JAL-3829 attempt to fix my changes to follow the Jira issue

[jalview.git] / src / jalview / fts / service / threedbeacons / TDBeaconsFTSRestClient.java

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index 884dced..7c06f05 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -143,7 +143,6 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
           Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
   {
     FTSRestResponse searchResult = new FTSRestResponse();
-    //searchResult.setNumberOfItemsFound(1);
     List<FTSData> result = null;
     
     try
@@ -152,28 +151,26 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       {
         jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
       }
-      System.out.println(jsonObj);
-      //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
       
-      //System.out.println((Map<String, Object>) jsonObj.get("uniprot_entry")); 
+      Object uniprot_entry = jsonObj.get("uniprot_entry"); 
       Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
-      System.out.println(seqLength);
-      result = new ArrayList<>();
+      //System.out.println(uniprot_entry);
+      //System.out.println(jsonObj);
+      //System.out.println("seqLenght :" + seqLength);
+      
+      //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
       List<Object> structures = (List<Object>) jsonObj.get("structures");
-      //System.out.println(jsonObj.get("structures"));
-      //System.out.println(structures);
-      System.out.println("ZERO : " + structures.get(0));
-      System.out.println("1 : " + structures.get(1));
+      result = new ArrayList<>();
+      
       int numFound = 0;
-      for (Iterator<Object> strucIter = structures.iterator(); strucIter
-              .hasNext();)
+      for (Iterator<Object> strucIter = structures.iterator(); strucIter.hasNext();)
       {
         Map<String, Object> structure = (Map<String, Object>) strucIter.next();
         result.add(getFTSData(structure, tdbRestRequest));
         numFound++;
         //System.out.println(structure);
       }
-      //System.out.println(structures);
+      
       System.out.println("1 : " + structures.get(1));
       searchResult.setNumberOfItemsFound(numFound); 
       searchResult.setSearchSummary(result);
@@ -195,9 +192,12 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
     Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
     int colCounter = 0;
     summaryRowData = new Object[displayFields.size()];
+    
     for (FTSDataColumnI field : displayFields) {
+      System.out.println("Field " + field);
       String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " " 
               : tdbJsonStructure.get(field.getCode()).toString();
+      System.out.println("Field Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
@@ -220,7 +220,7 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
                                           : fieldData;
         } catch (Exception e)
         {
-          e.printStackTrace();
+          //e.printStackTrace();
           System.out.println("offending value:" + fieldData);
         }
       }