X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=bd4d3525dcb2763eaeb749f4bdcad681c6275ac7;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=96a6f6bf0a57e7e595ae2d7c41d7317d7ca5c03d;hpb=b0b2035ac995961a10d420f337a91a08a3014298;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 96a6f6b..bd4d352 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,40 +1,52 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
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.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;
@@ -50,11 +62,64 @@ import compbio.ws.client.Services;
* @author JimP
*
*/
-public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
+public class Jws2Discoverer
+ implements Runnable, WSMenuEntryProviderI, ApplicationSingletonI
{
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
+ public static Jws2Discoverer getInstance()
+ {
+ return (Jws2Discoverer) ApplicationSingletonProvider
+ .getInstance(Jws2Discoverer.class);
+ }
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
+ */
+ private Jws2Discoverer()
+ {
+ // use getInstance();
+ }
+
+ public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
+
+ /*
+ * the .jalview_properties entry for JWS2 URLS
+ */
+ private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ /*
+ * Override for testing only
+ */
+ private static List testUrls = null;
+
+ // preferred url has precedence over others
+ private String preferredUrl;
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
+ private Vector invalidServiceUrls = null;
+
+ private Vector urlsWithoutServices = null;
+
+ private Vector validServiceUrls = null;
+
+ private volatile boolean running = false;
+
+ private volatile boolean aborted = false;
+
+ private Thread oldthread = null;
+
+ /**
+ * holds list of services.
+ */
+ protected Vector services;
+
/**
* change listeners are notified of "services" property changes
*
@@ -79,8 +144,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false, aborted = false;
-
/**
* @return the aborted
*/
@@ -98,10 +161,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
this.aborted = aborted;
}
- Thread oldthread = null;
-
+ @Override
public void run()
{
+
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
@@ -112,27 +175,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
try
{
- Cache.log
- .debug("Waiting around for old discovery thread to finish.");
+ Cache.log.debug(
+ "Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
} catch (Exception e)
{
}
}
+ aborted = false;
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
- changeSupport.firePropertyChange("services", services, new Vector());
+
+ // first set up exclusion list if needed
+ final Set ignoredServices = new HashSet<>();
+ for (String ignored : Cache
+ .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+ changeSupport.firePropertyChange("services", services,
+ new Vector());
oldthread = Thread.currentThread();
try
{
- Class foo = getClass().getClassLoader().loadClass(
- "compbio.ws.client.Jws2Client");
+ getClass().getClassLoader()
+ .loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
- System.err
- .println("Not enabling JABA Webservices : client jar is not available."
+ System.err.println(
+ "Not enabling JABA Webservices : client jar is not available."
+ "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
@@ -154,18 +228,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
validServiceUrls.removeAllElements();
}
- ArrayList svctypes=new ArrayList();
+ ArrayList svctypes = new ArrayList<>();
- List qrys = new ArrayList();
- for (final String jwsservers : getServiceUrls())
+ List qrys = new ArrayList<>();
+ for (final String jwsserver : getServiceUrls())
{
- JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
- if (svctypes.size()==0)
+ JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
+ if (svctypes.size() == 0)
{
- // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services
- for (Services sv:squery.JABAWS2SERVERS)
+ // TODO: remove this ugly hack to get Canonical JABA service ordering
+ // for all possible services
+ for (Services sv : squery.JABAWS2SERVERS)
{
- svctypes.add(sv.toString());
+ if (!ignoredServices.contains(sv.toString()))
+ {
+ svctypes.add(sv.toString());
+ }
}
}
@@ -175,22 +253,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
boolean finished = true;
do
{
- finished=true;
+ finished = true;
try
{
Thread.sleep(100);
} catch (Exception e)
{
}
- ;
for (JabaWsServerQuery squery : qrys)
{
- finished = finished && !squery.isRunning();
+ if (squery.isRunning())
+ {
+ finished = false;
+ }
}
if (aborted)
{
- Cache.log.debug("Aborting " + qrys.size()
- + " JABAWS discovery threads.");
+ Cache.log.debug(
+ "Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
squery.setQuit(true);
@@ -200,29 +280,35 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
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)
+ // also ensure services for each host are ordered in same way.
