X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hb=9d80cca5113c0411aa06559d4bd3f86454459ce7;hp=f6b3a47b6c07e73a55d474db4a9bb22b6b85d1e7;hpb=48af50e7fa4ebb62e2cd629b01ffc8142fc7164d;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index f6b3a47..9b56d6b 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -23,18 +23,18 @@ 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; /** @@ -117,28 +117,66 @@ 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)); } /** - * Returns the gene id related to the given identifier (which may be for a - * gene, transcript or protein) + * 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(Map val) { - return parseGeneId(getResult(identifier, null)); + 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; } /** @@ -151,7 +189,7 @@ public class EnsemblLookup extends EnsemblRestClient public String getSpecies(String identifier) { String species = null; - JSONObject json = getResult(identifier, null); + Map json = getResult(identifier, null); if (json != null) { Object o = json.get(SPECIES); @@ -164,7 +202,7 @@ public class EnsemblLookup extends EnsemblRestClient } /** - * Calls the /lookup/id rest service and returns the response as a JSONObject, + * Calls the /lookup/id rest service and returns the response as a Map, * or null if any error * * @param identifier @@ -172,80 +210,24 @@ public class EnsemblLookup extends EnsemblRestClient * (optional) * @return */ - protected JSONObject getResult(String identifier, String objectType) + @SuppressWarnings("unchecked") + protected Map getResult(String identifier, String objectType) { List ids = Arrays.asList(new String[] { identifier }); - BufferedReader br = null; try { - URL url = getUrl(identifier, objectType); - if (url != null) - { - br = getHttpResponse(url, ids); - } - return br == null ? null : (JSONObject) (new JSONParser().parse(br)); - } catch (IOException | ParseException e) + return (Map) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null); + } + catch (IOException | ParseException e) { System.err.println("Error parsing " + identifier + " lookup response " + e.getMessage()); return null; - } finally - { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } } } /** - * 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, - * specifying that object_type should be Transcript. - * - * @param jsonObject - * @return - */ - protected String parseGeneId(JSONObject json) - { - if (json == null) - { - // e.g. lookup failed with 404 not found - return null; - } - - String geneId = null; - String type = json.get(OBJECT_TYPE).toString(); - if (OBJECT_TYPE_GENE.equalsIgnoreCase(type)) - { - // got the gene - just returns its id - geneId = json.get(JSON_ID).toString(); - } - else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type)) - { - // got the transcript - return its (Gene) Parent - geneId = json.get(PARENT).toString(); - } - else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type)) - { - // got the protein - look up its Parent, restricted to type Transcript - String transcriptId = json.get(PARENT).toString(); - geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT)); - } - - return geneId; - } - - /** * Calls the /lookup/id rest service for the given id, and if successful, * parses and returns the gene's chromosomal coordinates * @@ -265,7 +247,7 @@ public class EnsemblLookup extends EnsemblRestClient * @param json * @return */ - GeneLociI parseGeneLoci(JSONObject json) + GeneLociI parseGeneLoci(Map json) { if (json == null) { @@ -288,34 +270,10 @@ public class EnsemblLookup extends EnsemblRestClient fromEnd }); List toRange = Collections.singletonList(new int[] { toStart, toEnd }); - final MapList map = new MapList(fromRange, toRange, 1, 1); - return new GeneLociI() - { - - @Override - public String getSpeciesId() - { - return species == null ? "" : species; - } - - @Override - public String getAssemblyId() - { - return assembly; - } - - @Override - public String getChromosomeId() - { - return chromosome; - } - - @Override - public MapList getMap() - { - return map; - } - }; + final Mapping map = new Mapping( + new MapList(fromRange, toRange, 1, 1)); + return new GeneLocus(species == null ? "" : species, assembly, + chromosome, map); } catch (NullPointerException | NumberFormatException e) { Cache.log.error("Error looking up gene loci: " + e.getMessage());