X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=de7f380132869ccbc607fc1c5fcd004b2aed8676;hb=788e840cc150aa4777a370cebfdf5d17589bbbaf;hp=7257d0c47492c6ea2472d9d1b0ab4831749a31fa;hpb=831ad693b1320d74143011e1fe510496876e148a;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 7257d0c..de7f380 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,25 +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.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;
@@ -29,15 +43,11 @@ 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;
-
/**
*
*/
-public class DasSourceRegistry implements DasSourceRegistryI,
- MultipleConnectionPropertyProviderI
+public class DasSourceRegistry
+ implements DasSourceRegistryI, MultipleConnectionPropertyProviderI
{
// private org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
private List dasSources = null;
@@ -46,7 +56,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
private Hashtable localSources = null;
- public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/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
@@ -58,6 +69,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
return loadingDasSources;
}
+ @Override
public String getDasRegistryURL()
{
String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
@@ -69,6 +81,13 @@ 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;
}
@@ -82,7 +101,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
private List getDASSources()
{
- return getDASSources(getDasRegistryURL());
+ return getDASSources(getDasRegistryURL(), this);
}
/**
@@ -91,7 +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
{
@@ -103,16 +123,35 @@ public class DasSourceRegistry implements DasSourceRegistryI,
List dassources = sources.getSOURCE();
ArrayList dsrc = new ArrayList();
+ HashMap latests = new HashMap();
+ Integer latest;
for (SOURCE src : dassources)
{
- dsrc.add(new JalviewSource(src, false));
+ 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: Ignored older source " + jsrc.getTitle());
+ }
+ }
+ else
+ {
+ latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size()));
+ dsrc.add(jsrc);
+ }
}
return dsrc;
} catch (Exception ex)
{
- System.err.println("Failed to contact DAS1 registry at "
- + registryURL);
- ex.printStackTrace();
+ System.out.println(
+ "DAS1 registry at " + registryURL + " no longer exists");
return new ArrayList();
}
}
@@ -142,13 +181,21 @@ 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:"))
@@ -157,8 +204,25 @@ 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++;
}
}
}
@@ -194,8 +258,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
}
/*
- *
- */
+ *
+ */
@Override
public jalviewSourceI createLocalSource(String url, String name,
@@ -207,7 +271,7 @@ 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;
}
@@ -308,8 +372,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
{
String token = en.nextElement().toString();
jalviewSourceI srco = localSources.get(token);
- sb.append(token + "|"
- + (srco.isSequenceSource() ? "sequence:" : "")
+ sb.append(token + "|" + (srco.isSequenceSource() ? "sequence:" : "")
+ srco.getUri() + "\t");
}
return sb.toString();
@@ -325,8 +388,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
try
{
// TODO: allow same credentials for https and http
- authStash.put(new URL(
- "http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
+ authStash.put(
+ new URL("http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
"Basic SmltOm1pSg==");
} catch (MalformedURLException e)
{