JAL-3829 fixed up the 3d-beacons data columns definitions, tests and client.

diff --git a/resources/fts/tdbeacons_data_columns.txt b/resources/fts/tdbeacons_data_columns.txt
index 350b9e8..4eb9b98 100644 (file)
--- a/resources/fts/tdbeacons_data_columns.txt
+++ b/resources/fts/tdbeacons_data_columns.txt
@@ -40,11 +40,18 @@ _data_column.max_col_width
 _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
-Model id;model_identifier;String;g2;80;150;85;true;true
-Sequence;aligned_sequence;String;g1;80;150;85;true;true
-Provider;provider;String;g1;80;150;85;true;true
-Uniprot Id;id;String;g2;80;150;85;true;true
-UniProt Accession;uniprot_accession;String;g2;50;400;95;true;false
-Entry Name;entry_name;String;g2;100;150;105;true;true 
-Url;model_url;String;g1;100;150;105;true;true
+Model id;model_identifier;String;g2;80;150;85;true;false
+Sequence;aligned_sequence;String;g1;80;150;85;false;false
+Provider;provider;String;g1;80;150;85;true;false
+Uniprot Id;id;String;g2;80;150;85;false;false
+UniProt Accession;uniprot_accession;String;g2;50;400;95;false;true
+Entry Name;entry_name;String;g2;100;150;105;true;false 
+Url;model_url;String;g1;100;150;105;false;false
 Qmean;qmean_avg_local_score;double;g2;100;150;105;true;false
+Uniprot Start;uniprot_start;Integer;g3;3;8;3;true;false
+Uniprot End;uniprot_end;Integer;g3;3;8;3;true;false
+Resolution;resolution;double;g3;3;8;3;true;false
+Coverage;coverage;double;g3;3;8;3;true;false
+Sequence Identity;sequence_identity;Float;g3;3;8;3;false;false
+Model Category;model_category;String;g3;3;8;3;true;false
+Created Date;created;string;g3;3;8;3;true;false
\ No newline at end of file

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index b55d9b1..7a556b5 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -32,7 +32,7 @@ import jalview.util.Platform;
 public class TDBeaconsFTSRestClient extends FTSRestClient
 {
   private static final String DEFAULT_THREEDBEACONS_DOMAIN = 
-          "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
+          "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
   
   private static FTSRestClientI instance = null;
   
@@ -196,7 +196,7 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
         primaryKey = fieldData;
         summaryRowData[colCounter++] = primaryKey;
       }
-      else if (fieldData == null || fieldData.isEmpty())
+      else if (fieldData == null || fieldData.trim().isEmpty())
       {
         summaryRowData[colCounter++] = null;
       }

diff --git a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
index 0656d67..06e1869 100644 (file)
--- a/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
+++ b/test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
@@ -71,7 +71,7 @@ public class TDBeaconsFTSRestClientTest
     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
             .isEmpty());
     Assert.assertEquals(ftsRestClient
-            .getAllDefaultDisplayedFTSDataColumns().size(), 8);
+            .getAllDefaultDisplayedFTSDataColumns().size(), 10);
   }
   
   @Test(groups = { "Functional" })
@@ -85,10 +85,10 @@ public class TDBeaconsFTSRestClientTest
       Assert.assertEquals(foundIndex, -1);
       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
               false);
-      Assert.assertEquals(foundIndex, 1);
+      Assert.assertEquals(foundIndex, 0);
       foundIndex = ftsRestClient
               .getPrimaryKeyColumIndex(wantedFields, true);
-      Assert.assertEquals(foundIndex, 2);
+      Assert.assertEquals(foundIndex, 1);
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -105,7 +105,7 @@ public class TDBeaconsFTSRestClientTest
     String actual = ftsRestClient
             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
     Assert.assertEquals(actual,
-            "aligned_sequence,model_identifier,provider,id,uniprot_accession,entry_name,model_url,qmean_avg_local_score");
+            "model_identifier,provider,entry_name,qmean_avg_local_score,uniprot_start,uniprot_end,resolution,coverage,model_category,created");
   }
   
   @Test(groups = { "Functional" })
@@ -115,7 +115,7 @@ public class TDBeaconsFTSRestClientTest
             .getAllFTSDataColumns();
     Assert.assertNotNull(allFields);
     //System.out.println(allFields.size());
-    Assert.assertEquals(allFields.size(), 8);
+    Assert.assertEquals(allFields.size(), 15);
   }
   
   @Test(groups = { "Functional" })
@@ -126,7 +126,7 @@ public class TDBeaconsFTSRestClientTest
             .getSearchableDataColumns();
     Assert.assertNotNull(searchableFields);
     //System.out.println(searchableFields.size());
-    Assert.assertEquals(searchableFields.size(), 6); //only 1, as of first 3DB test
+    Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
   }
   
   @Test(groups = { "Functional" })
@@ -278,13 +278,19 @@ public class TDBeaconsFTSRestClientTest
     try
     {
       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
-              .getDataColumnByNameOrCode("Model_id"));
+              .getDataColumnByNameOrCode("Model Id"));
       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("model_url"));
       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("provider"));
       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+              .getDataColumnByNameOrCode("model_category"));
+      wantedFields.add(TDBeaconsFTSRestClient.getInstance()
               .getDataColumnByNameOrCode("qmean_avg_local_score"));
+      wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+              .getDataColumnByNameOrCode("uniprot_start"));
+      wantedFields.add(TDBeaconsFTSRestClient.getInstance()
+              .getDataColumnByNameOrCode("uniprot_end"));
     } catch (Exception e1)
     {
       e1.printStackTrace();
@@ -293,8 +299,8 @@ public class TDBeaconsFTSRestClientTest
 
     FTSRestRequest request = new FTSRestRequest();
     request.setResponseSize(100);
-    request.setFieldToSearchBy("P");
-    request.setSearchTerm("01318.json");
+    request.setFieldToSearchBy("");
+    request.setSearchTerm("P01318.json");
     request.setWantedFields(wantedFields);
     System.out.println("request : " + request.getFieldToSearchBy());
     //System.out.println(request.toString());