From: gmungoc Date: Wed, 19 Nov 2014 12:55:39 +0000 (+0000) Subject: JAL-1342 new command-line parameter -jabaws X-Git-Tag: Release_2_8_2b1^2~20 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9d139ca8d1af8f0f2d78193d418ae9e9168a3e8a JAL-1342 new command-line parameter -jabaws --- diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 24ed1b4..3b0a23e 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -150,6 +150,7 @@ import org.apache.log4j.SimpleLayout; *
  • FOLLOW_SELECTIONS (true) Controls whether a new alignment view should * respond to selections made in other alignments containing the same sequences. *
    • + *
  • JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services
    • *
  • SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery * warning dialog box is displayed.
    • *
  • ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 184c267..f80f341 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -24,6 +24,7 @@ import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -34,6 +35,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; +import java.net.MalformedURLException; import java.net.URI; import java.net.URL; import java.net.URLDecoder; @@ -106,40 +108,7 @@ public class Jalview if (aparser.contains("help") || aparser.contains("h")) { - System.out - .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" - + "-nodisplay\tRun Jalview without User Interface.\n" - + "-props FILE\tUse the given Jalview properties file instead of users default.\n" - + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" - + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" - + "-tree FILE\tLoad the given newick format tree file onto the alignment\n" - + "-features FILE\tUse the given file to mark features on the alignment.\n" - + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n" - + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n" - + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n" - + "-msf FILE\tCreate alignment file FILE in MSF format.\n" - + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" - + "-pir FILE\tCreate alignment file FILE in PIR format.\n" - + "-blc FILE\tCreate alignment file FILE in BLC format.\n" - + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" - + "-png FILE\tCreate PNG image FILE from alignment.\n" - + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" - + "-eps FILE\tCreate EPS file FILE from alignment.\n" - + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" - + "-noquestionnaire\tTurn off questionnaire check.\n" - + "-nousagestats\tTurn off google analytics tracking for this session.\n" - + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" - // + - // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" - + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" - + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" - // + - // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" - // + "-vses vamsas-session\tJoin session with given URN\n" - + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" - + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + showUsage(); System.exit(0); } if (aparser.contains("nodisplay") || aparser.contains("nogui") @@ -150,6 +119,20 @@ public class Jalview } Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! + + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + } catch (MalformedURLException e) + { + System.err.println("Invalid jabaws parameter: " + jabawsUrl + + " ignored"); + } + } + String defs = aparser.getValue("setprop"); while (defs != null) { @@ -619,6 +602,45 @@ public class Jalview } } + private static void showUsage() + { + System.out + .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + + "-nodisplay\tRun Jalview without User Interface.\n" + + "-props FILE\tUse the given Jalview properties file instead of users default.\n" + + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" + + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" + + "-tree FILE\tLoad the given newick format tree file onto the alignment\n" + + "-features FILE\tUse the given file to mark features on the alignment.\n" + + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n" + + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n" + + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n" + + "-msf FILE\tCreate alignment file FILE in MSF format.\n" + + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + + "-png FILE\tCreate PNG image FILE from alignment.\n" + + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" + + "-eps FILE\tCreate EPS file FILE from alignment.\n" + + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" + + "-noquestionnaire\tTurn off questionnaire check.\n" + + "-nousagestats\tTurn off google analytics tracking for this session.\n" + + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" + // + + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" + + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" + + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" + + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" + // + + // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" + // + "-vses vamsas-session\tJoin session with given URN\n" + + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" + + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + } + private static void startUsageStats(final Desktop desktop) { /** diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 23ba893..7a1202c 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -2602,7 +2602,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements + ermsg + "" + "

    It may be that you have invalid JABA URLs
    in your web service preferences," - + " or mis-configured HTTP proxy settings.

    " + + "
    or as a command-line argument, or mis-configured HTTP proxy settings.

    " + "

    Check the Connections and Web services tab
    of the" + " Tools->Preferences dialog box to change them.

    "), "Web Service Configuration Problem", diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java index 00d9c79..4a74c9c 100644 --- a/src/jalview/gui/WsJobParameters.java +++ b/src/jalview/gui/WsJobParameters.java @@ -956,7 +956,7 @@ public class WsJobParameters extends JPanel implements ItemListener, { Vector services = new Vector(); services.addElement(args[p++]); - Jws2Discoverer.setServiceUrls(services); + Jws2Discoverer.getDiscoverer().setServiceUrls(services); } try { diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java index 0674352..527750c 100644 --- a/src/jalview/gui/WsPreferences.java +++ b/src/jalview/gui/WsPreferences.java @@ -33,6 +33,7 @@ import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.net.URL; +import java.util.List; import java.util.Vector; import javax.swing.JLabel; @@ -52,7 +53,9 @@ public class WsPreferences extends GWsPreferences initFromPreferences(); } - Vector wsUrls, oldUrls, rsbsUrls, oldRsbsUrls; + List wsUrls; + + Vector oldUrls, rsbsUrls, oldRsbsUrls; private boolean needWsMenuUpdate; @@ -62,8 +65,8 @@ public class WsPreferences extends GWsPreferences private void initFromPreferences() { - wsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls(); - if (wsUrls != null) + wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls(); + if (!wsUrls.isEmpty()) { oldUrls = new Vector(wsUrls); } @@ -235,7 +238,7 @@ public class WsPreferences extends GWsPreferences private void updateServiceList() { - jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls); + Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls); } private void updateRsbsServiceList() @@ -256,7 +259,7 @@ public class WsPreferences extends GWsPreferences int sel = wsList.getSelectedRow(); if (sel > -1) { - wsUrls.removeElementAt(sel); + wsUrls.remove(sel); update++; updateList(); } @@ -274,21 +277,22 @@ public class WsPreferences extends GWsPreferences int sel = wsList.getSelectedRow(); if (sel > -1) { - String url = editUrl(wsUrls.elementAt(sel), MessageManager.getString("label.edit_jabaws_url")); + String url = editUrl(wsUrls.get(sel), + MessageManager.getString("label.edit_jabaws_url")); if (url != null) { int present = wsUrls.indexOf(url); if (present == -1) { update++; - wsUrls.setElementAt(url, sel); + wsUrls.set(sel, url); updateList(); } else { if (present != sel) { - wsUrls.removeElementAt(sel); + wsUrls.remove(sel); updateList(); } } @@ -406,8 +410,8 @@ public class WsPreferences extends GWsPreferences if (p > -1 && p < wsUrls.size() - 1) { String t = wsUrls.get(p + 1); - wsUrls.setElementAt(wsUrls.elementAt(p), p + 1); - wsUrls.setElementAt(t, p); + wsUrls.set(p + 1, wsUrls.get(p)); + wsUrls.set(p, t); updateList(); wsList.getSelectionModel().setSelectionInterval(p + 1, p + 1); update++; @@ -428,8 +432,8 @@ public class WsPreferences extends GWsPreferences if (p > 0) { String t = wsUrls.get(p - 1); - wsUrls.setElementAt(wsUrls.elementAt(p), p - 1); - wsUrls.setElementAt(t, p); + wsUrls.set(p - 1, wsUrls.get(p)); + wsUrls.set(p, t); updateList(); wsList.getSelectionModel().setSelectionInterval(p - 1, p - 1); update++; @@ -487,7 +491,7 @@ public class WsPreferences extends GWsPreferences if (validate == JOptionPane.OK_OPTION) { - if (jalview.ws.jws2.Jws2Discoverer.testServiceUrl(foo)) + if (Jws2Discoverer.testServiceUrl(foo)) { return foo.toString(); } @@ -544,11 +548,11 @@ public class WsPreferences extends GWsPreferences int selind = wsList.getSelectedRow(); if (selind > -1) { - wsUrls.insertElementAt(url, selind); + wsUrls.add(selind, url); } else { - wsUrls.addElement(url); + wsUrls.add(url); } update++; updateList(); @@ -651,8 +655,8 @@ public class WsPreferences extends GWsPreferences @Override protected void resetWs_actionPerformed(ActionEvent e) { - jalview.ws.jws2.Jws2Discoverer.setServiceUrls(null); - Vector nwsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls(); + Jws2Discoverer.getDiscoverer().setServiceUrls(null); + List nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls(); if (!wsUrls.equals(nwsUrls)) { update++; diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java index a08a233..74dce4d 100644 --- a/src/jalview/ws/jws2/JabaWsServerQuery.java +++ b/src/jalview/ws/jws2/JabaWsServerQuery.java @@ -27,6 +27,9 @@ import jalview.bin.Cache; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.jws2.jabaws2.Jws2InstanceFactory; +import java.io.IOException; +import java.net.MalformedURLException; +import java.net.URL; import java.util.HashSet; import java.util.Set; @@ -44,7 +47,7 @@ public class JabaWsServerQuery implements Runnable Jws2Discoverer jws2Discoverer = null; - String jwsservers = null; + String jwsserver = null; boolean quit = false, running = false; @@ -65,10 +68,10 @@ public class JabaWsServerQuery implements Runnable this.quit = quit; } - public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers) + public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server) { this.jws2Discoverer = jws2Discoverer; - this.jwsservers = jwsservers; + this.jwsserver = server; } Services[] JABAWS1SERVERS = new Services[] @@ -92,7 +95,9 @@ public class JabaWsServerQuery implements Runnable running = true; try { - if (Jws2Client.validURL(jwsservers)) + // TODO this test doesn't seem to attempt a connection - should it? + // would save a lot of failed tries with UnknownHostException + if (isValidUrl(jwsserver)) { compbio.data.msa.RegistryWS registry = null; Set svccategories = null; @@ -109,7 +114,7 @@ public class JabaWsServerQuery implements Runnable try { // JBPNote: why is RegistryWS in compbio.data.msa ? - registry = Jws2Client.connectToRegistry(jwsservers); + registry = Jws2Client.connectToRegistry(jwsserver); if (registry != null) { // System.err.println("Test Services Output\n" @@ -137,7 +142,7 @@ public class JabaWsServerQuery implements Runnable ex.printStackTrace(); // if that failed, then we are probably working with a JABAWS1 server. // in that case, look for each service endpoint - System.err.println("JWS2 Discoverer: " + jwsservers + System.err.println("JWS2 Discoverer: " + jwsserver + " is a JABAWS1 server. Using hardwired list."); for (Services srv : JABAWS1SERVERS) { @@ -161,18 +166,18 @@ public class JabaWsServerQuery implements Runnable JABAService service = null; try { - service = Jws2Client.connect(jwsservers, srv); + service = Jws2Client.connect(jwsserver, srv); } catch (Exception e) { System.err.println("Jws2 Discoverer: Problem on " - + jwsservers + " with service " + srv + ":\n" + + jwsserver + " with service " + srv + ":\n" + e.getMessage()); if (!(e instanceof javax.xml.ws.WebServiceException)) { e.printStackTrace(); } // For moment, report service as a problem. - jws2Discoverer.addInvalidServiceUrl(jwsservers); + jws2Discoverer.addInvalidServiceUrl(jwsserver); } ; if (service != null) @@ -184,16 +189,16 @@ public class JabaWsServerQuery implements Runnable String description = registry.getServiceDescription(srv); - svc = Jws2InstanceFactory.newJws2Instance(jwsservers, + svc = Jws2InstanceFactory.newJws2Instance(jwsserver, srv.toString(), cat.name, description, service); } if (svc == null) { - svc = Jws2InstanceFactory.newJws2Instance(jwsservers, + svc = Jws2InstanceFactory.newJws2Instance(jwsserver, srv.toString(), cat.name, "JABAWS 1 Alignment Service", service); } - jws2Discoverer.addService(jwsservers, svc); + jws2Discoverer.addService(jwsserver, svc); } } @@ -201,25 +206,53 @@ public class JabaWsServerQuery implements Runnable if (noservices) { - jws2Discoverer.addUrlwithnoservices(jwsservers); + jws2Discoverer.addUrlwithnoservices(jwsserver); } } else { - jws2Discoverer.addInvalidServiceUrl(jwsservers); - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); + jws2Discoverer.addInvalidServiceUrl(jwsserver); + Cache.log.info("Ignoring invalid Jws2 service url " + jwsserver); } } catch (Exception e) { e.printStackTrace(); Cache.log.warn("Exception when discovering Jws2 services.", e); - jws2Discoverer.addInvalidServiceUrl(jwsservers); + jws2Discoverer.addInvalidServiceUrl(jwsserver); } catch (Error e) { Cache.log.error("Exception when discovering Jws2 services.", e); - jws2Discoverer.addInvalidServiceUrl(jwsservers); + jws2Discoverer.addInvalidServiceUrl(jwsserver); } running = false; } + /** + * Check if the URL is valid and responding. + * + * @return + */ + private boolean isValidUrl(String server) + { + // return Jws2Client.validURL(jwsserver); // checks syntax only + boolean result = false; + if (server != null) { + try { + URL url = new URL(server); + url.openStream().close(); + result = true; + } catch (MalformedURLException e) + { + System.err.println("Invalid server URL: " + server); + result = false; + } catch (IOException e) + { + System.err.println("Error connecting to server: " + server + ": " + + e.toString()); + result = false; + } + } + return result; + } + } diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 910b749..a111d68 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -34,6 +34,8 @@ 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; @@ -60,9 +62,48 @@ 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 testUrls = null; + + // preferred url has precedence over others + private