X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDiscoverer.java;h=02028b41acb25e5276f30cdee71f92537f1ace7a;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=4a83ba79a5782c57d04e810fbd8678e28d6a99ea;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java index 4a83ba7..02028b4 100755 --- a/src/jalview/ws/Discoverer.java +++ b/src/jalview/ws/Discoverer.java @@ -1,21 +1,21 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.ws; /** @@ -30,11 +30,11 @@ package jalview.ws; * @author not attributable * @version 1.0 */ +import java.util.*; + +import javax.swing.*; + import ext.vamsas.*; -import java.util.Vector; -import java.util.Hashtable; -import java.util.StringTokenizer; -import javax.swing.JOptionPane; public class Discoverer extends Thread implements Runnable @@ -111,12 +111,14 @@ public class Discoverer 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"); - try{ + try + { StringTokenizer st = new StringTokenizer(RootServiceURLs, ","); while (st.hasMoreElements()) { @@ -125,24 +127,36 @@ public class Discoverer { java.net.URL u = new java.net.URL(url = st.nextToken()); if (!urls.contains(u)) + { urls.add(u); + } else - jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list"); + { + jalview.bin.Cache.log.info( + "Ignoring duplicate url in DISCOVERY_URLS list"); + } } catch (Exception 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 DISCOVERY_URLS entry of $(HOME)/.jalview_properties)"); - jalview.bin.Cache.log.debug("Exception was ",ex); + ( (url != null) ? url : "") + "'"); + 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);} - if (urls.size()>0) + } + catch (Exception ex) + { + jalview.bin.Cache.log.warn( + "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex); + } + if (urls.size() > 0) + { return urls; + } return null; } @@ -164,19 +178,20 @@ public class Discoverer jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. - ServiceHandle[] defServices = { + 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", "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", + "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", "MAFFT Multiple Sequence Alignment"), new ServiceHandle( @@ -191,8 +206,9 @@ public class Discoverer "Cuff J. A and Barton G.J (2000) Application of " + "multiple sequence alignment profiles to improve protein secondary structure prediction, " + "Proteins 40:502-511", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction" - )}; + "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", + "JNet Secondary Structure Prediction" + )}; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); @@ -207,6 +223,7 @@ public class Discoverer } } + // TODO: JBPNote : make this discover more services based on list of // discovery service urls, break cyclic references to the same url and // duplicate service entries (same endpoint *and* same interface) @@ -218,20 +235,27 @@ public class Discoverer jalview.bin.Cache.log.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } - catch (org.apache.axis.AxisFault f) { + catch (org.apache.axis.AxisFault f) + { // JBPNote - should do this a better way! - if (f.getFaultReason().indexOf("(407)")>-1) { - if (jalview.gui.Desktop.desktop!=null) + if (f.getFaultReason().indexOf("(407)") > -1) + { + if (jalview.gui.Desktop.desktop != null) + { JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window", - "Proxy Authorization Failed", - JOptionPane.WARNING_MESSAGE); - } else { + "Proxy Authorization Failed", + JOptionPane.WARNING_MESSAGE); + } + } + else + { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Axis Fault", f); } } - catch (Exception e) { + catch (Exception e) + { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Discovery Service General Exception", e); @@ -252,7 +276,7 @@ public class Discoverer * @return boolean */ static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat, - Hashtable sscat) + Hashtable sscat) { boolean seenNewDiscovery = false; for (int i = 0, j = sh.length; i < j; i++) @@ -260,9 +284,9 @@ public class Discoverer if (!cat.contains(sh[i])) { jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + - " service called " + - sh[i].getName() + " exists at " + - sh[i].getEndpointURL() + "\n"); + " service called " + + sh[i].getName() + " exists at " + + sh[i].getEndpointURL() + "\n"); if (!sscat.containsKey(sh[i].getAbstractName())) { sscat.put(sh[i].getAbstractName(), cat = new Vector()); @@ -307,9 +331,10 @@ public class Discoverer Vector cat = new Vector(); ServiceHandle sh[] = null; int s_url = 0; - if (ServiceURLList==null) + if (ServiceURLList == null) { - jalview.bin.Cache.log.debug("No service endpoints to use for service discovery."); + jalview.bin.Cache.log.debug( + "No service endpoints to use for service discovery."); return; } while (s_url < ServiceURLList.size()) @@ -318,11 +343,13 @@ public class Discoverer { buildServiceLists(sh, cat, sscat); - } else { + } + else + { jalview.bin.Cache.log.warn( "No services at " - +((java.net.URL) ServiceURLList.get(s_url)) - +" - check DISCOVERY_URLS property in .jalview_properties"); + + ( (java.net.URL) ServiceURLList.get(s_url)) + + " - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } @@ -343,8 +370,10 @@ public class Discoverer public void run() { final Discoverer discoverer = this; - Thread discoverThread = new Thread() { - public void run() { + Thread discoverThread = new Thread() + { + public void run() + { discoverer.doDiscovery(); discoverer.discoverServices(); }