*/
package jalview.ext.ensembl;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
+import jalview.util.MapList;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
-import java.util.function.Function;
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
+ * A client for the Ensembl /lookup REST endpoint, used to find the gene
+ * identifier given a gene, transcript or protein identifier, or to extract the
+ * species or chromosomal coordinates from the same service response
*
* @author gmcarstairs
*/
{
private static final String SPECIES = "species";
- private static final String PARENT = "Parent";
-
- private static final String OBJECT_TYPE_TRANSLATION = "Translation";
- private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
- private static final String ID = "id";
- private static final String OBJECT_TYPE_GENE = "Gene";
- private static final String OBJECT_TYPE = "object_type";
-
/**
* Default constructor (to use rest.ensembl.org)
*/
protected URL getUrl(List<String> ids) throws MalformedURLException
{
String identifier = ids.get(0);
- return getUrl(identifier);
+ return getUrl(identifier, null);
}
/**
+ * Gets the url for lookup of the given identifier, optionally with objectType
+ * also specified in the request
+ *
* @param identifier
+ * @param objectType
* @return
*/
- protected URL getUrl(String identifier)
+ protected URL getUrl(String identifier, String objectType)
{
String url = getDomain() + "/lookup/id/" + identifier
+ CONTENT_TYPE_JSON;
+ if (objectType != null)
+ {
+ url += "&" + OBJECT_TYPE + "=" + objectType;
+ }
+
try
{
return new URL(url);
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
+ /**
+ * Returns the gene id related to the given identifier (which may be for a
+ * gene, transcript or protein), or null if none is found
+ *
+ * @param identifier
+ * @return
+ */
+ public String getGeneId(String identifier)
{
- return "application/json";
+ return getGeneId(identifier, null);
}
- @Override
- protected String getResponseMimeType()
+ /**
+ * Returns the gene id related to the given identifier (which may be for a
+ * gene, transcript or protein), or null if none is found
+ *
+ * @param identifier
+ * @param objectType
+ * @return
+ */
+ public String getGeneId(String identifier, String objectType)
{
- return "application/json";
+ return parseGeneId(getResult(identifier, objectType));
}
/**
- * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
- * given identifier, or null if not found
+ * Parses the JSON response and returns the gene identifier, or null if not
+ * found. If the returned object_type is Gene, returns the id, if Transcript
+ * returns the Parent. If it is Translation (peptide identifier), then the
+ * Parent is the transcript identifier, so we redo the search with this value.
*
- * @param identifier
+ * @param br
* @return
*/
- public String getGeneId(String identifier)
+ protected String parseGeneId(JSONObject val)
{
- return getResult(identifier, br -> parseGeneId(br));
+ if (val == null)
+ {
+ return null;
+ }
+ String geneId = null;
+ String type = val.get(OBJECT_TYPE).toString();
+ if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+ {
+ // got the gene - just returns its id
+ geneId = val.get(JSON_ID).toString();
+ }
+ else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+ {
+ // got the transcript - return its (Gene) Parent
+ geneId = val.get(PARENT).toString();
+ }
+ else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+ {
+ // got the protein - get its Parent, restricted to type Transcript
+ String transcriptId = val.get(PARENT).toString();
+ geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+ }
+
+ return geneId;
}
/**
*/
public String getSpecies(String identifier)
{
- return getResult(identifier, br -> getAttribute(br, SPECIES));
+ String species = null;
+ JSONObject json = getResult(identifier, null);
+ if (json != null)
+ {
+ Object o = json.get(SPECIES);
+ if (o != null)
+ {
+ species = o.toString();
+ }
+ }
+ return species;
}
/**
+ * Calls the /lookup/id rest service and returns the response as a JSONObject,
+ * or null if any error
+ *
* @param identifier
- * @param attribute
+ * @param objectType
+ * (optional)
* @return
*/
- protected String getResult(String identifier,
- Function<BufferedReader, String> parser)
+ protected JSONObject getResult(String identifier, String objectType)
{
List<String> ids = Arrays.asList(new String[] { identifier });
BufferedReader br = null;
try
{
- URL url = getUrl(identifier);
+ URL url = getUrl(identifier, objectType);
+
if (url != null)
{
br = getHttpResponse(url, ids);
}
- return br == null ? null : parser.apply(br);
- } catch (IOException e)
+ return br == null ? null : (JSONObject) (new JSONParser().parse(br));
+ } catch (IOException | ParseException e)
{
- // ignore
+ System.err.println("Error parsing " + identifier + " lookup response "
+ + e.getMessage());
return null;
} finally
{
}
/**
- * Answers the value of 'attribute' from the JSON response, or null if not
- * found
+ * Calls the /lookup/id rest service for the given id, and if successful,
+ * parses and returns the gene's chromosomal coordinates
*
- * @param br
- * @param attribute
+ * @param geneId
* @return
*/
- protected String getAttribute(BufferedReader br, String attribute)
+ public GeneLociI getGeneLoci(String geneId)
{
- String value = null;
- JSONParser jp = new JSONParser();
- try
- {
- JSONObject val = (JSONObject) jp.parse(br);
- value = val.get(attribute).toString();
- } catch (ParseException | NullPointerException | IOException e)
- {
- // ignore
- }
- return value;
+ return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
}
/**
- * Parses the JSON response and returns the gene identifier, or null if not
- * found. If the returned object_type is Gene, returns the id, if Transcript
- * returns the Parent. If it is Translation (peptide identifier), then the
- * Parent is the transcript identifier, so we redo the search with this value.
+ * Parses the /lookup/id response for species, asssembly_name,
+ * seq_region_name, start, end and returns an object that wraps them, or null
+ * if unsuccessful
*
- * @param br
+ * @param json
* @return
*/
- protected String parseGeneId(BufferedReader br)
+ GeneLociI parseGeneLoci(JSONObject json)
{
- String geneId = null;
- JSONParser jp = new JSONParser();
+ if (json == null)
+ {
+ return null;
+ }
+
try
{
- JSONObject val = (JSONObject) jp.parse(br);
- String type = val.get(OBJECT_TYPE).toString();
- if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
- {
- geneId = val.get(ID).toString();
- }
- else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
- {
- geneId = val.get(PARENT).toString();
- }
- else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
- {
- String transcriptId = val.get(PARENT).toString();
- try
- {
- geneId = getGeneId(transcriptId);
- } catch (StackOverflowError e)
- {
- /*
- * unlikely data condition error!
- */
- System.err
- .println("** Ensembl lookup "
- + getUrl(transcriptId).toString()
- + " looping on Parent!");
- }
- }
- } catch (ParseException | IOException e)
+ final String species = json.get("species").toString();
+ final String assembly = json.get("assembly_name").toString();
+ final String chromosome = json.get("seq_region_name").toString();
+ String strand = json.get("strand").toString();
+ int start = Integer.parseInt(json.get("start").toString());
+ int end = Integer.parseInt(json.get("end").toString());
+ int fromEnd = end - start + 1;
+ boolean reverseStrand = "-1".equals(strand);
+ int toStart = reverseStrand ? end : start;
+ int toEnd = reverseStrand ? start : end;
+ List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+ fromEnd });
+ List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+ toEnd });
+ final Mapping map = new Mapping(
+ new MapList(fromRange, toRange, 1, 1));
+ return new GeneLocus(species == null ? "" : species, assembly,
+ chromosome, map);
+ } catch (NullPointerException | NumberFormatException e)
{
- // ignore
+ Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ e.printStackTrace();
}
- return geneId;
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff