/*
* the .jalview_properties entry for JWS2 URLS
*/
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+ private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
/*
* Singleton instance
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
- Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
- validServiceUrls = null;
+ private Vector<String> invalidServiceUrls = null;
- boolean running = false, aborted = false;
+ private Vector<String> urlsWithoutServices = null;
- Thread oldthread = null;
+ private Vector<String> validServiceUrls = null;
+
+ private volatile boolean running = false;
+
+ private volatile boolean aborted = false;
+
+ private Thread oldthread = null;
/**
* holds list of services.
public void setAborted(boolean aborted)
{
this.aborted = aborted;
-
}
+
+ @Override
public void run()
{
{
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;
// first set up exclusion list if needed
- final Set<String> ignoredServices = new HashSet<String>();
- for (String ignored : Cache.getDefault(
- "IGNORED_JABAWS_SERVICETYPES", "")
- .split("\\|"))
+ final Set<String> ignoredServices = new HashSet<>();
+ for (String ignored : Cache
+ .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
{
ignoredServices.add(ignored);
}
- changeSupport.firePropertyChange("services", services, new Vector());
+ changeSupport.firePropertyChange("services", services,
+ new Vector<Jws2Instance>());
oldthread = Thread.currentThread();
try
{
- Class foo = getClass().getClassLoader().loadClass(
- "compbio.ws.client.Jws2Client");
+ Class foo = 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;
{
validServiceUrls.removeAllElements();
}
- ArrayList<String> svctypes = new ArrayList<String>();
+ ArrayList<String> svctypes = new ArrayList<>();
- List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+ List<JabaWsServerQuery> qrys = new ArrayList<>();
for (final String jwsserver : getServiceUrls())
{
JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
}
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);
if (!aborted)
{
// resort services according to order found in jabaws service list
- // also ensure servics for each host are ordered in same way.
+ // also ensure services for each host are ordered in same way.
if (services != null && services.size() > 0)
{
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
- spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
- + svctypes.indexOf(svc.serviceType);
+ spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHostURL()) + 1
+ + svctypes.indexOf(svc.getName());
}
jalview.util.QuickSort.sort(spos, svcs);
- services = new Vector<Jws2Instance>();
+ services = new Vector<>();
for (Jws2Instance svc : svcs)
{
- if (!ignoredServices.contains(svc.serviceType))
+ if (!ignoredServices.contains(svc.getName()))
{
services.add(svc);
}
}
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services", new Vector(), services);
+ changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
+ services);
}
/**
{
if (services == null)
{
- services = new Vector<Jws2Instance>();
+ services = new Vector<>();
}
- System.out.println("Discovered service: " + jwsservers + " "
- + service.toString());
+ System.out.println(
+ "Discovered service: " + jwsservers + " " + service.toString());
// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
// service2);
service.hasParameters();
if (validServiceUrls == null)
{
- validServiceUrls = new Vector();
+ validServiceUrls = new Vector<>();
}
validServiceUrls.add(jwsservers);
}
* 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.
{
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<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+ List<Jws2Instance> enumerableServices = new ArrayList<>();
// jws2al.removeAll();
- Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
- Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<>();
for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
{
- if (!isRecalculable(service.action))
+ // TODO: check this behaves with refactored serviceType to getName
+ if (!isRecalculable(service.getName()))
{
// add 'one shot' services to be displayed using the classic menu
// structure
}
else
{
- if (!preferredHosts.containsKey(service.serviceType))
+ if (!preferredHosts.containsKey(service.getName()))
{
Jws2Instance preferredInstance = getPreferredServiceFor(
- alignFrame, service.serviceType);
+ alignFrame, service.getName());
if (preferredInstance != null)
{
- preferredHosts.put(service.serviceType, preferredInstance);
