package jalview.ws.dbsources;
-import jalview.ws.uimodel.PDBSearchResultPojo;
-import jalview.ws.uimodel.PDBSummaryListModel;
+import jalview.ws.uimodel.PDBSearchRequest;
+import jalview.ws.uimodel.PDBSearchResponse;
+import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import java.util.ArrayList;
import java.util.Iterator;
+import java.util.List;
-import javax.swing.DefaultListModel;
import javax.ws.rs.core.MediaType;
import org.json.simple.JSONArray;
{
private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
-
public static void main(String[] args)
{
- new PDBRestClient().searchResult("pfam_name", "Lipoc*");
+ 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);
}
- private String executeRestSearch(String qParam,
- String searchTerm)
+ public PDBSearchResponse executeRequest(PDBSearchRequest request)
{
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()) ? ""
+ : " AND molecule_sequence:['' TO *]");
+
+ String wantedFields = getFieldsAsCommaDelimitedString(request
+ .getWantedFields());
+
+ String responseSize = (request.getResponseSize() == 0) ? "200" : String
+ .valueOf(request.getResponseSize());
+ String sortParam = (request.getFieldToSortBy() == null || request
+ .getFieldToSortBy().trim().isEmpty()) ? ""
+ : (request
+ .getFieldToSortBy() + (request.isAscending() ? " asc" : " desc"));
+
WebResource webResource = client.resource(pdbSearchEndpoint)
- .queryParam("wt", "json")
- .queryParam("q", qParam + ":" + searchTerm);
+ .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)
{
+ if (clientResponse.getStatus() == 400)
+ {
+ throw new RuntimeException(parseException(responseString));
+ }
+ else
+ {
throw new RuntimeException("Failed : HTTP error code : "
+ clientResponse.getStatus());
+ }
+ }
+ // System.out.println("--------------> " + responseString);
+ return parseResponse(responseString, request.getWantedFields(),
+ request.getAssociatedSequence());
+ }
+
+ private String parseException(String jsonResponse)
+ {
+ String errorMessage = "RunTime error";
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonResponse);
+ JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+ errorMessage = errorResponse.get("msg").toString();
+
+ JSONObject responseHeader = (JSONObject) jsonObj
+ .get("responseHeader");
+ errorMessage += responseHeader.get("params").toString();
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
}
- return responseString;
+ return errorMessage;
}
- public PDBSearchResultPojo searchResult(String qParam,
- String searchTerm)
+ @SuppressWarnings("unchecked")
+ private PDBSearchResponse parseResponse(String jsonResponse,
+ List<PDBDocField> wantedFields, String associatedSequence)
{
- String jsonResponseString = executeRestSearch(qParam, searchTerm);
- PDBSearchResultPojo searchResult = new PDBSearchResultPojo();
- DefaultListModel<PDBSummaryListModel> result = null;
+ PDBSearchResponse searchResult = new PDBSearchResponse();
+ List<PDBResponseSummary> result = null;
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser
- .parse(jsonResponseString);
+.parse(jsonResponse);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
{
- result = new DefaultListModel<PDBSummaryListModel>();
+ result = new ArrayList<PDBResponseSummary>();
JSONArray docs = (JSONArray) pdbResponse.get("docs");
for (Iterator<JSONObject> docIter = docs.iterator(); docIter
.hasNext();)
{
JSONObject doc = docIter.next();
- if (doc.get("molecule_sequence") != null)
- {
- result.addElement(new PDBSummaryListModel(doc));
- }
+ // if (doc.get("molecule_sequence") != null)
+ // {
+ result.add(searchResult.new PDBResponseSummary(doc, wantedFields,
+ associatedSequence));
+ // }
}
- searchResult.setItemFound(numFound);
+ searchResult.setItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
}
return searchResult;
}
+ private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ {
+ String result = "";
+ if (fields != null && !fields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : fields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+
+ public enum PDBDocField
+ {
+ PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
+ "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
+ "molecule_type"), MOLECULE_SEQUENCE("Sequence",
+ "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features",
+ "uniprot_features"), PFAM_ACCESSION("PFAM Accession",
+ "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession",
+ "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession",
+ "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION(
+ "Resolution", "resolution"), DATA_QUALITY("Data Quality",
+ "data_quality"), OVERALL_QUALITY("Overall Quality",
+ "overall_quality"), POLYMER_COUNT("Polymer Count",
+ "number_of_polymers"), PROTEIN_CHAIN_COUNT(
+ "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
+ "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");
+
+ private String name;
+
+ private String code;
+
+ PDBDocField(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String toString()
+ {
+ return name;
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff