-package uk.ac.vamsas.client.simpleclient;
-
-import uk.ac.vamsas.client.*;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutput;
-import java.io.ObjectOutputStream;
-import java.io.OutputStream;
-import java.util.Vector;
-
-/**
- * Handler for the clientsFile within a vamsas session thread.
- * @author jim
- */
-public class ClientsFile extends ListFile {
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(ClientsFile.class);
- /**
- * number of my client in list - passed back when a client
- * is added to list, and used (if valid) for quickly
- * looking up presence of client handle in the list.
- */
- private int syncnum = 1;
-
- public ClientsFile(File filelist) throws IOException {
- super(filelist);
- }
-
- /**
- * internal method for getting clientList - ensures a lock has been made but
- * does not release it.
- *
- * @return list of clients
- */
- private ClientHandle[] retrieveClientHandles() {
- if (lockFile()) {
- try {
- ClientHandle[] clients=null;
- if (fileLock.length()>0) {
-
- ObjectInputStream is = new ObjectInputStream(fileLock.getBufferedInputStream(true));
- Object o;
- o=is.readObject();
- if (o!=null) {
- try {
- clients = (ClientHandle[]) o;
- }
- catch (Exception e) {
- System.err.println("Garbage in the clientHandle list "+this.sessionFile);
- }
- }
- }
- return clients;
- } catch (FileNotFoundException e) {
- // TODO Auto-generated catch block
- e.printStackTrace(System.err);
- } catch (Exception e) {
- e.printStackTrace(System.err);
- }
- }
- return null;
- }
- /**
- * get the clientList from the file. May return null if lock failed!
- * @return clientList
- */
- public ClientHandle[] retrieveClientList() {
- if (lockFile()) {
- ClientHandle[] clients = retrieveClientHandles();
- unlockFile();
- return clients;
- }
- return null;
- }
- /**
- * get list from the locked ClientList.
- * @param extantlock
- * @return clientList or null if lock failed (or file was empty)
- */
- public ClientHandle[] retrieveClientList(Lock extantlock) {
- if (lockFile(extantlock)) {
- ClientHandle[] clients = retrieveClientHandles();
- unlockFile();
- return clients;
- }
- return null;
- }
- /**
- * adds clientHandle me to the clientList under an existing lock extantLock.
- * @param me
- * @param extantLock
- * @return client index in list or 0 if lock was invalid or addClient operation failed.
- */
- public int addClient(ClientHandle me, Lock extantLock) {
- return addClient(me, true, extantLock);
- }
-
- /**
- * adds clientHandle me to the clientList under an existing lock.
- * @param me - clientHandle
- * @param disambig - if true then add will fail if an identical clientHandle already exists
- * @param extantLock - existing lock
- * @return client index in list or 0 if addClient (or the lock) failed.
- */
-
- public int addClient(ClientHandle me, boolean disambig, Lock extantLock) {
- if (lockFile(extantLock)) {
- syncnum = addClient(me, disambig);
- unlockFile();
- return syncnum;
- }
- return 0;
- }
-
- /**
- * adds the ClientHandle to the list - if it is not unique, then the
- * ClientHandle object is modified to make it unique in the list. returns the
- * clientNumber for the client in the session.
- *
- * @param me
- * @return
- */
-
- public int addClient(ClientHandle me) {
- syncnum = addClient(me, true);
- unlockFile();
- return syncnum;
- }
-
- /**
- * removes 'me' from the session ClientList without complaint if 'me' isn't in the clientList already.
- * @param me client handle to be removed
- * @param clientlock existing lock passed from watcher.
- */
- public void removeClient(ClientHandle me, Lock clientlock) {
- int mynum=-1;
- if (lockFile(clientlock)) {
- ClientHandle[] clients = retrieveClientHandles();
- if (clients != null) {
- if ((syncnum<=0 || syncnum>clients.length) || clients[syncnum-1]!=me) {
- for (int i = 0, j = clients.length; i < j; i++)
- if (clients[i].equals(me)) {
- mynum=i;
- break;
- }
- } else {
- mynum=syncnum-1;
- }
- if (mynum>-1) {
- ClientHandle[] newlist = new ClientHandle[clients.length - 1];
- for (int k=0,i = 0, j = clients.length; i < j; i++)
- if (i!=mynum)
- newlist[k++] = clients[i];
- if (!putClientList(newlist))
- throw new Error("Failed to write new clientList!"); // failed to put the clientList to disk.
- }
- }
- unlockFile();
- } else {
- throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in ClientsFile" : sessionFile.getAbsolutePath()));
- }
- }
- /**
- * Adds a ClientHandle to the ClientList file - optionally disambiguating
- * the ClientHandle (modifes the URN).
