+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
+
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.io.Closeable;
-import java.net.ConnectException;
+import java.beans.PropertyChangeSupport;
+import java.net.MalformedURLException;
import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import org.apache.log4j.Level;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.ws.WSMenuEntryProviderI;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.RunnerConfig;
-import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
/**
*/
public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
+
+ /*
+ * the .jalview_properties entry for JWS2 URLS
+ */
+ final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ /*
+ * Singleton instance
+ */
+ private static Jws2Discoverer discoverer;
+
+ /*
+ * Override for testing only
+ */
+ private static List<String> testUrls = null;
+
+ // preferred url has precedence over others
+ private String preferredUrl;
+
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
+ Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
+ validServiceUrls = null;
+
+ boolean running = false, aborted = false;
+
+ Thread oldthread = null;
+
+ /**
+ * holds list of services.
+ */
+ protected Vector<Jws2Instance> services;
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
+ */
+ private Jws2Discoverer()
+ {
+ }
+
/**
* change listeners are notified of "services" property changes
*
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false;
+ /**
+ * @return the aborted
+ */
+ public boolean isAborted()
+ {
+ return aborted;
+ }
- Thread oldthread = null;
+ /**
+ * @param aborted
+ * the aborted to set
+ */
+ public void setAborted(boolean aborted)
+ {
+ this.aborted = aborted;
+
+ }
public void run()
{
+
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;
+
+ // first set up exclusion list if needed
+ final Set<String> ignoredServices = new HashSet<String>();
+ for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
+ "").split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+ changeSupport.firePropertyChange("services", services, new Vector());
oldthread = Thread.currentThread();
try
{
} 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)
{
- try
+ urlsWithoutServices.removeAllElements();
+ }
+ if (invalidServiceUrls != null)
+ {
+ invalidServiceUrls.removeAllElements();
+ }
+ if (validServiceUrls != null)
+ {
+ validServiceUrls.removeAllElements();
+ }
+ ArrayList<String> svctypes = new ArrayList<String>();
+
+ List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+ for (final String jwsserver : getServiceUrls())
+ {
+ JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
+ if (svctypes.size() == 0)
{
- if (Jws2Client.validURL(jwsservers))
+ // TODO: remove this ugly hack to get Canonical JABA service ordering
+ // for all possible services
+ for (Services sv : squery.JABAWS2SERVERS)
{
- // look for services
- for (Services srv : Services.values())
+ if (!ignoredServices.contains(sv.toString()))
{
- 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);
- }
+ svctypes.add(sv.toString());
}
-
}
- else
+
+ }
+ qrys.add(squery);
+ new Thread(squery).start();
+ }
+ boolean finished = true;
+ do
+ {
+ finished = true;
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+ }
+ ;
+ for (JabaWsServerQuery squery : qrys)
+ {
+ if (squery.isRunning())
{
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ finished = false;
}
- } catch (Exception e)
+ }
+ if (aborted)
{
- e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- } catch (Error e)
+ Cache.log.debug("Aborting " + qrys.size()
+ + " JABAWS discovery threads.");
+ for (JabaWsServerQuery squery : qrys)
+ {
+ squery.setQuit(true);
+ }
+ }
+ } while (!aborted && !finished);
+ if (!aborted)
+ {
+ // resort services according to order found in jabaws service list
+ // also ensure servics for each host are ordered in same way.
+
+ if (services != null && services.size() > 0)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ Jws2Instance[] svcs = new Jws2Instance[services.size()];
+ int[] spos = new int[services.size()];
+ int ipos = 0;
+ List<String> svcUrls = getServiceUrls();
+ for (Jws2Instance svc : services)
+ {
+ svcs[ipos] = svc;
+ spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
+ + svctypes.indexOf(svc.serviceType);
+ }
+ jalview.util.QuickSort.sort(spos, svcs);
+ services = new Vector<Jws2Instance>();
+ for (Jws2Instance svc : svcs)
+ {
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ services.add(svc);
+ }
+ }
}
}
oldthread = null;
* @param srv
* @param service2
*/
- private void addService(String jwsservers, Services srv, MsaWS service2)
+ synchronized void addService(String jwsservers, Jws2Instance service)
{
if (services == null)
{
services = new Vector<Jws2Instance>();
}
System.out.println("Discovered service: " + jwsservers + " "
- + srv.toString());
- services.add(new Jws2Instance(jwsservers, srv.toString(), service2));
+ + service.toString());
+ // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+ // service2);
+
+ services.add(service);
+ // retrieve the presets and parameter set and cache now
+ ParamDatastoreI pds = service.getParamStore();
+ if (pds != null)
+ {
+ pds.getPresets();
+ }
+ service.hasParameters();
+ if (validServiceUrls == null)
+ {
+ validServiceUrls = new Vector();
+ }
+ validServiceUrls.add(jwsservers);
}
- public class Jws2Instance
+ /**
+ * attach all available web services to the appropriate submenu in the given
+ * JMenu
+ */
+ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
- public String hosturl;
-
- public String serviceType;
+ // dynamically regenerate service list.
+ populateWSMenuEntry(wsmenu, alignFrame, null);
+ }
- public MsaWS service;
+ private boolean isRecalculable(String action)
+ {
+ return (action != null && action.equalsIgnoreCase("conservation"));
+ }
- public Jws2Instance(String hosturl, String serviceType, MsaWS service)
+ private void populateWSMenuEntry(JMenu jws2al,
+ final AlignFrame alignFrame, String typeFilter)
+ {
+ if (running || services == null || services.size() == 0)
{
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
- this.service = service;
+ return;
}
-
- PresetManager presets = null;
-
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+ .getDefault("WSMENU_BYTYPE", false);
/**
- * non thread safe - gets the presets for this service (blocks whilst it
- * calls the service to get the preset set)
- *
- * @return service presets or null if exceptions were raised.
+ * eventually, JWS2 services will appear under the same align/etc submenus.
+ * for moment we keep them separate.
*/
- public PresetManager getPresets()
+ JMenu atpoint;
+ List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+ // jws2al.removeAll();
+ Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
{
- if (presets == null)
+ if (!isRecalculable(service.action))
{
- try
+ // add 'one shot' services to be displayed using the classic menu
+ // structure
+ enumerableServices.add(service);
+ }
+ else
+ {
+ if (!preferredHosts.containsKey(service.serviceType))
{
- presets = service.getPresets();
- } catch (Exception ex)
+ Jws2Instance preferredInstance = getPreferredServiceFor(
+ alignFrame, service.serviceType);
+ if (preferredInstance != null)
+ {
+ preferredHosts.put(service.serviceType, preferredInstance);
+ }
+ else
+ {
+ preferredHosts.put(service.serviceType, service);
+ }
+ }
+ List<Jws2Instance> ph = alternates.get(service.serviceType);
+ if (preferredHosts.get(service.serviceType) != service)
{
- System.err
- .println("Exception when retrieving presets for service "
- + serviceType + " at " + hosturl);
+ if (ph == null)
+ {
+ ph = new ArrayList<Jws2Instance>();
+ }
+ ph.add(service);
+ alternates.put(service.serviceType, ph);
}
}
- return presets;
- }
- public String getHost()
- {
- return hosturl;
- /*
- * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
- * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
- * serviceurl.getHost(); } catch (Exception e) {
- * System.err.println("Failed to parse service URL '" + hosturl +
- * "' as a valid URL!"); } return null;
- */
}
- /**
- * @return short description of what the service will do
- */
- public String getActionText()
+ // create GUI element for classic services
+ addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+ // and the instantaneous services
+ for (final Jws2Instance service : preferredHosts.values())
{
- return "Align with " + serviceType;
- }
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+ JMenuItem hitm;
+ if (atpoint.getItemCount() > 1)
+ {
+ // previous service of this type already present
+ atpoint.addSeparator();
+ }
+ atpoint.add(hitm = new JMenuItem(service.getHost()));
+ hitm.setForeground(Color.blue);
+ hitm.addActionListener(new ActionListener()
+ {
- /**
- * non-thread safe - blocks whilst accessing service to get complete set of
- * available options and parameters
- *
- * @return
- */
- public RunnerConfig getRunnerConfig()
- {
- return service.getRunnerOptions();
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(service.getHost());
+ }
+ });
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+ MessageManager.getString("label.open_jabaws_web_page")));
- @Override
- protected void finalize() throws Throwable
- {
- if (service != null)
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ if (alternates.containsKey(service.serviceType))
{
- try
- {
- Closeable svc = (Closeable) service;
- service = null;
- svc.close();
- } catch (Exception e)
+ atpoint.add(hitm = new JMenu(MessageManager
+ .getString("label.switch_server")));
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+ MessageManager.getString("label.choose_jabaws_server")));
+ for (final Jws2Instance sv : alternates.get(service.serviceType))
{
- }
- ;
- }
- super.finalize();
- }
- };
+ JMenuItem itm;
+ hitm.add(itm = new JMenuItem(sv.getHost()));
+ itm.setForeground(Color.blue);
+ itm.addActionListener(new ActionListener()
+ {
- /**
- * holds list of services.
