X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=943305ef50b7672b74aebb1f498f843fa8783e47;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=629b3d602d285f32d8180a3ab4e78f5b7cade6de;hpb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;p=jalview.git diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 629b3d6..943305e 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,52 @@ */ package jalview.ws.jws1; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.gui.JvOptionPane; import jalview.util.MessageManager; -import java.util.*; +import java.net.URL; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; -import javax.swing.*; +import ext.vamsas.IRegistry; +import ext.vamsas.IRegistryServiceLocator; +import ext.vamsas.RegistryServiceSoapBindingStub; +import ext.vamsas.ServiceHandle; +import ext.vamsas.ServiceHandles; -import ext.vamsas.*; - -public class Discoverer implements Runnable +public class Discoverer implements Runnable, ApplicationSingletonI { - ext.vamsas.IRegistry registry; // the root registry service. + + public static Discoverer getInstance() + { + return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class); + } + + private Discoverer() + { + // use getInstance() + } + + private java.net.URL RootServiceURL = null; + + private Vector ServiceURLList = null; + + private boolean reallyDiscoverServices = true; + + private Hashtable> services = null; + + public Hashtable> getServices() + { + return services; + } + + private Vector serviceList = null; + + // private ext.vamsas.IRegistry registry; // the root registry service. + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); @@ -92,9 +127,9 @@ public class Discoverer implements Runnable // timeout } catch (Exception ex) { - jalview.bin.Cache.log - .error("Serious! Service location failed\nfor URL :" + WsURL - + "\n", ex); + jalview.bin.Cache.log.error( + "Serious! Service location failed\nfor URL :" + WsURL + "\n", + ex); return null; } @@ -104,26 +139,11 @@ public class Discoverer implements Runnable return server; } - static private java.net.URL RootServiceURL = null; - - static public Vector ServiceURLList = null; - - static private boolean reallyDiscoverServices = true; - - public static java.util.Hashtable services = null; // vectors of services - - // stored by - // abstractServiceType - // string - - public static java.util.Vector serviceList = null; // flat list of services - - static private Vector getDiscoveryURLS() + static private Vector getDiscoveryURLS() { - Vector urls = new Vector(); - String RootServiceURLs = jalview.bin.Cache - .getDefault("DISCOVERY_URLS", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); + Vector urls = new Vector<>(); + String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try { @@ -148,17 +168,17 @@ public class Discoverer implements Runnable 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" + jalview.bin.Cache.log.warn( + "This was probably due to a malformed comma separated list" + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)"); jalview.bin.Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { - jalview.bin.Cache.log - .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.", - ex); + jalview.bin.Cache.log.warn( + "Error parsing comma separated list of urls in DISCOVERY_URLS.", + ex); } if (urls.size() > 0) { @@ -174,58 +194,64 @@ public class Discoverer implements Runnable { jalview.bin.Cache.log .debug("(Re)-Initialising the discovery URL list."); + Discoverer d = getInstance(); try { - reallyDiscoverServices = jalview.bin.Cache.getDefault( - "DISCOVERY_START", false); - if (reallyDiscoverServices) + d.reallyDiscoverServices = jalview.bin.Cache + .getDefault("DISCOVERY_START", false); + if (d.reallyDiscoverServices) { - ServiceURLList = getDiscoveryURLS(); + d.ServiceURLList = getDiscoveryURLS(); } else { jalview.bin.Cache.log.debug("Setting default services"); - services = new Hashtable(); + d.services = new Hashtable<>(); // Muscle, Clustal and JPred. - ServiceHandle[] defServices = - { - new ServiceHandle( - "MsaWS", - "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " - + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", - MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")), - new ServiceHandle( - "MsaWS", - "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " - + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" - + " Nucleic Acids Research, 33 511-518", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", - MessageManager.getString("label.mafft_multiple_sequence_alignment")), - new ServiceHandle( - "MsaWS", - "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" - + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." - + " Nucleic Acids Research, 22 4673-4680", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", - MessageManager.getString("label.clustalw_multiple_sequence_alignment")), - new ServiceHandle( - "SecStrPred", - "Cole C., Barber J. D., Barton G.J (2008) " - + "The Jpred 3 secondary structure prediction server " - + "Nucleic Acids Research, 36 W197-W201", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JNet Secondary Structure Prediction") }; - services = new Hashtable(); - serviceList = new Vector(); - buildServiceLists(defServices, serviceList, services); + ServiceHandle[] defServices = new ServiceHandle[0]; + try + { + // BH 2020.03.18 issue with applet branch Module problem. + defServices = new ServiceHandle[] { new ServiceHandle("MsaWS", + "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", + MessageManager.getString( + "label.muscle_multiple_protein_sequence_alignment")), + new ServiceHandle("MsaWS", + "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " + + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" + + " Nucleic Acids Research, 33 511-518", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", + MessageManager.getString( + "label.mafft_multiple_sequence_alignment")), + new