+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.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.ws.rs.core.MediaType;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-import org.json.simple.parser.ParseException;
-
-import com.sun.jersey.api.client.Client;
-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;
-
-/**
- * A rest client for querying the Search endpoing of the PDB REST API
- *
- * @author tcnofoegbu
- *
- */
-public class PDBRestClient
-{
- public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
-
- private static int DEFAULT_RESPONSE_SIZE = 200;
-
- /**
- * 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
- {
- 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 = null;
- if (pdbRestRequest.getFieldToSortBy() == null
- || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
- {
- sortParam = "";
- }
- else
- {
- if (pdbRestRequest.getFieldToSortBy()
- .equalsIgnoreCase("Resolution"))
- {
- sortParam = pdbRestRequest.getFieldToSortBy()
- + (pdbRestRequest.isAscending() ? " asc" : " desc");
- }
- else
- {
- sortParam = pdbRestRequest.getFieldToSortBy()
- + (pdbRestRequest.isAscending() ? " desc" : " asc");
- }
- }
-
- String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
- .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
- .getFacetPivot();
- String facetPivotMinCount = String.valueOf(pdbRestRequest
- .getFacetPivotMinCount());
-
- // Build request parameters for the REST Request
- WebResource webResource = null;
- if (pdbRestRequest.isFacet())
- {
- webResource = client.resource(PDB_SEARCH_ENDPOINT)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", String.valueOf(responseSize))
- .queryParam("q", pdbRestRequest.getQuery())
- .queryParam("sort", sortParam).queryParam("facet", "true")
- .queryParam("facet.pivot", facetPivot)
- .queryParam("facet.pivot.mincount", facetPivotMinCount);
- }
- else
- {
- 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);
- // System.out.println("query >>>>>>> " + pdbRestRequest.toString());
-
- // 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;
- }
- }
- }
-
- public String getMessageByHTTPStatusCode(int code)
- {
- 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)
- {
- e.printStackTrace();
- }
- 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")
- public static PDBRestResponse parsePDBJsonResponse(
- String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
- {
- PDBRestResponse searchResult = new PDBRestResponse();
- List<PDBResponseSummary> result = null;
- try
- {
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser
- .parse(pdbJsonResponseString);
-
- JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
- String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
- "QTime").toString();
- int numFound = Integer
- .valueOf(pdbResponse.get("numFound").toString());
- if (numFound > 0)
- {
- result = new ArrayList<PDBResponseSummary>();
- JSONArray docs = (JSONArray) pdbResponse.get("docs");
- for (Iterator<JSONObject> docIter = docs.iterator(); docIter
- .hasNext();)
- {
- JSONObject doc = docIter.next();
- result.add(searchResult.new PDBResponseSummary(doc,
- pdbRestRequest));
- }
- searchResult.setNumberOfItemsFound(numFound);
- searchResult.setResponseTime(queryTime);
- searchResult.setSearchSummary(result);
- }
- } catch (ParseException e)
- {
- 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<PDBDocField> 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<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;
- }
-
- public static PDBDocField getPDBDocFieldByCode(String fieldCode)
- throws Exception
- {
- for (PDBDocField curPDBDocField : PDBDocField.values())
- {
- if (curPDBDocField.getCode().equalsIgnoreCase(fieldCode))
- {
- return curPDBDocField;
- }
- }
- throw new Exception("PDB doc Field not found!");
- }
-
- /**
- * This enum represents the fields available in the PDB JSON response
- *
- */