- */
- protected Vector<Jws2Instance> services;
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ setPreferredServiceFor(alignFrame, sv.serviceType,
+ sv.action, sv);
+ changeSupport.firePropertyChange("services",
+ new Vector(), services);
+ };
+ }).start();
- /**
- * find or add a submenu with the given title in the given menu
- *
- * @param menu
- * @param submenu
- * @return the new or existing submenu
- */
- private JMenu findOrCreateMenu(JMenu menu, String submenu)
- {
- JMenu submenuinstance = null;
- for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
- {
- if (menu.getMenuComponent(i) instanceof JMenu
- && ((JMenu) menu.getMenuComponent(i)).getText().equals(
- submenu))
- {
- submenuinstance = (JMenu) menu.getMenuComponent(i);
+ }
+ });
+ }
+ /*
+ * hitm.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent arg0) { new
+ * Thread(new Runnable() {
+ *
+ * @Override public void run() { new SetPreferredServer(alignFrame,
+ * service.serviceType, service.action); } }).start(); } });
+ */
}
}
- if (submenuinstance == null)
- {
- submenuinstance = new JMenu(submenu);
- menu.add(submenuinstance);
- }
- return submenuinstance;
-
}
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+ /**
+ * add services using the Java 2.5/2.6/2.7 system which optionally creates
+ * submenus to index by host and service program type
+ */
+ private void addEnumeratedServices(final JMenu jws2al,
+ final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
{
- if (running || services == null || services.size() == 0)
- {
- return;
- }
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
- .getDefault("WSMENU_BYTYPE", true);
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+ .getDefault("WSMENU_BYTYPE", false);
/**
* eventually, JWS2 services will appear under the same align/etc submenus.
* for moment we keep them separate.
*/
- JMenu atpoint, jws2al = new JMenu("JABA Alignment");
+ JMenu atpoint;
MsaWSClient msacl = new MsaWSClient();
- Vector hostLabels = new Vector();
- for (final Jws2Instance service : services)
+ List<String> hostLabels = new ArrayList<String>();
+ Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+ ArrayList<String> hostlist = new ArrayList<String>();
+ for (Jws2Instance service : enumerableServices)
{
- atpoint = jws2al;
- String host = service.getHost();
- String type = service.serviceType;
- if (byhost)
+ ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+ if (hostservices == null)
{
- atpoint = findOrCreateMenu(atpoint, host);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText("Services at " + host);
- }
+ hosts.put(service.getHost(),
+ hostservices = new ArrayList<Jws2Instance>());
+ hostlist.add(service.getHost());
}
- if (bytype)
+ hostservices.add(service);
+ }
+ // now add hosts in order of the given array
+ for (String host : hostlist)
+ {
+ Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
+ new Jws2Instance[1]);
+ String sortbytype[] = new String[orderedsvcs.length];
+ for (int i = 0; i < sortbytype.length; i++)
{
- atpoint = findOrCreateMenu(atpoint, type);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText(service.getActionText());
- }
+ sortbytype[i] = orderedsvcs[i].serviceType;
}
- if (!byhost && !hostLabels.contains(host + service.getActionText()))
+ jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
+ for (final Jws2Instance service : orderedsvcs)
{
- // 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();
- atpoint.add(hitm = new JMenuItem(host));
- hitm.setForeground(Color.blue);
- hostLabels.addElement(host);
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+ String type = service.serviceType;
+ if (byhost)
+ {
+ atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText(MessageManager.formatMessage(
+ "label.services_at", new String[] { host }));
+ }
+ }
+ if (bytype)
+ {
+ atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText(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;
+ if (hostLabels.contains(host))
+ {
+ atpoint.addSeparator();
+ }
+ else
+ {
+ hostLabels.add(host);
+ }
+ if (lasthostFor.get(service.action) == null
+ || !lasthostFor.get(service.action).equals(host))
+ {
+ atpoint.add(hitm = new JMenuItem(host));
+ hitm.setForeground(Color.blue);
+ hitm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(service.getHost());
+ }
+ });
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_jabaws_web_page")));