ServiceHandle("MsaWS", + "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." + + " Nucleic Acids Research, 22 4673-4680", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", + MessageManager.getString( + "label.clustalw_multiple_sequence_alignment")), + new ServiceHandle("SecStrPred", + "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server" + + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" + + "\ndoi://10.1093/nar/gkv332", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", + "JPred Secondary Structure Prediction") }; + } catch (Throwable e) + { + + } + d.services = new Hashtable<>(); + d.serviceList = new Vector<>(); + buildServiceLists(defServices, d.serviceList, d.services); } } catch (Exception e) { - System.err - .println("jalview.rootRegistry is not a proper url!\nWas set to " - + RootServiceURL + "\n" + e); + System.err.println( + "jalview.rootRegistry is not a proper url!\nWas set to " + + d.RootServiceURL + "\n" + e); } } @@ -245,14 +271,13 @@ public class Discoverer implements Runnable // JBPNote - should do this a better way! if (f.getFaultReason().indexOf("(407)") > -1) { - if (jalview.gui.Desktop.desktop != null) + if (jalview.gui.Desktop.getDesktopPane() != null) { - JOptionPane - .showMessageDialog( - jalview.gui.Desktop.desktop, - MessageManager.getString("label.set_proxy_settings"), - MessageManager.getString("label.proxy_authorization_failed"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(), + MessageManager.getString("label.set_proxy_settings"), + MessageManager + .getString("label.proxy_authorization_failed"), + JvOptionPane.WARNING_MESSAGE); } } else @@ -284,8 +309,9 @@ public class Discoverer implements Runnable * Hashtable * @return boolean */ - static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat, - Hashtable sscat) + static private boolean buildServiceLists(ServiceHandle[] sh, + Vector cat, + Hashtable> sscat) { boolean seenNewDiscovery = false; for (int i = 0, j = sh.length; i < j; i++) @@ -297,33 +323,33 @@ public class Discoverer implements Runnable + sh[i].getEndpointURL() + "\n"); if (!sscat.containsKey(sh[i].getAbstractName())) { - sscat.put(sh[i].getAbstractName(), cat = new Vector()); + sscat.put(sh[i].getAbstractName(), cat = new Vector<>()); } else { - cat = (Vector) sscat.get(sh[i].getAbstractName()); + cat = sscat.get(sh[i].getAbstractName()); } cat.add(sh[i]); if (sh[i].getAbstractName().equals("Registry")) { - for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++) + Vector list = getInstance().ServiceURLList; + for (int s = 0, sUrls = list.size(); s < sUrls; s++) { java.net.URL disc_serv = null; try { disc_serv = new java.net.URL(sh[i].getEndpointURL()); - if (!ServiceURLList.contains(disc_serv)) + if (!list.contains(disc_serv)) { - jalview.bin.Cache.log - .debug("Adding new discovery service at " - + disc_serv); - ServiceURLList.add(disc_serv); + jalview.bin.Cache.log.debug( + "Adding new discovery service at " + disc_serv); + list.add(disc_serv); seenNewDiscovery = true; } } catch (Exception e) { - jalview.bin.Cache.log.debug( - "Ignoring bad discovery service URL " + jalview.bin.Cache.log + .debug("Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } } @@ -335,8 +361,8 @@ public class Discoverer implements Runnable public void discoverServices() { - Hashtable sscat = new Hashtable(); - Vector cat = new Vector(); + Hashtable> sscat = new Hashtable<>(); + Vector cat = new Vector<>(); ServiceHandle sh[] = null; int s_url = 0; if (ServiceURLList == null) @@ -347,17 +373,17 @@ public class Discoverer implements Runnable } while (s_url < ServiceURLList.size()) { - if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null) + if ((sh = getServices( + ServiceURLList.get(s_url))) != null) { buildServiceLists(sh, cat, sscat); } else { - jalview.bin.Cache.log - .warn("No services at " - + ((java.net.URL) ServiceURLList.get(s_url)) - + " - check DISCOVERY_URLS property in .jalview_properties"); + jalview.bin.Cache.log.warn("No services at " + + (ServiceURLList.get(s_url)) + + " - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } @@ -366,7 +392,7 @@ public class Discoverer implements Runnable // so no need to access original discovery thread. // Curent decision is to change properties then notify listeners with old // and new values. - Hashtable oldServices = services; + Hashtable> oldServices = services; // Vector oldServicelist = serviceList; services = sscat; serviceList = cat; @@ -376,14 +402,16 @@ public class Discoverer implements Runnable /** * creates a new thread to call discoverServices() */ + @Override public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { + @Override public void run() { - discoverer.doDiscovery(); + Discoverer.doDiscovery(); discoverer.discoverServices(); } }; @@ -393,24 +421,24 @@ public class Discoverer implements Runnable /** * binding service abstract name to handler class */ - private static Hashtable serviceClientBindings; + private static Hashtable serviceClientBindings; public static WS1Client getServiceClient(ServiceHandle sh) { if (serviceClientBindings == null) { // get a list from Config or create below - serviceClientBindings = new Hashtable(); + serviceClientBindings = new Hashtable<>(); serviceClientBindings.put("MsaWS", new MsaWSClient()); serviceClientBindings.put("SecStrPred", new JPredClient()); serviceClientBindings.put("SeqSearch", new SeqSearchWSClient()); } - WS1Client instance = (WS1Client) serviceClientBindings.get(sh - .getAbstractName()); + WS1Client instance = serviceClientBindings + .get(sh.getAbstractName()); if (instance == null) { - System.err - .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for " + System.err.println( + "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for " + sh.getAbstractName()); } else