X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fthreedbeacons%2FTDBeaconsFTSRestClient.java;h=ac02a5fa1705775e9bd87b2800e70e6cf34ce46f;hb=d654b1f014790b7ae25e6eec631847170a930987;hp=9c6f45a2df3c6af21969770861d72a57c1f75eb1;hpb=a848ed8eb380e5f9d915b0d7a062feec4f9d3dad;p=jalview.git

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index 9c6f45a..ac02a5f 100644
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.service.threedbeacons;
 
 import java.net.URI;
@@ -21,25 +41,37 @@ import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
 import jalview.fts.core.FTSRestClient;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 public class TDBeaconsFTSRestClient extends FTSRestClient
+        implements StructureFTSRestClientI
 {
-  private static final String DEFAULT_THREEDBEACONS_DOMAIN = 
-          "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
-  
-  private static FTSRestClientI instance = null;
-  
+  /**
+   * production server URI
+   */
+  private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+  /**
+   * dev server URI
+   */
+  private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+  private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
+
+  public static FTSRestClientI instance = null;
+
   protected TDBeaconsFTSRestClient()
-  {   
+  {
   }
-  
+
   @SuppressWarnings("unchecked")
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
@@ -47,8 +79,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
   {
     try
     {
-      String query = tdbRestRequest.getFieldToSearchBy()
-              + tdbRestRequest.getSearchTerm();
+      String query = tdbRestRequest.getSearchTerm();
       Client client;
       Class<ClientResponse> clientResponseClass;
       if (Platform.isJS())
@@ -60,29 +91,41 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
       else
       /**
        * Java only
+       * 
        * @j2sIgnore
        */
       {
         client = Client.create(new DefaultClientConfig());
         clientResponseClass = ClientResponse.class;
       }
+
       WebResource webResource;
-      webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN)
-              .path(query);
+      webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
+
       URI uri = webResource.getURI();
       System.out.println(uri.toString());
-        
+
       // Execute the REST request
-      ClientResponse clientResponse = webResource
-              .accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
-  
+      ClientResponse clientResponse;
+      if (isMocked())
+      {
+        clientResponse = null;
+      }
+      else
+      {
+        clientResponse = webResource.accept(MediaType.APPLICATION_JSON)
+                .get(clientResponseClass);
+      }
+
       // Get the JSON string from the response object or directly from the
       // client (JavaScript)
       Map<String, Object> jsonObj = null;
       String responseString = null;
-  
+
       // Check the response status and report exception if one occurs
-      int responseStatus = clientResponse.getStatus();
+      int responseStatus = isMocked()
+              ? (mockQueries.containsKey(query) ? 200 : 404)
+              : clientResponse.getStatus();
       switch (responseStatus)
       {
       // if success
@@ -93,89 +136,106 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
         }
         else
         {
-          responseString = clientResponse.getEntity(String.class);
+          responseString = isMocked() ? mockQueries.get(query)
+                  : clientResponse.getEntity(String.class);
         }
         break;
       case 400:
         throw new Exception(parseJsonExceptionString(responseString));
+      case 404:
+        return emptyTDBeaconsJsonResponse();
       default:
         throw new Exception(
                 getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
       }
       // Process the response and return the result to the caller.
-      return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
+      return parseTDBeaconsJsonResponse(responseString, jsonObj,
+              tdbRestRequest);
     } catch (Exception e)
     {
       String exceptionMsg = e.getMessage();
-      if (exceptionMsg.contains("SocketException"))
-      {
-        // No internet connection
-        throw new Exception(MessageManager.getString(
-                "exception.unable_to_detect_internet_connection"));
-      }
-      else if (exceptionMsg.contains("UnknownHostException"))
+      if (exceptionMsg != null)
       {
-        // The server is unreachable
-        throw new Exception(MessageManager.formatMessage(
-                "exception.fts_server_unreachable", "3DB Hub"));
-      }
-      else
-      {
-        throw e;
+        if (exceptionMsg.contains("SocketException"))
+        {
+          // No internet connection
+          throw new Exception(MessageManager.getString(
+                  "exception.unable_to_detect_internet_connection"));
+        }
+        else if (exceptionMsg.contains("UnknownHostException"))
+        {
+          // The server is unreachable
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.fts_server_unreachable", "3DB Hub"));
+        }
       }
+      throw e;
+
     }
-      
+
   }
-  
-  public String setSearchTerm(String term) {
+
+  /**
+   * returns response for when the 3D-Beacons service doesn't have a record for
+   * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
+   * 
+   * @return null
+   */
+  private FTSRestResponse emptyTDBeaconsJsonResponse()
+  {
+    return null;
+  }
+
+  public String setSearchTerm(String term)
+  {
     return term;
   }
-  
+
   public static FTSRestResponse parseTDBeaconsJsonResponse(
           String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
   {
     return parseTDBeaconsJsonResponse(tdbJsonResponseString,
             (Map<String, Object>) null, tdbRestRequest);
   }
-  
+
   @SuppressWarnings("unchecked")
-  public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString,
-          Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
+  public static FTSRestResponse parseTDBeaconsJsonResponse(
+          String tdbJsonResponseString, Map<String, Object> jsonObj,
+          FTSRestRequest tdbRestRequest)
   {
     FTSRestResponse searchResult = new FTSRestResponse();
     List<FTSData> result = null;
-    
+
     try
     {
       if (jsonObj == null)
       {
-        jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
+        jsonObj = (Map<String, Object>) JSONUtils
+                .parse(tdbJsonResponseString);
       }
-      
-      Object uniprot_entry = jsonObj.get("uniprot_entry"); 
-      Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
-      //System.out.println(uniprot_entry);
-      //System.out.println(jsonObj);
-      //System.out.println("seqLenght :" + seqLength);
-      
-      //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
+
+      Object uniprot_entry = jsonObj.get("uniprot_entry");
+      // TODO: decide if anything from uniprot_entry needs to be reported via
+      // the FTSRestResponse object
+      // Arnaud added seqLength = (Long) ((Map<String, Object>)
+      // jsonObj.get("uniprot_entry")).get("sequence_length");
+
       List<Object> structures = (List<Object>) jsonObj.get("structures");
       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();
+        Map<String, Object> structure = (Map<String, Object>) strucIter
+                .next();
         result.add(getFTSData(structure, tdbRestRequest));
         numFound++;
-        //System.out.println(structure);
       }
-      
-      //System.out.println("1 : " + structures.get(1));
-      searchResult.setNumberOfItemsFound(numFound); 
+
+      searchResult.setNumberOfItemsFound(numFound);
       searchResult.setSearchSummary(result);
-      searchResult.setSequenceLength(seqLength);
-        
+
     } catch (ParseException e)
     {
       e.printStackTrace();
@@ -183,30 +243,43 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
     return searchResult;
   }
 
