-/**
+/*
+ * 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 <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;
-
/**
*
*/
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,
- registry=registry.substring(0, registry.lastIndexOf("sources.xml")));
+ jalview.bin.Cache.setProperty(
+ jalview.bin.Cache.DAS_REGISTRY_URL,
+ registry = registry.substring(0,
+ registry.lastIndexOf("sources.xml")));
}
return registry;
}
* @param registryURL
* return sources from registryURL
*/
- private static List<jalviewSourceI> getDASSources(String registryURL, MultipleConnectionPropertyProviderI registry)
+ private static List<jalviewSourceI> getDASSources(String registryURL,
+ MultipleConnectionPropertyProviderI registry)
{
try
{
List<SOURCE> dassources = sources.getSOURCE();
ArrayList<jalviewSourceI> dsrc = new ArrayList<jalviewSourceI>();
- HashMap<String,Integer> latests=new HashMap<String, Integer>();
+ HashMap<String, Integer> latests = new HashMap<String, Integer>();
Integer latest;
for (SOURCE src : dassources)
{
- JalviewSource jsrc=new JalviewSource(src, registry, 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);
}
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>();
}
}
}
return appendLocalSources();
}
-
+
/**
* generate Sources from the local das source list
*
{
// 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,
git://source.jalview.org / jalview.git / blobdiff