X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPDBRestClient.java;h=320b1c57d670e0027d0660f1df25b8cf43f69629;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=0c41d61769a40dcfbc5745ed2ee874b52c7e1609;hpb=f09bee67bc24f1e401b4834f8ecb14812620568c;p=jalview.git diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 0c41d61..320b1c5 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -1,11 +1,15 @@ package jalview.ws.dbsources; -import jalview.ws.uimodel.PDBSearchResultPojo; -import jalview.ws.uimodel.PDBSummaryListModel; +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 javax.swing.DefaultListModel; import javax.ws.rs.core.MediaType; import org.json.simple.JSONArray; @@ -18,52 +22,196 @@ 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?"; + private static int DEFAULT_RESPONSE_SIZE = 200; - public static void main(String[] args) + /** + * 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 { - new PDBRestClient().searchResult("pfam_name", "Lipoc*"); + 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) + { + 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")) + { + // The server 'www.ebi.ac.uk' is unreachable + throw new Exception( + MessageManager + .getString("exception.pdb_server_unreachable")); + } + else + { + throw e; + } + } } - private String executeRestSearch(String qParam, - String searchTerm) + public String getMessageByHTTPStatusCode(int code) { - ClientConfig clientConfig = new DefaultClientConfig(); - clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING, - Boolean.TRUE); - Client client = Client.create(clientConfig); - WebResource webResource = client.resource(pdbSearchEndpoint) - .queryParam("wt", "json") -.queryParam("rows", "100") - .queryParam("q", qParam + ":" + searchTerm); - ClientResponse clientResponse = webResource.accept( - MediaType.APPLICATION_JSON).get(ClientResponse.class); - - String responseString = clientResponse.getEntity(String.class); - if (clientResponse.getStatus() != 200) + 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(jsonErrorResponse); + JSONObject errorResponse = (JSONObject) jsonObj.get("error"); + + JSONObject responseHeader = (JSONObject) jsonObj + .get("responseHeader"); + 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) { - throw new RuntimeException("Failed : HTTP error code : " - + clientResponse.getStatus()); + e.printStackTrace(); } - return responseString; + return errorMessage.toString(); } - public PDBSearchResultPojo searchResult(String qParam, - String searchTerm) + /** + * 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") + public static PDBRestResponse parsePDBJsonResponse( + String pdbJsonResponseString, PDBRestRequest pdbRestRequest) { - String jsonResponseString = executeRestSearch(qParam, searchTerm); - PDBSearchResultPojo searchResult = new PDBSearchResultPojo(); - DefaultListModel result = null; + PDBRestResponse searchResult = new PDBRestResponse(); + List result = null; try { JSONParser jsonParser = new JSONParser(); JSONObject jsonObj = (JSONObject) jsonParser - .parse(jsonResponseString); + .parse(pdbJsonResponseString); JSONObject pdbResponse = (JSONObject) jsonObj.get("response"); String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get( @@ -72,18 +220,16 @@ public class PDBRestClient .valueOf(pdbResponse.get("numFound").toString()); if (numFound > 0) { - result = new DefaultListModel(); + result = new ArrayList(); JSONArray docs = (JSONArray) pdbResponse.get("docs"); for (Iterator docIter = docs.iterator(); docIter .hasNext();) { JSONObject doc = docIter.next(); - if (doc.get("molecule_sequence") != null) - { - result.addElement(new PDBSummaryListModel(doc)); - } + result.add(searchResult.new PDBResponseSummary(doc, + pdbRestRequest)); } - searchResult.setItemFound(numFound); + searchResult.setNumberOfItemsFound(numFound); searchResult.setResponseTime(queryTime); searchResult.setSearchSummary(result); } @@ -91,8 +237,166 @@ public class PDBRestClient { e.printStackTrace(); } - return searchResult; } -} + /** + * 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 (pdbDocfields != null && !pdbDocfields.isEmpty()) + { + StringBuilder returnedFields = new StringBuilder(); + for (PDBDocField field : pdbDocfields) + { + returnedFields.append(",").append(field.getCode()); + } + 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 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"), 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; + + 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; + } + } +} \ No 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