+ lasthostFor.put(service.action, host);
+ }
+ hostLabels.add(host + service.serviceType
+ + service.getActionText());
+ }
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
}
- msacl.attachWSMenuEntry(atpoint, service, alignFrame);
- /*
- * JMenuItem sitem = new JMenuItem(service.serviceType);
- * sitem.setToolTipText("Hosted at " + service.hosturl);
- * sitem.addActionListener(new ActionListener() {
- *
- * @Override public void actionPerformed(ActionEvent e) { AlignmentView
- * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
- * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(),
- * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
- * alignFrame); } });
- */
- }
- if (services.size() > 0)
- {
- wsmenu.add(jws2al);
}
-
}
public static void main(String[] args)
{
- Thread runner = new Thread(getDiscoverer());
- getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
+ if (args.length > 0)
{
-
- public void propertyChange(PropertyChangeEvent evt)
+ testUrls = new ArrayList<String>();
+ for (String url : args)
{
- System.out.println("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
+ testUrls.add(url);
}
- });
- runner.start();
+ ;
+ }
+ Thread runner = getDiscoverer().startDiscoverer(
+ new PropertyChangeListener()
+ {
+
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (getDiscoverer().services != null)
+ {
+ System.out.println("Changesupport: There are now "
+ + getDiscoverer().services.size() + " services");
+ int i = 1;
+ for (Jws2Instance instance : getDiscoverer().services)
+ {
+ System.out.println("Service " + i++ + " "
+ + instance.getClass() + "@"
+ + instance.getHost() + ": "
+ + instance.getActionText());
+ }
+
+ }
+ }
+ });
while (runner.isAlive())
{
try
}
;
}
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
}
- private static Jws2Discoverer discoverer;
-
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
public static Jws2Discoverer getDiscoverer()
{
if (discoverer == null)
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
return running;
}
- /**
- * the jalview .properties entry for JWS2 URLS
- */
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
- public static void setServiceUrls(Vector<String> urls)
+ public void setServiceUrls(List<String> wsUrls)
{
- if (urls != null)
+ if (wsUrls != null && !wsUrls.isEmpty())
{
- StringBuffer urlbuffer = new StringBuffer();
+ StringBuilder urls = new StringBuilder(128);
String sep = "";
- for (String url : urls)
+ for (String url : wsUrls)
{
- urlbuffer.append(sep);
- urlbuffer.append(url);
+ urls.append(sep);
+ urls.append(url);
sep = ",";
}
- Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ Cache.setProperty(JWS2HOSTURLS, urls.toString());
}
else
{
}
}
- public static Vector<String> getServiceUrls()
+ /**
+ * Returns web service URLs, in the order in which they should be tried (or an
+ * empty list).
+ *
+ * @return
+ */
+ public List<String> getServiceUrls()
{
- String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://www.compbio.dundee.ac.uk/jabaws");
- Vector<String> urls = new Vector<String>();
+ if (testUrls != null)
+ {
+ // return test urls, if there are any, instead of touching cache
+ return testUrls;
+ }
+ List<String> urls = new ArrayList<String>();
+
+ if (this.preferredUrl != null)
+ {
+ urls.add(preferredUrl);
+ }
+
+ String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
String url = null;
try
{
- java.net.URL u = new java.net.URL(url = st.nextToken());
+ url = st.nextToken();
+ new URL(url);
if (!urls.contains(url))
{
urls.add(url);
}
else
{
- jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ Cache.log.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
- } catch (Exception ex)
+ } catch (MalformedURLException ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
- + ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log
+ Cache.log.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
+ Cache.log
.warn("This was probably due to a malformed comma separated list"
+ " in the "
+ JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
- "Error parsing comma separated list of urls in "
- + JWS2HOSTURLS + " preference.", ex);
- }
- if (urls.size() >= 0)
- {
- return urls;
+ Cache.log.warn("Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
}
- return null;
+ return urls;
}
public Vector<Jws2Instance> getServices()
/**
* test the given URL with the JabaWS test code
+ *
* @param foo
* @return
*/
public static boolean testServiceUrl(URL foo)
{
- try {
- compbio.ws.client.WSTester.main(new String[] { "-h="+foo.toString()});
+ try
+ {
+ compbio.ws.client.WSTester
+ .main(new String[] { "-h=" + foo.toString() });
} catch (Exception e)
{
+ e.printStackTrace();
return false;
- }
- catch (OutOfMemoryError e)
+ } catch (OutOfMemoryError e)
{
+ e.printStackTrace();
return false;
- }
- catch (Error e)
+ } 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;
+ }
+
+ /**
+ * @return the invalidServiceUrls
+ */
+ public Vector<String> getInvalidServiceUrls()
+ {
+ return invalidServiceUrls;
+ }
+
+ /**
+ * @return the urlsWithoutServices
+ */
+ public Vector<String> 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<String>();
+ }
+
+ 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<String>();
+ }
+ 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(MessageManager.getString("warn.urls_not_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(MessageManager.getString("warn.urls_no_jaba") + ": \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;
+ }
+
+ public int getServerStatusFor(String url)
+ {
+ if (validServiceUrls != null && validServiceUrls.contains(url))
+ {
+ return 1;
+ }
+ if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+ {
+ return 0;
+ }
+ if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
+ {
+ return -1;
+ }
+ return -2;
+ }
+
+ /**
+ * pick the user's preferred service based on a set of URLs (jaba server
+ * locations) and service URIs (specifying version and service interface
+ * class)
+ *
+ * @param serviceURL
+ * @return null or best match for given uri/ls.
+ */
+ public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
+ {
+ HashSet<String> urls = new HashSet<String>();
+ urls.addAll(Arrays.asList(serviceURLs));
+ Jws2Instance match = null;
+ if (services != null)
+ {
+ for (Jws2Instance svc : services)
+ {
+ if (urls.contains(svc.getServiceTypeURI()))
+ {
+ if (match == null)
+ {
+ // for moment we always pick service from server ordered first in
+ // user's preferences
+ match = svc;
+ }
+ if (urls.contains(svc.getUri()))
+ {
+ // stop and return - we've matched type URI and URI for service
+ // endpoint
+ return svc;
+ }
+ }
+ }
+ }
+ return match;
+ }
+
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+
+ /**
+ * get current preferred service of the given type, or global default
+ *
+ * @param af
+ * null or a specific alignFrame
+ * @param serviceType
+ * Jws2Instance.serviceType for service
+ * @return null if no service of this type is available, the preferred service
+ * for the serviceType and af if specified and if defined.
+ */
+ public Jws2Instance getPreferredServiceFor(AlignFrame af,
+ String serviceType)
+ {
+ String serviceurl = null;
+ synchronized (preferredServiceMap)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (afid.length() > 0 && prefmap == null)
+ {
+ // recover global setting, if any
+ prefmap = preferredServiceMap.get("");
+ }
+ if (prefmap != null)
+ {
+ serviceurl = prefmap.get(serviceType);
+ }
+
+ }
+ Jws2Instance response = null;
+ for (Jws2Instance svc : services)
+ {
+ if (svc.serviceType.equals(serviceType))
+ {
+ if (serviceurl == null || serviceurl.equals(svc.getHost()))
+ {
+ response = svc;
+ break;
+ }
+ }
+ }
+ return response;
+ }
+
+ public void setPreferredServiceFor(AlignFrame af, String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ if (preferredServiceMap == null)
+ {
+ preferredServiceMap = new HashMap<String, Map<String, String>>();
+ }
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (prefmap == null)
+ {
+ prefmap = new HashMap<String, String>();
+ preferredServiceMap.put(afid, prefmap);
+ }
+ prefmap.put(serviceType, selectedServer.getHost());
+ prefmap.put(serviceAction, selectedServer.getHost());
+ }
+
+ public void setPreferredServiceFor(String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+ }
+
+ /**
+ * Set a URL to try before any others. For use with command-line parameter to
+ * configure a local Jabaws installation without the need to add to property
+ * files.
+ *
+ * @param value
+ * @throws MalformedURLException
+ */
+ public void setPreferredUrl(String value) throws MalformedURLException
+ {
+ if (value != null && value.trim().length() > 0)
+ {
+ new URL(value);
+ preferredUrl = value;
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff