+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.ws.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import jalview.util.MessageManager;
+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;
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?";
- 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);
- }
+ private static int DEFAULT_RESPONSE_SIZE = 200;
- public PDBSearchResponse executeRequest(PDBSearchRequest request)
+ /**
+ * Takes a PDBRestRequest object and returns a response upon execution
+ *
+ * @param pdbRestRequest
+ * 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 = 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("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
+ {
+ 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"));
+ // Build request parameters for the REST Request
+ WebResource 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);
+
+ // 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)
{
- if (clientResponse.getStatus() == 400)
+ 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"))
{
- throw new RuntimeException(parseException(responseString));
+ // The server 'www.ebi.ac.uk' is unreachable
+ throw new Exception(
+ MessageManager
+ .getString("exception.pdb_server_unreachable"));
}
else
{
- throw new RuntimeException("Failed : HTTP error code : "
- + clientResponse.getStatus());
+ throw e;
}
}
- // System.out.println("--------------> " + responseString);
- return parseResponse(responseString, request.getWantedFields(),
- request.getAssociatedSequence());
}
- private String parseException(String jsonResponse)
+ public String getMessageByHTTPStatusCode(int code)
{
- String errorMessage = "RunTime error";
+ 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;
+ }
+ 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
+ */
+ public static String parseJsonExceptionString(String jsonErrorResponse)
+ {
+ StringBuilder errorMessage = new StringBuilder(
+ "\n============= PDB Rest Client RunTime error =============\n");
+
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();
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 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
+ * @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' Field values into
+ * a comma delimited string.
+ *
+ * @param pdbDocfields
+ * the collection of PDBDocField to process
+ * @return the comma delimited string from the pdbDocFields collection
+ */
+ 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());
}
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 wantedFields
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ public static int getPDBIdColumIndex(
+ Collection<PDBDocField> wantedFields, boolean hasRefSeq)
+ {
+
+ // 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 (field.equals(PDBDocField.PDB_ID))
+ {
+ break; // Once PDB Id index is determined exit iteration
+ }
+ ++pdbFieldIndexCounter;
+ }
+ return pdbFieldIndexCounter;
+ }
+ /**
+ * This enum represents the fields available in the PDB JSON 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"), 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"), 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(
+ "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