+/*
+ * 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.ext.ensembl;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.util.DBRefUtils;
+import jalview.util.JSONUtils;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
* service
*
* @author gmcarstairs
- *
+ * @see http://rest.ensembl.org/documentation/info/xref_id
*/
class EnsemblXref extends EnsemblRestClient
{
+ private static final String GO_GENE_ONTOLOGY = "GO";
+
+ private String dbName = "ENSEMBL (xref)";
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblXref(String d, String dbSource, String version)
+ {
+ super(d);
+ dbName = dbSource;
+ xrefVersion = dbSource + ":" + version;
+
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (xref)";
+ return dbName;
}
@Override
@Override
protected URL getUrl(List<String> ids) throws MalformedURLException
{
- // TODO Auto-generated method stub
- return null;
+ return getUrl(ids.get(0));
}
@Override
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
* names. The "dbname" returned by Ensembl is canonicalised to Jalview's
- * standard version, and a DBRefEntry constructed. If no databases are
- * specified, all available cross-references are retrieved.
+ * standard version, and a DBRefEntry constructed. Currently takes all
+ * identifiers apart from GO terms and synonyms.
*
* @param identifier
- * @param databases
+ * an Ensembl stable identifier
* @return
*/
- public List<DBRefEntry> getCrossReferences(String identifier,
- List<String> databases)
+ @SuppressWarnings("unchecked")
+ public List<DBRefEntry> getCrossReferences(String identifier)
{
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- List<String> ids = new ArrayList<String>();
+ List<DBRefEntry> result = new ArrayList<>();
+ List<String> ids = new ArrayList<>();
ids.add(identifier);
- BufferedReader br = null;
try
{
- URL url = getUrl(identifier);
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- }
- return (parseResponse(br, databases));
- } catch (IOException e)
- {
- // ignore
- } finally
- {
- if (br != null)
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
+ while (rvals.hasNext())
{
- try
- {
- br.close();
- } catch (IOException e)
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+ String db = val.get("dbname").toString();
+ String id = val.get("primary_id").toString();
+ if (db != null && id != null
+ && !GO_GENE_ONTOLOGY.equals(db))
{
- // ignore
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
+ result.add(dbref);
}
}
+ } catch (ParseException | IOException e)
+ {
+ // ignore
}
-
return result;
}
+// /**
+// * Parses "primary_id" and "dbname" values from the JSON response and
+// * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
+// * don't parse "synonyms" as they appear to be either redirected or obsolete
+// * in Uniprot.
+// *
+// * @param br
+// * @return
+// * @throws IOException
+// */
+// @SuppressWarnings("unchecked")
+//protected List<DBRefEntry> parseResponse(BufferedReader br)
+// throws IOException
+// {
+// return result;
+// }
+//
+ private String xrefVersion = "ENSEMBL:0";
+
/**
- * Parses "primary_id" and "dbname" values from the JSON response and
- * constructs a DBRefEntry if the dbname is in the list supplied. Returns a
- * list of DBRefEntry created.
+ * version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
*
- * @param br
- * @param databases
* @return
- * @throws IOException
*/
- protected List<DBRefEntry> parseResponse(BufferedReader br,
- List<String> databases)
- throws IOException
+ public String getXRefVersion()
{
- JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- try
- {
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
- {
- JSONObject val = (JSONObject) rvals.next();
- String dbName = val.get("dbname").toString();
- if (databases != null && !databases.isEmpty()
- && !databases.contains(dbName))
- {
- continue;
- }
- String id = val.get("primary_id").toString();
- if (dbName != null && id != null)
- {
- dbName = DBRefUtils.getCanonicalName(dbName);
- DBRefEntry dbref = new DBRefEntry(dbName, "0", id);
- result.add(dbref);
- }
- }
- } catch (ParseException e)
- {
- // ignore
- }
- return result;
+ return xrefVersion;
}
/**
*/
protected URL getUrl(String identifier)
{
- String url = ENSEMBL_REST + "/xrefs/id/" + identifier
- + "?content-type=application/json&all_levels=1";
+ String url = getDomain() + "/xrefs/id/" + identifier
+ + CONTENT_TYPE_JSON + "&all_levels=1";
try
{
return new URL(url);
git://source.jalview.org / jalview.git / blobdiff