+ preferredHosts.put(service.getName(), preferredInstance);
}
else
{
- preferredHosts.put(service.serviceType, service);
+ preferredHosts.put(service.getName(), service);
}
}
- List<Jws2Instance> ph = alternates.get(service.serviceType);
- if (preferredHosts.get(service.serviceType) != service)
+ List<Jws2Instance> ph = alternates.get(service.getName());
+ if (preferredHosts.get(service.getName()) != service)
{
if (ph == null)
{
- ph = new ArrayList<Jws2Instance>();
+ ph = new ArrayList<>();
}
ph.add(service);
- alternates.put(service.serviceType, ph);
+ alternates.put(service.getName(), ph);
}
}
// and the instantaneous services
for (final Jws2Instance service : preferredHosts.values())
{
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
+ service.getServiceType());
JMenuItem hitm;
if (atpoint.getItemCount() > 1)
{
// previous service of this type already present
atpoint.addSeparator();
}
- atpoint.add(hitm = new JMenuItem(service.getHost()));
+ atpoint.add(hitm = new JMenuItem(service.getHostURL()));
hitm.setForeground(Color.blue);
hitm.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- Desktop.showUrl(service.getHost());
+ Desktop.showUrl(service.getHostURL());
}
});
hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
MessageManager.getString("label.open_jabaws_web_page")));
service.attachWSMenuEntry(atpoint, alignFrame);
- if (alternates.containsKey(service.serviceType))
+ if (alternates.containsKey(service.getName()))
{
- 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))
+ 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.getName()))
{
JMenuItem itm;
- hitm.add(itm = new JMenuItem(sv.getHost()));
+ hitm.add(itm = new JMenuItem(sv.getHostURL()));
itm.setForeground(Color.blue);
itm.addActionListener(new ActionListener()
{
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
- setPreferredServiceFor(alignFrame, sv.serviceType,
- sv.action, sv);
+ setPreferredServiceFor(alignFrame, sv.getName(),
+ sv.getServiceType(), sv);
changeSupport.firePropertyChange("services",
- new Vector(), services);
+ new Vector<Jws2Instance>(), services);
};
}).start();
}
});
}
- /*
- * 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(); } });
- */
}
}
}
* submenus to index by host and service program type
*/
private void addEnumeratedServices(final JMenu jws2al,
- final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+ final AlignFrame alignFrame,
+ List<Jws2Instance> enumerableServices)
{
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
- .getDefault("WSMENU_BYTYPE", false);
+ 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();
- 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>();
+
+ List<String> hostLabels = new ArrayList<>();
+ Hashtable<String, String> lasthostFor = new Hashtable<>();
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+ ArrayList<String> hostlist = new ArrayList<>();
for (Jws2Instance service : enumerableServices)
{
- ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+ ArrayList<Jws2Instance> hostservices = hosts
+ .get(service.getHostURL());
if (hostservices == null)
{
- hosts.put(service.getHost(),
- hostservices = new ArrayList<Jws2Instance>());
- hostlist.add(service.getHost());
+ hosts.put(service.getHostURL(),
+ hostservices = new ArrayList<>());
+ hostlist.add(service.getHostURL());
}
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]);
+ Jws2Instance orderedsvcs[] = hosts.get(host)
+ .toArray(new Jws2Instance[1]);
String sortbytype[] = new String[orderedsvcs.length];
for (int i = 0; i < sortbytype.length; i++)
{
- sortbytype[i] = orderedsvcs[i].serviceType;
+ sortbytype[i] = orderedsvcs[i].getName();
}
jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
for (final Jws2Instance service : orderedsvcs)
{
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
- String type = service.serviceType;
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al,
+ service.getAction());
+ String type = service.getName();
if (byhost)
{
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText(MessageManager.formatMessage("label.services_at", new String[]{host}));
+ atpoint.setToolTipText(MessageManager
+ .formatMessage("label.services_at", new String[]
+ { host }));
}
}
if (bytype)
atpoint.setToolTipText(service.getActionText());
}
}
- if (!byhost
- && !hostLabels.contains(host + service.serviceType
- + service.getActionText()))
+ if (!byhost && !hostLabels.contains(
+ host + service.getName() + service.getActionText()))
// !hostLabels.contains(host + (bytype ?