- * Note: Caller is left to release the lock on the ClientList.
- * @param me
- * @param disambiguate -
- * flag indicating if the URN for me should be disambiguated to
- * differentiate between sessions.
- * @return index of clientHandle in new list, or -1-position of existing
- * clientHandle (if disambiguate is true)
- */
- protected int addClient(ClientHandle me, boolean disambiguate) {
- int newclient = 0;
- int tries=5;
- while (tries-->0 && !lockFile())
- try { Thread.sleep(1); } catch (Exception e){};
- if (lockFile()) {
- ClientHandle[] clients = retrieveClientHandles();
- if (me.getClientUrn()==null) {
- // TODO: move this into ClientUrn as a standard form method.
- me.setClientUrn("vamsas://"+me.getClientName()+":"+me.getVersion()+"/");
- }
- if (clients == null) {
- clients = new ClientHandle[1];
- clients[0] = me;
- newclient = 1;
- } else {
- int k = 0;
- for (int i = 0, j = clients.length; i < j; i++) {
- if (clients[i].equals(me)) {
- if (disambiguate) {
- while (clients[i].equals(me)) {
- 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;
- ClientHandle[] newlist = new ClientHandle[clients.length + 1];
- for (i = 0, j = clients.length; i < j; i++)
- newlist[i] = clients[i];
- newlist[j] = me;
- clients = newlist;
- newclient = j+1;
- }
- if (!putClientList(clients))
- return 0; // failed to put the clientList to disk.
- }
- return newclient;
- }
- /**
- * 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;
- /**
- * safely writes clients array to the file referred to by sessionFile.
- *
- * @param clients
- * @return true if successful write. Throws Errors otherwise.
- */
- protected boolean putClientList(ClientHandle[] clients) {
- if (lockFile()) {
- File templist=null;
- if (backup) {
- templist = backupSessionFile();
- }
- if (!backup || (templist != null)) {
- int retries=3;
- while (retries-->0) {
- try {
- ObjectOutputStream os =
- new ObjectOutputStream(fileLock.getBufferedOutputStream(true));
- log.debug("About to write "+clients.length+" clientHandles to output stream.");
- os.writeObject(clients);
- os.close();
- // All done - remove the backup.
- if (backup)
- templist.delete();
- templist = null;
- retries=-1;
- } catch (Exception e) {
- System.err
- .println("Serious - problems writing to sessionFile.");
- if (retries>0 && templist != null) {
- System.err.println("Recovering from Backup in "
- + templist.getAbsolutePath());
- templist.renameTo(fileLock.target);
- }
- e.printStackTrace(System.err);
- }
- }
- if (retries>-2) {
- System.err
- .println("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: "
- + ((sessionFile == null) ? "Unitialized ClientsFile"
- : " failed to get lock on " + sessionFile.getAbsolutePath()));
- }
- // successful!
- return true;
- }
-
- public void clearList() {
- if (lockFile()) {
- try {
- FileOutputStream fout = fileLock.getFileOutputStream(true);
- fout.flush();
- fout.close();
- } catch (Exception e) {
- throw new Error("Problems trying to clear clientlist!",e);
-
- }
- }
-
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.client.simpleclient;\r
+\r
+import uk.ac.vamsas.client.*;\r
+\r
+import java.io.BufferedInputStream;\r
+import java.io.BufferedOutputStream;\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileOutputStream;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.io.ObjectInputStream;\r
+import java.io.ObjectOutput;\r
+import java.io.ObjectOutputStream;\r
+import java.io.OutputStream;\r
+import java.util.Vector;\r
+\r
+/**\r
+ * Handler for the clientsFile within a vamsas session thread.\r
+ * \r
+ * @author jim\r
+ */\r
+public class ClientsFile extends ListFile {\r
+ private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory\r
+ .getLog(ClientsFile.class);\r
+\r
+ /**\r
+ * number of my client in list - passed back when a client is added to list,\r
+ * and used (if valid) for quickly looking up presence of client handle in the\r
+ * list.\r
+ */\r
+ private int syncnum = 1;\r
+\r
+ public ClientsFile(File filelist) throws IOException {\r
+ super(filelist);\r
+ }\r
+\r
+ /**\r
