X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=4a8f512e563c31054a551f346d570b8f306d020d;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=ba4054e27164a9bea8166ec8d8350ef9fb3f373b;hpb=cd4e2687751aab1c9c5974e6966e610a3332236b;p=jalview.git diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index ba4054e..4a8f512 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -20,9 +20,12 @@ */ package jalview.ws.jws1; +import jalview.bin.Cache; +import jalview.bin.Console; import jalview.gui.JvOptionPane; import jalview.util.MessageManager; +import java.net.URL; import java.util.Hashtable; import java.util.StringTokenizer; import java.util.Vector; @@ -97,9 +100,9 @@ public class Discoverer implements Runnable // timeout } catch (Exception ex) { - jalview.bin.Cache.log - .error("Serious! Service location failed\nfor URL :" + WsURL - + "\n", ex); + Console.error( + "Serious! Service location failed\nfor URL :" + WsURL + "\n", + ex); return null; } @@ -111,24 +114,22 @@ public class Discoverer implements Runnable static private java.net.URL RootServiceURL = null; - static public Vector ServiceURLList = null; + static public Vector ServiceURLList = null; static private boolean reallyDiscoverServices = true; - public static java.util.Hashtable services = null; // vectors of services - + public static java.util.Hashtable> services = null; // stored by // abstractServiceType // string - public static java.util.Vector serviceList = null; // flat list of services + public static java.util.Vector serviceList = null; - 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 = Cache.getDefault("DISCOVERY_URLS", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try { @@ -145,25 +146,23 @@ public class Discoverer implements Runnable } else { - jalview.bin.Cache.log - .info("Ignoring duplicate url in DISCOVERY_URLS list"); + Console.info("Ignoring duplicate url in DISCOVERY_URLS list"); } } catch (Exception ex) { - jalview.bin.Cache.log - .warn("Problem whilst trying to make a URL from '" + Console.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" + Console.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); + Console.debug("Exception was ", ex); } } } catch (Exception ex) { - jalview.bin.Cache.log - .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.", - ex); + Console.warn( + "Error parsing comma separated list of urls in DISCOVERY_URLS.", + ex); } if (urls.size() > 0) { @@ -177,61 +176,55 @@ public class Discoverer implements Runnable */ static public void doDiscovery() { - jalview.bin.Cache.log - .debug("(Re)-Initialising the discovery URL list."); + Console.debug("(Re)-Initialising the discovery URL list."); try { - reallyDiscoverServices = jalview.bin.Cache.getDefault( - "DISCOVERY_START", false); + reallyDiscoverServices = Cache + .getDefault("DISCOVERY_START", false); if (reallyDiscoverServices) { ServiceURLList = getDiscoveryURLS(); } else { - jalview.bin.Cache.log.debug("Setting default services"); - services = new Hashtable(); + Console.debug("Setting default services"); + 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", + 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", + 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", + 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") }; - services = new Hashtable(); - serviceList = new Vector(); + services = new Hashtable<>(); + serviceList = new Vector<>(); buildServiceLists(defServices, serviceList, services); } } catch (Exception e) { - System.err - .println("jalview.rootRegistry is not a proper url!\nWas set to " + System.err.println( + "jalview.rootRegistry is not a proper url!\nWas set to " + RootServiceURL + "\n" + e); } @@ -245,7 +238,7 @@ public class Discoverer implements Runnable ServiceHandles shs = null; try { - jalview.bin.Cache.log.debug("Discovering services using " + location); + Console.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } catch (org.apache.axis.AxisFault f) { @@ -263,13 +256,13 @@ public class Discoverer implements Runnable } else { - jalview.bin.Cache.log.warn("No Discovery service at " + location); - jalview.bin.Cache.log.debug("Axis Fault", f); + Console.warn("No Discovery service at " + location); + Console.debug("Axis Fault", f); } } catch (Exception e) { - jalview.bin.Cache.log.warn("No Discovery service at " + location); - jalview.bin.Cache.log.debug("Discovery Service General Exception", e); + Console.warn("No Discovery service at " + location); + Console.debug("Discovery Service General Exception", e); } if ((shs != null) && shs.getServices().length > 0) { @@ -290,24 +283,25 @@ 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++) { if (!cat.contains(sh[i])) { - jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + Console.debug("A " + sh[i].getAbstractName() + " 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()); + 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")) @@ -320,16 +314,14 @@ public class Discoverer implements Runnable disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { - jalview.bin.Cache.log - .debug("Adding new discovery service at " - + disc_serv); + Console.debug( + "Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; } } catch (Exception e) { - jalview.bin.Cache.log.debug( - "Ignoring bad discovery service URL " + Console.debug("Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } } @@ -341,29 +333,28 @@ 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) { - jalview.bin.Cache.log - .debug("No service endpoints to use for service discovery."); + Console.debug("No service endpoints to use for service discovery."); return; } 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 " - + (ServiceURLList.get(s_url)) - + " - check DISCOVERY_URLS property in .jalview_properties"); + Console.warn("No services at " + + (ServiceURLList.get(s_url)) + + " - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } @@ -372,7 +363,7 @@ 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; @@ -391,7 +382,7 @@ public class Discoverer implements Runnable @Override public void run() { - discoverer.doDiscovery(); + Discoverer.doDiscovery(); discoverer.discoverServices(); } }; @@ -401,24 +392,24 @@ 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