// service.serviceType+service.getActionText() : "")))
{
{
hostLabels.add(host);
}
- if (lasthostFor.get(service.action) == null
- || !lasthostFor.get(service.action).equals(host))
+ if (lasthostFor.get(service.getAction()) == null
+ || !lasthostFor.get(service.getAction()).equals(host))
{
atpoint.add(hitm = new JMenuItem(host));
hitm.setForeground(Color.blue);
@Override
public void actionPerformed(ActionEvent e)
{
- Desktop.showUrl(service.getHost());
+ Desktop.showUrl(service.getHostURL());
}
});
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip(true, MessageManager.getString("label.open_jabaws_web_page")));
- lasthostFor.put(service.action, host);
+ hitm.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.open_jabaws_web_page")));
+ lasthostFor.put(service.getAction(), host);
}
- hostLabels.add(host + service.serviceType
- + service.getActionText());
+ hostLabels.add(
+ host + service.getName() + service.getActionText());
}
service.attachWSMenuEntry(atpoint, alignFrame);
{
if (args.length > 0)
{
- testUrls = new ArrayList<String>();
+ testUrls = new ArrayList<>();
for (String url : args)
{
testUrls.add(url);
}
;
}
- Thread runner = getDiscoverer().startDiscoverer(
- new PropertyChangeListener()
+ Thread runner = getDiscoverer()
+ .startDiscoverer(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (getDiscoverer().services != null)
{
System.out.println("Service " + i++ + " "
+ instance.getClass() + "@"
- + instance.getHost() + ": "
- + instance.getActionText());
+ + instance.getHostURL()
+ + ": " + instance.getActionText());
}
}
// return test urls, if there are any, instead of touching cache
return testUrls;
}
- List<String> urls = new ArrayList<String>();
+ List<String> urls = new ArrayList<>();
if (this.preferredUrl != null)
{
}
} catch (MalformedURLException ex)
{
- 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
+ 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)");
Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- Cache.log.warn(
- "Error parsing comma separated list of urls in "
- + JWS2HOSTURLS + " preference.", ex);
+ Cache.log.warn("Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
}
return urls;
}
public Vector<Jws2Instance> getServices()
{
- return (services == null) ? new Vector<Jws2Instance>()
- : new Vector<Jws2Instance>(services);
+ return (services == null) ? new Vector<>()
+ : new Vector<>(services);
}
/**
{
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();
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
*/
public Thread startDiscoverer(PropertyChangeListener changeSupport2)
{
+ /* if (restart())
+ {
+ return;
+ }
+ else
+ {
+ Thread thr = new Thread(this);
+ thr.start();
+ }
+ */
if (isRunning())
{
setAborted(true);
{
if (urlsWithoutServices == null)
{
- urlsWithoutServices = new Vector<String>();
+ urlsWithoutServices = new Vector<>();
}
- if ((invalidServiceUrls == null || !invalidServiceUrls
- .contains(jwsservers))
+ if ((invalidServiceUrls == null
+ || !invalidServiceUrls.contains(jwsservers))
&& !urlsWithoutServices.contains(jwsservers))
{
urlsWithoutServices.add(jwsservers);
{
if (invalidServiceUrls == null)
{
- invalidServiceUrls = new Vector<String>();
+ invalidServiceUrls = new Vector<>();
}
if (!invalidServiceUrls.contains(jwsservers))
{
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)
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)
*/
public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
{
- HashSet<String> urls = new HashSet<String>();
+ HashSet<String> urls = new HashSet<>();
urls.addAll(Arrays.asList(serviceURLs));
Jws2Instance match = null;
if (services != null)
{
for (Jws2Instance svc : services)
{
- if (urls.contains(svc.getServiceTypeURI()))
+ // TODO getNameURI Should return a versioned URI for the service, but
+ // doesn't as of 2.11
+ if (urls.contains(svc.getNameURI()))
{
if (match == null)
{
return match;
}
- Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();;
/**
- * get current preferred service of the given type, or global default
+ * get current preferred endpoint of the given Jabaws service, or global
+ * default
*
* @param af
* null or a specific alignFrame
- * @param serviceType
- * Jws2Instance.serviceType for service
+ * @param serviceName
+ * Jws2Instance.getName() 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 serviceName)
{
String serviceurl = null;
synchronized (preferredServiceMap)
}
if (prefmap != null)
{
- serviceurl = prefmap.get(serviceType);
+ serviceurl = prefmap.get(serviceName);
}
}
Jws2Instance response = null;
for (Jws2Instance svc : services)
{
- if (svc.serviceType.equals(serviceType))
+ if (svc.getName().equals(serviceName))
{
- if (serviceurl == null || serviceurl.equals(svc.getHost()))
+ if (serviceurl == null || serviceurl.equals(svc.getHostURL()))
{
response = svc;
break;
return response;
}
- public void setPreferredServiceFor(AlignFrame af, String serviceType,
+ public void setPreferredServiceFor(AlignFrame af, String serviceName,
String serviceAction, Jws2Instance selectedServer)
{
+ // TODO: pull out and generalise for the selectedServer's attributes
String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
if (preferredServiceMap == null)
{
- preferredServiceMap = new HashMap<String, Map<String, String>>();
+ preferredServiceMap = new HashMap<>();
}
Map<String, String> prefmap = preferredServiceMap.get(afid);
if (prefmap == null)
{
- prefmap = new HashMap<String, String>();
+ prefmap = new HashMap<>();
preferredServiceMap.put(afid, prefmap);
}
- prefmap.put(serviceType, selectedServer.getHost());
- prefmap.put(serviceAction, selectedServer.getHost());
+ prefmap.put(serviceName, selectedServer.getHostURL());
+ prefmap.put(serviceAction, selectedServer.getHostURL());
}
public void setPreferredServiceFor(String serviceType,
String serviceAction, Jws2Instance selectedServer)
{
- setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+ setPreferredServiceFor(null, serviceType, serviceAction,
+ selectedServer);
}
/**
git://source.jalview.org / jalview.git / blobdiff