+ * internal method for getting clientList - ensures a lock has been made but\r
+ * does not release it.\r
+ * \r
+ * @return list of clients\r
+ */\r
+ private ClientHandle[] retrieveClientHandles() {\r
+ if (lockFile()) {\r
+ try {\r
+ ClientHandle[] clients = null;\r
+ if (fileLock.length() > 0) {\r
+\r
+ ObjectInputStream is = new ObjectInputStream(fileLock\r
+ .getBufferedInputStream(true));\r
+ Object o;\r
+ o = is.readObject();\r
+ if (o != null) {\r
+ try {\r
+ clients = (ClientHandle[]) o;\r
+ } catch (Exception e) {\r
+ System.err.println("Garbage in the clientHandle list "\r
+ + this.sessionFile);\r
+ }\r
+ }\r
+ }\r
+ return clients;\r
+ } catch (FileNotFoundException e) {\r
+ // TODO Auto-generated catch block\r
+ e.printStackTrace(System.err);\r
+ } catch (Exception e) {\r
+ e.printStackTrace(System.err);\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get the clientList from the file. May return null if lock failed!\r
+ * \r
+ * @return clientList\r
+ */\r
+ public ClientHandle[] retrieveClientList() {\r
+ if (lockFile()) {\r
+ ClientHandle[] clients = retrieveClientHandles();\r
+ unlockFile();\r
+ return clients;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get list from the locked ClientList.\r
+ * \r
+ * @param extantlock\r
+ * @return clientList or null if lock failed (or file was empty)\r
+ */\r
+ public ClientHandle[] retrieveClientList(Lock extantlock) {\r
+ if (lockFile(extantlock)) {\r
+ ClientHandle[] clients = retrieveClientHandles();\r
+ unlockFile();\r
+ return clients;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * adds clientHandle me to the clientList under an existing lock extantLock.\r
+ * \r
+ * @param me\r
+ * @param extantLock\r
+ * @return client index in list or 0 if lock was invalid or addClient\r
+ * operation failed.\r
+ */\r
+ public int addClient(ClientHandle me, Lock extantLock) {\r
+ return addClient(me, true, extantLock);\r
+ }\r
+\r
+ /**\r
+ * adds clientHandle me to the clientList under an existing lock.\r
+ * \r
+ * @param me\r
+ * - clientHandle\r
+ * @param disambig\r
+ * - if true then add will fail if an identical clientHandle already\r
+ * exists\r
+ * @param extantLock\r
+ * - existing lock\r
+ * @return client index in list or 0 if addClient (or the lock) failed.\r
+ */\r
+\r
+ public int addClient(ClientHandle me, boolean disambig, Lock extantLock) {\r
+ if (lockFile(extantLock)) {\r
+ syncnum = addClient(me, disambig);\r
+ unlockFile();\r
+ return syncnum;\r
+ }\r
+ return 0;\r
+ }\r
+\r
+ /**\r
+ * adds the ClientHandle to the list - if it is not unique, then the\r
+ * ClientHandle object is modified to make it unique in the list. returns the\r
+ * clientNumber for the client in the session.\r
+ * \r
+ * @param me\r
+ * @return\r
+ */\r
+\r
+ public int addClient(ClientHandle me) {\r
+ syncnum = addClient(me, true);\r
+ unlockFile();\r
+ return syncnum;\r
+ }\r
+\r
+ /**\r
+ * removes 'me' from the session ClientList without complaint if 'me' isn't in\r
+ * the clientList already.\r
+ * \r
+ * @param me\r
+ * client handle to be removed\r
+ * @param clientlock\r
+ * existing lock passed from watcher.\r
+ */\r
+ public void removeClient(ClientHandle me, Lock clientlock) {\r
+ int mynum = -1;\r
+ if (lockFile(clientlock)) {\r
+ ClientHandle[] clients = retrieveClientHandles();\r
+ if (clients != null) {\r
+ if ((syncnum <= 0 || syncnum > clients.length)\r
+ || clients[syncnum - 1] != me) {\r
+ for (int i = 0, j = clients.length; i < j; i++)\r
+ if (clients[i].equals(me)) {\r
+ mynum = i;\r
+ break;\r
+ }\r
+ } else {\r
+ mynum = syncnum - 1;\r
+ }\r
+ if (mynum > -1) {\r
+ ClientHandle[] newlist = new ClientHandle[clients.length - 1];\r
+ for (int k = 0, i = 0, j = clients.length; i < j; i++)\r
+ if (i != mynum)\r
+ newlist[k++] = clients[i];\r
+ if (!putClientList(newlist))\r
+ throw new Error("Failed to write new clientList!"); // failed to put\r
+ // the\r
+ // clientList to\r
+ // disk.\r
+ }\r
+ }\r
+ unlockFile();\r
+ } else {\r
+ throw new Error("Couldn't get lock for "\r
+ + ((sessionFile == null) ? "Unitialised sessionFile in ClientsFile"\r
+ : sessionFile.getAbsolutePath()));\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Adds a ClientHandle to the ClientList file - optionally disambiguating the\r
+ * ClientHandle (modifes the URN). Note: Caller is left to release the lock on\r
+ * the ClientList.\r
+ * \r
+ * @param me\r
+ * @param disambiguate\r
+ * - flag indicating if the URN for me should be disambiguated to\r
+ * differentiate between sessions.\r
+ * @return index of clientHandle in new list, or -1-position of existing\r
+ * clientHandle (if disambiguate is true)\r
+ */\r
+ protected int addClient(ClientHandle me, boolean disambiguate) {\r
+ int newclient = 0;\r
+ int tries = 5;\r
+ while (tries-- > 0 && !lockFile())\r
+ try {\r
+ Thread.sleep(1);\r
+ } catch (Exception e) {\r
+ }\r
+ ;\r
+ if (lockFile()) {\r
+ ClientHandle[] clients = retrieveClientHandles();\r
+ if (me.getClientUrn() == null) {\r
+ // TODO: move this into ClientUrn as a standard form method.\r
+ me.setClientUrn("vamsas://" + me.getClientName() + ":"\r
+ + me.getVersion() + "/");\r
+ }\r
+ if (clients == null) {\r
+ clients = new ClientHandle[1];\r
+ clients[0] = me;\r
+ newclient = 1;\r
+ } else {\r
+ int k = 0;\r
+ for (int i = 0, j = clients.length; i < j; i++) {\r
+ if (clients[i].equals(me)) {\r
+ if (disambiguate) {\r
+ while (clients[i].equals(me)) {\r
+ me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better\r
+ // disambiguation of\r
+ // urn.\r
+ }\r
+ } else {\r
+ // will not write the ambiguous clientHandle to disk, just return\r
+ // its index.\r
+ return -1 - i;\r
+ }\r
+ }\r
+ }\r
+ int i, j;\r
+ ClientHandle[] newlist = new ClientHandle[clients.length + 1];\r
+ for (i = 0, j = clients.length; i < j; i++)\r
+ newlist[i] = clients[i];\r
+ newlist[j] = me;\r
+ clients = newlist;\r
+ newclient = j + 1;\r
+ }\r
+ if (!putClientList(clients))\r
+ return 0; // failed to put the clientList to disk.\r
+ }\r
+ return newclient;\r
+ }\r
+\r
+ /**\r
+ * when set true - get FileNotFoundExceptions on WinXP when writing to locked\r
+ * stream after the backup has been made (via the backupFile method)\r
+ */\r
+ boolean backup = false;\r
+\r
+ /**\r
+ * safely writes clients array to the file referred to by sessionFile.\r
+ * \r
+ * @param clients\r
+ * @return true if successful write. Throws Errors otherwise.\r
+ */\r
+ protected boolean putClientList(ClientHandle[] clients) {\r
+ if (lockFile()) {\r
+ File templist = null;\r
+ if (backup) {\r
+ templist = backupSessionFile();\r
+ }\r
+ if (!backup || (templist != null)) {\r
+ int retries = 3;\r
+ while (retries-- > 0) {\r
+ try {\r
+ ObjectOutputStream os = new ObjectOutputStream(fileLock\r
+ .getBufferedOutputStream(true));\r
+ log.debug("About to write " + clients.length\r
+ + " clientHandles to output stream.");\r
+ os.writeObject(clients);\r
+ os.close();\r
+ // All done - remove the backup.\r
+ if (backup)\r
+ templist.delete();\r
+ templist = null;\r
+ retries = -1;\r
+ } catch (Exception e) {\r
+ System.err.println("Serious - problems writing to sessionFile.");\r
+ if (retries > 0 && templist != null) {\r
+ System.err.println("Recovering from Backup in "\r
+ + templist.getAbsolutePath());\r
+ templist.renameTo(fileLock.target);\r
+ }\r
+ e.printStackTrace(System.err);\r
+ }\r
+ }\r
+ if (retries > -2) {\r
+ System.err\r
+ .println("Serious - problems writing to sessionFile. Giving Up.");\r
+ return false;\r
+ }\r
+ } else {\r
+ throw new Error(\r
+ "Couldn't create backup of the clientList before writing to it!");\r
+ }\r
+ } else {\r
+ throw new Error("Could not lock the clientList: "\r
+ + ((sessionFile == null) ? "Unitialized ClientsFile"\r
+ : " failed to get lock on " + sessionFile.getAbsolutePath()));\r
+ }\r
+ // successful!\r
+ return true;\r
+ }\r
+\r
+ public void clearList() {\r
+ if (lockFile()) {\r
+ try {\r
+ FileOutputStream fout = fileLock.getFileOutputStream(true);\r
+ fout.flush();\r
+ fout.close();\r
+ } catch (Exception e) {\r
+ throw new Error("Problems trying to clear clientlist!", e);\r
+\r
+ }\r
+ }\r
+\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff