/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
 * 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 <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 = (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<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;
  }

  /**
   * 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;
    }
  }
}