+
+ if (services != null && services.size() > 0)
{
- Jws2Instance[] svcs=new Jws2Instance[services.size()];
- int[] spos=new int[services.size()];
- int ipos=0;
- Vector svcUrls = getServiceUrls();
- for (Jws2Instance svc:services)
+ Jws2Instance[] svcs = new Jws2Instance[services.size()];
+ int[] spos = new int[services.size()];
+ int ipos = 0;
+ List svcUrls = getServiceUrls();
+ for (Jws2Instance svc : services)
{
- svcs[ipos]=svc;
- spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType);
+ svcs[ipos] = svc;
+ spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
+ + svctypes.indexOf(svc.serviceType);
}
jalview.util.QuickSort.sort(spos, svcs);
- services=new Vector();
- for (Jws2Instance svc:svcs) {
- services.add(svc);
+ services = new Vector<>();
+ for (Jws2Instance svc : svcs)
+ {
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ services.add(svc);
+ }
}
}
}
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services", new Vector(), services);
+ changeSupport.firePropertyChange("services", new Vector(),
+ services);
}
/**
@@ -236,63 +322,188 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
if (services == null)
{
- services = new Vector();
+ services = new Vector<>();
}
- System.out.println("Discovered service: " + jwsservers + " "
- + service.toString());
-// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
-// service2);
+ System.out.println(
+ "Discovered service: " + jwsservers + " " + service.toString());
+ // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+ // service2);
services.add(service);
// retrieve the presets and parameter set and cache now
- service.getParamStore().getPresets();
+ ParamDatastoreI pds = service.getParamStore();
+ if (pds != null)
+ {
+ pds.getPresets();
+ }
service.hasParameters();
- if (validServiceUrls==null)
+ if (validServiceUrls == null)
{
- validServiceUrls=new Vector();
+ validServiceUrls = new Vector<>();
}
validServiceUrls.add(jwsservers);
}
/**
- * holds list of services.
- */
- protected Vector services;
- /**
- * attach all available web services to the appropriate submenu in the given JMenu
+ * attach all available web services to the appropriate submenu in the given
+ * JMenu
*/
+ @Override
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
// dynamically regenerate service list.
populateWSMenuEntry(wsmenu, alignFrame, null);
}
- private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+ private boolean isRecalculable(String action)
+ {
+ return (action != null && action.equalsIgnoreCase("conservation"));
+ }
+
+ private void populateWSMenuEntry(JMenu jws2al,
+ final AlignFrame alignFrame, String typeFilter)
{
if (running || services == null || services.size() == 0)
{
return;
}
- 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;
+ List enumerableServices = new ArrayList<>();
+ // jws2al.removeAll();
+ Map preferredHosts = new HashMap<>();
+ Map> alternates = new HashMap<>();
+ for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
+ {
+ if (!isRecalculable(service.action))
+ {
+ // add 'one shot' services to be displayed using the classic menu
+ // structure
+ enumerableServices.add(service);
+ }
+ else
+ {
+ if (!preferredHosts.containsKey(service.serviceType))
+ {
+ Jws2Instance preferredInstance = getPreferredServiceFor(
+ alignFrame, service.serviceType);
+ if (preferredInstance != null)
+ {
+ preferredHosts.put(service.serviceType, preferredInstance);
+ }
+ else
+ {
+ preferredHosts.put(service.serviceType, service);
+ }
+ }
+ List ph = alternates.get(service.serviceType);
+ if (preferredHosts.get(service.serviceType) != service)
+ {
+ if (ph == null)
+ {
+ ph = new ArrayList<>();
+ }
+ ph.add(service);
+ alternates.put(service.serviceType, ph);
+ }
+ }
+
+ }
+
+ // create GUI element for classic services
+ addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+ // and the instantaneous services
+ for (final Jws2Instance service : preferredHosts.values())
+ {
+ 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()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(service.getHost());
+ }
+ });
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+ MessageManager.getString("label.open_jabaws_web_page")));
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ if (alternates.containsKey(service.serviceType))
+ {
+ 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))
+ {
+ JMenuItem itm;
+ hitm.add(itm = new JMenuItem(sv.getHost()));
+ itm.setForeground(Color.blue);
+ itm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ setPreferredServiceFor(alignFrame, sv.serviceType,
+ sv.action, sv);
+ changeSupport.firePropertyChange("services",
+ new Vector(), services);
+ }
+ }).start();
+
+ }
+ });
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 enumerableServices)
+ {
+ 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;
- MsaWSClient msacl = new MsaWSClient();
- Vector hostLabels = new Vector();
