package jalview.ws.dbsources;
-import jalview.ws.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.util.ArrayList;
import java.util.Iterator;
{
private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
- public static void main(String[] args)
- {
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(100);
- request.setFieldToSearchBy("pfam_name");
- request.setSearchTerm("Lipoc*");
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
- wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
- wantedFields.add(PDBDocField.TITLE);
- request.setWantedFields(wantedFields);
- new PDBRestClient().executeRequest(request);
- }
-
- public PDBSearchResponse executeRequest(PDBSearchRequest request)
+ /**
+ * 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
+ */
+ public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
{
ClientConfig clientConfig = new DefaultClientConfig();
clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
Boolean.TRUE);
Client client = Client.create(clientConfig);
- String query = request.getFieldToSearchBy()
- + request.getSearchTerm()
- + ((request.isAllowEmptySeq()) ? ""
+ String query = pdbRestRequest.getFieldToSearchBy()
+ + pdbRestRequest.getSearchTerm()
+ + ((pdbRestRequest.isAllowEmptySeq()) ? ""
: " AND molecule_sequence:['' TO *]");
- String wantedFields = getFieldsAsCommaDelimitedString(request
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
.getWantedFields());
- String responseSize = (request.getResponseSize() == 0) ? "200" : String
- .valueOf(request.getResponseSize());
- String sortParam = (request.getFieldToSortBy() == null || request
+ String responseSize = (pdbRestRequest.getResponseSize() == 0) ? "200"
+ : String.valueOf(pdbRestRequest.getResponseSize());
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
.getFieldToSortBy().trim().isEmpty()) ? ""
- : (request
- .getFieldToSortBy() + (request.isAscending() ? " asc" : " desc"));
+ : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
WebResource webResource = client.resource(pdbSearchEndpoint)
.queryParam("wt", "json").queryParam("fl", wantedFields)
{
if (clientResponse.getStatus() == 400)
{
- throw new RuntimeException(parseException(responseString));
+ throw new RuntimeException(parseJsonExceptionString(responseString));
}
else
{
+ clientResponse.getStatus());
}
}
- // System.out.println("--------------> " + responseString);
- return parseResponse(responseString, request.getWantedFields(),
- request.getAssociatedSequence());
+ clientResponse = null;
+ client = null;
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
}
- private String parseException(String jsonResponse)
+ /**
+ * 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
+ */
+ public static String parseJsonExceptionString(String jsonErrorResponse)
{
String errorMessage = "RunTime error";
try
{
JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonResponse);
+ JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
JSONObject errorResponse = (JSONObject) jsonObj.get("error");
errorMessage = errorResponse.get("msg").toString();
return errorMessage;
}
+ /**
+ * 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.
+ *
+ * @param pdbJsonResponseString
+ * the json string to be parsed
+ * @param pdbRestRequest
+ * the request object which contains parameters used to process the
+ * json string
+ * @return
+ */
@SuppressWarnings("unchecked")
- private PDBSearchResponse parseResponse(String jsonResponse,
- List<PDBDocField> wantedFields, String associatedSequence)
+ public static PDBRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString,
+ PDBRestRequest pdbRestRequest)
{
- PDBSearchResponse searchResult = new PDBSearchResponse();
+ PDBRestResponse searchResult = new PDBRestResponse();
List<PDBResponseSummary> result = null;
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser
-.parse(jsonResponse);
+ .parse(pdbJsonResponseString);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
JSONObject doc = docIter.next();
// if (doc.get("molecule_sequence") != null)
// {
- result.add(searchResult.new PDBResponseSummary(doc, wantedFields,
- associatedSequence));
+ result.add(searchResult.new PDBResponseSummary(doc, pdbRestRequest));
// }
}
- searchResult.setItemsFound(numFound);
+ searchResult.setNumberOfItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
}
return searchResult;
}
- private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ /**
+ * Takes a collection of PDBDocField and converts it into a comma delimited
+ * string.
+ *
+ * @param pdbDocfields
+ * @return
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ List<PDBDocField> pdbDocfields)
{
String result = "";
- if (fields != null && !fields.isEmpty())
+ if (pdbDocfields != null && !pdbDocfields.isEmpty())
{
StringBuilder returnedFields = new StringBuilder();
- for (PDBDocField field : fields)
+ for (PDBDocField field : pdbDocfields)
{
returnedFields.append(",").append(field.getCode());
}
- returnedFields.deleteCharAt(0);
+ returnedFields.deleteCharAt(0);
result = returnedFields.toString();
}
return result;
}
+ /**
+ * Represents the fields retrievable from a PDB Document response
+ *
+ */
public enum PDBDocField
{
PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
"Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
"Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE(
"UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME(
- "Gene Name", "gene_name"), ALL("ALL", "text");
+ "Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), ALL("ALL",
+ "text");
private String name;
git://source.jalview.org / jalview.git / blobdiff