JAL-1720 JAL-2002 improvement for 'uniprot coverage' filter using facet pivot query

[jalview.git] / src / jalview / ws / dbsources / PDBRestClient.java

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index 09c10ef..2c05acd 100644 (file)
--- 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 ($$Version-Rel$$)
+ * 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.ws.dbsources;
 
+import jalview.util.MessageManager;
 import jalview.ws.uimodel.PDBRestRequest;
 import jalview.ws.uimodel.PDBRestResponse;
 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
@@ -22,7 +43,6 @@ import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.ClientConfig;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
-
 /**
  * A rest client for querying the Search endpoing of the PDB REST API
  * 
@@ -59,20 +79,39 @@ public class PDBRestClient
               .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
               .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
               : " desc"));
-
+      String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
+              .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
+              .getFacetPivot();
+      String facetPivotMinCount = String.valueOf(pdbRestRequest
+              .getFacetPivotMinCount());
+      
       // 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);
-
+      WebResource webResource = null;
+      if (pdbRestRequest.isFacet())
+      {
+        webResource = client.resource(PDB_SEARCH_ENDPOINT)
+                .queryParam("wt", "json").queryParam("fl", wantedFields)
+                .queryParam("rows", String.valueOf(responseSize))
+                .queryParam("q", pdbRestRequest.getQuery())
+                .queryParam("sort", sortParam).queryParam("facet", "true")
+                .queryParam("facet.pivot", facetPivot)
+                .queryParam("facet.pivot.mincount", facetPivotMinCount);
+      }
+      else
+      {
+        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);
+      System.out.println("query >>>>>>> " + pdbRestRequest.toString());
 
       // Check the response status and report exception if one occurs
       if (clientResponse.getStatus() != 200)
@@ -103,16 +142,17 @@ public class PDBRestClient
       String exceptionMsg = e.getMessage();
       if (exceptionMsg.contains("SocketException"))
       {
-        throw new Exception(
-                "Jalview is unable to detect an internet connection");
         // No internet connection
+        throw new Exception(
+                MessageManager
+                        .getString("exception.unable_to_detect_internet_connection"));
       }
       else if (exceptionMsg.contains("UnknownHostException"))
       {
-        throw new Exception(
-                "Jalview is unable to reach the host server \'www.ebi.ac.uk\'. "
-                        + "\nPlease ensure that you are connected to the internet and try again.");
         // The server 'www.ebi.ac.uk' is unreachable
+        throw new Exception(
+                MessageManager
+                        .getString("exception.pdb_server_unreachable"));
       }
       else
       {
@@ -127,11 +167,12 @@ public class PDBRestClient
     switch (code)
     {
     case 410:
-      message = "PDB Rest Service no longer exists!";
+      message = MessageManager
+              .getString("exception.pdb_rest_service_no_longer_available");
       break;
     case 403:
     case 404:
-      message = "The requested resource could not be found";
+      message = MessageManager.getString("exception.resource_not_be_found");
       break;
     case 408:
     case 409:
@@ -141,7 +182,7 @@ public class PDBRestClient
     case 503:
     case 504:
     case 505:
-      message = "There seems to be an error from the PDB Rest API server.";
+      message = MessageManager.getString("exception.pdb_server_error");
       break;
 
     default:
@@ -393,9 +434,10 @@ public class PDBRestClient
       return code;
     }
 
+    @Override
     public String toString()
     {
       return name;
     }
   }
-}
\ No newline at end of file
+}