- //jws2al.removeAll();
- Hashtable lasthostFor = new Hashtable();
- Hashtable> hosts = new Hashtable>();
- ArrayList hostlist=new ArrayList();
- for (Jws2Instance service : services)
+
+ List hostLabels = new ArrayList<>();
+ Hashtable lasthostFor = new Hashtable<>();
+ Hashtable> hosts = new Hashtable<>();
+ ArrayList hostlist = new ArrayList<>();
+ for (Jws2Instance service : enumerableServices)
{
ArrayList hostservices = hosts.get(service.getHost());
if (hostservices == null)
{
hosts.put(service.getHost(),
- hostservices = new ArrayList());
+ hostservices = new ArrayList<>());
hostlist.add(service.getHost());
}
hostservices.add(service);
@@ -300,8 +511,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
// now add hosts in order of the given array
for (String host : hostlist)
{
- Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
- new Jws2Instance[1]);
+ Jws2Instance orderedsvcs[] = hosts.get(host)
+ .toArray(new Jws2Instance[1]);
String sortbytype[] = new String[orderedsvcs.length];
for (int i = 0; i < sortbytype.length; i++)
{
@@ -310,14 +521,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
for (final Jws2Instance service : orderedsvcs)
{
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
String type = service.serviceType;
if (byhost)
{
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText("Services at " + host);
+ atpoint.setToolTipText(MessageManager
+ .formatMessage("label.services_at", new String[]
+ { host }));
}
}
if (bytype)
@@ -328,9 +541,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
atpoint.setToolTipText(service.getActionText());
}
}
- if (!byhost
- && !hostLabels.contains(host + service.serviceType
- + service.getActionText()))
+ if (!byhost && !hostLabels.contains(
+ host + service.serviceType + service.getActionText()))
// !hostLabels.contains(host + (bytype ?
// service.serviceType+service.getActionText() : "")))
{
@@ -339,8 +551,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
// contiguous
// group
JMenuItem hitm;
- atpoint.addSeparator();
- if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host))
+ 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);
@@ -353,58 +573,52 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
Desktop.showUrl(service.getHost());
}
});
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
- lasthostFor.put(service.action,host);
+ hitm.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.open_jabaws_web_page")));
+ lasthostFor.put(service.action, host);
}
- hostLabels.addElement(host + service.serviceType
- + service.getActionText());
- // hostLabels.addElement(host + (bytype ?
- // service.serviceType+service.getActionText() : ""));
+ hostLabels.add(
+ host + service.serviceType + service.getActionText());
}
-
+
service.attachWSMenuEntry(atpoint, 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); }
- * });
- */
}
}
-
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
- if (args.length>0)
+ if (args.length > 0)
{
- testUrls = new Vector();
- for (String url:args)
+ testUrls = new ArrayList<>();
+ for (String url : args)
{
testUrls.add(url);
- };
+ }
}
- Thread runner = getDiscoverer().startDiscoverer(
- new PropertyChangeListener()
+ Thread runner = getInstance()
+ .startDiscoverer(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (getDiscoverer().services != null)
+ if (getInstance().services != null)
{
System.out.println("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
- int i=1;
- for (Jws2Instance instance:getDiscoverer().services)
+ + getInstance().services.size() + " services");
+ int i = 1;
+ for (Jws2Instance instance : getInstance().services)
{
- System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+ System.out.println("Service " + i++ + " "
+ + instance.getClass() + "@" + instance.getHost()
+ + ": " + instance.getActionText());
}
}
@@ -418,27 +632,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
} catch (InterruptedException e)
{
}
- ;
}
- try {
+ try
+ {
Thread.sleep(50);
- } catch (InterruptedException x) {}
- }
-
- private static Jws2Discoverer discoverer;
-
- public static Jws2Discoverer getDiscoverer()
- {
- if (discoverer == null)
+ } catch (InterruptedException x)
{
- discoverer = new Jws2Discoverer();
}
- return discoverer;
}
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
@@ -447,24 +651,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return running;
}
- /**
- * the jalview .properties entry for JWS2 URLS
- */
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
- public static void setServiceUrls(Vector urls)
+ public void setServiceUrls(List 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
{
@@ -472,17 +671,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
}
- private static Vector testUrls=null;
- public static Vector getServiceUrls()
+ /**
+ * Returns web service URLs, in the order in which they should be tried (or an
+ * empty list).
+ *
+ * @return
+ */
+ public List getServiceUrls()
{
- if (testUrls!=null)
+ if (testUrls != null)
{
// return test urls, if there are any, instead of touching cache
return testUrls;
}
- String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://www.compbio.dundee.ac.uk/jabaws");
- Vector urls = new Vector();
+ List urls = new ArrayList<>();
+
+ if (this.preferredUrl != null)
+ {
+ urls.add(preferredUrl);
+ }
+
+ String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
@@ -491,46 +700,40 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
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 : "") + "'");
- jalview.bin.Cache.log
- .warn("This was probably due to a malformed comma separated list"
- + " in the "
- + JWS2HOSTURLS
+ Cache.log.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "") + "'");
+ 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 getServices()
{
- return (services == null) ? new Vector()
- : new Vector(services);
+ return (services == null) ? new Vector<>()
+ : new Vector<>(services);
}
/**
@@ -543,8 +746,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
try
{
- compbio.ws.client.WSTester.main(new String[]
- { "-h=" + foo.toString() });
+ compbio.ws.client.WSTester
+ .main(new String[]
+ { "-h=" + foo.toString() });
} catch (Exception e)
{
e.printStackTrace();
@@ -562,6 +766,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return true;
}
+ public boolean restart()
+ {
+ synchronized (this)
+ {
+ if (running)
+ {
+ aborted = true;
+ }
+ else
+ {
+ running = true;
+ }
+ return aborted;
+ }
+ }
+
/**
* 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
@@ -572,6 +792,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
*/
public Thread startDiscoverer(PropertyChangeListener changeSupport2)
{
+ /* if (restart())
+ {
+ return;
+ }
+ else
+ {
+ Thread thr = new Thread(this);
+ thr.start();
+ }
+ */
if (isRunning())
{
setAborted(true);
@@ -582,8 +812,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return thr;
}
- Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
-
/**
* @return the invalidServiceUrls
*/
@@ -610,11 +838,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
if (urlsWithoutServices == null)
{
- urlsWithoutServices = new Vector();
+ urlsWithoutServices = new Vector<>();
}
- if ((invalidServiceUrls == null || !invalidServiceUrls
- .contains(jwsservers))
+ if ((invalidServiceUrls == null
+ || !invalidServiceUrls.contains(jwsservers))
&& !urlsWithoutServices.contains(jwsservers))
{
urlsWithoutServices.add(jwsservers);
@@ -630,7 +858,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
if (invalidServiceUrls == null)
{
- invalidServiceUrls = new Vector();
+ invalidServiceUrls = new Vector<>();
}
if (!invalidServiceUrls.contains(jwsservers))
{
@@ -652,7 +880,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
if (getInvalidServiceUrls() != null
&& getInvalidServiceUrls().size() > 0)
{
- ermsg.append("URLs that could not be contacted: \n");
+ ermsg.append(MessageManager.getString("warn.urls_not_contacted")
+ + ": \n");
for (String svcurl : getInvalidServiceUrls())
{
if (list)
@@ -668,7 +897,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
if (getUrlsWithoutServices() != null
&& getUrlsWithoutServices().size() > 0)
{
- ermsg.append("URLs without any JABA Services : \n");
+ ermsg.append(
+ MessageManager.getString("warn.urls_no_jaba") + ": \n");
for (String svcurl : getUrlsWithoutServices())
{
if (list)
@@ -691,13 +921,15 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public int getServerStatusFor(String url)
{
- if (validServiceUrls!=null && validServiceUrls.contains(url))
+ if (validServiceUrls != null && validServiceUrls.contains(url))
{
return 1;
}
- if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
- return 0;
- if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+ if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+ {
+ return 0;
+ }
+ if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
return -1;
}
@@ -705,31 +937,127 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
/**
- * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class)
+ * 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 urls=new HashSet();
+ HashSet urls = new HashSet<>();
urls.addAll(Arrays.asList(serviceURLs));
- Jws2Instance match=null;
- for (Jws2Instance svc:services)
+ Jws2Instance match = null;
+ if (services != null)
{
- if (urls.contains(svc.getServiceTypeURI()))
+ for (Jws2Instance svc : services)
{
- if (match==null) {
- // for moment we always pick service from server ordered first in user's preferences
- match=svc;
- }
- if (urls.contains(svc.getUri()))
+ if (urls.contains(svc.getServiceTypeURI()))
{
- // stop and return - we've matched type URI and URI for service endpoint
- return svc;
+ 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> preferredServiceMap = new HashMap<>();
+
+ /**
+ * 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 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<>();
+ }
+ Map prefmap = preferredServiceMap.get(afid);
+ if (prefmap == null)
+ {
+ prefmap = new HashMap<>();
+ 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;
+ }
+ }
}