X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FSessionsFile.java;h=ab26d201a367f2de4262a76d8f2b8a80397df152;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=230c633ff5840fee76c265bb2eb380c410547bdc;hpb=9cb512e89c7e3016e8149d9e3df8ae6fcf9a410d;p=vamsas.git
diff --git a/src/uk/ac/vamsas/client/simpleclient/SessionsFile.java b/src/uk/ac/vamsas/client/simpleclient/SessionsFile.java
index 230c633..ab26d20 100644
--- a/src/uk/ac/vamsas/client/simpleclient/SessionsFile.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SessionsFile.java
@@ -1,302 +1,347 @@
-/*
- *
-* VAMSAS Project
-*
-* Dec 13, 2006 - VamsasClient
-*
-*/
-
-package uk.ac.vamsas.client.simpleclient;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.SessionHandle;
-
-/**
- * @author Pierre MARGUERITE
- *
- *
- */
-public class SessionsFile extends ListFile {
-
- private static Log log = LogFactory.getLog(SessionsFile.class);
- /**
- * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method)
- */
- boolean backup=false;
- /**
- * number of my session in list - passed back when a session
- * is added to list, and used (if valid) for quickly
- * looking up presence of session handle in the list.
- */
- private int syncnum = 1;
- /**
- * @param file
- */
- public SessionsFile(File file) throws java.io.IOException {
- super(file);
- }
-
-
- /**
- * internal method for getting sessionsList - ensures a lock has been made but
- * does not release it.
- *
- * @return list of clients
- */
- private SessionHandle[] retrieveSessionHandles() {
- if (lockFile()) {
- try {
- SessionHandle[] sessions =null;
- if (this.fileLock.length()>0) {
-
- ObjectInputStream is = new ObjectInputStream(this.fileLock.getBufferedInputStream(true));
- Object o;
- o=is.readObject();
- if (o!=null) {
- try {
- sessions = (SessionHandle[]) o;
- }
- catch (Exception e) {
- log.error("Garbage in the clientHandle list "+this.sessionFile,e);
- }
- }
- // is.close();
- }
- return sessions;
- } catch (FileNotFoundException e) {
- // e.printStackTrace(System.err);
- log.error(e);
- } catch (Exception e) {
- log.error(e);
- //e.printStackTrace(System.err);
- }
- }
- return null;
- }
-
- /**
- * get the SessionsList from the file. May return null if lock failed!
- * @return sessionsList
- */
- public SessionHandle[] retrieveSessionsList() {
- if (lockFile()) {
- SessionHandle[] clients = retrieveSessionHandles();
- unlockFile();
- return clients;
- }
- return null;
- }
-
- /**
- * get list from the locked SessionsList.
- * @param extantlock
- * @return sessionList or null if lock failed (or file was empty)
- */
- public SessionHandle[] retrieveSessionsList(Lock extantlock) {
- if (lockFile(extantlock)) {
- SessionHandle[] sessions = retrieveSessionHandles();
- unlockFile();
- return sessions;
- }
- return null;
- }
-
-
- /**
- * adds SessionHandle me to the sessionList under an existing lock extantLock.
- * @param newSession
- * @param extantLock
- * @return session index in list or 0 if lock was invalid or addSession operation failed.
- */
- public int addSession(SessionHandle newSession, Lock extantLock) {
- return addSession(newSession, true, extantLock);
- }
-
- /**
- * adds SessionsHandle me to the sessionsList under an existing lock.
- * @param newSession - sessionsHandle
- * @param disambig - if true then add will fail if an identical sessionHandle already exists
- * @param extantLock - existing lock
- * @return client index in list or 0 if addSession (or the lock) failed.
- */
-
- public int addSession(SessionHandle newSession, boolean disambig, Lock extantLock) {
- if (lockFile(extantLock)) {
- this.syncnum = addSession(newSession, disambig);
- unlockFile();
- return this.syncnum;
- }
- return 0;
- }
-
- /**
- * removes the current session from the SessionsList without complaint if the session isn't in the sessionsList already.
- * @param session session handle to be removed
- * @param sessionlock existing lock passed from watcher.
- */
- public void removeSession(SessionHandle session, Lock sessionlock) {
- int mynum =-1;
- if (lockFile(sessionlock)) {
-
- SessionHandle[] sessions = retrieveSessionHandles();
- if (sessions != null) {
- if ((this.syncnum<=0 || this.syncnum>sessions.length) || !sessions[this.syncnum-1].equals(session)) {
- for (int i = 0, j = sessions.length; i < j; i++)
- { if (sessions[i].equals(session)) {
- mynum=i;
- break;
- }
- }
- } else {
- mynum=this.syncnum-1;
- }
-
- if (mynum>-1) {
- SessionHandle[] newlist = new SessionHandle[sessions.length - 1];
- for (int k=0,i = 0, j = sessions.length; i < j; i++)
- if (i!=mynum)
- newlist[k++] = sessions[i];
- if (!putSessionsList(newlist))
- throw new Error("Failed to write new sessionsList!"); // failed to put the sessionList to disk.
- }
- }
- unlockFile();
- } else {
- throw new Error("Couldn't get lock for "+((this.sessionFile==null) ? "Unitialised sessionFile in SessionsFile" : this.sessionFile.getAbsolutePath()));
- }
- }
- /**
- * Adds a SessionHandle to the SessionList file - optionally disambiguating
- * the SessionHandle (modifes the URN).
- * Note: Caller is left to release the lock on the SessionList.
- * @param session
- * @param disambiguate -
- * flag indicating if the URN for me should be disambiguated to
- * differentiate between sessions.
- * @return index of sessionHandle in new list, or -1-position of existing
- * sessionHandle (if disambiguate is true)
- */
- protected int addSession(SessionHandle session, boolean disambiguate) {
- int newsession = 0;
- int tries=5;
- while (tries-->0 && !lockFile())
- try { Thread.sleep(1); } catch (Exception e){};
- if (lockFile()) {
- SessionHandle[] sessions = retrieveSessionHandles();
-
- if (sessions == null) {
- sessions = new SessionHandle[1];
- sessions[0] = session;
- newsession = 1;
- } else {
- int k = 0;
- for (int i = 0, j = sessions.length; i < j; i++) {
- if ( sessions[i].equals(session)) {
- if (disambiguate) {
- while (sessions[i].equals(session)) {
- // me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better
- // disambiguation of
- // urn.
- }
- } else {
- // will not write the ambiguous clientHandle to disk, just return
- // its index.
- return -1 - i;
- }
- }
- }
- int i, j;
- SessionHandle[] newlist = new SessionHandle[sessions.length + 1];
- for (i = 0, j = sessions.length; i < j; i++)
- newlist[i] = sessions[i];
- newlist[j] = session;
- sessions = newlist;
- newsession = j+1;
- }
- if (!putSessionsList(sessions))
- return 0; // failed to put the clientList to disk.
- }
- return newsession;
- }
-
-
- /**
- * safely writes sessions array to the file referred to by sessionFile.
- *
- * @param clients
- * @return true if successful write. Throws Errors otherwise.
- */
- protected boolean putSessionsList(SessionHandle[] clients) {
- if (lockFile()) {
- File templist=null;
- if (!this.backup || (templist = backupSessionFile()) != null) {
- int retries=3;
- while (retries-->0) {
- try {
- ObjectOutputStream os =
- new ObjectOutputStream(this.fileLock.getBufferedOutputStream(true));
- log.debug("About to write "+clients.length+" sessionHandles to output stream.");
- os.writeObject(clients);
- // os.flush();
- os.close();
- // All done - remove the backup.
- if (this.backup)
- templist.delete();
- templist = null;
- retries=-1;
- } catch (Exception e) {
- // System.err
- //.println("Serious - problems writing to sessionFile.");
- log.error("Serious - problems writing to sessionFile.",e);
- if (retries>0 && templist != null) {
- // System.err.println("Recovering from Backup in "
- // + templist.getAbsolutePath());
- log.error("Recovering from Backup in "+ templist.getAbsolutePath());
- templist.renameTo(this.fileLock.target);
- }
- //e.printStackTrace(System.err);
- log.error(e);
- }
- }
- if (retries>-2) {
- // System.err
- // .println("Serious - problems writing to sessionFile. Giving Up.");
- log.error("Serious - problems writing to sessionFile. Giving Up.");
- return false;
- }
- } else {
- throw new Error(
- "Couldn't create backup of the clientList before writing to it!");
- }
- } else {
- throw new Error("Could not lock the clientList: "
- + ((this.sessionFile == null) ? "Unitialized ClientsFile"
- : " failed to get lock on " + this.sessionFile.getAbsolutePath()));
- }
- // successful!
- return true;
- }
-
- public void clearList() {
- if (lockFile()) {
- try {
- FileOutputStream fout = this.fileLock.getFileOutputStream(true);
- fout.flush();
- fout.close();
- } catch (Exception e) {
- throw new Error("Problems trying to clear clientlist!",e);
-
- }
- }
-
- }
-}
+/*
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client 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 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client 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. 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 the Vamsas Client. If not, see .
+ */
+package uk.ac.vamsas.client.simpleclient;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import uk.ac.vamsas.client.SessionHandle;
+import uk.ac.vamsas.client.simpleclient.SimpleSessionHandle;
+
+/**
+ * @author Pierre MARGUERITE
+ *
+ *
+ */
+public class SessionsFile extends ListFile {
+
+ private static Log log = LogFactory.getLog(SessionsFile.class);
+
+ /**
+ * when set true - get FileNotFoundExceptions on WinXP when writing to locked
+ * stream after the backup has been made (via the backupFile method)
+ */
+ boolean backup = false;
+
+ /**
+ * number of my session in list - passed back when a session is added to list,
+ * and used (if valid) for quickly looking up presence of session handle in
+ * the list.
+ */
+ private int syncnum = 1;
+
+ /**
+ * @param file
+ */
+ public SessionsFile(File file) throws java.io.IOException {
+ super(file);
+ }
+
+ /**
+ * internal method for getting sessionsList - ensures a lock has been made but
+ * does not release it.
+ *
+ * @return list of clients
+ */
+ private SimpleSessionHandle[] retrieveSessionHandles() {
+ if (lockFile()) {
+ try {
+ SimpleSessionHandle[] sessions = null;
+ if (this.fileLock.length() > 0) {
+
+ ObjectInputStream is = new ObjectInputStream(this.fileLock
+ .getBufferedInputStream(true));
+ Object o;
+ o = is.readObject();
+ if (o != null) {
+ try {
+ sessions = (SimpleSessionHandle[]) o;
+ } catch (Exception e) {
+ log.error("Garbage in the clientHandle list " + this.sessionFile,
+ e);
+ }
+ }
+ // is.close();
+ }
+ return sessions;
+ } catch (FileNotFoundException e) {
+ // e.printStackTrace(System.err);
+ log.error(e);
+ } catch (Exception e) {
+ log.error(e);
+ // e.printStackTrace(System.err);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * get the SessionsList from the file. May return null if lock failed!
+ *
+ * @return sessionsList
+ */
+ public SimpleSessionHandle[] retrieveSessionsList() {
+ if (lockFile()) {
+ SimpleSessionHandle[] clients = retrieveSessionHandles();
+ unlockFile();
+ return clients;
+ }
+ return null;
+ }
+
+ /**
+ * get list from the locked SessionsList.
+ *
+ * @param extantlock
+ * @return sessionList or null if lock failed (or file was empty)
+ */
+ public SimpleSessionHandle[] retrieveSessionsList(Lock extantlock) {
+ if (lockFile(extantlock)) {
+ SimpleSessionHandle[] sessions = retrieveSessionHandles();
+ unlockFile();
+ return sessions;
+ }
+ return null;
+ }
+
+ /**
+ * adds SessionHandle me to the sessionList under an existing lock extantLock.
+ *
+ * @param newSession
+ * @param extantLock
+ * @return session index in list or 0 if lock was invalid or addSession
+ * operation failed.
+ */
+ public int addSession(SimpleSessionHandle newSession, Lock extantLock) {
+ return addSession(newSession, true, extantLock);
+ }
+
+ /**
+ * adds SessionsHandle me to the sessionsList under an existing lock.
+ *
+ * @param newSession
+ * - sessionsHandle
+ * @param disambig
+ * - if true then add will fail if an identical sessionHandle already
+ * exists
+ * @param extantLock
+ * - existing lock
+ * @return client index in list or 0 if addSession (or the lock) failed.
+ */
+
+ public int addSession(SimpleSessionHandle newSession, boolean disambig,
+ Lock extantLock) {
+ if (lockFile(extantLock)) {
+ this.syncnum = addSession(newSession, disambig);
+ unlockFile();
+ return this.syncnum;
+ }
+ return 0;
+ }
+
+ /**
+ * removes the current session from the SessionsList without complaint if the
+ * session isn't in the sessionsList already.
+ *
+ * @param session
+ * session handle to be removed
+ * @param sessionlock
+ * existing lock passed from watcher.
+ */
+ public void removeSession(SessionHandle session, Lock sessionlock) {
+ int mynum = -1;
+ if (lockFile(sessionlock)) {
+
+ SimpleSessionHandle[] sessions = retrieveSessionHandles();
+ if (sessions != null) {
+ if ((this.syncnum <= 0 || this.syncnum > sessions.length)
+ || !session.equals(sessions[this.syncnum - 1])) {
+ for (int i = 0, j = sessions.length; i < j; i++) {
+ if (sessions[i].equals(session)) {
+ mynum = i;
+ break;
+ }
+ }
+ } else {
+ mynum = this.syncnum - 1;
+ }
+
+ if (mynum > -1) {
+ SimpleSessionHandle[] newlist = new SimpleSessionHandle[sessions.length - 1];
+ for (int k = 0, i = 0, j = sessions.length; i < j; i++)
+ if (i != mynum)
+ newlist[k++] = sessions[i];
+ if (!putSessionsList(newlist))
+ throw new Error("Failed to write new sessionsList!"); // failed to
+ // put the
+ // sessionList
+ // to disk.
