+/*
+ * 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;
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
try
{
ClientConfig clientConfig = new DefaultClientConfig();
- clientConfig.getFeatures().put(
- JSONConfiguration.FEATURE_POJO_MAPPING, Boolean.TRUE);
Client client = Client.create(clientConfig);
String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
.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)
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 couldn't reach the host server @ www.ebi.ac.uk"
- + "\nPlease ensure that you are connected to the internet.");
// The server 'www.ebi.ac.uk' is unreachable
+ throw new Exception(
+ MessageManager
+ .getString("exception.pdb_server_unreachable"));
}
else
{
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:
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:
* 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;
}
/**
return code;
}
+ @Override
public String toString()
{
return name;
}
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff