X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=b184ff22e4190261b7286dbdc12fec7023970629;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=2bc33b6979524a4797d1782e46bab8a1749a910c;hpb=1dd6842f276f27ba69d7e1cfbc1c9b6519f3d22c;p=jalview.git diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java index 2bc33b6..b184ff2 100644 --- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java +++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java @@ -1,26 +1,39 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. * + * Jalview 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 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.dbsources.das.datamodel; +import jalview.bin.Cache; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.dbsources.das.api.jalviewSourceI; + import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; -import java.util.Collection; import java.util.Enumeration; import java.util.HashMap; -import java.util.HashSet; import java.util.Hashtable; import java.util.List; -import java.util.Map; -import java.util.Set; import java.util.StringTokenizer; -import java.util.Vector; -import javax.swing.JOptionPane; - -import org.apache.http.auth.InvalidCredentialsException; import org.biodas.jdas.client.ConnectionPropertyProviderI; import org.biodas.jdas.client.SourcesClient; import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI; @@ -30,10 +43,6 @@ import org.biodas.jdas.schema.sources.SOURCE; import org.biodas.jdas.schema.sources.SOURCES; import org.biodas.jdas.schema.sources.VERSION; -import jalview.bin.Cache; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; -import jalview.ws.dbsources.das.api.jalviewSourceI; - /** * */ @@ -47,7 +56,8 @@ public class DasSourceRegistry implements DasSourceRegistryI, private Hashtable localSources = null; - public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/"; + // public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/"; + public static String DEFAULT_REGISTRY = "http://www.ebi.ac.uk/das-srv/registry/das/"; /** * true if thread is running and we are talking to DAS registry service @@ -70,6 +80,14 @@ public class DasSourceRegistry implements DasSourceRegistryI, DEFAULT_REGISTRY); registry = DEFAULT_REGISTRY; } + if (registry.lastIndexOf("sources.xml") == registry.length() - 11) + { + // no trailing sources.xml document for registry in JDAS + jalview.bin.Cache.setProperty( + jalview.bin.Cache.DAS_REGISTRY_URL, + registry = registry.substring(0, + registry.lastIndexOf("sources.xml"))); + } return registry; } @@ -83,7 +101,7 @@ public class DasSourceRegistry implements DasSourceRegistryI, private List getDASSources() { - return getDASSources(getDasRegistryURL()); + return getDASSources(getDasRegistryURL(), this); } /** @@ -92,7 +110,8 @@ public class DasSourceRegistry implements DasSourceRegistryI, * @param registryURL * return sources from registryURL */ - private static List getDASSources(String registryURL) + private static List getDASSources(String registryURL, + MultipleConnectionPropertyProviderI registry) { try { @@ -104,21 +123,26 @@ public class DasSourceRegistry implements DasSourceRegistryI, List dassources = sources.getSOURCE(); ArrayList dsrc = new ArrayList(); - HashMap latests=new HashMap(); + HashMap latests = new HashMap(); Integer latest; for (SOURCE src : dassources) { - JalviewSource jsrc=new JalviewSource(src, false); - latest=latests.get(jsrc.getSourceURL()); - if (latest!=null) + JalviewSource jsrc = new JalviewSource(src, registry, false); + latest = latests.get(jsrc.getSourceURL()); + if (latest != null) { if (jsrc.isNewerThan(dsrc.get(latest.intValue()))) { dsrc.set(latest.intValue(), jsrc); - } else { - System.out.println("Debug: Ingored older source "+jsrc.getTitle()); } - } else { + else + { + System.out.println("Debug: Ignored older source " + + jsrc.getTitle()); + } + } + else + { latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size())); dsrc.add(jsrc); } @@ -147,7 +171,7 @@ public class DasSourceRegistry implements DasSourceRegistryI, } return appendLocalSources(); } - + /** * generate Sources from the local das source list * @@ -158,13 +182,21 @@ public class DasSourceRegistry implements DasSourceRegistryI, { // get local sources from properties and initialise the local source list String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); + if (local != null) { + int n = 1; StringTokenizer st = new StringTokenizer(local, "\t"); while (st.hasMoreTokens()) { String token = st.nextToken(); int bar = token.indexOf("|"); + if (bar == -1) + { + System.err + .println("Warning: DAS user local source appears to have no nickname (expected a '|' followed by nickname)\nOffending definition: '" + + token + "'"); + } String url = token.substring(bar + 1); boolean features = true, sequence = false; if (url.startsWith("sequence:")) @@ -173,8 +205,25 @@ public class DasSourceRegistry implements DasSourceRegistryI, // this source also serves sequences as well as features sequence = true; } - createLocalSource(url, token.substring(0, bar), sequence, - features); + try + { + if (bar > -1) + { + createLocalSource(url, token.substring(0, bar), sequence, + features); + } + else + { + createLocalSource(url, "User Source" + n, sequence, features); + } + } catch (Exception q) + { + System.err + .println("Unexpected exception when creating local source from '" + + token + "'"); + q.printStackTrace(); + } + n++; } } } @@ -210,8 +259,8 @@ public class DasSourceRegistry implements DasSourceRegistryI, } /* - * - */ + * + */ @Override public jalviewSourceI createLocalSource(String url, String name, @@ -223,7 +272,7 @@ public class DasSourceRegistry implements DasSourceRegistryI, { localSources = new Hashtable(); } - jalviewSourceI src = new JalviewSource(local, true); + jalviewSourceI src = new JalviewSource(local, this, true); localSources.put(local.getTitle(), src); return src; }