X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=b184ff22e4190261b7286dbdc12fec7023970629;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=6d62d974cbfb7a6e425c5291ce75666a0f468c59;hpb=be78a936034455f8ab1be4df53736000631d87ff;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 6d62d97..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/sources";
+ // 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;
}