String preferredUrl; + + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); + Vector invalidServiceUrls = null, urlsWithoutServices = null, + validServiceUrls = null; + + boolean running = false, aborted = false; + + Thread oldthread = null; + + /** + * holds list of services. + */ + protected Vector services; + + /** + * Private constructor enforces use of singleton via getDiscoverer() + */ + private Jws2Discoverer() + { + } + /** * change listeners are notified of "services" property changes * @@ -87,8 +128,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false, aborted = false; - /** * @return the aborted */ @@ -104,10 +143,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public void setAborted(boolean aborted) { this.aborted = aborted; - } - - Thread oldthread = null; + } public void run() { @@ -135,7 +172,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // first set up exclusion list if needed final Set ignoredServices = new HashSet(); - for (String ignored : jalview.bin.Cache.getDefault( + for (String ignored : Cache.getDefault( "IGNORED_JABAWS_SERVICETYPES", "") .split("\\|")) { @@ -176,9 +213,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ArrayList svctypes = new ArrayList(); List qrys = new ArrayList(); - for (final String jwsservers : getServiceUrls()) + for (final String jwsserver : getServiceUrls()) { - JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver); if (svctypes.size() == 0) { // TODO: remove this ugly hack to get Canonical JABA service ordering @@ -233,7 +270,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Jws2Instance[] svcs = new Jws2Instance[services.size()]; int[] spos = new int[services.size()]; int ipos = 0; - Vector svcUrls = getServiceUrls(); + List svcUrls = getServiceUrls(); for (Jws2Instance svc : services) { svcs[ipos] = svc; @@ -290,11 +327,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } /** - * holds list of services. - */ - protected Vector services; - - /** * attach all available web services to the appropriate submenu in the given * JMenu */ @@ -545,7 +577,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (args.length > 0) { - testUrls = new Vector(); + testUrls = new ArrayList(); for (String url : args) { testUrls.add(url); @@ -592,8 +624,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } - private static Jws2Discoverer discoverer; - + /** + * Returns the singleton instance of this class. + * + * @return + */ public static Jws2Discoverer getDiscoverer() { if (discoverer == null) @@ -605,7 +640,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { - // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } @@ -614,24 +648,19 @@ 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 { @@ -639,18 +668,27 @@ 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) { // 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, ","); @@ -659,40 +697,37 @@ 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.info("Ignoring duplicate url " + url + " in " + JWS2HOSTURLS + " list"); } - } catch (Exception ex) + } catch (MalformedURLException ex) { - jalview.bin.Cache.log + Cache.log .warn("Problem whilst trying to make a URL from '" + ((url != null) ? url : "") + "'"); - jalview.bin.Cache.log + 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( + Cache.log.warn( "Error parsing comma separated list of urls in " + JWS2HOSTURLS + " preference.", ex); } - if (urls.size() >= 0) - { - return urls; - } - return null; + return urls; } public Vector getServices() @@ -750,9 +785,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null, - validServiceUrls = null; - /** * @return the invalidServiceUrls */ @@ -865,7 +897,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return 1; } if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) + { return 0; + } if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) { return -1; @@ -979,4 +1013,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { 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; + } + } } diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java index 295c3bf..c206323 100644 --- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java +++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java @@ -20,7 +20,8 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.*; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; import jalview.ws.jws2.Jws2Discoverer; import java.util.Vector; @@ -73,7 +74,7 @@ public class JalviewJabawsTestUtils services.add(url); } ; - Jws2Discoverer.setServiceUrls(services); + Jws2Discoverer.getDiscoverer().setServiceUrls(services); } try {