-private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+  private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
           FTSRestRequest tdbRequest)
   {
-    // TODO Auto-generated method stub
     String primaryKey = null;
     Object[] summaryRowData;
+
+    SequenceI associatedSequence;
+
     Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
+    SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
     int colCounter = 0;
-    summaryRowData = new Object[displayFields.size()];
-    
-    for (FTSDataColumnI field : displayFields) {
-      String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " " 
+    summaryRowData = new Object[(associatedSeq != null)
+            ? displayFields.size() + 1
+            : displayFields.size()];
+    if (associatedSeq != null)
+    {
+      associatedSequence = associatedSeq;
+      summaryRowData[0] = associatedSequence;
+      colCounter = 1;
+    }
+
+    for (FTSDataColumnI field : displayFields)
+    {
+      String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
+              ? " "
               : tdbJsonStructure.get(field.getCode()).toString();
-      System.out.println("Field : " + field + "  Data : " + fieldData);
+      // System.out.println("Field : " + field + " Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;
         summaryRowData[colCounter++] = primaryKey;
       }
-      else if (fieldData == null || fieldData.isEmpty())
+      else if (fieldData == null || fieldData.trim().isEmpty())
       {
         summaryRowData[colCounter++] = null;
       }
-      else 
+      else
       {
         try
         {
@@ -219,75 +292,31 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
                                           : fieldData;
         } catch (Exception e)
         {
-          //e.printStackTrace();
+          // e.printStackTrace();
           System.out.println("offending value:" + fieldData + fieldData);
         }
       }
     }
     final String primaryKey1 = primaryKey;
     final Object[] summaryRowData1 = summaryRowData;
-    
-    return new FTSData()
-    {
-
-      @Override
-      public Object[] getSummaryData()
-      {
-        return summaryRowData1;
-      }
-
-      @Override
-      public Object getPrimaryKey()
-      {
-        return primaryKey1;
-      }
-      
-      /**
-       * Returns a string representation of this object;
-       */
-      @Override
-      public String toString()
-      {
-        StringBuilder summaryFieldValues = new StringBuilder();
-        for (Object summaryField : summaryRowData1)
-        {
-          summaryFieldValues.append(
-                  summaryField == null ? " " : summaryField.toString())
-                  .append("\t");
-        }
-        return summaryFieldValues.toString();
-      }
-      
-      /**
-       * Returns hash code value for this object
-       */
-      @Override
-      public int hashCode()
-      {
-        return Objects.hash(primaryKey1, this.toString());
-      }
 
-      @Override
-      public boolean equals(Object that)
-      {
-        return this.toString().equals(that.toString());
-      }
-    };
+    return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1);
   }
 
-//  private static FTSData getFTSData(Map<String, Object> doc,
-//          FTSRestRequest tdbRestRequest)
-//  {
-//    String primaryKey = null;
-//
-//    Object[] summaryRowData;
-//
-//    Collection<FTSDataColumnI> displayFields = tdbRestRequest.getWantedFields();
-//    int colCounter = 0;
-//    summaryRowData = new Object[displayFields.size() + 1];
-// 
-//    return null;
-//  }
+  // private static FTSData getFTSData(Map<String, Object> doc,
+  // FTSRestRequest tdbRestRequest)
+  // {
+  // String primaryKey = null;
+  //
+  // Object[] summaryRowData;
+  //
+  // Collection<FTSDataColumnI> displayFields =
+  // tdbRestRequest.getWantedFields();
+  // int colCounter = 0;
+  // summaryRowData = new Object[displayFields.size() + 1];
+  //
+  // return null;
+  // }
 
   private String parseJsonExceptionString(String jsonErrorString)
   {
@@ -300,7 +329,7 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
   {
     return "/fts/tdbeacons_data_columns.txt";
   }
-  
+
   public static FTSRestClientI getInstance()
   {
     if (instance == null)
@@ -309,7 +338,7 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
     }
     return instance;
   }
-  
+
   private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
 
   public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
@@ -323,5 +352,26 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
     }
     return allDefaultDisplayedStructureDataColumns;
   }
-  
+
+  @Override
+  public String[] getPreferencesColumnsFor(PreferenceSource source)
+  {
+    String[] columnNames = null;
+    switch (source)
+    {
+    case SEARCH_SUMMARY:
+      columnNames = new String[] { "", "Display", "Group" };
+      break;
+    case STRUCTURE_CHOOSER:
+      columnNames = new String[] { "", "Display", "Group" };
+      break;
+    case PREFERENCES:
+      columnNames = new String[] { "3DB Beacons Field",
+          "Show in search summary", "Show in structure summary" };
+      break;
+    default:
+      break;
+    }
+    return columnNames;
+  }
 }