookmarks();
- BookmarksUtil.saveBookmark(bookmarks, zos);
-
- zos.closeEntry();
+ try {
+ bookmarks = Cytoscape.getBookmarks();
+ BookmarksUtil.saveBookmark(bookmarks, zos);
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
}
/**
@@ -380,18 +400,19 @@
String xgmmlFile = getValidFileName( network.getTitle() +
XGMML_EXT );
CyNetworkView view =
Cytoscape.getNetworkView(network.getIdentifier());
- zos.putNextEntry(new ZipEntry(sessionDir + xgmmlFile) );
- Writer writer = new OutputStreamWriter(zos, "UTF-8");
-
- // Write the XGMML file *without* our graphics attributes
- // We'll let the Vizmapper handle those
- XGMMLWriter xgmmlWriter = new XGMMLWriter(network, view, true);
- xgmmlWriter.write(writer);
-
- zos.closeEntry();
-
- writer = null;
- xgmmlWriter = null;
+ zos.putNextEntry(new ZipEntry(sessionDir + xgmmlFile));
+ Writer writer = new OutputStreamWriter(zos, "UTF-8");
+ try {
+ // Write the XGMML file *without* our graphics attributes
+ // We'll let the Vizmapper handle those
+ XGMMLWriter xgmmlWriter = new XGMMLWriter(network, view, true);
+ xgmmlWriter.write(writer);
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
}
/**
@@ -418,10 +439,14 @@
zos.putNextEntry(new ZipEntry(sessionDir + CYSESSION_FILE_NAME)
);
- m.marshal(session, zos);
-
- zos.closeEntry();
- m = null;
+ try {
+ m.marshal(session, zos);
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
session = null;
}
@@ -454,14 +479,25 @@
zos.putNextEntry(new ZipEntry(
sessionDir + "plugins/" + pluginName +
"/" +
theFile.getName() ) );
- // copy the file contents to the zip
output stream
- FileInputStream fileIS = new
FileInputStream(theFile);
- int numRead = 0;
- while ((numRead = fileIS.read(buf)) > -1)
- zos.write(buf, 0, numRead);
- fileIS.close();
-
- zos.closeEntry();
+ try {
+ // copy the file contents to the zip output stream
+ FileInputStream fileIS = new FileInputStream(theFile);
+ try {
+ int numRead = 0;
+ while ((numRead = fileIS.read(buf)) > -1)
+ zos.write(buf, 0, numRead);
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
+ }
+ finally {
+ if (zos != null) {
+ zos.closeEntry();
+ }
+ }
}
}
}
Modified: cytoscape/trunk/src/cytoscape/plugin/InstallablePlugin.java
===================================================================
--- cytoscape/trunk/src/cytoscape/plugin/InstallablePlugin.java 2009-08-13
04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/plugin/InstallablePlugin.java 2009-08-13
10:01:38 UTC (rev 17805)
@@ -19,6 +19,7 @@
import cytoscape.util.URLUtil;
import cytoscape.util.ZipUtil;
import cytoscape.logger.CyLogger;
+import java.util.zip.ZipFile;
/**
* @author skillcoy
@@ -270,8 +271,14 @@
switch (Type) {
case JAR:
JarFile Jar = new JarFile(FileName);
- PluginClassName =
getManifestAttribute(Jar.getManifest());
- Jar.close();
+ try {
+ PluginClassName = getManifestAttribute(Jar.getManifest());
+ }
+ finally {
+ if (Jar != null) {
+ Jar.close();
+ }
+ }
break;
case ZIP:
@@ -285,18 +292,38 @@
+ " does not
contain any jar files or is not a zip file.");
}
- for (ZipEntry Entry : Entries) {
- String EntryName = Entry.getName();
+ ZipFile zf = null;
- InputStream is = ZipUtil.readFile(FileName,
EntryName);
- JarInputStream jis = new JarInputStream(is);
- PluginClassName =
getManifestAttribute(jis.getManifest());
- jis.close();
- is.close();
- }
+ zf = new ZipFile(FileName);
+ try {
+ for (ZipEntry Entry : Entries) {
+ String EntryName = Entry.getName();
