X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;fp=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSourceRegistry.java;h=0000000000000000000000000000000000000000;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=de7f380132869ccbc607fc1c5fcd004b2aed8676;hpb=d943fcd0dc04fd4974344eddd13902c89fb595b2;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
deleted file mode 100644
index de7f380..0000000
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ /dev/null
@@ -1,484 +0,0 @@
-/*
- * 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.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-
-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;
-import org.biodas.jdas.schema.sources.SOURCES;
-import org.biodas.jdas.schema.sources.VERSION;
-
-/**
- *
- */
-public class DasSourceRegistry
- implements DasSourceRegistryI, MultipleConnectionPropertyProviderI
-{
- // private org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
- private List dasSources = null;
-
- private Hashtable sourceNames = null;
-
- private Hashtable localSources = null;
-
- // 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
- */
- private boolean loadingDasSources = false;
-
- public boolean isLoadingDasSources()
- {
- return loadingDasSources;
- }
-
- @Override
- public String getDasRegistryURL()
- {
- String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
- DEFAULT_REGISTRY);
-
- if (registry.indexOf("/registry/das1/sources/") > -1)
- {
- jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
- 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;
- }
-
- /**
- * query the default DAS Source Registry for sources. Uses value of jalview
- * property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that
- * doesn't exist.
- *
- * @return list of sources
- */
- private List getDASSources()
- {
-
- return getDASSources(getDasRegistryURL(), this);
- }
-
- /**
- * query the given URL for DasSources.
- *
- * @param registryURL
- * return sources from 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);
-
- List dassources = sources.getSOURCE();
- ArrayList dsrc = new ArrayList();
- HashMap latests = new HashMap();
- Integer latest;
- for (SOURCE src : dassources)
- {
- 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.out.println(
- "DAS1 registry at " + registryURL + " no longer exists");
- return new ArrayList();
- }
- }
-
- public void run()
- {
- getSources();
- }
-
- @Override
- public List getSources()
- {
- if (dasSources == null)
- {
- dasSources = getDASSources();
- }
- return appendLocalSources();
- }
-
- /**
- * generate Sources from the local das source list
- *
- */
- private void addLocalDasSources()
- {
- if (localSources == null)
- {
- // 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:"))
- {
- 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++;
- }
- }
- }
- }
-
- private List appendLocalSources()
- {
- List srclist = new ArrayList();
- addLocalDasSources();
- sourceNames = new Hashtable();
- if (dasSources != null)
- {
- for (jalviewSourceI src : dasSources)
- {
- sourceNames.put(src.getTitle(), src);
- srclist.add(src);
- }
- }
-
- if (localSources == null)
- {
- return srclist;
- }
- Enumeration en = localSources.keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- jalviewSourceI jvsrc = localSources.get(key);
- sourceNames.put(key, jvsrc);
- srclist.add(jvsrc);
- }
- return srclist;
- }
-
- /*
- *
- */
-
- @Override
- public jalviewSourceI createLocalSource(String url, String name,
- boolean sequence, boolean features)
- {
- SOURCE local = _createLocalSource(url, name, sequence, features);
-
- if (localSources == null)
- {
- localSources = new Hashtable();
- }
- jalviewSourceI src = new JalviewSource(local, this, true);
- localSources.put(local.getTitle(), src);
- return src;
- }
-
- private SOURCE _createLocalSource(String url, String name,
- boolean sequence, boolean features)
- {
- SOURCE local = new SOURCE();
-
- local.setUri(url);
- local.setTitle(name);
- local.setVERSION(new ArrayList());
- VERSION v = new VERSION();
- List cp = new ArrayList();
- if (sequence)
- {
- /*
- * Could try and synthesize a coordinate system for the source if needbe
- * COORDINATES coord = new COORDINATES(); coord.setAuthority("NCBI");
- * coord.setSource("Chromosome"); coord.setTaxid("9606");
- * coord.setVersion("35"); version.getCOORDINATES().add(coord);
- */
- CAPABILITY cap = new CAPABILITY();
- cap.setType("das1:" + Capabilities.SEQUENCE.getName());
- cap.setQueryUri(url + "/sequence");
- cp.add(cap);
- }
- if (features)
- {
- CAPABILITY cap = new CAPABILITY();
- cap.setType("das1:" + Capabilities.FEATURES.getName());
- cap.setQueryUri(url + "/features");
- cp.add(cap);
- }
-
- v.getCAPABILITY().addAll(cp);
- local.getVERSION().add(v);
-
- return local;
- }
-
- @Override
- public jalviewSourceI getSource(String nickname)
- {
- return sourceNames.get(nickname);
- }
-
- @Override
- public boolean removeLocalSource(jalviewSourceI source)
- {
- if (localSources.containsValue(source))
- {
- localSources.remove(source.getTitle());
- sourceNames.remove(source.getTitle());
- dasSources.remove(source);
- jalview.bin.Cache.setProperty("DAS_LOCAL_SOURCE",
- getLocalSourceString());
-
- return true;
- }
- return false;
- }
-
- @Override
- public void refreshSources()
- {
- dasSources = null;
- sourceNames = null;
- run();
- }
-
- @Override
- public List resolveSourceNicknames(List sources)
- {
- ArrayList resolved = new ArrayList();
- if (sourceNames != null)
- {
- for (String src : sources)
- {
- jalviewSourceI dsrc = sourceNames.get(src);
- if (dsrc != null)
- {
- resolved.add(dsrc);
- }
- }
- }
- return resolved;
- }
-
- @Override
- public String getLocalSourceString()
- {
- if (localSources != null)
- {
- StringBuffer sb = new StringBuffer();
- Enumeration en = localSources.keys();
- while (en.hasMoreElements())
- {
- String token = en.nextElement().toString();
- jalviewSourceI srco = localSources.get(token);
- sb.append(token + "|" + (srco.isSequenceSource() ? "sequence:" : "")
- + srco.getUri() + "\t");
- }
- return sb.toString();
- }
- return "";
- }
-
- private static final Hashtable authStash;
- static
- {
- authStash = new Hashtable();
-
- try
- {
- // TODO: allow same credentials for https and http
- authStash.put(
- new URL("http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
- "Basic SmltOm1pSg==");
- } catch (MalformedURLException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- @Override
- public MultipleConnectionPropertyProviderI getSessionHandler()
- {
- return this;
- }
-
- @Override
- public ConnectionPropertyProviderI getConnectionPropertyProviderFor(
- String arg0)
- {
-
- final ConnectionPropertyProviderI conprov = new ConnectionPropertyProviderI()
- {
- boolean authed = false;
-
- @Override
- public void setConnectionProperties(HttpURLConnection connection)
- {
- String auth = authStash.get(connection.getURL());
- if (auth != null && auth.length() > 0)
- {
- connection.setRequestProperty("Authorisation", auth);
- authed = true;
- }
- else
- {
- authed = false;
- }
- }
-
- @Override
- public boolean getResponseProperties(HttpURLConnection connection)
- {
- String auth = authStash.get(connection.getURL());
- if (auth != null && auth.length() == 0)
- {
- // don't attempt to check if we authed or not - user entered empty
- // password
- return false;
- }
- if (!authed)
- {
- if (auth != null)
- {
- // try and pass credentials.
- return true;
- }
- // see if we should try and create a new auth record.
- String ameth = connection.getHeaderField("X-DAS-AuthMethods");
- Cache.log.debug("Could authenticate to " + connection.getURL()
- + " with : " + ameth);
- // TODO: search auth string and raise login box - return if auth was
- // provided
- return false;
- }
- else
- {
- // check to see if auth was successful
- String asuc = connection
- .getHeaderField("X-DAS_AuthenticatedUser");
- if (asuc != null && asuc.trim().length() > 0)
- {
- // authentication was successful
- 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
- // want to attempt authentication again.
- authStash.remove(connection.getURL());
- // open a new login/password dialog with cancel button
- // set new authStash content with password and return true
- return true; //
- // User cancelled auth - so put empty string in stash to indicate we
- // don't want to auth with this server.
- // authStash.put(connection.getURL(), "");
- // return false;
- }
- }
- };
- return conprov;
- }
-
-}