X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSRestClient.java;h=87d640b3ab79e908fe2578df7e0d7adbf217b043;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=b4e56606fb9a48f906e7b521b4493b5977c9fb7a;hpb=8e7cf85a7f61f425e808cac53ead7bc27e402242;p=jalview.git

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index b4e5660..87d640b 100644
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -20,7 +20,8 @@
  */
 package jalview.fts.service.pdb;
 
-import jalview.bin.Jalview;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
@@ -30,6 +31,7 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.net.URI;
 import java.util.ArrayList;
@@ -53,15 +55,19 @@ import com.sun.jersey.api.client.config.DefaultClientConfig;
  * 
  * @author tcnofoegbu
  */
-public class PDBFTSRestClient extends FTSRestClient
+public class PDBFTSRestClient extends FTSRestClient implements ApplicationSingletonI
 {
-
-  private static FTSRestClientI instance = null;
-
   public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?";
 
-  protected PDBFTSRestClient()
+  public static FTSRestClientI getInstance()
+  {
+    return (FTSRestClientI) ApplicationSingletonProvider
+            .getInstance(PDBFTSRestClient.class);
+  }
+
+  private PDBFTSRestClient()
   {
+    // singleton -- use getInstance()
   }
 
   /**
@@ -125,15 +131,19 @@ public class PDBFTSRestClient extends FTSRestClient
       // different from the ones in Java yet still allow this to be correct for Java
       Client client;
       Class<ClientResponse> clientResponseClass;
-      if (Jalview.isJS())
+      if (Platform.isJS())
       {
         // JavaScript only -- coerce types to Java types for Java
         client = (Client) (Object) new jalview.javascript.web.Client();
         clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
       }
       else
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
-        // Java only
         client = Client.create(new DefaultClientConfig());
         clientResponseClass = ClientResponse.class;
       }
@@ -161,29 +171,34 @@ public class PDBFTSRestClient extends FTSRestClient
 
       URI uri = webResource.getURI();
 
+      System.out.println(uri);
+
       // Execute the REST request
       ClientResponse clientResponse = webResource
               .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
 
-      // Get the JSON string from the response object
-      String responseString = clientResponse.getEntity(String.class);
+      int status = clientResponse.getStatus();
+
+      // Get the JSON string from the response object or directly from the
+      // client (JavaScript)
+      Map<String, Object> jsonObj = (Platform.isJS() && status == 200
+              ? clientResponse.getEntity(Map.class)
+              : null);
+      String responseString = (jsonObj == null
+              ? clientResponse.getEntity(String.class)
+              : null);
+
       // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
 
       // Check the response status and report exception if one occurs
-      if (clientResponse.getStatus() != 200)
+      switch (status)
       {
-        String errorMessage = "";
-        if (clientResponse.getStatus() == 400)
-        {
-          errorMessage = parseJsonExceptionString(responseString);
-          throw new Exception(errorMessage);
-        }
-        else
-        {
-          errorMessage = getMessageByHTTPStatusCode(
-                  clientResponse.getStatus(), "PDB");
-          throw new Exception(errorMessage);
-        }
+      case 200:
+        break;
+      case 400:
+        throw new Exception(parseJsonExceptionString(responseString));
+      default:
+        throw new Exception(getMessageByHTTPStatusCode(status, "PDB"));
       }
 
       // Make redundant objects eligible for garbage collection to conserve
@@ -192,7 +207,7 @@ public class PDBFTSRestClient extends FTSRestClient
       client = null;
 
       // Process the response and return the result to the caller.
-      return parsePDBJsonResponse(responseString, pdbRestRequest);
+      return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
     } catch (Exception e)
     {
       String exceptionMsg = e.getMessage();
@@ -285,15 +300,26 @@ public static String parseJsonExceptionString(String jsonErrorResponse)
    *          JSON string
    * @return
    */
-  @SuppressWarnings("unchecked")
   public static FTSRestResponse parsePDBJsonResponse(
           String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
   {
+    return parsePDBJsonResponse(pdbJsonResponseString,
+            (Map<String, Object>) null, pdbRestRequest);
+  }
+
+  @SuppressWarnings("unchecked")
+  public static FTSRestResponse parsePDBJsonResponse(
+          String pdbJsonResponseString, Map<String, Object> jsonObj,
+          FTSRestRequest pdbRestRequest)
+  {
     FTSRestResponse searchResult = new FTSRestResponse();
     List<FTSData> result = null;
     try
     {
-      Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+      if (jsonObj == null)
+      {
+        jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+      }
       Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
       String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
               .get("QTime").toString();
@@ -301,7 +327,7 @@ public static String parseJsonExceptionString(String jsonErrorResponse)
               .valueOf(pdbResponse.get("numFound").toString());
       if (numFound > 0)
       {
-        result = new ArrayList<FTSData>();
+        result = new ArrayList<>();
         List<Object> docs = (List<Object>) pdbResponse.get("docs");
         for (Iterator<Object> docIter = docs.iterator(); docIter
                 .hasNext();)
@@ -439,15 +465,6 @@ public static String parseJsonExceptionString(String jsonErrorResponse)
     return "/fts/pdb_data_columns.txt";
   }
 
-  public static FTSRestClientI getInstance()
-  {
-    if (instance == null)
-    {
-      instance = new PDBFTSRestClient();
-    }
-    return instance;
-  }
-
   private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
 
   public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
@@ -455,39 +472,12 @@ public static String parseJsonExceptionString(String jsonErrorResponse)
     if (allDefaultDisplayedStructureDataColumns == null
             || allDefaultDisplayedStructureDataColumns.isEmpty())
     {
-      allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+      allDefaultDisplayedStructureDataColumns = new ArrayList<>();
       allDefaultDisplayedStructureDataColumns
               .addAll(super.getAllDefaultDisplayedFTSDataColumns());
     }
     return allDefaultDisplayedStructureDataColumns;
   }
   
-  @SuppressWarnings("unchecked")
-public static void main(String[] args) {
-    
-    
-    // check for transpiler fix associated with JSONParser yylex.java use of charAt()
-    // instead of codePointAt()
-
-    String s = "e";
-    char c = 'c';
-    char f = 'f';
-    s += c | f; 
-    int x = c&f;
-    int y = 2 & c;
-    int z = c ^ 5;
-    String result = s +x + y + z;
-    assert (result == "e103982102");
-    try
-    {
-      Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse("{\"a\":3}");
-      System.out.println(jsonObj);
-    } catch (ParseException e)
-    {
-      e.printStackTrace();
-    }
-    
-  }
-  
   
 }