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=e55605d92effa83d313b57fd886a1d4818b34d3d;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java index e55605d..e188986 100644 --- a/src/jalview/ext/ensembl/EnsemblLookup.java +++ b/src/jalview/ext/ensembl/EnsemblLookup.java @@ -20,21 +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.Map; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; /** @@ -47,17 +47,6 @@ import org.json.simple.parser.ParseException; public class EnsemblLookup extends EnsemblRestClient { private static final String SPECIES = "species"; - private static final String OBJECT_TYPE_TRANSLATION = "Translation"; - private static final String PARENT = "Parent"; - 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"; - - /** - * keep track of last identifier retrieved to break loops - */ - private String lastId; /** * Default constructor (to use rest.ensembl.org) @@ -128,28 +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; } /** @@ -162,7 +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); @@ -175,99 +202,33 @@ public class EnsemblLookup extends EnsemblRestClient } /** - * Calls the /lookup/id rest service and returns the response as a JSONObject, - * or null if any error + * Calls the /lookup/id rest service and returns the response as a Map, or null if any error * * @param identifier * @param objectType * (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 (identifier.equals(lastId)) - { - System.err.println("** Ensembl lookup " + url.toString() - + " looping on Parent!"); - return null; - } - - lastId = identifier; - - if (url != null) - { - br = getHttpResponse(url, ids); - } - return br == null ? null : (JSONObject) (new JSONParser().parse(br)); + return (Map) getJSON(getUrl(identifier, objectType), + ids, -1, MODE_MAP, null); } catch (IOException | ParseException e) { - System.err.println("Error parsing " + identifier + " lookup response " + jalview.bin.Console.errPrintln("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 * @@ -287,7 +248,7 @@ public class EnsemblLookup extends EnsemblRestClient * @param json * @return */ - GeneLociI parseGeneLoci(JSONObject json) + GeneLociI parseGeneLoci(Map json) { if (json == null) { @@ -306,41 +267,19 @@ public class EnsemblLookup extends EnsemblRestClient 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; - } - }; + 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;