X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=04a1b6054295dc59094406485a6c52f874e031cb;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=b17f7f25f3852bff0a16bccc722d5ddff515292a;hpb=339ed5130c391c6028e01222e8ba293b8209b524;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index b17f7f2..04a1b60 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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;
@@ -7,21 +22,15 @@ 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;
import org.biodas.jdas.dassources.Capabilities;
import org.biodas.jdas.schema.sources.CAPABILITY;
import org.biodas.jdas.schema.sources.SOURCE;
@@ -35,7 +44,8 @@ import jalview.ws.dbsources.das.api.jalviewSourceI;
/**
*
*/
-public class DasSourceRegistry implements DasSourceRegistryI
+public class DasSourceRegistry implements DasSourceRegistryI,
+ MultipleConnectionPropertyProviderI
{
// private org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
private List dasSources = null;
@@ -44,7 +54,7 @@ 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/";
/**
* true if thread is running and we are talking to DAS registry service
@@ -67,6 +77,14 @@ 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;
}
@@ -80,7 +98,7 @@ public class DasSourceRegistry implements DasSourceRegistryI
private List getDASSources()
{
- return getDASSources(getDasRegistryURL());
+ return getDASSources(getDasRegistryURL(), this);
}
/**
@@ -89,20 +107,42 @@ 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
{
URL url = new URL(registryURL);
org.biodas.jdas.client.SourcesClientInterface client = new SourcesClient();
- SOURCES sources = client.fetchDataRegistry(registryURL, null, null, null, null, null, null);
+ SOURCES sources = client.fetchDataRegistry(registryURL, null, null,
+ null, null, null, null);
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)
@@ -114,7 +154,6 @@ public class DasSourceRegistry implements DasSourceRegistryI
}
}
-
public void run()
{
getSources();
@@ -136,30 +175,60 @@ public class DasSourceRegistry implements DasSourceRegistryI
*/
private void addLocalDasSources()
{
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
- if (local != null)
+ if (localSources == null)
{
- StringTokenizer st = new StringTokenizer(local, "\t");
- while (st.hasMoreTokens())
+ // get local sources from properties and initialise the local source list
+ String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+
+ if (local != null)
{
- String token = st.nextToken();
- int bar = token.indexOf("|");
- String url = token.substring(bar + 1);
- boolean features = true, sequence = false;
- if (url.startsWith("sequence:"))
+ int n = 1;
+ StringTokenizer st = new StringTokenizer(local, "\t");
+ while (st.hasMoreTokens())
{
- url = url.substring(9);
- // this source also serves sequences as well as features
- sequence = true;
+ 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:"))
+ {
+ url = url.substring(9);
+ // this source also serves sequences as well as features
+ sequence = true;
+ }
+ 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++;
}
- createLocalSource(url, token.substring(0, bar), sequence, features);
}
}
}
private List appendLocalSources()
{
- List srclist=new ArrayList();
+ List srclist = new ArrayList();
addLocalDasSources();
sourceNames = new Hashtable();
if (dasSources != null)
@@ -200,7 +269,7 @@ 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;
}
@@ -225,14 +294,14 @@ public class DasSourceRegistry implements DasSourceRegistryI
*/
CAPABILITY cap = new CAPABILITY();
cap.setType("das1:" + Capabilities.SEQUENCE.getName());
- cap.setQueryUri(url+"/sequence");
+ cap.setQueryUri(url + "/sequence");
cp.add(cap);
}
if (features)
{
CAPABILITY cap = new CAPABILITY();
cap.setType("das1:" + Capabilities.FEATURES.getName());
- cap.setQueryUri(url+"/features");
+ cap.setQueryUri(url + "/features");
cp.add(cap);
}
@@ -256,6 +325,9 @@ public class DasSourceRegistry implements DasSourceRegistryI
localSources.remove(source.getTitle());
sourceNames.remove(source.getTitle());
dasSources.remove(source);
+ jalview.bin.Cache.setProperty("DAS_LOCAL_SOURCE",
+ getLocalSourceString());
+
return true;
}
return false;
@@ -326,8 +398,16 @@ public class DasSourceRegistry implements DasSourceRegistryI
}
@Override
- public Map getSessionHandler()
+ public MultipleConnectionPropertyProviderI getSessionHandler()
{
+ return this;
+ }
+
+ @Override
+ public ConnectionPropertyProviderI getConnectionPropertyProviderFor(
+ String arg0)
+ {
+
final ConnectionPropertyProviderI conprov = new ConnectionPropertyProviderI()
{
boolean authed = false;
@@ -380,8 +460,8 @@ public class DasSourceRegistry implements DasSourceRegistryI
if (asuc != null && asuc.trim().length() > 0)
{
// authentication was successful
- Cache.log.debug("Authenticated successfully as " + asuc
- + " with " + connection.getURL().toString());
+ Cache.log.debug("Authenticated successfully to "
+ + connection.getURL().toString());
return false;
}
// it wasn't - so we should tell the user it failed and ask if they
@@ -397,95 +477,7 @@ public class DasSourceRegistry implements DasSourceRegistryI
}
}
};
- return new Map()
- {
-
- @Override
- public void clear()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean containsKey(Object key)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public boolean containsValue(Object value)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public Set> entrySet()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public ConnectionPropertyProviderI get(Object key)
- {
- return conprov;
- }
-
- @Override
- public boolean isEmpty()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public Set keySet()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public ConnectionPropertyProviderI put(String key,
- ConnectionPropertyProviderI value)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void putAll(
- Map m)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public ConnectionPropertyProviderI remove(Object key)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public int size()
- {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public Collection values()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- };
+ return conprov;
}
}