X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPDBRestClient.java;h=16b3f55fb7d30b1bac3ceef1c73ef5d70507a065;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c5642a9c08929069562f7596e682dc45e3f765e1;hpb=a49a5c83b2616e58475c57a37b9a5127d1551a64;p=jalview.git

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index c5642a9..16b3f55 100644
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.ws.dbsources;
 
+import jalview.util.MessageManager;
 import jalview.ws.uimodel.PDBRestRequest;
 import jalview.ws.uimodel.PDBRestResponse;
 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
@@ -21,7 +42,6 @@ import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
-import com.sun.jersey.api.json.JSONConfiguration;
 
 /**
  * A rest client for querying the Search endpoing of the PDB REST API
@@ -31,7 +51,7 @@ import com.sun.jersey.api.json.JSONConfiguration;
  */
 public class PDBRestClient
 {
-  private static String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
+  public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
 
   private static int DEFAULT_RESPONSE_SIZE = 200;
 
@@ -41,61 +61,114 @@ public class PDBRestClient
    * @param pdbRestRequest
    *          the PDBRestRequest instance to be processed
    * @return the pdbResponse object for the given request
+   * @throws Exception
    */
   public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
+          throws Exception
   {
-    ClientConfig clientConfig = new DefaultClientConfig();
-    clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
-            Boolean.TRUE);
-    Client client = Client.create(clientConfig);
-
-    String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
-            .getWantedFields());
-    int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
-            : pdbRestRequest.getResponseSize();
-    String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
-            .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
-            .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
-            : " desc"));
-
-    // Build request parameters for the REST Request
-    WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
-            .queryParam("wt", "json").queryParam("fl", wantedFields)
-            .queryParam("rows", String.valueOf(responseSize))
-            .queryParam("q", pdbRestRequest.getQuery())
-            .queryParam("sort", sortParam);
-
-    // Execute the REST request
-    ClientResponse clientResponse = webResource.accept(
-            MediaType.APPLICATION_JSON).get(ClientResponse.class);
-
-    // Get the JSON string from the response object
-    String responseString = clientResponse.getEntity(String.class);
-
-    // Check the response status and report exception if one occurs
-    if (clientResponse.getStatus() != 200)
+    try
     {
-      String errorMessage = "";
-      if (clientResponse.getStatus() == 400)
+      ClientConfig clientConfig = new DefaultClientConfig();
+      Client client = Client.create(clientConfig);
+
+      String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
+              .getWantedFields());
+      int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+              : pdbRestRequest.getResponseSize();
+      String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
+              .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
+              .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+              : " desc"));
+      // Build request parameters for the REST Request
+      WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
+              .queryParam("wt", "json").queryParam("fl", wantedFields)
+              .queryParam("rows", String.valueOf(responseSize))
+              .queryParam("q", pdbRestRequest.getQuery())
+              .queryParam("sort", sortParam);
+
+      // Execute the REST request
+      ClientResponse clientResponse = webResource.accept(
+              MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+      // Get the JSON string from the response object
+      String responseString = clientResponse.getEntity(String.class);
+
+      // Check the response status and report exception if one occurs
+      if (clientResponse.getStatus() != 200)
       {
-        errorMessage = parseJsonExceptionString(responseString);
-        throw new RuntimeException(errorMessage);
+        String errorMessage = "";
+        if (clientResponse.getStatus() == 400)
+        {
+          errorMessage = parseJsonExceptionString(responseString);
+          throw new Exception(errorMessage);
+        }
+        else
+        {
+          errorMessage = getMessageByHTTPStatusCode(clientResponse
+                  .getStatus());
+          throw new Exception(errorMessage);
+        }
+      }
+
+      // Make redundant objects eligible for garbage collection to conserve
+      // memory
+      clientResponse = null;
+      client = null;
+
+      // Process the response and return the result to the caller.
+      return parsePDBJsonResponse(responseString, pdbRestRequest);
+    } 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"))
+      {
+        // The server 'www.ebi.ac.uk' is unreachable
+        throw new Exception(
+                MessageManager
+                        .getString("exception.pdb_server_unreachable"));
       }
       else
       {
-        errorMessage = "Failed : HTTP error code : "
-                + clientResponse.getStatus();
-        throw new RuntimeException(errorMessage);
+        throw e;
       }
     }
+  }
 
-    // Make redundant objects eligible for garbage collection to conserve
-    // memory
-    clientResponse = null;
-    client = null;
-
-    // Process the response and return the result to the caller.
-    return parsePDBJsonResponse(responseString, pdbRestRequest);
+  public String getMessageByHTTPStatusCode(int code)
+  {
+    String message = "";
+    switch (code)
+    {
+    case 410:
+      message = MessageManager
+              .getString("exception.pdb_rest_service_no_longer_available");
+      break;
+    case 403:
+    case 404:
+      message = MessageManager.getString("exception.resource_not_be_found");
+      break;
+    case 408:
+    case 409:
+    case 500:
+    case 501:
+    case 502:
+    case 503:
+    case 504:
+    case 505:
+      message = MessageManager.getString("exception.pdb_server_error");
+      break;
+
+    default:
+      break;
+    }
+    return message;
   }
 
   /**
@@ -217,27 +290,27 @@ public class PDBRestClient
    * table. The PDB Id serves as a unique identifier for a given row in the
    * summary table
    * 
-   * @param wantedFeilds
+   * @param wantedFields
    *          the available table columns in no particular order
    * @return the pdb id field column index
    */
   public static int getPDBIdColumIndex(
-          Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
+          Collection<PDBDocField> wantedFields, boolean hasRefSeq)
   {
 
     // If a reference sequence is attached then start counting from 1 else
     // start from zero
-    int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+    int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
 
-    for (PDBDocField feild : wantedFeilds)
+    for (PDBDocField field : wantedFields)
     {
-      if (feild.equals(PDBDocField.PDB_ID))
+      if (field.equals(PDBDocField.PDB_ID))
       {
         break; // Once PDB Id index is determined exit iteration
       }
-      ++pdbFeildIndexCounter;
+      ++pdbFieldIndexCounter;
     }
-    return pdbFeildIndexCounter;
+    return pdbFieldIndexCounter;
   }
 
   /**
@@ -346,4 +419,4 @@ public class PDBRestClient
       return name;
     }
   }
-}
\ No newline at end of file
+}