JAL-3210 Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / ext / ensembl / EnsemblFeatures.java

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 99ebc69..e28cc7f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.JSONUtils;
+import jalview.util.Platform;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -35,10 +36,8 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 /**
@@ -92,16 +91,14 @@ class EnsemblFeatures extends EnsemblRestClient
   public AlignmentI getSequenceRecords(String query) throws IOException
   {
     // TODO: use a vararg String... for getSequenceRecords instead?
+         
     List<String> queries = new ArrayList<>();
     queries.add(query);
-    BufferedReader fp = getSequenceReader(queries);
-    if (fp == null)
-    {
-      return null;
-    }
-
-    SequenceI seq = parseFeaturesJson(fp);
+    SequenceI seq = parseFeaturesJson(queries);
+    if (seq == null)
+       return null;
     return new Alignment(new SequenceI[] { seq });
+
   }
 
   /**
@@ -111,20 +108,22 @@ class EnsemblFeatures extends EnsemblRestClient
    * @param br
    * @return
    */
-  private SequenceI parseFeaturesJson(BufferedReader br)
+  @SuppressWarnings("unchecked")
+  private SequenceI parseFeaturesJson(List<String> queries)
   {
     SequenceI seq = new Sequence("Dummy", "");
-
-    JSONParser jp = new JSONParser();
     try
     {
-      JSONArray responses = (JSONArray) jp.parse(br);
-      Iterator rvals = responses.iterator();
-      while (rvals.hasNext())
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+      if (rvals == null)
       {
+         return null;
+      }
+      while (rvals.hasNext())
+      {          
         try
         {
-          JSONObject obj = (JSONObject) rvals.next();
+          Map<String, Object> obj = (Map<String, Object>) rvals.next();
           String type = obj.get("feature_type").toString();
           int start = Integer.parseInt(obj.get("start").toString());
           int end = Integer.parseInt(obj.get("end").toString());
@@ -132,10 +131,10 @@ class EnsemblFeatures extends EnsemblRestClient
           String strand = obj.get("strand").toString();
           Object phase = obj.get("phase");
           String alleles = JSONUtils
-                  .arrayToList((JSONArray) obj.get("alleles"));
+                  .arrayToStringList((List<Object>) obj.get("alleles"));
           String clinSig = JSONUtils
-                  .arrayToList(
-                          (JSONArray) obj.get("clinical_significance"));
+                  .arrayToStringList(
+                          (List<Object>) obj.get("clinical_significance"));
 
           /*
            * convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
@@ -150,7 +149,7 @@ class EnsemblFeatures extends EnsemblRestClient
           {
             type = SequenceOntologyI.CDS;
           }
-          
+
           String desc = getFirstNotNull(obj, "alleles", "external_name",
                   JSON_ID);
           SequenceFeature sf = new SequenceFeature(type, desc, start, end,
@@ -167,6 +166,7 @@ class EnsemblFeatures extends EnsemblRestClient
           sf.setValue("clinical_significance", clinSig);
 
           seq.addSequenceFeature(sf);
+          
         } catch (Throwable t)
         {
           // ignore - keep trying other features
@@ -174,6 +174,7 @@ class EnsemblFeatures extends EnsemblRestClient
       }
     } catch (ParseException | IOException e)
     {
+       e.printStackTrace();
       // ignore
     }
 
@@ -189,17 +190,16 @@ class EnsemblFeatures extends EnsemblRestClient
    * @param keys
    * @return
    */
-  protected String getFirstNotNull(JSONObject obj, String... keys)
+  @SuppressWarnings("unchecked")
+  protected String getFirstNotNull(Map<String, Object> obj, String... keys)
   {
-    String desc = null;
-
     for (String key : keys)
     {
       Object val = obj.get(key);
       if (val != null)
       {
-        String s = val instanceof JSONArray
-                ? JSONUtils.arrayToList((JSONArray) val)
+        String s = val instanceof List<?>
+                ? JSONUtils.arrayToStringList((List<Object>) val)
                 : val.toString();
         if (!s.isEmpty())
         {
@@ -207,7 +207,7 @@ class EnsemblFeatures extends EnsemblRestClient
         }
       }
     }
-    return desc;
+    return null;
   }
 
   /**
@@ -218,7 +218,7 @@ class EnsemblFeatures extends EnsemblRestClient
    * @param obj
    * @param key
    */
-  protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+  protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
           String key)
   {
     Object object = obj.get(key);