+/*
+ * 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 java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
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;
+/**
+ * A client for the Ensembl xrefs/symbol REST service;
+ *
+ * @see http://rest.ensembl.org/documentation/info/xref_external
+ * @author gmcarstairs
+ *
+ */
public class EnsemblSymbol extends EnsemblXref
{
+ private static final String GENE = "gene";
+
+ private static final String TYPE = "type";
+
/**
- * Returns the first "id" value in gene identifier format from the JSON
- * response, or null if none found
+ * Constructor given the target domain to fetch data from
*
- * @param br
- * @return
- * @throws IOException
+ * @param domain
+ * @param dbName
+ * @param dbVersion
*/
- protected String parseResponse(BufferedReader br)
- throws IOException
+ public EnsemblSymbol(String domain, String dbName, String dbVersion)
{
- JSONParser jp = new JSONParser();
- String result = null;
- try
- {
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
- {
- JSONObject val = (JSONObject) rvals.next();
- String id = val.get("id").toString();
- if (id != null && isGeneIdentifier(id))
- {
- result = id;
- break;
- }
- }
- } catch (ParseException e)
- {
- // ignore
- }
- return result;
+ super(domain, dbName, dbVersion);
}
- protected URL getUrl(String id, Species species)
+ // /**
+ // * Returns the first "id" value in gene identifier format from the JSON
+ // * response, or null if none found
+ // *
+ // * @param br
+ // * @return
+ // * @throws IOException
+ // */
+ // @SuppressWarnings("unchecked")
+ // protected String parseSymbolResponse(BufferedReader br) throws IOException
+ // {
+ // }
+
+ /**
+ * Constructs the URL for the REST symbol endpoint
+ *
+ * @param id
+ * the accession id (Ensembl or external)
+ * @param species
+ * a species name recognisable by Ensembl
+ * @param type
+ * an optional type to filter the response (gene, transcript,
+ * translation)
+ * @return
+ */
+ protected URL getUrl(String id, Species species, String... type)
{
- String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
- + id
- + "?content-type=application/json";
+ StringBuilder sb = new StringBuilder();
+ sb.append(getDomain()).append("/xrefs/symbol/")
+ .append(species.toString()).append("/").append(id)
+ .append(CONTENT_TYPE_JSON);
+ for (String t : type)
+ {
+ sb.append("&object_type=").append(t);
+ }
try
{
+ String url = sb.toString();
return new URL(url);
} catch (MalformedURLException e)
{
* @param identifier
* @return
*/
- public List<String> getIds(String identifier)
+ @SuppressWarnings("unchecked")
+ public List<String> getGeneIds(String identifier)
{
List<String> result = new ArrayList<String>();
List<String> ids = new ArrayList<String>();
ids.add(identifier);
-
+
String[] queries = identifier.split(getAccessionSeparator());
- BufferedReader br = null;
try
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
- if (taxon.isModelOrganism())
+ String geneId = null;/// parseSymbolResponse(br);
+ try
{
- URL url = getUrl(query, taxon);
- if (url != null)
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR,
+ null);
+ if (rvals == null)
+ continue;
+ while (rvals.hasNext())
{
- br = getHttpResponse(url, ids);
- }
- String geneId = parseResponse(br);
- if (geneId != null)
- {
- result.add(geneId);
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+ String id = val.get(JSON_ID).toString();
+ String type = val.get(TYPE).toString();
+ if (id != null && GENE.equals(type))
+ {
+ geneId = id;
+ break;
+ }
}
+ } catch (ParseException e)
+ {
+ // ignore
+ }
+
+ if (geneId != null && !result.contains(geneId))
+ {
+ result.add(geneId);
}
}
}
} catch (IOException e)
{
// ignore
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
return result;
}
git://source.jalview.org / jalview.git / blobdiff