X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=b412849f408a86f65bb639e64778d5f755ed873b;hb=ed96e73a6db654d52a6a1b1d27c2ee707876a4c7;hp=4c4328160db4877e59bc3044223f86e8ade59973;hpb=d38847f4c9170385c3b4c8fbc5e6f5c95a15a196;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index 4c43281..b412849 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -23,6 +23,8 @@ 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; @@ -32,7 +34,6 @@ 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; @@ -118,28 +119,66 @@ 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(JSONObject val) { - return (String) getResult(identifier, null, 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; } /** @@ -151,22 +190,29 @@ public class EnsemblLookup extends EnsemblRestClient */ public String getSpecies(String identifier) { - return (String) getResult(identifier, null, - 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 delegates parsing of the JSON - * response to the supplied parser + * Calls the /lookup/id rest service and returns the response as a JSONObject, + * or null if any error * * @param identifier * @param objectType * (optional) - * @param parser * @return */ - protected Object getResult(String identifier, String objectType, - Function parser) + protected JSONObject getResult(String identifier, String objectType) { List ids = Arrays.asList(new String[] { identifier }); @@ -174,14 +220,16 @@ public class EnsemblLookup extends EnsemblRestClient try { 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 { @@ -199,71 +247,6 @@ public class EnsemblLookup extends EnsemblRestClient } /** - * Answers the value of 'attribute' from the JSON response, or null if not - * found - * - * @param br - * @param attribute - * @return - */ - protected String getAttribute(BufferedReader br, String attribute) - { - 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; - } - - /** - * 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 br - * @return - */ - protected String parseGeneId(BufferedReader br) - { - String geneId = null; - JSONParser jp = new JSONParser(); - try - { - JSONObject val = (JSONObject) jp.parse(br); - 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 = (String) getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT, - reader -> parseGeneId(reader)); - } - } catch (ParseException | IOException e) - { - // ignore - } - return geneId; - } - - /** * Calls the /lookup/id rest service for the given id, and if successful, * parses and returns the gene's chromosomal coordinates * @@ -272,8 +255,7 @@ public class EnsemblLookup extends EnsemblRestClient */ public GeneLociI getGeneLoci(String geneId) { - return (GeneLociI) getResult(geneId, OBJECT_TYPE_GENE, - br -> parseGeneLoci(br)); + return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE)); } /** @@ -281,21 +263,24 @@ public class EnsemblLookup extends EnsemblRestClient * seq_region_name, start, end and returns an object that wraps them, or null * if unsuccessful * - * @param br + * @param json * @return */ - GeneLociI parseGeneLoci(BufferedReader br) + GeneLociI parseGeneLoci(JSONObject json) { - JSONParser jp = new JSONParser(); + if (json == null) + { + return null; + } + try { - JSONObject val = (JSONObject) jp.parse(br); - final String species = val.get("species").toString(); - final String assembly = val.get("assembly_name").toString(); - final String chromosome = val.get("seq_region_name").toString(); - String strand = val.get("strand").toString(); - int start = Integer.parseInt(val.get("start").toString()); - int end = Integer.parseInt(val.get("end").toString()); + 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; @@ -304,36 +289,11 @@ 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; - } - }; - } catch (ParseException | NullPointerException | IOException - | NumberFormatException | ClassCastException e) + 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()); e.printStackTrace();