package jalview.fts.service.threedbeacons;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;

import org.json.JSONArray;
import org.json.JSONObject;

import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;

@SuppressWarnings("serial")
public class TDBeaconsFTSPanel extends GFTSPanel
{       
  private static String defaultFTSFrameTitle = MessageManager
          .getString("label.pdb_sequence_fetcher");

  private static Map<String, Integer> tempUserPrefs = new HashMap<>();

  private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";

  private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
  
  private static HttpURLConnection connection;
  
  public TDBeaconsFTSPanel(SequenceFetcher fetcher)
  {
    super(fetcher);
    pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
    this.seqFetcher = fetcher;
    this.progressIndicator = (fetcher == null) ? null
            : fetcher.getProgressIndicator();
  }
  
//  public int TDBeaconsFTSPanel2(String result)
//  {
//    int seqlength = executeParse(result);
//    return seqlength;
//  }
  
  public static int executeParse(String query) {
    BufferedReader reader;
    String line;
    StringBuffer responseContent = new StringBuffer();
    try {
      URL url = new URL("https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/" + query + ".json");
      connection = (HttpURLConnection) url.openConnection();
      connection.setRequestMethod("GET");
      connection.setConnectTimeout(5000); // <=>5seconds
      connection.setReadTimeout(5000);
      // Status check up, 200 = connection succesful
      int status = connection.getResponseCode();
      // System.out.println(status);

      if (status > 299) {
              reader = new BufferedReader(new InputStreamReader(connection.getErrorStream()));
              while ((line = reader.readLine()) != null) {
                      responseContent.append(line);
              }
              reader.close();
      } else {
              reader = new BufferedReader(new InputStreamReader(connection.getInputStream()));
              while ((line = reader.readLine()) != null) {
                      responseContent.append(line);
              }
              reader.close();
      }
      //System.out.println(responseContent.toString());
      int seq = parse(responseContent.toString());
      return seq;

      } catch (MalformedURLException e) {
        e.printStackTrace();
      } catch (IOException e) {
        e.printStackTrace();
      } finally {
      connection.disconnect();
      }
      return (Integer) null;
      
  }
  
  public static int parse(String jsonString) {
    JSONObject entry = new JSONObject(jsonString);
    System.out.println(entry);
    int length = entry.getJSONObject("uniprot_entry").getInt("sequence_length");
    String  ac = entry.getJSONObject("uniprot_entry").getString("ac");
    
    JSONArray structures = entry.getJSONArray("structures");
    for (int i=0 ; i < structures.length() ; i++) {
            String id = structures.getJSONObject(i).getString("model_identifier");
            //System.out.println("identifier num " + i + " : " + id);
    }
    System.out.println("length : " + length + "; access name : " + ac);
    return length;
    
}

  @Override
  public void searchAction(boolean isFreshSearch)
  {
    mainFrame.requestFocusInWindow();
    if (isFreshSearch)
    {
      offSet = 0;
    }
    new Thread()
    {
      @Override
      public void run()
      {
        reset();
        boolean allowEmptySequence = false;
        if (getTypedText().length() > 0)
        {
          setSearchInProgress(true);
          long startTime = System.currentTimeMillis();

          String searchTarget = ((FTSDataColumnI) cmb_searchTarget
                  .getSelectedItem()).getCode();
          wantedFields = TDBeaconsFTSRestClient.getInstance()
                  .getAllDefaultDisplayedFTSDataColumns();
          String searchTerm = getTypedText(); // to add : decodeSearchTerm

          FTSRestRequest request = new FTSRestRequest();
          request.setAllowEmptySeq(allowEmptySequence);
          request.setResponseSize(100);
          request.setFieldToSearchBy("(" + searchTarget + ":");
          request.setSearchTerm(searchTerm + ")");
          request.setOffSet(offSet);
          request.setWantedFields(wantedFields);
          FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
          FTSRestResponse resultList;
          try
          {
            resultList = tdbRestClient.executeRequest(request);
          } catch (Exception e)
          {
            setErrorMessage(e.getMessage());
            checkForErrors();
            setSearchInProgress(false);
            return;
          }

          if (resultList.getSearchSummary() != null
                  && resultList.getSearchSummary().size() > 0)
          {
            getResultTable().setModel(FTSRestResponse.getTableModel(request,
                    resultList.getSearchSummary()));
            FTSRestResponse.configureTableColumn(getResultTable(),
                    wantedFields, tempUserPrefs);
            getResultTable().setVisible(true);
          }

          long endTime = System.currentTimeMillis();
          totalResultSetCount = resultList.getNumberOfItemsFound();
          resultSetCount = resultList.getSearchSummary() == null ? 0
                  : resultList.getSearchSummary().size();
          String result = (resultSetCount > 0)
                  ? MessageManager.getString("label.results")
                  : MessageManager.getString("label.result");

          if (isPaginationEnabled() && resultSetCount > 0)
          {
            String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
            String f2 = totalNumberformatter
                    .format(Integer.valueOf(offSet + resultSetCount));
            String f3 = totalNumberformatter
                    .format(Integer.valueOf(totalResultSetCount));
            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
                    + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
                    + (endTime - startTime) + " milli secs)");
          }
          else
          {
            updateSearchFrameTitle(defaultFTSFrameTitle + " - "
                    + resultSetCount + " " + result + " ("
                    + (endTime - startTime) + " milli secs)");
          }

          setSearchInProgress(false);
          refreshPaginatorState();
          updateSummaryTableSelections();
        }
        txt_search.updateCache();
      }
    }.start();
  }
  
  @Override
  public void okAction()
  {
    // mainFrame.dispose();
    disableActionButtons();
    StringBuilder selectedIds = new StringBuilder();
    HashSet<String> selectedIdsSet = new HashSet<>();
    int primaryKeyColIndex = 0;
    try
    {
      primaryKeyColIndex = getFTSRestClient()
              .getPrimaryKeyColumIndex(wantedFields, false);
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    int[] selectedRows = getResultTable().getSelectedRows();
    String searchTerm = getTypedText();
    for (int summaryRow : selectedRows)
    {
      String idStr = getResultTable()
              .getValueAt(summaryRow, primaryKeyColIndex).toString();
      selectedIdsSet.add(searchTerm);
    }

    for (String idStr : paginatorCart)
    {
      selectedIdsSet.add(searchTerm);
    }

    for (String selectedId : selectedIdsSet)
    {
      selectedIds.append(selectedId).append(";");
    }

    String ids = selectedIds.toString();
    seqFetcher.setQuery(ids);
    Thread worker = new Thread(seqFetcher);
    worker.start();
    delayAndEnableActionButtons();
  }
  
  @Override
  public FTSRestClientI getFTSRestClient()
  {
    return TDBeaconsFTSRestClient.getInstance();
  }
  
  @Override
  public String getFTSFrameTitle()
  {
    return defaultFTSFrameTitle;
  }

  @Override
  public boolean isPaginationEnabled()
  {
    return true;
  }

  @Override
  public Map<String, Integer> getTempUserPrefs()
  {
    return tempUserPrefs;
  }

  @Override
  public String getCacheKey()
  {
    return THREEDB_FTS_CACHE_KEY;
  }

  @Override
  public String getAutosearchPreference()
  {
    return THREEDB_AUTOSEARCH;
  }

  @Override
  protected void showHelp()
  {
    System.out.println("No help implemented yet.");
    
  }
  
  public static String decodeSearchTerm(String enteredText) {
    // no multiple query support yet
    return enteredText;
  }
}