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.Collection;
import java.util.Iterator;
import java.util.List;
{
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(
.hasNext();)
{
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);
}
{
e.printStackTrace();
}
-
return searchResult;
}
- private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ /**
+ * Takes a collection of PDBDocField and converts its code values into a comma
+ * delimited string.
+ *
+ * @param pdbDocfields
+ * @return
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ Collection<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;
}
+ /**
+ * Determines the column index for 'PDB Id' Fields in the dynamic summary
+ * table. The PDB Id serves as a unique identifier for a given row in the
+ * summary table
+ *
+ * @param wantedFeilds
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ 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
+ for (PDBDocField feild : wantedFeilds)
+ {
+ if (feild.equals(PDBDocField.PDB_ID))
+ {
+ break; // once PDB Id index is determined exit iteration
+ }
+ ++pdbFeildIndexCounter;
+ }
+ return pdbFeildIndexCounter;
+ }
+ /**
+ * Represents the fields retrievable from a PDB Document response
+ *
+ */
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");
+ "molecule_sequence"), PFAM_ACCESSION("PFAM Accession",
+ "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
+ "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
+ "InterPro Accession", "interpro_accession"), UNIPROT_ID(
+ "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
+ "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
+ "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
+ "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
+ "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
+ "Data Quality", "data_quality"), OVERALL_QUALITY(
+ "Overall Quality", "overall_quality"), POLYMER_COUNT(
+ "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
+ "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
+ "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
+ "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
+ "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), GO_ID("GO Id",
+ "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
+ "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
+ "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
+ "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
+ "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
+ "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
+ "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
+ "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
+ "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
+ "Model Quality", "model_quality"), PIVOT_RESOLUTION(
+ "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
+ "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
+ "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(
+ "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(
+ "Interacting Ligands", "interacting_ligands"), JOURNAL(
+ "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
+ "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
+ "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
+ "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
+ "Structure Determination Method",
+ "structure_determination_method"), SYNCHROTON_SITE(
+ "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
+ "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
+ "Entry Authors", "entry_authors"), CITATION_TITLE(
+ "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
+ "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
+ "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
+ "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
+ "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
+ "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
+ "Data Scalling Software", "data_scaling_software"), DETECTOR(
+ "Detector", "detector"), DETECTOR_TYPE("Detector Type",
+ "detector_type"), MODIFIED_RESIDUE_FLAG(
+ "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
+ "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
+ "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
+ "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
+ "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
+ "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
+ "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
+ "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
+ "beam_source_name"), PROCESSING_SITE("Processing Site",
+ "processing_site"), ENTITY_WEIGHT("Entity Weight",
+ "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
+ "text");
private String name;
git://source.jalview.org / jalview.git / blobdiff