+
+ InputStream is = ZipUtil.readFile(zf, EntryName);
+ try {
+ JarInputStream jis = new JarInputStream(is);
+ try {
+ PluginClassName =
getManifestAttribute(jis.getManifest());
+ }
+ finally {
+ if (jis != null) {
+ jis.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
+ }
+ finally {
+ zf.close();
+ }
}
- ;
- return PluginClassName;
+
+ return PluginClassName;
}
/*
Modified: cytoscape/trunk/src/cytoscape/plugin/PluginManager.java
===================================================================
--- cytoscape/trunk/src/cytoscape/plugin/PluginManager.java 2009-08-13
04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/plugin/PluginManager.java 2009-08-13
10:01:38 UTC (rev 17805)
@@ -64,6 +64,7 @@
import java.util.jar.JarInputStream;
import java.util.jar.Manifest;
import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
/**
* @author skillcoy
@@ -997,8 +998,14 @@
switch (Type) {
case JAR:
JarFile Jar = new JarFile(FileName);
- PluginClassName =
getManifestAttribute(Jar.getManifest());
- Jar.close();
+ try {
+ PluginClassName = getManifestAttribute(Jar.getManifest());
+ }
+ finally {
+ if (Jar != null) {
+ Jar.close();
+ }
+ }
break;
case ZIP:
@@ -1012,15 +1019,36 @@
+ " does not
contain any jar files or is not a zip file.");
}
- for (ZipEntry Entry : Entries) {
- String EntryName = Entry.getName();
+ ZipFile zf = null;
+ zf = new ZipFile(FileName);
+ try {
+ for (ZipEntry Entry : Entries) {
+ String EntryName = Entry.getName();
- InputStream is = ZipUtil.readFile(FileName,
EntryName);
- JarInputStream jis = new JarInputStream(is);
- PluginClassName =
getManifestAttribute(jis.getManifest());
- jis.close();
- is.close();
+ InputStream is = ZipUtil.readFile(zf, EntryName);
+ try {
+ JarInputStream jis = new JarInputStream(is);
+ try {
+ PluginClassName =
getManifestAttribute(jis.getManifest());
+ }
+ finally {
+ if (jis != null) {
+ jis.close();
+ }
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
}
+ finally {
+ if (zf != null) {
+ zf.close();
+ }
+ }
}
return PluginClassName;
}
Modified: cytoscape/trunk/src/cytoscape/util/URLUtil.java
===================================================================
--- cytoscape/trunk/src/cytoscape/util/URLUtil.java 2009-08-13 04:16:54 UTC
(rev 17804)
+++ cytoscape/trunk/src/cytoscape/util/URLUtil.java 2009-08-13 10:01:38 UTC
(rev 17805)
@@ -51,10 +51,6 @@
private static final String JAR = ".jar";
private static int msConnectionTimeout = 2000;
- /**
- *
- */
- public static boolean STOP = false;
/**
* Gets the an input stream given a URL.
@@ -156,57 +152,71 @@
*/
public static void download(String urlString, File downloadFile,
TaskMonitor taskMonitor) throws IOException {
- URL url = new URL(urlString);
- InputStream is = null;
-// Proxy CytoProxyHandler = ProxyHandler.getProxyServer();
- int maxCount = 0; // -1 if unknown
- int progressCount = 0;
-// if (CytoProxyHandler == null) {
- URLConnection conn = getURLConnection(url);
- //URLConnection conn = url.openConnection();
- // Ensure we are reading the real content from url,
- // and not some out-of-date cached content:
- //conn.setUseCaches(false);
- maxCount = conn.getContentLength();
- is = conn.getInputStream();
-// } else {
-// URLConnection conn =
url.openConnection(CytoProxyHandler);
-// // Ensure we are reading the real content from url,
-// // and not some out-of-date cached content:
-// conn.setUseCaches(false);
-// conn.setConnectTimeout(msConnectionTimeout);
+ boolean stop = false;
+
+ try {
+ URL url = new URL(urlString);
+ InputStream is = null;
+// Proxy CytoProxyHandler = ProxyHandler.getProxyServer();
+ int maxCount = 0; // -1 if unknown
+ int progressCount = 0;
+// if (CytoProxyHandler == null) {
+ URLConnection conn = getURLConnection(url);
+ //URLConnection conn = url.openConnection();
+ // Ensure we are reading the real content from url,
+ // and not some out-of-date cached content:
+ //conn.setUseCaches(false);
+ maxCount = conn.getContentLength();
+ is = conn.getInputStream();
+// } else {
+// URLConnection conn =
url.openConnection(CytoProxyHandler);
+// // Ensure we are reading the real content from url,
+// // and not some out-of-date cached content:
+// conn.setUseCaches(false);
+// conn.setConnectTimeout(msConnectionTimeout);
//
-// maxCount = conn.getContentLength();
-// is = conn.getInputStream();
-// }
- FileOutputStream os = new FileOutputStream(downloadFile);
- double percent = 0.0d;
- byte[] buffer = new byte[1];
- while (((is.read(buffer)) != -1) && !STOP) {
- progressCount += buffer.length;
- // Report on Progress
- if (taskMonitor != null) {
- percent = ((double) progressCount / maxCount) *
100.0;
- if (maxCount == -1) { // file size unknown
- percent = -1;
- }
- JTask jTask = (JTask) taskMonitor;
- if (jTask.haltRequested()) { // abort
- downloadFile = null;
- taskMonitor.setStatus("Canceling the
download ...");
- taskMonitor.setPercentCompleted(100);
- break;
- }
- taskMonitor.setPercentCompleted((int) percent);
- }
- os.write(buffer);
- }
- os.flush();
- os.close();
- is.close();
- if (STOP) {
- downloadFile.delete();
- }
+// maxCount = conn.getContentLength();
+// is = conn.getInputStream();
+// }
+ FileOutputStream os = new FileOutputStream(downloadFile);
+ try {
+ double percent = 0.0d;
+ byte[] buffer = new byte[1];
+ while (((is.read(buffer)) != -1) && !stop) {
+ progressCount += buffer.length;
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount / maxCount) * 100.0;
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
+ JTask jTask = (JTask) taskMonitor;
+ if (jTask.haltRequested()) { // abort
+ stop = true;
+ taskMonitor.setStatus("Canceling the download
...");
+ taskMonitor.setPercentCompleted(100);
+ break;
+ }
+ taskMonitor.setPercentCompleted((int) percent);
+ }
+ os.write(buffer);
+ }
+ os.flush();
+ }
+ finally {
+ if (os != null) {
+ os.close();
+ }
+ if (is != null) {
+ is.close();
+ }
+ }
+ }
+ finally {
+ if (stop) {
+ downloadFile.delete();
+ }
+ }
}
/**
@@ -220,10 +230,18 @@
InputStream is = getInputStream(source);
StringBuffer buffer = new StringBuffer();
int c;
- while ((c = is.read()) != -1) {
- buffer.append((char) c);
- }
- is.close();
+
+ try {
+ while ((c = is.read()) != -1) {
+ buffer.append((char) c);
+ }
+ }
+ finally {
+ if (is != null) {
+ is.close();
+ }
+ }
+
return buffer.toString();
}
}
Modified: cytoscape/trunk/src/cytoscape/util/ZipUtil.java
===================================================================
--- cytoscape/trunk/src/cytoscape/util/ZipUtil.java 2009-08-13 04:16:54 UTC
(rev 17804)
+++ cytoscape/trunk/src/cytoscape/util/ZipUtil.java 2009-08-13 10:01:38 UTC
(rev 17805)
@@ -162,45 +162,50 @@
final byte[] rgb = new byte[5000];
final ZipOutputStream zipOS = new ZipOutputStream(new
BufferedOutputStream(new FileOutputStream(zipArchiveName)));
- // Tuning performance
