/*
* 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 .
* 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 = (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;
}
}
}
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 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();
JSONArray docs = (JSONArray) pdbResponse.get("docs");
for (Iterator 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 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;
}
}
}