X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=f96f1d5a4f36ad9c42349782b9031477365678c6;hp=9229379788f2661c7b380d0a465ab2d12d55a482;hb=f59dd9efbb3dfc313ab0b0507832e21cd0076fe1;hpb=035d24444cbba067a84958c75fba709d54b6f1c2

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 9229379..f96f1d5 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -28,12 +28,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.exceptions.JalviewException;
-import jalview.io.FastaFile;
-import jalview.io.FileParse;
 import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
@@ -42,6 +41,7 @@ import jalview.util.DBRefUtils;
 import jalview.util.IntRangeComparator;
 import jalview.util.MapList;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -50,6 +50,10 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
 /**
  * Base class for Ensembl sequence fetchers
  * 
@@ -385,50 +389,44 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       inProgress = false;
       throw new JalviewException("ENSEMBL Rest API not available.");
     }
-    FileParse fp = getSequenceReader(ids);
-    if (fp == null)
+    BufferedReader br = getSequenceReader(ids);
+    if (br == null)
     {
       return alignment;
     }
 
-    FastaFile fr = new FastaFile(fp);
-    if (fr.hasWarningMessage())
+    List<SequenceI> seqs = parseSequenceJson(br);
+
+    if (seqs.isEmpty())
     {
-      System.out.println(
-              String.format("Warning when retrieving %d ids %s\n%s",
-                      ids.size(), ids.toString(), fr.getWarningMessage()));
+      throw new IOException("No data returned for " + ids);
     }
-    else if (fr.getSeqs().size() != ids.size())
+
+    if (seqs.size() != ids.size())
     {
       System.out.println(String.format(
               "Only retrieved %d sequences for %d query strings",
-              fr.getSeqs().size(), ids.size()));
+              seqs.size(), ids.size()));
     }
 
-    if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0)
+    if (!seqs.isEmpty())
     {
-      /*
-       * POST request has returned an empty FASTA file e.g. for invalid id
-       */
-      throw new IOException("No data returned for " + ids);
-    }
-
-    if (fr.getSeqs().size() > 0)
-    {
-      AlignmentI seqal = new Alignment(fr.getSeqsAsArray());
-      for (SequenceI sq : seqal.getSequences())
+      AlignmentI seqal = new Alignment(
+              seqs.toArray(new SequenceI[seqs.size()]));
+      for (SequenceI seq : seqs)
       {
-        if (sq.getDescription() == null)
+        if (seq.getDescription() == null)
         {
-          sq.setDescription(getDbName());
+          seq.setDescription(getDbName());
         }
-        String name = sq.getName();
+        String name = seq.getName();
         if (ids.contains(name)
                 || ids.contains(name.replace("ENSP", "ENST")))
         {
-          DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
+          // TODO JAL-3077 use true accession version in dbref
+          DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
                   getEnsemblDataVersion(), name);
-          sq.addDBRef(dbref);
+          seq.addDBRef(dbref);
         }
       }
       if (alignment == null)
@@ -444,6 +442,49 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
+   * Parses a JSON response into a list of sequences
+   * 
+   * @param br
+   * @return
+   * @see http://rest.ensembl.org/documentation/info/sequence_id
+   */
+  protected List<SequenceI> parseSequenceJson(BufferedReader br)
+  {
+    JSONParser jp = new JSONParser();
+    List<SequenceI> result = new ArrayList<>();
+    try
+    {
+      /*
+       * for now, assumes only one sequence returned; refactor if needed
+       * in future to handle a JSONArray with more than one
+       */
+      final JSONObject val = (JSONObject) jp.parse(br);
+      Object s = val.get("desc");
+      String desc = s == null ? null : s.toString();
+      s = val.get("id");
+      String id = s == null ? null : s.toString();
+      s = val.get("seq");
+      String seq = s == null ? null : s.toString();
+      Sequence sequence = new Sequence(id, seq);
+      if (desc != null)
+      {
+        sequence.setDescription(desc);
+      }
+      // todo JAL-3077 make a DBRefEntry with true accession version
+      // s = val.get("version");
+      // String version = s == null ? "0" : s.toString();
+      // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id);
+      // sequence.addDBRef(dbref);
+      result.add(sequence);
+    } catch (ParseException | IOException e)
+    {
+      System.err.println("Error processing JSON response: " + e.toString());
+      // ignore
+    }
+    return result;
+  }
+
+  /**
    * Returns the URL for the REST call
    * 
    * @return
@@ -464,7 +505,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     }
     // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
     urlstring.append("?type=").append(getSourceEnsemblType().getType());
-    urlstring.append(("&Accept=text/x-fasta"));
+    urlstring.append(("&Accept=application/json"));
+    urlstring.append(("&Content-Type=application/json"));
 
     String objectType = getObjectType();
     if (objectType != null)
@@ -504,18 +546,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     return false;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return multipleIds ? "application/json" : "text/x-fasta";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "text/x-fasta";
-  }
-
   /**
    * 
    * @return the configured sequence return type for this source
@@ -656,6 +686,20 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
           String accId);
 
   /**
+   * Answers a list of sequence features that mark positions of the genomic
+   * sequence feature which are within the sequence being retrieved. For
+   * example, an 'exon' feature whose parent is the target transcript marks the
+   * cdna positions of the transcript. For a gene sequence, this is trivially
+   * just the 'gene' feature with matching gene id.
+   * 
+   * @param seq
+   * @param accId
+   * @return
+   */
+  protected abstract List<SequenceFeature> getIdentifyingFeatures(
+          SequenceI seq, String accId);
+
+  /**
    * Transfers the sequence feature to the target sequence, locating its start
    * and end range based on the mapping. Features which do not overlap the
    * target sequence are ignored.