- zipOS.setMethod(ZipOutputStream.DEFLATED);
+ try {
+ // Tuning performance
+ zipOS.setMethod(ZipOutputStream.DEFLATED);
- if ((compressionLevel >= 0) && (compressionLevel <= 9)) {
- zipOS.setLevel(compressionLevel);
- } else {
- zipOS.setLevel(DEF_COMPRESSION_LEVEL);
- }
+ if ((compressionLevel >= 0) && (compressionLevel <= 9)) {
+ zipOS.setLevel(compressionLevel);
+ } else {
+ zipOS.setLevel(DEF_COMPRESSION_LEVEL);
+ }
- String targetName = "";
+ String targetName = "";
- for (int i = 0; i < fileCount; i++) {
- final File file = new File(inputFileDir +
inputFiles[i]);
- targetName = sessionDirName + FS + inputFiles[i];
- addEntryToZip(file, targetName, zipOS, crc32, rgb);
- }
+ for (int i = 0; i < fileCount; i++) {
+ final File file = new File(inputFileDir + inputFiles[i]);
+ targetName = sessionDirName + FS + inputFiles[i];
+ addEntryToZip(file, targetName, zipOS, crc32, rgb);
+ }
- if ((pluginFileMap != null) && (pluginFileMap.size() > 0)) {
- Set<String> pluginSet = pluginFileMap.keySet();
+ if ((pluginFileMap != null) && (pluginFileMap.size() > 0)) {
+ Set<String> pluginSet = pluginFileMap.keySet();
- for (String pluginName : pluginSet) {
- List<File> theFileList = (List<File>)
pluginFileMap.get(pluginName);
+ for (String pluginName : pluginSet) {
+ List<File> theFileList = (List<File>)
pluginFileMap.get(pluginName);
- if ((theFileList == null) ||
(theFileList.size() == 0))
- continue;
+ if ((theFileList == null) || (theFileList.size() == 0))
+ continue;
- for (File theFile : theFileList) {
- if ((theFile == null) ||
(!theFile.exists()))
- continue;
+ for (File theFile : theFileList) {
+ if ((theFile == null) || (!theFile.exists()))
+ continue;
- targetName = sessionDirName + FS +
"plugins" + FS + pluginName + FS
- + theFile.getName();
- addEntryToZip(theFile, targetName,
zipOS, crc32, rgb);
- }
- }
- }
+ targetName = sessionDirName + FS + "plugins" + FS +
pluginName + FS
+ + theFile.getName();
+ addEntryToZip(theFile, targetName, zipOS, crc32, rgb);
+ }
+ }
+ }
+ }
+ finally {
+ if (zipOS != null) {
+ zipOS.close();
+ }
+ }
- zipOS.close();
-
// final double stop = System.currentTimeMillis();
// final double diff = stop - start;
// CyLogger.getLogger().info("Compression time 3 = " + diff /
1000 + " sec.");
@@ -225,27 +230,43 @@
// Set CRC
FileInputStream fileIS = new FileInputStream(srcFile);
- while ((numRead = fileIS.read(rgb)) > -1) {
- crc32.update(rgb, 0, numRead);
- }
+ try {
+ while ((numRead = fileIS.read(rgb)) > -1) {
+ crc32.update(rgb, 0, numRead);
+ }
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
- fileIS.close();
-
final ZipEntry zipEntry = new ZipEntry(targetName);
zipEntry.setSize(srcFile.length());
zipEntry.setTime(srcFile.lastModified());
zipEntry.setCrc(crc32.getValue());
zipOS.putNextEntry(zipEntry);
- // Write the file
- fileIS = new FileInputStream(srcFile);
+ try {
+ // Write the file
+ fileIS = new FileInputStream(srcFile);
- while ((numRead = fileIS.read(rgb)) > -1) {
- zipOS.write(rgb, 0, numRead);
- }
-
- fileIS.close();
- zipOS.closeEntry();
+ try {
+ while ((numRead = fileIS.read(rgb)) > -1) {
+ zipOS.write(rgb, 0, numRead);
+ }
+ }
+ finally {
+ if (fileIS != null) {
+ fileIS.close();
+ }
+ }
+ }
+ finally {
+ if (zipOS != null) {
+ zipOS.closeEntry();
+ }
+ }
}
/**
@@ -265,24 +286,89 @@
* clutter from the zip file.
* @return An InputStream of the zip entry identified by the regular
* expression or null if nothing matches.
+ * @throws IOexception
+ * @deprecated
*/
+ @Deprecated
public static InputStream readFile(String zipName, String fileNameRegEx)
throws IOException {
final ZipFile sessionZipFile = new ZipFile(zipName);
- final Enumeration zipEntries = sessionZipFile.entries();
+ final Enumeration zipEntries = sessionZipFile.entries();
- while (zipEntries.hasMoreElements()) {
- final ZipEntry zent = (ZipEntry)
zipEntries.nextElement();
+ try {
+ while (zipEntries.hasMoreElements()) {
+ final ZipEntry zent = (ZipEntry) zipEntries.nextElement();
- if (zent.getName().matches(fileNameRegEx)) {
- return sessionZipFile.getInputStream(zent);
- }
- }
- sessionZipFile.close();
+ if (zent.getName().matches(fileNameRegEx)) {
+ return sessionZipFile.getInputStream(zent);
+ }
+ }
+ }
+ catch (Exception e) {
+ // This is not an ideal way to address bug 1988 for this method,
+ // as sessionZipFile must remain open for the stream on the entry
+ // to be usable.
+ // Therefore sessionZipFile can only be closed explicitly when an
+ // exception has occured.
+ // More importantly sessionZipFile cannot otherwise be closed and
+ // so will remain open until the finalize is called on it.
+ // This is the reason for deprecating this method for one that
+ // allows the enclosing method to timely close the ZipFile object
+ // and otherwise properly manage it's lifetime.
+ if (sessionZipFile != null) {
+ sessionZipFile.close();
+ }
+ if (e instanceof RuntimeException) {
+ throw (RuntimeException)e;
+ }
+ else if (e instanceof IOException) {
+ throw (IOException)e;
+ }
+ else {
+ throw new RuntimeException(e);
+ }
+ }
+
return null;
}
/**
+ * Reads a file contained within a zip file and returns an InputStream
for the
+ * specific file you want from within the zip file.
+ *
+ * @param sessionZipFile
+ * The ZipFile in which to look for an entry matching
+ * fileNameRegEx.
+ * @param fileNameRegEx
+ * A regular expression that identifies the file to be read.
In
+ * general this should just be the file name you're looking
for.
+ * If more than one file matches the regular expression,
only the
+ * first will be returned. If you're looking for a specific
file
+ * remeber to build your regular expression correctly. For
+ * example, if you're looking for the file 'vizmap.props',
make
+ * your regular expression '.*vizmap.props' to accomodate any
+ * clutter from the zip file.
+ * @return An InputStream of the zip entry identified by the regular
+ * expression or null if nothing matches.
+ * @throws IOexception
+ */
+ public static InputStream readFile(ZipFile sessionZipFile, String
fileNameRegEx)
+ throws IOException {
+ //final ZipFile sessionZipFile = new ZipFile(zipName);
+ final Enumeration zipEntries = sessionZipFile.entries();
+
+ while (zipEntries.hasMoreElements()) {
+ final ZipEntry zent = (ZipEntry) zipEntries.nextElement();
+
+ if (zent.getName().matches(fileNameRegEx)) {
+ return sessionZipFile.getInputStream(zent);
+ }
+ }
+
+ return null;
+ }
+
+ /**
* Reads zip file, returns a list of all entries that match the given
* regular expression
* @param zipName
@@ -294,16 +380,23 @@
List<ZipEntry> Matching = new ArrayList<ZipEntry>();
ZipFile Zip = new ZipFile(zipName);
- Enumeration Entries = Zip.entries();
-
- while (Entries.hasMoreElements()) {
- ZipEntry CurrentEntry = (ZipEntry)
Entries.nextElement();
- if (CurrentEntry.getName().matches(fileNameRegEx)) {
- Matching.add(CurrentEntry);
- }
- }
- Zip.close();
- return Matching;
+ try {
+ Enumeration Entries = Zip.entries();
+
+ while (Entries.hasMoreElements()) {
+ ZipEntry CurrentEntry = (ZipEntry) Entries.nextElement();
+ if (CurrentEntry.getName().matches(fileNameRegEx)) {
+ Matching.add(CurrentEntry);
+ }
+ }
+ }
+ finally {
+ if (Zip != null) {
+ Zip.close();
+ }
+ }
+
+ return Matching;
}
@@ -327,64 +420,90 @@
double percent = 0.0d;
ZipFile Zip = new ZipFile(zipName);
- Enumeration Entries = Zip.entries();
- int BUFFER = 2048;
-
- while(Entries.hasMoreElements()) {
- ZipEntry CurrentEntry = (ZipEntry)Entries.nextElement();
- File ZipFile = new File(unzipDir +
CurrentEntry.getName());
- if (!CurrentEntry.isDirectory()) {
- if (ZipFile.getParent() != null) {
- File ParentDirs = new
File(ZipFile.getParent());
-
- if (!ParentDirs.exists()) {
- ParentDirs.mkdirs();
- }
- }
- } else { // entry is directory, create and move on
- if (!ZipFile.exists()) {
- ZipFile.mkdirs();
- }
- continue;
- }
+ try {
+ Enumeration Entries = Zip.entries();
+ int BUFFER = 2048;
- InputStream zis = Zip.getInputStream(CurrentEntry);
- maxCount = zis.available();
-
- FileOutputStream fos = new FileOutputStream(ZipFile);
- BufferedOutputStream dest = new
BufferedOutputStream(fos, BUFFER);
+ while(Entries.hasMoreElements()) {
+ ZipEntry CurrentEntry = (ZipEntry)Entries.nextElement();
+ File ZipFile = new File(unzipDir + CurrentEntry.getName());
+ if (!CurrentEntry.isDirectory()) {
+ if (ZipFile.getParent() != null) {
+ File ParentDirs = new File(ZipFile.getParent());
- // write the files to the disk
- int count;
- byte[] data = new byte[BUFFER];
+ if (!ParentDirs.exists()) {
+ ParentDirs.mkdirs();
+ }
+ }
+ } else { // entry is directory, create and move on
+ if (!ZipFile.exists()) {
+ ZipFile.mkdirs();
+ }
+ continue;
+ }
- while ((count = zis.read(data, 0, BUFFER)) != -1) {
- dest.write(data, 0, count);
- // Report on Progress
- if (taskMonitor != null) {
- percent = ((double) progressCount /
maxCount) * 100.0;
- if (maxCount == -1) { // file size
unknown
- percent = -1;
- }
+ InputStream zis = Zip.getInputStream(CurrentEntry);
+ try {
+ maxCount = zis.available();
- JTask jTask = (JTask) taskMonitor;
- // TODO erm...how?
- if (jTask.haltRequested()) { //abort
-
taskMonitor.setStatus("Canceling the unzip ...");
-
taskMonitor.setPercentCompleted(100);
- break;
- }
- taskMonitor.setPercentCompleted((int)
percent);
- }
- }
+ FileOutputStream fos = new FileOutputStream(ZipFile);
+ try {
+ BufferedOutputStream dest = new
BufferedOutputStream(fos, BUFFER);
- dest.flush();
- dest.close();
- zis.close();
-
- UnzippedFiles.add(ZipFile.getAbsolutePath());
- }
- Zip.close();
+ try {
+ // write the files to the disk
+ int count;
+ byte[] data = new byte[BUFFER];
+
+ while ((count = zis.read(data, 0, BUFFER)) != -1) {
+ dest.write(data, 0, count);
+ // Report on Progress
+ if (taskMonitor != null) {
+ percent = ((double) progressCount /
maxCount) * 100.0;
+ if (maxCount == -1) { // file size unknown
+ percent = -1;
+ }
+
+ JTask jTask = (JTask) taskMonitor;
+ // TODO erm...how?
+ if (jTask.haltRequested()) { //abort
+ taskMonitor.setStatus("Canceling the
unzip ...");
+ taskMonitor.setPercentCompleted(100);
+ break;
+ }
+ taskMonitor.setPercentCompleted((int)
percent);
+ }
+ }
+
+ dest.flush();
+ }
+ finally {
+ if (dest != null) {
+ dest.close();
+ }
+ }
+ }
+ finally {
+ if (fos != null) {
+ fos.close();
+ }
+ }
+ }
+ finally {
+ if (zis != null) {
+ zis.close();
+ }
+ }
+
+ UnzippedFiles.add(ZipFile.getAbsolutePath());
+ }
+ }
+ finally {
+ if (Zip != null) {
+ Zip.close();
+ }
+ }
+
return UnzippedFiles;
}
Modified: cytoscape/trunk/src/cytoscape/visual/CalculatorIO.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/CalculatorIO.java 2009-08-13
04:16:54 UTC (rev 17804)
+++ cytoscape/trunk/src/cytoscape/visual/CalculatorIO.java 2009-08-13
10:01:38 UTC (rev 17805)
@@ -122,8 +122,12 @@
*/
public static void storeCatalog(CalculatorCatalog catalog, File
outFile) throws IOException {
final Writer writer = new FileWriter(outFile);
- storeCatalog(catalog, writer);
- writer.close();
+ try {
+ storeCatalog(catalog, writer);
+ }
+ finally {
+ writer.close();
+ }
}
/**
@@ -151,44 +155,51 @@
// get a Properties description of the catalog
final Properties props = getProperties(catalog);
- // and dump it to a buffer of bytes
- buffer = new ByteArrayOutputStream();
- props.store(buffer, header.toString());
-
- // convert the bytes to a String we can read from
- reader = new BufferedReader(new
StringReader(buffer.toString()));
-
// read all the lines and store them in a container object
// store the header lines separately so they don't get sorted
final List<String> headerLines = new ArrayList<String>();
final List<String> lines = new ArrayList<String>();
- String oneLine = reader.readLine();
+ // and dump it to a buffer of bytes
+ buffer = new ByteArrayOutputStream();
+ try {
+ props.store(buffer, header.toString());
- while (oneLine != null) {
- if (oneLine.startsWith("#"))
- headerLines.add(oneLine);
- else {
- boolean test = true;
- for (String key : OLD_CALC_KEYS) {
- if (oneLine.toUpperCase().contains(key)
== false)
- continue;
- else {
- test = false;
- break;
- }
- }
+ // convert the bytes to a String we can read from
+ reader = new BufferedReader(new StringReader(buffer.toString()));
- if (test)
- lines.add(oneLine);
- }
+ try {
+ String oneLine = reader.readLine();
- oneLine = reader.readLine();
- }
+ while (oneLine != null) {
+ if (oneLine.startsWith("#"))
+ headerLines.add(oneLine);
+ else {
+ boolean test = true;
+ for (String key : OLD_CALC_KEYS) {
+ if (oneLine.toUpperCase().contains(key) == false)
+ continue;
+ else {
+ test = false;
+ break;
+ }
+ }
- buffer.close();
- reader.close();
+ if (test)
+ lines.add(oneLine);
+ }
+ oneLine = reader.readLine();
+ }
+ }
+ finally {
+ reader.close();
+ }
+ }
+ finally {
+ buffer.close();
+ }
+
// now sort all the non-header lines
Collections.sort(lines);
Added:
cytoscape/trunk/tests/cytoscape/data/readers/CytoscapeSessionReaderTest.java
===================================================================
---
cytoscape/trunk/tests/cytoscape/data/readers/CytoscapeSessionReaderTest.java
(rev 0)
+++
cytoscape/trunk/tests/cytoscape/data/readers/CytoscapeSessionReaderTest.java
2009-08-13 10:01:38 UTC (rev 17805)
@@ -0,0 +1,79 @@
+/*
+ File: XGMMLWriterTest.java
+
+ Copyright (c) 2009, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package cytoscape.data.readers;
+
+import cytoscape.Cytoscape;
+import junit.framework.TestCase;
+
+/**
+ * Tests the CytoscapeSessionReader class.
+ *
+ * @author noel.ruddock
+ */
+public class CytoscapeSessionReaderTest extends TestCase {
+ public void testDummy() throws Exception {
+ }
+
+ // These test work and pass, but are commented out because they disturb
+ // one of the PluginManager tests when run using "ant test"
+ // All tests function undisturbed when run using "ant test-slow"
+// public void testBug0001929a() throws Exception {
+// CytoscapeSessionReader sr;
+//
+// Cytoscape.buildOntologyServer();
+// sr = new CytoscapeSessionReader("testData/Bug1929TestA.cys", null);
+// sr.read();
+// }
+//
+// public void testBug0001929b() throws Exception {
+// CytoscapeSessionReader sr;
+//
+// //new CytoscapeInit().init(null);
+// Cytoscape.buildOntologyServer();
+// sr = new CytoscapeSessionReader("testData/Bug1929TestB.cys", null);
+// sr.read();
+// }
+//
+// public void testBug0001929c() throws Exception {
+// CytoscapeSessionReader sr;
+//
+// //new CytoscapeInit().init(null);
+// Cytoscape.buildOntologyServer();
+// sr = new CytoscapeSessionReader("testData/Bug1929TestC.cys", null);
+// sr.read();
+// }
+}
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