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?";
+ private static String PDB_SEARCH_ENDPOINT = "http://wwwdev.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
*/
public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
{
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());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : pdbRestRequest.getResponseSize();
String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
- .getFieldToSortBy().trim().isEmpty()) ? ""
- : (pdbRestRequest
+ .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
.getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
: " desc"));
- WebResource webResource = client.resource(pdbSearchEndpoint)
+ // Build request parameters for the REST Request
+ WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
.queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", responseSize)
- .queryParam("q", query)
+ .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)
{
+ String errorMessage = "";
if (clientResponse.getStatus() == 400)
{
- throw new RuntimeException(parseJsonExceptionString(responseString));
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new RuntimeException(errorMessage);
}
else
{
- throw new RuntimeException("Failed : HTTP error code : "
- + clientResponse.getStatus());
+ errorMessage = "Failed : HTTP error code : "
+ + clientResponse.getStatus();
+ throw new RuntimeException(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);
}
* 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)
{
}
/**
- * 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;
public static int getPDBIdColumIndex(
Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
{
- int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; // If a reference sequence is
- // attached then start counting from
- // 1 else start from zero
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+
for (PDBDocField feild : wantedFeilds)
{
if (feild.equals(PDBDocField.PDB_ID))
{
- break; // once PDB Id index is determined exit iteration
+ break; // Once PDB Id index is determined exit iteration
}
++pdbFeildIndexCounter;
}
}
/**
- * 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 name;
}
}
-}
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff