/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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;
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<jalviewSourceI> dasSources = null;
private Hashtable<String, jalviewSourceI> 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
return loadingDasSources;
}
+ @Override
public String getDasRegistryURL()
{
String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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,
+ jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
registry = registry.substring(0,
registry.lastIndexOf("sources.xml")));
}
}
else
{
- System.out.println("Debug: Ignored older source "
- + jsrc.getTitle());
+ System.out.println(
+ "Debug: Ignored older source " + jsrc.getTitle());
}
}
else
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<jalviewSourceI>();
}
}
{
// 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:"))
// 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++;
}
}
}
}
/*
- *
- */
+ *
+ */
@Override
public jalviewSourceI createLocalSource(String url, String name,
{
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();
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)
{