- public enum PDBDocField
- {
- PDB_ID("PDB Id", "pdb_id", Group.CROSS_REFS), TITLE(
- "Title",
- "title", Group.MISCELLENOUS),
- MOLECULE_NAME("Molecule",
- "molecule_name",
- Group.NAMES_AND_TAXONOMY), MOLECULE_TYPE(
- "Molecule Type", "molecule_type", Group.NAMES_AND_TAXONOMY), MOLECULE_SEQUENCE(
- "Sequence", "molecule_sequence", Group.MISCELLENOUS), PFAM_ACCESSION(
- "PFAM Accession", "pfam_accession",
- Group.CROSS_REFS), PFAM_NAME(
- "PFAM Name", "pfam_name", Group.NAMES_AND_TAXONOMY), INTERPRO_NAME(
- "InterPro Name", "interpro_name", Group.NAMES_AND_TAXONOMY), INTERPRO_ACCESSION(
- "InterPro Accession", "interpro_accession",
- Group.CROSS_REFS), UNIPROT_ID("UniProt Id",
- "uniprot_id", Group.CROSS_REFS), UNIPROT_ACCESSION(
- "UniProt Accession", "uniprot_accession",
- Group.CROSS_REFS),
-
- UNIPROT_COVERAGE(
- "UniProt Coverage", "uniprot_coverage", Group.MISCELLENOUS), UNIPROT_FEATURES(
- "Uniprot Features", "uniprot_features", Group.MISCELLENOUS), R_FACTOR(
-"R Factor",
- "r_factor", Group.QUALITY_MEASURES), RESOLUTION("Resolution",
- "resolution", Group.QUALITY_MEASURES), DATA_QUALITY(
- "Data Quality", "data_quality", Group.QUALITY_MEASURES), OVERALL_QUALITY(
- "Overall Quality", "overall_quality", Group.QUALITY_MEASURES), POLYMER_COUNT(
- "Number of Polymers", "number_of_polymers", Group.MISCELLENOUS), PROTEIN_CHAIN_COUNT(
- "Number of Protein Chains", "number_of_protein_chains",
- Group.MISCELLENOUS), BOUND_MOLECULE_COUNT(
- "Number of Bound Molecule", "number_of_bound_molecules",
- Group.MISCELLENOUS), POLYMER_RESIDUE_COUNT(
- "Number of Polymer Residue", "number_of_polymer_residues",
- Group.MISCELLENOUS), GENUS("GENUS", "genus",
- Group.NAMES_AND_TAXONOMY), GENE_NAME("Gene Name", "gene_name",
- Group.NAMES_AND_TAXONOMY), EXPERIMENTAL_METHOD(
- "Experimental Method", "experimental_method",
- Group.PROCEDURE_AND_SOFTWARE), GO_ID("GO Id", "go_id",
- Group.CROSS_REFS), ASSEMBLY_ID("Assembly Id",
- "assembly_id", Group.CROSS_REFS), ASSEMBLY_FORM(
- "Assembly Form", "assembly_form", Group.MISCELLENOUS), ASSEMBLY_TYPE(
- "Assembly Type", "assembly_type", Group.MISCELLENOUS), SPACE_GROUP(
- "Space Group", "spacegroup", Group.MISCELLENOUS), CATH_CODE(
- "Cath Code", "cath_code", Group.CROSS_REFS), TAX_ID(
- "Tax Id", "tax_id", Group.CROSS_REFS), TAX_QUERY(
- "Tax Query", "tax_query", Group.CROSS_REFS), INTERACTING_ENTITY_ID(
- "Interacting Entity Id", "interacting_entity_id",
- Group.CROSS_REFS), INTERACTING_MOLECULES(
- "Interacting Molecules", "interacting_molecules",
- Group.MISCELLENOUS), PUBMED_ID("Pubmed Id", "pubmed_id",
- Group.CROSS_REFS), STATUS("Status", "status",
- Group.MISCELLENOUS), MODEL_QUALITY("Model Quality",
- "model_quality", Group.QUALITY_MEASURES), PIVOT_RESOLUTION(
- "Pivot Resolution", "pivot_resolution", Group.QUALITY_MEASURES), DATA_REDUCTION_SOFTWARE(
- "Data reduction software", "data_reduction_software",
- Group.PROCEDURE_AND_SOFTWARE), MAX_OBSERVED_RES(
- "Max observed residues",
- "max_observed_residues", Group.MISCELLENOUS), ORG_SCI_NAME(
- "Organism scientific name", "organism_scientific_name",
- Group.NAMES_AND_TAXONOMY), SUPER_KINGDOM("Super kingdom",
- "superkingdom", Group.NAMES_AND_TAXONOMY), RANK("Rank", "rank",
- Group.NAMES_AND_TAXONOMY), CRYSTALLISATION_PH(
- "Crystallisation Ph",
- "crystallisation_ph", Group.MISCELLENOUS), BIOLOGICAL_FUNCTION(
- "Biological Function", "biological_function",
- Group.MISCELLENOUS), BIOLOGICAL_PROCESS("Biological Process",
- "biological_process", Group.MISCELLENOUS), BIOLOGICAL_CELL_COMPONENT(
- "Biological Cell Component", "biological_cell_component",
- Group.MISCELLENOUS), COMPOUND_NAME("Compound Name",
- "compound_name", Group.NAMES_AND_TAXONOMY), COMPOUND_ID(
- "Compound Id", "compound_id", Group.CROSS_REFS), COMPOUND_WEIGHT(
- "Compound Weight", "compound_weight", Group.MISCELLENOUS), COMPOUND_SYSTEMATIC_NAME(
- "Compound Systematic Name", "compound_systematic_name",
