/*
* 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.ext.ensembl;
import jalview.datamodel.AlignmentI;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
import java.util.List;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
* A client for the Ensembl lookup REST endpoint; used to find the Parent gene
* identifier given a transcript identifier.
*
* @author gmcarstairs
*
*/
public class EnsemblLookup extends EnsemblRestClient
{
/**
* Default constructor (to use rest.ensembl.org)
*/
public EnsemblLookup()
{
super();
}
/**
* Constructor given the target domain to fetch data from
*
* @param
*/
public EnsemblLookup(String d)
{
super(d);
}
@Override
public String getDbName()
{
return "ENSEMBL";
}
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
return null;
}
@Override
protected URL getUrl(List ids) throws MalformedURLException
{
String identifier = ids.get(0);
return getUrl(identifier);
}
/**
* @param identifier
* @return
*/
protected URL getUrl(String identifier)
{
String url = getDomain() + "/lookup/id/" + identifier
+ "?content-type=application/json";
try
{
return new URL(url);
} catch (MalformedURLException e)
{
return null;
}
}
@Override
protected boolean useGetRequest()
{
return true;
}
@Override
protected String getRequestMimeType(boolean multipleIds)
{
return "application/json";
}
@Override
protected String getResponseMimeType()
{
return "application/json";
}
/**
* Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
* given identifier, or null if not found
*
* @param identifier
* @return
*/
public String getParent(String identifier)
{
List ids = Arrays.asList(new String[] { identifier });
BufferedReader br = null;
try
{
URL url = getUrl(identifier);
if (url != null)
{
br = getHttpResponse(url, ids);
}
return (parseResponse(br));
} catch (IOException e)
{
// ignore
return null;
} finally
{
if (br != null)
{
try
{
br.close();
} catch (IOException e)
{
// ignore
}
}
}
}
/**
* Parses "Parent" from the JSON response and returns the value, or null if
* not found
*
* @param br
* @return
* @throws IOException
*/
protected String parseResponse(BufferedReader br) throws IOException
{
String parent = null;
JSONParser jp = new JSONParser();
try
{
JSONObject val = (JSONObject) jp.parse(br);
parent = val.get("Parent").toString();
} catch (ParseException e)
{
// ignore
}
return parent;
}
}