X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPDBRestClient.java;h=16b3f55fb7d30b1bac3ceef1c73ef5d70507a065;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=e00d9ac19bc7aae710e0a61cc96c00d788d476a0;hpb=0ae0771700df811f421f8548e40dae2cd11cfae0;p=jalview.git diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index e00d9ac..16b3f55 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -1,10 +1,32 @@ +/* + * 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 . + * 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; @@ -20,108 +42,196 @@ import com.sun.jersey.api.client.ClientResponse; 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 wantedFields = new ArrayList(); - 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 wantedFields, String associatedSequence) + public static PDBRestResponse parsePDBJsonResponse( + String pdbJsonResponseString, PDBRestRequest pdbRestRequest) { - PDBSearchResponse searchResult = new PDBSearchResponse(); + PDBRestResponse searchResult = new PDBRestResponse(); List 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( @@ -136,13 +246,10 @@ public class PDBRestClient .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); } @@ -150,17 +257,25 @@ public class PDBRestClient { e.printStackTrace(); } - return searchResult; } - private String getFieldsAsCommaDelimitedString(List 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 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()); } @@ -170,26 +285,114 @@ public class PDBRestClient 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 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;