- Group.NAMES_AND_TAXONOMY), INTERACTING_LIG(
- "Interacting Ligands",
- "interacting_ligands", Group.MISCELLENOUS), JOURNAL("Journal",
- "journal", Group.MISCELLENOUS), ALL_AUTHORS("All Authors",
- "all_authors", Group.MISCELLENOUS), EXPERIMENTAL_DATA_AVAILABLE(
- "Experiment Data Available", "experiment_data_available",
- Group.MISCELLENOUS), DIFFRACTION_PROTOCOL(
- "Diffraction Protocol", "diffraction_protocol",
- Group.PROCEDURE_AND_SOFTWARE), REFINEMENT_SOFTWARE(
- "Refinement Software", "refinement_software",
- Group.PROCEDURE_AND_SOFTWARE), STRUCTURE_DETERMINATION_METHOD(
- "Structure Determination Method",
- "structure_determination_method", Group.PROCEDURE_AND_SOFTWARE), SYNCHROTON_SITE(
- "Synchrotron Site", "synchrotron_site", Group.MISCELLENOUS), SAMPLE_PREP_METHOD(
- "Sample Preparation Method", "sample_preparation_method",
- Group.PROCEDURE_AND_SOFTWARE), ENTRY_AUTHORS("Entry Authors",
- "entry_authors", Group.MISCELLENOUS), CITATION_TITLE(
- "Citation Title", "citation_title", Group.MISCELLENOUS), STRUCTURE_SOLUTION_SOFTWARE(
- "Structure Solution Software", "structure_solution_software",
- Group.PROCEDURE_AND_SOFTWARE), ENTRY_ENTITY("Entry Entity",
- "entry_entity", Group.MISCELLENOUS), R_FREE("R Free", "r_free",
- Group.QUALITY_MEASURES), NO_OF_POLYMER_ENTITIES(
- "Number of Polymer Entities", "number_of_polymer_entities",
- Group.MISCELLENOUS), NO_OF_BOUND_ENTITIES(
- "Number of Bound Entities", "number_of_bound_entities",
- Group.MISCELLENOUS), CRYSTALLISATION_RESERVOIR(
- "Crystallisation Reservoir", "crystallisation_reservoir",
- Group.MISCELLENOUS), DATA_SCALING_SW("Data Scalling Software",
- "data_scaling_software", Group.PROCEDURE_AND_SOFTWARE), DETECTOR(
- "Detector", "detector", Group.MISCELLENOUS), DETECTOR_TYPE(
- "Detector Type", "detector_type", Group.MISCELLENOUS), MODIFIED_RESIDUE_FLAG(
- "Modified Residue Flag", "modified_residue_flag",
- Group.MISCELLENOUS), NUMBER_OF_COPIES("Number of Copies",
- "number_of_copies", Group.MISCELLENOUS), STRUCT_ASYM_ID(
- "Struc Asym Id", "struct_asym_id",
- Group.CROSS_REFS), HOMOLOGUS_PDB_ENTITY_ID(
- "Homologus PDB Entity Id", "homologus_pdb_entity_id",
- Group.CROSS_REFS), MOLECULE_SYNONYM(
- "Molecule Synonym",
- "molecule_synonym", Group.MISCELLENOUS), DEPOSITION_SITE(
- "Deposition Site", "deposition_site", Group.MISCELLENOUS), SYNCHROTRON_BEAMLINE(
- "Synchrotron Beamline", "synchrotron_beamline",
- Group.MISCELLENOUS), ENTITY_ID("Entity Id", "entity_id",
- Group.CROSS_REFS), BEAM_SOURCE_NAME(
- "Beam Source Name",
- "beam_source_name",
- Group.NAMES_AND_TAXONOMY), PROCESSING_SITE(
- "Processing Site", "processing_site", Group.MISCELLENOUS), ENTITY_WEIGHT(
- "Entity Weight", "entity_weight", Group.MISCELLENOUS), VERSION(
- "Version", "_version_", Group.MISCELLENOUS), ALL("ALL", "text",
- Group.MISCELLENOUS);
-
- public enum Group
- {
- DATE_OF("Date Of", 5), NAMES_AND_TAXONOMY("Names & Taxonomy", 3),
- MISCELLENOUS("Miscellenous", 6), QUALITY_MEASURES("Quality Measures",
- 1), CROSS_REFS("Cross References", 2),
- PROCEDURE_AND_SOFTWARE("Procedures & Softwares", 4);
-
- Group(String name, int sortOrder)
- {
- this.name = name;
- this.sortOrder = sortOrder;
- }
-
- private String name;
-
- private int sortOrder;
-
- public String getName()
- {
- return this.name;
- }
-
- public int getSortOrder()
- {
- return sortOrder;
- }
-
- @Override
- public String toString()
- {
- return this.name;
- }
- };
- private String name;
-
- private String code;
-
- private Group group;
-
- PDBDocField(String name, String code, Group group)
- {
- this.name = name;
- this.code = code;
- this.group = group;
- }
-
- public String getName()
- {
- return name;
- }
-
- public String getCode()
- {
- return code;
- }
-
- public Group getGroup()
- {
- return group;
- }
-
- @Override
- public String toString()
- {
- return name;
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff