X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hb=9d80cca5113c0411aa06559d4bd3f86454459ce7;hp=eb8f90ee738dcb1391137e6d0e755284df00bdf4;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index eb8f90e..9b56d6b 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -20,28 +20,33 @@ */ 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.Map; -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. + * 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 - * */ public class EnsemblLookup extends EnsemblRestClient { + private static final String SPECIES = "species"; /** * Default constructor (to use rest.ensembl.org) @@ -77,17 +82,26 @@ public class EnsemblLookup extends EnsemblRestClient protected URL getUrl(List 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=application/json"; + + CONTENT_TYPE_JSON; + if (objectType != null) + { + url += "&" + OBJECT_TYPE + "=" + objectType; + } + try { return new URL(url); @@ -103,78 +117,169 @@ public class EnsemblLookup extends EnsemblRestClient 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)); + } + + /** + * 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 br + * @return + */ + protected String parseGeneId(Map val) + { + 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; } /** - * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the + * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the * given identifier, or null if not found * * @param identifier * @return */ - public String getParent(String identifier) + public String getSpecies(String identifier) + { + String species = null; + Map 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 Map, + * or null if any error + * + * @param identifier + * @param objectType + * (optional) + * @return + */ + @SuppressWarnings("unchecked") + protected Map getResult(String identifier, String objectType) { 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) + return (Map) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null); + } + catch (IOException | ParseException e) { - // ignore + System.err.println("Error parsing " + identifier + " lookup response " + + e.getMessage()); 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 + * Calls the /lookup/id rest service for the given id, and if successful, + * parses and returns the gene's chromosomal coordinates * - * @param br + * @param geneId + * @return + */ + public GeneLociI getGeneLoci(String geneId) + { + return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE)); + } + + /** + * 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 json * @return - * @throws IOException */ - protected String parseResponse(BufferedReader br) throws IOException + GeneLociI parseGeneLoci(Map json) { - String parent = null; - JSONParser jp = new JSONParser(); + if (json == null) + { + return null; + } + try { - JSONObject val = (JSONObject) jp.parse(br); - parent = val.get("Parent").toString(); - } catch (ParseException 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 fromRange = Collections.singletonList(new int[] { 1, + fromEnd }); + List 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 parent; + return null; } }