X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=e188986f3fc4b0bf03d319ab497b2b765932cb46;hb=refs%2Fheads%2Fspike%2FJAL-4047%2FJAL-4048_columns_in_sequenceID;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..e188986 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -20,22 +20,21 @@ */ package jalview.ext.ensembl; -import jalview.bin.Cache; +import jalview.bin.Console; 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 java.util.Map; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; /** @@ -118,149 +117,115 @@ public class EnsemblLookup extends EnsemblRestClient return true; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return "application/json"; - } - - @Override - protected String getResponseMimeType() - { - return "application/json"; - } - /** * Returns the gene id related to the given identifier (which may be for a - * gene, transcript or protein) + * gene, transcript or protein), or null if none is found * * @param identifier * @return */ public String getGeneId(String identifier) { - return (String) getResult(identifier, null, br -> parseGeneId(br)); + return getGeneId(identifier, null); } /** - * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the - * given identifier, or null if not found + * 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 getSpecies(String identifier) + public String getGeneId(String identifier, String objectType) { - return (String) getResult(identifier, null, - br -> getAttribute(br, SPECIES)); + return parseGeneId(getResult(identifier, objectType)); } /** - * Calls the /lookup/id rest service and delegates parsing of the JSON - * response to the supplied parser + * 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 objectType - * (optional) - * @param parser + * @param br * @return */ - protected Object getResult(String identifier, String objectType, - Function parser) + protected String parseGeneId(Map val) { - List ids = Arrays.asList(new String[] { identifier }); - - BufferedReader br = null; - try + if (val == null) { - URL url = getUrl(identifier, objectType); - if (url != null) - { - br = getHttpResponse(url, ids); - } - return br == null ? null : parser.apply(br); - } catch (IOException e) - { - // ignore return null; - } finally + } + String geneId = null; + String type = val.get(OBJECT_TYPE).toString(); + if (OBJECT_TYPE_GENE.equalsIgnoreCase(type)) { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + // 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; } /** - * Answers the value of 'attribute' from the JSON response, or null if not - * found + * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the + * given identifier, or null if not found * - * @param br - * @param attribute + * @param identifier * @return */ - protected String getAttribute(BufferedReader br, String attribute) + public String getSpecies(String identifier) { - String value = null; - JSONParser jp = new JSONParser(); - try + String species = null; + Map json = getResult(identifier, null); + if (json != null) { - JSONObject val = (JSONObject) jp.parse(br); - value = val.get(attribute).toString(); - } catch (ParseException | NullPointerException | IOException e) - { - // ignore + Object o = json.get(SPECIES); + if (o != null) + { + species = o.toString(); + } } - return value; + return species; } /** - * 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. + * Calls the /lookup/id rest service and returns the response as a Map, or null if any error * - * @param br + * @param identifier + * @param objectType + * (optional) * @return */ - protected String parseGeneId(BufferedReader br) + @SuppressWarnings("unchecked") + protected Map getResult(String identifier, + String objectType) { - String geneId = null; - JSONParser jp = new JSONParser(); + List ids = Arrays.asList(new String[] { identifier }); + 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) + return (Map) getJSON(getUrl(identifier, objectType), + ids, -1, MODE_MAP, null); + } catch (IOException | ParseException e) { - // ignore + jalview.bin.Console.errPrintln("Error parsing " + identifier + " lookup response " + + e.getMessage()); + return null; } - return geneId; } /** @@ -272,8 +237,7 @@ 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)); } /** @@ -281,61 +245,41 @@ 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(Map 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; int toEnd = reverseStrand ? start : end; - List fromRange = Collections.singletonList(new int[] { 1, - 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) + 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) { - Cache.log.error("Error looking up gene loci: " + e.getMessage()); + Console.error("Error looking up gene loci: " + e.getMessage()); e.printStackTrace(); } return null;