+ }
+ }
+ unlockFile();
+ } else {
+ throw new Error(
+ "Couldn't get lock for "
+ + ((this.sessionFile == null) ? "Unitialised sessionFile in SessionsFile"
+ : this.sessionFile.getAbsolutePath()));
+ }
+ }
+
+ /**
+ * Adds a SessionHandle to the SessionList file - optionally disambiguating
+ * the SessionHandle (modifes the URN). Note: Caller is left to release the
+ * lock on the SessionList.
+ *
+ * @param session
+ * @param disambiguate
+ * - flag indicating if the URN for me should be disambiguated to
+ * differentiate between sessions.
+ * @return index of sessionHandle in new list, or -1-position of existing
+ * sessionHandle (if disambiguate is true)
+ */
+ protected int addSession(SimpleSessionHandle session, boolean disambiguate) {
+ int newsession = 0;
+ int tries = 5;
+ while (tries-- > 0 && !lockFile())
+ try {
+ Thread.sleep(1);
+ } catch (Exception e) {
+ }
+ ;
+ if (lockFile()) {
+ SimpleSessionHandle[] sessions = retrieveSessionHandles();
+
+ if (sessions == null) {
+ sessions = new SimpleSessionHandle[1];
+ sessions[0] = session;
+ newsession = 1;
+ } else {
+ int k = 0;
+ for (int i = 0, j = sessions.length; i < j; i++) {
+ if (sessions[i].equals(session)) {
+ if (disambiguate) {
+ while (sessions[i].equals(session)) {
+ // me.setClientUrn(me.getClientUrn() + k++); // TODO: make a
+ // better
+ // disambiguation of
+ // urn.
+ }
+ } else {
+ // will not write the ambiguous clientHandle to disk, just return
+ // its index.
+ return -1 - i;
+ }
+ }
+ }
+ int i, j;
+ SimpleSessionHandle[] newlist = new SimpleSessionHandle[sessions.length + 1];
+ for (i = 0, j = sessions.length; i < j; i++)
+ newlist[i] = sessions[i];
+ newlist[j] = session;
+ sessions = newlist;
+ newsession = j + 1;
+ }
+ if (!putSessionsList(sessions))
+ return 0; // failed to put the clientList to disk.
+ }
+ return newsession;
+ }
+
+ /**
+ * safely writes sessions array to the file referred to by sessionFile.
+ *
+ * @param clients
+ * @return true if successful write. Throws Errors otherwise.
+ */
+ protected boolean putSessionsList(SimpleSessionHandle[] clients) {
+ if (lockFile()) {
+ File templist = null;
+ if (!this.backup || (templist = backupSessionFile()) != null) {
+ int retries = 3;
+ while (retries-- > 0) {
+ try {
+ ObjectOutputStream os = new ObjectOutputStream(this.fileLock
+ .getBufferedOutputStream(true));
+ log.debug("About to write " + clients.length
+ + " sessionHandles to output stream.");
+ os.writeObject(clients);
+ // os.flush();
+ os.close();
+ // All done - remove the backup.
+ if (this.backup)
+ templist.delete();
+ templist = null;
+ retries = -1;
+ } catch (Exception e) {
+ // System.err
+ // .println("Serious - problems writing to sessionFile.");
+ log.error("Serious - problems writing to sessionFile.", e);
+ if (retries > 0 && templist != null) {
+ // System.err.println("Recovering from Backup in "
+ // + templist.getAbsolutePath());
+ log.error("Recovering from Backup in "
+ + templist.getAbsolutePath());
+ templist.renameTo(this.fileLock.target);
+ }
+ // e.printStackTrace(System.err);
+ log.error(e);
+ }
+ }
+ if (retries > -2) {
+ // System.err
+ // .println("Serious - problems writing to sessionFile. Giving Up.");
+ log.error("Serious - problems writing to sessionFile. Giving Up.");
+ return false;
+ }
+ } else {
+ throw new Error(
+ "Couldn't create backup of the clientList before writing to it!");
+ }
+ } else {
+ throw new Error("Could not lock the clientList: "
+ + ((this.sessionFile == null) ? "Unitialized ClientsFile"
+ : " failed to get lock on " + this.sessionFile.getAbsolutePath()));
+ }
+ // successful!
+ return true;
+ }
+
+ public void clearList() {
+ if (lockFile()) {
+ try {
+ FileOutputStream fout = this.fileLock.getFileOutputStream(true);
+ fout.flush();
+ fout.close();
+ } catch (Exception e) {
+ throw new Error("Problems trying to clear clientlist!", e);
+
+ }
+ }
+
+ }
+}