+/*
+ * 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
+ *
+ * @author tcnofoegbu
+ *
+ */
public class PDBRestClient
{
- private String pdbSearchEndpoint = "http://wwwdev.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;
/**
* Takes a PDBRestRequest object and returns a response upon execution
*
* @param pdbRestRequest
- * the pdbRequest to be sent
- * @return the pdbResponse object for the given pdbRequest
+ * 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 query = pdbRestRequest.getFieldToSearchBy()
- + pdbRestRequest.getSearchTerm()
- + ((pdbRestRequest.isAllowEmptySeq()) ? ""
- : " AND molecule_sequence:['' TO *]");
-
- String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
- .getWantedFields());
-
- String responseSize = (pdbRestRequest.getResponseSize() == 0) ? "200"
- : String.valueOf(pdbRestRequest.getResponseSize());
- String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
- .getFieldToSortBy().trim().isEmpty()) ? ""
- : (pdbRestRequest
- .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
- : " desc"));
-
- WebResource webResource = client.resource(pdbSearchEndpoint)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", responseSize)
- .queryParam("q", query)
- .queryParam("sort", sortParam);
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
-
- String responseString = clientResponse.getEntity(String.class);
- if (clientResponse.getStatus() != 200)
+ try
{
- 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"));
+ 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 = null;
+ if (pdbRestRequest.isFacet())
{
- throw new RuntimeException(parseJsonExceptionString(responseString));
+ 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
{
- throw new RuntimeException("Failed : HTTP error code : "
- + clientResponse.getStatus());
+ 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 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
+ {
+ throw e;
+ }
+ }
+ }
+
+ 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;
}
- clientResponse = null;
- client = null;
- return parsePDBJsonResponse(responseString, pdbRestRequest);
+ return message;
}
/**
* Process error response from PDB server if/when one occurs.
*
* @param jsonResponse
- * the json string containing error message from the server
- * @return the processed error message from the json string
+ * the JSON string containing error message from the server
+ * @return the processed error message from the JSON string
*/
public static String parseJsonExceptionString(String jsonErrorResponse)
{
- String errorMessage = "RunTime error";
+ StringBuilder errorMessage = new StringBuilder(
+ "\n============= PDB Rest Client RunTime error =============\n");
+
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
JSONObject errorResponse = (JSONObject) jsonObj.get("error");
- errorMessage = errorResponse.get("msg").toString();
JSONObject responseHeader = (JSONObject) jsonObj
.get("responseHeader");
- errorMessage += responseHeader.get("params").toString();
+ JSONObject paramsObj = (JSONObject) responseHeader.get("params");
+ String status = responseHeader.get("status").toString();
+ String message = errorResponse.get("msg").toString();
+ String query = paramsObj.get("q").toString();
+ String fl = paramsObj.get("fl").toString();
+
+ errorMessage.append("Status: ").append(status).append("\n");
+ errorMessage.append("Message: ").append(message).append("\n");
+ errorMessage.append("query: ").append(query).append("\n");
+ errorMessage.append("fl: ").append(fl).append("\n");
+
} catch (ParseException e)
{
e.printStackTrace();
}
- return errorMessage;
+ return errorMessage.toString();
}
/**
- * Parses json response string from PDB REST API to a PDBRestResponse
- * instance. The parsed response is dynamic and based upon some of the request
- * parameters.
+ * Parses the JSON response string from PDB REST API. The response is dynamic
+ * hence, only fields specifically requested for in the 'wantedFields'
+ * parameter is fetched/processed
*
* @param pdbJsonResponseString
- * the json string to be parsed
+ * the JSON string to be parsed
* @param pdbRestRequest
* the request object which contains parameters used to process the
- * json string
+ * JSON string
* @return
*/
@SuppressWarnings("unchecked")
public static PDBRestResponse parsePDBJsonResponse(
- String pdbJsonResponseString,
- PDBRestRequest pdbRestRequest)
+ String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
{
PDBRestResponse searchResult = new PDBRestResponse();
List<PDBResponseSummary> result = null;
.hasNext();)
{
JSONObject doc = docIter.next();
- result.add(searchResult.new PDBResponseSummary(doc, pdbRestRequest));
+ result.add(searchResult.new PDBResponseSummary(doc,
+ pdbRestRequest));
}
searchResult.setNumberOfItemsFound(numFound);
searchResult.setResponseTime(queryTime);
}
/**
- * Takes a collection of PDBDocField and converts its code values into a comma
- * delimited string.
+ * Takes a collection of PDBDocField and converts its 'code' Field values into
+ * a comma delimited string.
*
* @param pdbDocfields
- * @return
+ * the collection of PDBDocField to process
+ * @return the comma delimited string from the pdbDocFields collection
*/
public static String getPDBDocFieldsAsCommaDelimitedString(
Collection<PDBDocField> pdbDocfields)
{
returnedFields.append(",").append(field.getCode());
}
- returnedFields.deleteCharAt(0);
+ returnedFields.deleteCharAt(0);
result = returnedFields.toString();
}
return result;
* 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)
{
- int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; // If a reference sequence is
- // attached then start counting from
- // 1 else start from zero
- for (PDBDocField feild : wantedFeilds)
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
+
+ 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
+ break; // Once PDB Id index is determined exit iteration
}
- ++pdbFeildIndexCounter;
+ ++pdbFieldIndexCounter;
}
- return pdbFeildIndexCounter;
+ return pdbFieldIndexCounter;
}
/**
- * Represents the fields retrievable from a PDB Document response
+ * This enum represents the fields available in the PDB JSON response
*
*/
public enum PDBDocField
"Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
"Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
"Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
- "Crystallisation Ph", "crystallisation_ph"), BIO_FUNCTION(
- "Biological Function", "biological_function"), BIO_PROCESS(
- "Biological Process", "biological_process"), BIO_CELL_COMP(
+ "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION(
+ "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
+ "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
"Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
"Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
"compound_id"), COMPOUND_WEIGHT("Compound Weight",
- "compound_weight"), COMP_SYS_NAME("Compound Systematic Name",
- "compound_systematic_name"), INTERACTING_LIG(
+ "compound_weight"), COMPOUND_SYSTEMATIC_NAME(
+ "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG(
"Interacting Ligands", "interacting_ligands"), JOURNAL(
"Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
"Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
return code;
}
+ @Override
public String toString()
{
return name;
git://source.jalview.org / jalview.git / blobdiff