1 package jalview.ws.dbsources;
3 import jalview.ws.uimodel.PDBRestRequest;
4 import jalview.ws.uimodel.PDBRestResponse;
5 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
7 import java.util.ArrayList;
8 import java.util.Collection;
9 import java.util.Iterator;
10 import java.util.List;
12 import javax.ws.rs.core.MediaType;
14 import org.json.simple.JSONArray;
15 import org.json.simple.JSONObject;
16 import org.json.simple.parser.JSONParser;
17 import org.json.simple.parser.ParseException;
19 import com.sun.jersey.api.client.Client;
20 import com.sun.jersey.api.client.ClientResponse;
21 import com.sun.jersey.api.client.WebResource;
22 import com.sun.jersey.api.client.config.ClientConfig;
23 import com.sun.jersey.api.client.config.DefaultClientConfig;
24 import com.sun.jersey.api.json.JSONConfiguration;
27 * A rest client for querying the Search endpoing of the PDB REST API
32 public class PDBRestClient
34 private static String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
36 private static int DEFAULT_RESPONSE_SIZE = 200;
39 * Takes a PDBRestRequest object and returns a response upon execution
41 * @param pdbRestRequest
42 * the PDBRestRequest instance to be processed
43 * @return the pdbResponse object for the given request
45 public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
47 ClientConfig clientConfig = new DefaultClientConfig();
48 clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
50 Client client = Client.create(clientConfig);
52 String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
54 int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
55 : pdbRestRequest.getResponseSize();
56 String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
57 .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
58 .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
61 // Build request parameters for the REST Request
62 WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
63 .queryParam("wt", "json").queryParam("fl", wantedFields)
64 .queryParam("rows", String.valueOf(responseSize))
65 .queryParam("q", pdbRestRequest.getQuery())
66 .queryParam("sort", sortParam);
68 // Execute the REST request
69 ClientResponse clientResponse = webResource.accept(
70 MediaType.APPLICATION_JSON).get(ClientResponse.class);
72 // Get the JSON string from the response object
73 String responseString = clientResponse.getEntity(String.class);
75 // Check the response status and report exception if one occurs
76 if (clientResponse.getStatus() != 200)
78 String errorMessage = "";
79 if (clientResponse.getStatus() == 400)
81 errorMessage = parseJsonExceptionString(responseString);
82 throw new RuntimeException(errorMessage);
86 errorMessage = "Failed : HTTP error code : "
87 + clientResponse.getStatus();
88 throw new RuntimeException(errorMessage);
92 // Make redundant objects eligible for garbage collection to conserve
94 clientResponse = null;
97 // Process the response and return the result to the caller.
98 return parsePDBJsonResponse(responseString, pdbRestRequest);
102 * Process error response from PDB server if/when one occurs.
104 * @param jsonResponse
105 * the JSON string containing error message from the server
106 * @return the processed error message from the JSON string
108 public static String parseJsonExceptionString(String jsonErrorResponse)
110 StringBuilder errorMessage = new StringBuilder(
111 "\n============= PDB Rest Client RunTime error =============\n");
115 JSONParser jsonParser = new JSONParser();
116 JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
117 JSONObject errorResponse = (JSONObject) jsonObj.get("error");
119 JSONObject responseHeader = (JSONObject) jsonObj
120 .get("responseHeader");
121 JSONObject paramsObj = (JSONObject) responseHeader.get("params");
122 String status = responseHeader.get("status").toString();
123 String message = errorResponse.get("msg").toString();
124 String query = paramsObj.get("q").toString();
125 String fl = paramsObj.get("fl").toString();
127 errorMessage.append("Status: ").append(status).append("\n");
128 errorMessage.append("Message: ").append(message).append("\n");
129 errorMessage.append("query: ").append(query).append("\n");
130 errorMessage.append("fl: ").append(fl).append("\n");
132 } catch (ParseException e)
136 return errorMessage.toString();
140 * Parses the JSON response string from PDB REST API. The response is dynamic
141 * hence, only fields specifically requested for in the 'wantedFields'
142 * parameter is fetched/processed
144 * @param pdbJsonResponseString
145 * the JSON string to be parsed
146 * @param pdbRestRequest
147 * the request object which contains parameters used to process the
151 @SuppressWarnings("unchecked")
152 public static PDBRestResponse parsePDBJsonResponse(
153 String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
155 PDBRestResponse searchResult = new PDBRestResponse();
156 List<PDBResponseSummary> result = null;
159 JSONParser jsonParser = new JSONParser();
160 JSONObject jsonObj = (JSONObject) jsonParser
161 .parse(pdbJsonResponseString);
163 JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
164 String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
166 int numFound = Integer
167 .valueOf(pdbResponse.get("numFound").toString());
170 result = new ArrayList<PDBResponseSummary>();
171 JSONArray docs = (JSONArray) pdbResponse.get("docs");
172 for (Iterator<JSONObject> docIter = docs.iterator(); docIter
175 JSONObject doc = docIter.next();
176 result.add(searchResult.new PDBResponseSummary(doc,
179 searchResult.setNumberOfItemsFound(numFound);
180 searchResult.setResponseTime(queryTime);
181 searchResult.setSearchSummary(result);
183 } catch (ParseException e)
191 * Takes a collection of PDBDocField and converts its 'code' Field values into
192 * a comma delimited string.
