+++ /dev/null
-/**
- *
- */
-package org.vamsas.test.simpleclient.simpleapp;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Vector;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-
-import org.vamsas.test.simpleclient.ArchiveClient;
-import org.vamsas.test.simpleclient.ClientDoc;
-
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-/**
- * @author jimp
- *
- */
-public class VamsasClient extends ArchiveClient {
- org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasClient.class);
- /**
- * create a new vamsas client session from the archive at sessionPath.
- * @param sessionPath
- */
- public VamsasClient(File sessionPath) {
- super(System.getProperty("user.name"),System.getProperty("host.name"), "SimpleVamsasClientApp","0.1",
- sessionPath);
- }
- /**
- * Called by gui to read anything from the vamsas session into the apps datamodel
- * after it has started up.
- *
- */
- public void initial_update() {
- log.info("Jalview loading the Vamsas Session.");
- // load in the vamsas archive for the first time
- ClientDoc cdoc = this.getUpdateable();
- updateJalview(cdoc);
- // TODO: flush any new VorbaIds to the document : updateVamsasClient may actually generate new Vamsas Document data in the form of vamsas element ids - these should be written back to the document.
- //doUpdate(cdoc); // JBPNote: this should flush new VorbaIds but I've not tested it yet.
- cdoc.closeDoc();
- // then tell app to update its display based on the datamodel changes.
- }
- VamsasClientWatcher watcher=null;
- /**
- * Called by app when internal datamodel should exported (syncrhonised outwards) to vamsas document
- *
- */
- public void push_update() {
-
- watchForChange=false; // this makes any watch(long) loops return.
- // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
- try {
- Thread.sleep(WATCH_SLEEP);
- } catch (Exception e) {
-
- };
-
- ClientDoc cdoc = getUpdateable();
- updateVamsasDocument(cdoc);
- doUpdate(cdoc);
- cdoc.closeDoc();
- cdoc=null;
- watchForChange=true;
- startWatcher();
- }
- public void end_session() {
- watchForChange=false; // this makes any watch(long) loops return.
- // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
- try {
- Thread.sleep(WATCH_SLEEP);
- } catch (Exception e) {
-
- };
-
- // stop any update/watcher thread.
- log.info("VamsasClientApplication disconnecting from the Vamsas Session.");
- }
- public void updateJalview(ClientDoc cdoc) {
- ensureVamsasBindings();
- VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry());
- vds.updateToJalview();
- }
- private void ensureVamsasBindings() {
- if (jv2vobj==null) {
- jv2vobj = new IdentityHashMap();
- vobj2jv = new Hashtable();
- }
- }
- /**
- * App's object binding to VorbaIds
- */
- IdentityHashMap jv2vobj = null;
- Hashtable vobj2jv = null;
- /**
- * called with a vamsas document which will be updated with new data from the app
- * @param doc
- */
- public void updateVamsasDocument(ClientDoc doc) {
- ensureVamsasBindings();
- VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry());
- // wander through frames
- vds.storeVAMSAS(new Object()); // Object is the apps datamodel ;)
- }
- /**
- *
- * @return a base provenance entry used by the VamsasDatastore object to get attributes from. this isn't particularly elegant either.
- */
- private Entry baseProvEntry() {
- uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
- pentry.setUser(this.getProvenanceUser());
- pentry.setApp(this.getClientHandle().getClientName());
- pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
- pentry.setAction("created");
- return pentry;
- }
- protected class VamsasClientWatcher extends Thread implements Runnable {
- /* (non-Javadoc)
- * @see java.lang.Thread#run()
- */
- VamsasClient client=null;
- VamsasClientWatcher(VamsasClient client) {
- this.client = client;
- }
- boolean running=false;
- public void run() {
- running=true;
- while (client.watchForChange) {
- ClientDoc docio = client.watch(0);
- if (docio!=null) {
- // VamsasClient GUI bits should be disabled whilst an update is in progress so the user doesn't screw anything up.
- client.disableGui(true);
- log.debug("Updating VamsasClient app from changed vamsas document.");
- client.updateJalview(docio);
- log.debug("Finished updating from document change.");
- docio.closeDoc();
- docio=null;
- client.disableGui(false);
- }
- }
- running=false;
-
- }
-
- }
- /**
- * @param args
- */
- public static void main(String[] args) {
- // TODO Auto-generated method stub
-
- }
- /**
- * disable (if b is true) or enable (if b is true) the VamsasClient's vamsas session gui bits whilst a document change is being updated to the app.
- * @param b
- */
- public void disableGui(boolean b) {
- // in jalview, we turn off the VAMSAS Session menu : Desktop.instance.setVamsasUpdate(b);
- }
- /**
- * spawn a new thread to start the VamsasClientWatcher.
- *
- */
- public void startWatcher() {
- if (watcher==null)
- watcher=new VamsasClientWatcher(this);
- Thread thr = new Thread() {
- public void run() {
- watcher.start();
- }
- };
- thr.start();
- }
-
-}
git://source.jalview.org / vamsas.git / blobdiff