X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=198f01d9872690467508996181dcf75d37251414;hb=a9514dd266ef856c485fd8f9108a3797b87add3f;hp=8e298178006e16b8baa47f800ab1dd76af783aed;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 8e29817..198f01d 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -25,8 +25,10 @@ import java.beans.PropertyChangeListener; import java.io.Closeable; import java.net.ConnectException; import java.net.URL; +import java.util.ArrayList; import java.util.HashSet; import java.util.Hashtable; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; @@ -41,6 +43,7 @@ import jalview.bin.Cache; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JalviewChangeSupport; import jalview.ws.WSMenuEntryProviderI; import jalview.ws.params.ParamDatastoreI; import compbio.data.msa.MsaWS; @@ -87,7 +90,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false; + boolean running = false, aborted = false; + + /** + * @return the aborted + */ + public boolean isAborted() + { + return aborted; + } + + /** + * @param aborted + * the aborted to set + */ + public void setAborted(boolean aborted) + { + this.aborted = aborted; + } Thread oldthread = null; @@ -95,7 +115,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (running && oldthread != null && oldthread.isAlive()) { - return; + if (!aborted) + { + return; + } + while (running) + { + try + { + Cache.log + .debug("Waiting around for old discovery thread to finish."); + // wait around until old discoverer dies + Thread.sleep(100); + } catch (Exception e) + { + } + } + Cache.log.debug("Old discovery thread has finished."); } running = true; oldthread = Thread.currentThread(); @@ -106,62 +142,62 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } catch (ClassNotFoundException e) { System.err - .println("Not enabling Jalview Webservices version 2: client jar is not available." + .println("Not enabling JABA Webservices : client jar is not available." + "\nPlease check that your webstart JNLP file is up to date!"); running = false; return; } + // reinitialise records of good and bad service URLs if (services != null) { services.removeAllElements(); } - for (String jwsservers : getServiceUrls()) + if (urlsWithoutServices != null) + { + urlsWithoutServices.removeAllElements(); + } + if (invalidServiceUrls != null) + { + invalidServiceUrls.removeAllElements(); + } + + List qrys = new ArrayList(); + for (final String jwsservers : getServiceUrls()) + { + JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + qrys.add(squery); + new Thread(squery).start(); + } + boolean finished = false; + do { try { - if (Jws2Client.validURL(jwsservers)) - { - // look for services - for (Services srv : Services.values()) - { - MsaWS service = null; - try - { - service = Jws2Client.connect(jwsservers, srv); - } catch (Exception e) - { - System.err.println("Jws2 Discoverer: Problem on " - + jwsservers + " with service " + srv + ":\n" - + e.getMessage()); - if (!(e instanceof javax.xml.ws.WebServiceException)) - { - e.printStackTrace(); - } - } - ; - if (service != null) - { - addService(jwsservers, srv, service); - } - } - - } - else - { - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); - } + Thread.sleep(100); } catch (Exception e) { - e.printStackTrace(); - Cache.log.warn("Exception when discovering Jws2 services.", e); - } catch (Error e) + } + ; + for (JabaWsServerQuery squery : qrys) { - Cache.log.error("Exception when discovering Jws2 services.", e); + finished |= !squery.isRunning(); } - } + if (aborted) + { + Cache.log.debug("Aborting " + qrys.size() + + " JABAWS discovery threads."); + for (JabaWsServerQuery squery : qrys) + { + squery.setQuit(true); + } + } + } while (!aborted && !finished); oldthread = null; running = false; - changeSupport.firePropertyChange("services", new Vector(), services); + if (!aborted) + { + changeSupport.firePropertyChange("services", new Vector(), services); + } } /** @@ -171,7 +207,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - private void addService(String jwsservers, Services srv, MsaWS service2) + synchronized void addService(String jwsservers, Services srv, + MsaWS service2) { if (services == null) { @@ -179,9 +216,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } System.out.println("Discovered service: " + jwsservers + " " + srv.toString()); - Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), service2); + Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), + service2); - services.add(service); + services.add(service); // retrieve the presets and parameter set and cache now service.getParamStore().getPresets(); service.hasParameters(); @@ -299,22 +337,25 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public String getUri() { // this is only valid for Jaba 1.0 - this formula might have to change! - return hosturl+(hosturl.lastIndexOf("/")==(hosturl.length()-1) ? "/" : "") +serviceType; + return hosturl + + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/" + : "") + serviceType; } - private boolean hasParams=false,lookedForParams=false; + + private boolean hasParams = false, lookedForParams = false; public boolean hasParameters() { if (!lookedForParams) { - lookedForParams=true; - try - { - hasParams = (getRunnerConfig().getArguments().size() > 0); - } catch (Exception e) - { + lookedForParams = true; + try + { + hasParams = (getRunnerConfig().getArguments().size() > 0); + } catch (Exception e) + { - } + } } return hasParams; } @@ -383,7 +424,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI }); wsmenu.add(jws2al); - + } private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) @@ -402,7 +443,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI MsaWSClient msacl = new MsaWSClient(); Vector hostLabels = new Vector(); jws2al.removeAll(); - String lasthost=null; + String lasthost = null; for (final Jws2Instance service : services) { atpoint = jws2al; @@ -424,22 +465,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI atpoint.setToolTipText(service.getActionText()); } } - if (!byhost && !hostLabels.contains(host + service.serviceType+service.getActionText())) - //!hostLabels.contains(host + (bytype ? service.serviceType+service.getActionText() : ""))) + if (!byhost + && !hostLabels.contains(host + service.serviceType + + service.getActionText())) + // !hostLabels.contains(host + (bytype ? + // service.serviceType+service.getActionText() : ""))) { // add a marker indicating where this service is hosted // relies on services from the same host being listed in a contiguous // group JMenuItem hitm; atpoint.addSeparator(); - if (lasthost==null || !lasthost.equals(host)) + if (lasthost == null || !lasthost.equals(host)) { atpoint.add(hitm = new JMenuItem(host)); hitm.setForeground(Color.blue); lasthost = host; } - hostLabels.addElement(host + service.serviceType+service.getActionText() ); - // hostLabels.addElement(host + (bytype ? service.serviceType+service.getActionText() : "")); + hostLabels.addElement(host + service.serviceType + + service.getActionText()); + // hostLabels.addElement(host + (bytype ? + // service.serviceType+service.getActionText() : "")); } msacl.attachWSMenuEntry(atpoint, service, alignFrame); /* @@ -458,17 +504,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public static void main(String[] args) { - Thread runner = new Thread(getDiscoverer()); - getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() - { + Thread runner = getDiscoverer().startDiscoverer( + new PropertyChangeListener() + { - public void propertyChange(PropertyChangeEvent evt) - { - System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); - } - }); - runner.start(); + public void propertyChange(PropertyChangeEvent evt) + { + if (getDiscoverer().services != null) + { + System.out.println("Changesupport: There are now " + + getDiscoverer().services.size() + " services"); + + } + } + }); while (runner.isAlive()) { try @@ -597,15 +646,145 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { "-h=" + foo.toString() }); } catch (Exception e) { + e.printStackTrace(); return false; } catch (OutOfMemoryError e) { + e.printStackTrace(); return false; } catch (Error e) { + e.printStackTrace(); return false; } + return true; } + /** + * Start a fresh discovery thread and notify the given object when we're + * finished. Any known existing threads will be killed before this one is + * started. + * + * @param changeSupport2 + * @return new thread + */ + public Thread startDiscoverer(PropertyChangeListener changeSupport2) + { + if (isRunning()) + { + setAborted(true); + } + addPropertyChangeListener(changeSupport2); + Thread thr = new Thread(this); + thr.start(); + return thr; + } + + Vector invalidServiceUrls = null, urlsWithoutServices = null; + + /** + * @return the invalidServiceUrls + */ + public Vector getInvalidServiceUrls() + { + return invalidServiceUrls; + } + + /** + * @return the urlsWithoutServices + */ + public Vector getUrlsWithoutServices() + { + return urlsWithoutServices; + } + + /** + * add an 'empty' JABA server to the list. Only servers not already in the 'bad URL' list will be added to this list. + * + * @param jwsservers + */ + public synchronized void addUrlwithnoservices(String jwsservers) + { + if (urlsWithoutServices == null) + { + urlsWithoutServices = new Vector(); + } + + if ((invalidServiceUrls == null || !invalidServiceUrls + .contains(jwsservers)) + && !urlsWithoutServices.contains(jwsservers)) + { + urlsWithoutServices.add(jwsservers); + } + } + + /** + * add a bad URL to the list + * + * @param jwsservers + */ + public synchronized void addInvalidServiceUrl(String jwsservers) + { + if (invalidServiceUrls == null) + { + invalidServiceUrls = new Vector(); + } + if (!invalidServiceUrls.contains(jwsservers)) + { + invalidServiceUrls.add(jwsservers); + } + } + + /** + * + * @return a human readable report of any problems with the service URLs used + * for discovery + */ + public String getErrorMessages() + { + if (!isRunning() && !isAborted()) + { + StringBuffer ermsg = new StringBuffer(); + boolean list = false; + if (getInvalidServiceUrls() != null + && getInvalidServiceUrls().size() > 0) + { + ermsg.append("URLs that could not be contacted: \n"); + for (String svcurl : getInvalidServiceUrls()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n\n"); + } + list = false; + if (getUrlsWithoutServices() != null + && getUrlsWithoutServices().size() > 0) + { + ermsg.append("URLs without any JABA Services : \n"); + for (String svcurl : getUrlsWithoutServices()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n"); + } + if (ermsg.length() > 1) + { + return ermsg.toString(); + } + + } + return null; + } + }