194 * @param pdbDocfields
195 * the collection of PDBDocField to process
196 * @return the comma delimited string from the pdbDocFields collection
198 public static String getPDBDocFieldsAsCommaDelimitedString(
199 Collection<PDBDocField> pdbDocfields)
202 if (pdbDocfields != null && !pdbDocfields.isEmpty())
204 StringBuilder returnedFields = new StringBuilder();
205 for (PDBDocField field : pdbDocfields)
207 returnedFields.append(",").append(field.getCode());
209 returnedFields.deleteCharAt(0);
210 result = returnedFields.toString();
216 * Determines the column index for 'PDB Id' Fields in the dynamic summary
217 * table. The PDB Id serves as a unique identifier for a given row in the
220 * @param wantedFeilds
221 * the available table columns in no particular order
222 * @return the pdb id field column index
224 public static int getPDBIdColumIndex(
225 Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
228 // If a reference sequence is attached then start counting from 1 else
230 int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
232 for (PDBDocField feild : wantedFeilds)
234 if (feild.equals(PDBDocField.PDB_ID))
236 break; // Once PDB Id index is determined exit iteration
238 ++pdbFeildIndexCounter;
240 return pdbFeildIndexCounter;
244 * This enum represents the fields available in the PDB JSON response
247 public enum PDBDocField
249 PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
250 "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
251 "molecule_type"), MOLECULE_SEQUENCE("Sequence",
252 "molecule_sequence"), PFAM_ACCESSION("PFAM Accession",
253 "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
254 "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
255 "InterPro Accession", "interpro_accession"), UNIPROT_ID(
256 "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
257 "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
258 "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
259 "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
260 "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
261 "Data Quality", "data_quality"), OVERALL_QUALITY(
262 "Overall Quality", "overall_quality"), POLYMER_COUNT(
263 "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
264 "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
265 "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
266 "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
267 "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
268 "Experimental Method", "experimental_method"), GO_ID("GO Id",
269 "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
270 "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
271 "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
272 "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
273 "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
274 "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
275 "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
276 "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
277 "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
278 "Model Quality", "model_quality"), PIVOT_RESOLUTION(
279 "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
280 "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
281 "Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
282 "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
283 "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
284 "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION(
285 "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
286 "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
287 "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
288 "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
289 "compound_id"), COMPOUND_WEIGHT("Compound Weight",
290 "compound_weight"), COMPOUND_SYSTEMATIC_NAME(
291 "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG(
292 "Interacting Ligands", "interacting_ligands"), JOURNAL(
293 "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
294 "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
295 "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
296 "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
297 "Structure Determination Method",
298 "structure_determination_method"), SYNCHROTON_SITE(
299 "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
300 "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
301 "Entry Authors", "entry_authors"), CITATION_TITLE(
302 "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
303 "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
304 "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
305 "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
306 "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
307 "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
308 "Data Scalling Software", "data_scaling_software"), DETECTOR(
309 "Detector", "detector"), DETECTOR_TYPE("Detector Type",
310 "detector_type"), MODIFIED_RESIDUE_FLAG(
311 "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
312 "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
313 "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
314 "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
315 "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
316 "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
317 "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
318 "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
319 "beam_source_name"), PROCESSING_SITE("Processing Site",
320 "processing_site"), ENTITY_WEIGHT("Entity Weight",
321 "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
328 PDBDocField(String name, String code)
334 public String getName()
339 public String getCode()
344 public String toString()