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[Genoviz-cmts] SF.net SVN: genoviz:[6230] trunk/genometryImpl/src/com/affymetrix/ genometryImpl/util/CacheScript.java
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From: <hi...@us...> - 2010-06-22 17:14:42
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Revision: 6230
http://genoviz.svn.sourceforge.net/genoviz/?rev=6230&view=rev
Author: hiralv
Date: 2010-06-22 17:14:33 +0000 (Tue, 22 Jun 2010)
Log Message:
-----------
Copy recursively if no error occurs.
Modified Paths:
--------------
trunk/genometryImpl/src/com/affymetrix/genometryImpl/util/CacheScript.java
Modified: trunk/genometryImpl/src/com/affymetrix/genometryImpl/util/CacheScript.java
===================================================================
--- trunk/genometryImpl/src/com/affymetrix/genometryImpl/util/CacheScript.java 2010-06-22 17:13:25 UTC (rev 6229)
+++ trunk/genometryImpl/src/com/affymetrix/genometryImpl/util/CacheScript.java 2010-06-22 17:14:33 UTC (rev 6230)
@@ -11,6 +11,7 @@
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.net.MalformedURLException;
@@ -40,9 +41,10 @@
public class CacheScript {
private static final String dsn = "dsn.xml";
+ private static final String temp = " temp";
/** Local path where data is cached. **/
- private static final String path = ".";
+ private static final String path = "/";
/** For files too be looked up on server. **/
private static final Set<String> quickloadFiles = new HashSet<String>();
@@ -65,15 +67,15 @@
/** Default server list. **/
private static final String defaultList = " <servers> " +
-// " <server type='das2' name='NetAffx Das2' url='http://netaffxdas.affymetrix.com/das2/genome' />" +
-// " <server type='quickload' name='NetAffx Quickload' url='http://netaffxdas.affymetrix.com/quickload_data' />" +
+ " <server type='das2' name='NetAffx Das2' url='http://netaffxdas.affymetrix.com/das2/genome' />" +
+ " <server type='quickload' name='NetAffx Quickload' url='http://netaffxdas.affymetrix.com/quickload_data' />" +
" <server type='das2' name='Bioviz Das2' url='http://bioviz.org/das2/genome' />" +
" <server type='quickload' name='Bioviz Quickload' url='http://bioviz.org/quickload/' />" +
-// " <server type='das' name='UCSC Das' url='http://genome.cse.ucsc.edu/cgi-bin/das/dsn' />" +
+ " <server type='das' name='UCSC Das' url='http://genome.cse.ucsc.edu/cgi-bin/das/dsn' />" +
-// " <server type='quickload' name='HughesLab' url='http://hugheslab.ccbr.utoronto.ca/igb/' />" +
+ " <server type='quickload' name='HughesLab' url='http://hugheslab.ccbr.utoronto.ca/igb/' />" +
// " <server type='das' name='Ensembl' url='http://www.ensembl.org/das/dsn' enabled='false' />" +
@@ -86,23 +88,24 @@
* Determines the server type and process it accordingly.
* @param gServer GenericServer to be processed.
*/
- private static void processServer(GenericServer gServer){
- String serverCachePath = path+gServer.serverName;
+ private static boolean processServer(GenericServer gServer){
+ String serverCachePath = path+gServer.serverName+temp;
makeDir(serverCachePath);
switch(gServer.serverType){
case QuickLoad:
- processQuickLoad(gServer, serverCachePath);
- break;
+ return processQuickLoad(gServer, serverCachePath);
+
case DAS2:
- processDas2Server(gServer, serverCachePath);
- break;
+ return processDas2Server(gServer, serverCachePath);
+
case DAS:
- processDasServer(gServer, serverCachePath);
- break;
+ return processDasServer(gServer, serverCachePath);
}
+
+ return false;
}
/**
@@ -223,9 +226,7 @@
for (DasSource source : sources.values()) {
- String localPath = serverCachePath + "/" + source.getID();
- makeDir(localPath);
- getAllDasFiles(source.getID(),source.getServerURL(), source.getMasterURL(), localPath);
+ getAllDasFiles(source.getID(),source.getServerURL(), source.getMasterURL(), serverCachePath);
}
return true;
@@ -236,7 +237,10 @@
* @param server_path Server path from where mapping is to be copied.
* @param local_path Local path from where mapping is to saved.
*/
- private static void getAllDasFiles(String id, URL server, URL master, String local_path){
+ private static boolean getAllDasFiles(String id, URL server, URL master, String local_path){
+ local_path += "/" + id;
+ makeDir(local_path);
+
File file;
final Map<String, String> DasFilePath = new HashMap<String, String>();
@@ -248,9 +252,15 @@
for(Entry<String, String> fileDet : DasFilePath.entrySet()){
file = getFile(fileDet.getKey());
- moveFileTo(file,fileDet.getValue(),local_path);
+
+ if(file == null)
+ continue;
+
+ if(!moveFileTo(file,fileDet.getValue(),local_path))
+ return false;
}
-
+
+ return true;
}
/**
@@ -287,12 +297,12 @@
* @param path Path where directory is to be created.
* @return
*/
- private static boolean makeDir(String path){
+ private static File makeDir(String path){
File dir = new File(path);
if(!dir.exists()){
dir.mkdir();
}
- return true;
+ return dir;
}
/**
@@ -367,53 +377,92 @@
}
/**
- * Runs caching script for given set of server list.
- * @param server_list List of server.
+ * Create serverMapping.txt and adds server name and corresponding directory to it.
+ * @param server_list
*/
- static public void runScript(Set<GenericServer> server_list){
-
+ private static void writeServerMapping(Set<GenericServer> server_list){
FileOutputStream fos = null;
- File mapping = new File(path + "/" + Constants.serverMapping);
try {
+ File mapping = new File(path + "/" + Constants.serverMapping);
mapping.createNewFile();
fos = new FileOutputStream(mapping);
final PrintStream out = new PrintStream(fos);
-
for (final GenericServer gServer : server_list) {
-
- final Timer ser_tim = new Timer();
- ExecutorService vexec = Executors.newSingleThreadExecutor();
- SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {
-
- protected Void doInBackground(){
- ser_tim.start();
- processServer(gServer);
- return null;
- }
-
- @Override
- public void done() {
- out.println(gServer.friendlyURL.toExternalForm() + "\t" + gServer.serverName);
- Logger.getLogger(CacheScript.class.getName()).log(Level.INFO, "Time required to cache " + gServer.serverName + " :" + (ser_tim.read()/ 1000f), ser_tim);
- }
-
- };
- vexec.execute(worker);
- vexec.shutdown();
+ out.println(gServer.friendlyURL.toExternalForm() + "\t" + gServer.serverName);
}
- } catch (Exception ex) {
+ } catch (IOException ex) {
Logger.getLogger(CacheScript.class.getName()).log(Level.SEVERE, null, ex);
} finally {
GeneralUtils.safeClose(fos);
}
}
+ /**
+ * Recursively copies data from source to destination.
+ * @param source Source directory.
+ * @param dest Destination directory.
+ */
+ private static void copyRecursively(File source, File dest){
+ for(File file: source.listFiles()){
+ if(file.isDirectory()){
+ copyRecursively(file,makeDir(dest.getPath()+ "/" +file.getName()));
+ }else{
+ moveFileTo(file,file.getName(),dest.getPath());
+ }
+ }
+ }
+
+ /**
+ * Recursively copies directory data for given server name.
+ * @param servername Name of the server.
+ */
+ private static void copyDirectoryFor(String servername){
+ File temp_dir = new File(path + servername + temp);
+
+ String perm_path = path + servername;
+ makeDir(perm_path);
+
+ File perm_dir = new File(perm_path);
+
+ copyRecursively(temp_dir,perm_dir);
+ }
+
+ /**
+ * Runs caching script for given set of server list.
+ * @param server_list List of server.
+ */
+ static public void runScript(Set<GenericServer> server_list) {
+
+ for (final GenericServer gServer : server_list) {
+
+ final Timer ser_tim = new Timer();
+ ExecutorService vexec = Executors.newSingleThreadExecutor();
+ SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {
+
+ protected Void doInBackground() {
+ ser_tim.start();
+ if(processServer(gServer))
+ copyDirectoryFor(gServer.serverName);
+ return null;
+ }
+
+ @Override
+ public void done() {
+ Logger.getLogger(CacheScript.class.getName()).log(Level.INFO, "Time required to cache " + gServer.serverName + " :" + (ser_tim.read() / 1000f), ser_tim);
+ }
+ };
+ vexec.execute(worker);
+ vexec.shutdown();
+ }
+ }
+
static public void main(String[] args){
InputStream istr = null;
try {
istr = new ByteArrayInputStream(defaultList.getBytes());
Set<GenericServer> server_list = parseServerList(istr);
runScript(server_list);
+ writeServerMapping(server_list);
} catch (Exception ex) {
Logger.getLogger(CacheScript.class.getName()).log(Level.SEVERE, null, ex);
} finally {
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