src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java

   1 package jalview.fts.service.threedbeacons;
   2
   3 import java.io.BufferedReader;
   4 import java.io.IOException;
   5 import java.io.InputStreamReader;
   6 import java.net.HttpURLConnection;
   7 import java.net.MalformedURLException;
   8 import java.net.URL;
   9 import java.util.HashMap;
  10 import java.util.HashSet;
  11 import java.util.Map;
  12
  13 import org.json.JSONArray;
  14 import org.json.JSONObject;
  15
  16 import jalview.fts.api.FTSDataColumnI;
  17 import jalview.fts.api.FTSRestClientI;
  18 import jalview.fts.core.FTSRestRequest;
  19 import jalview.fts.core.FTSRestResponse;
  20 import jalview.fts.core.GFTSPanel;
  21 import jalview.fts.service.pdb.PDBFTSRestClient;
  22 import jalview.gui.SequenceFetcher;
  23 import jalview.util.MessageManager;
  24
  25 @SuppressWarnings("serial")
  26 public class TDBeaconsFTSPanel extends GFTSPanel
  27 {
  28   private static String defaultFTSFrameTitle = MessageManager
  29           .getString("label.pdb_sequence_fetcher");
  30
  31   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  32
  33   private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
  34
  35   private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
  36
  37   private static HttpURLConnection connection;
  38
  39   public TDBeaconsFTSPanel(SequenceFetcher fetcher)
  40   {
  41     super(fetcher);
  42     pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
  43     this.seqFetcher = fetcher;
  44     this.progressIndicator = (fetcher == null) ? null
  45             : fetcher.getProgressIndicator();
  46   }
  47
  48 //  public int TDBeaconsFTSPanel2(String result)
  49 //  {
  50 //    int seqlength = executeParse(result);
  51 //    return seqlength;
  52 //  }
  53
  54   public static int executeParse(String query) {
  55     BufferedReader reader;
  56     String line;
  57     StringBuffer responseContent = new StringBuffer();
  58     try {
  59       URL url = new URL("https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/" + query + ".json");
  60       connection = (HttpURLConnection) url.openConnection();
  61       connection.setRequestMethod("GET");
  62       connection.setConnectTimeout(5000); // <=>5seconds
  63       connection.setReadTimeout(5000);
  64       // Status check up, 200 = connection succesful
  65       int status = connection.getResponseCode();
  66       // System.out.println(status);
  67
  68       if (status > 299) {
  69               reader = new BufferedReader(new InputStreamReader(connection.getErrorStream()));
  70               while ((line = reader.readLine()) != null) {
  71                       responseContent.append(line);
  72               }
  73               reader.close();
  74       } else {
  75               reader = new BufferedReader(new InputStreamReader(connection.getInputStream()));
  76               while ((line = reader.readLine()) != null) {
  77                       responseContent.append(line);
  78               }
  79               reader.close();
  80       }
  81       //System.out.println(responseContent.toString());
  82       int seq = parse(responseContent.toString());
  83       return seq;
  84
  85       } catch (MalformedURLException e) {
  86         e.printStackTrace();
  87       } catch (IOException e) {
  88         e.printStackTrace();
  89       } finally {
  90       connection.disconnect();
  91       }
  92       return (Integer) null;
  93
  94   }
  95
  96   public static int parse(String jsonString) {
  97     JSONObject entry = new JSONObject(jsonString);
  98     System.out.println(entry);
  99     int length = entry.getJSONObject("uniprot_entry").getInt("sequence_length");
 100     String  ac = entry.getJSONObject("uniprot_entry").getString("ac");
 101
 102     JSONArray structures = entry.getJSONArray("structures");
 103     for (int i=0 ; i < structures.length() ; i++) {
 104             String id = structures.getJSONObject(i).getString("model_identifier");
 105             //System.out.println("identifier num " + i + " : " + id);
 106     }
 107     System.out.println("length : " + length + "; access name : " + ac);
 108     return length;
 109
 110 }
 111
 112   @Override
 113   public void searchAction(boolean isFreshSearch)
 114   {
 115     mainFrame.requestFocusInWindow();
 116     if (isFreshSearch)
 117     {
 118       offSet = 0;
 119     }
 120     new Thread()
 121     {
 122       @Override
 123       public void run()
 124       {
 125         reset();
 126         boolean allowEmptySequence = false;
 127         if (getTypedText().length() > 0)
 128         {
 129           setSearchInProgress(true);
 130           long startTime = System.currentTimeMillis();
 131
 132           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
 133                   .getSelectedItem()).getCode();
 134           wantedFields = TDBeaconsFTSRestClient.getInstance()
 135                   .getAllDefaultDisplayedFTSDataColumns();
 136           String searchTerm = getTypedText(); // to add : decodeSearchTerm
 137
 138           FTSRestRequest request = new FTSRestRequest();
 139           request.setAllowEmptySeq(allowEmptySequence);
 140           request.setResponseSize(100);
 141           request.setFieldToSearchBy("(" + searchTarget + ":");
 142           request.setSearchTerm(searchTerm + ")");
 143           request.setOffSet(offSet);
 144           request.setWantedFields(wantedFields);
 145           FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
 146           FTSRestResponse resultList;
 147           try
 148           {
 149             resultList = tdbRestClient.executeRequest(request);
 150           } catch (Exception e)
 151           {
 152             setErrorMessage(e.getMessage());
 153             checkForErrors();
 154             setSearchInProgress(false);
 155             return;
 156           }
 157
 158           if (resultList.getSearchSummary() != null
 159                   && resultList.getSearchSummary().size() > 0)
 160           {
 161             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 162                     resultList.getSearchSummary()));
 163             FTSRestResponse.configureTableColumn(getResultTable(),
 164                     wantedFields, tempUserPrefs);
 165             getResultTable().setVisible(true);
 166           }
 167
 168           long endTime = System.currentTimeMillis();
 169           totalResultSetCount = resultList.getNumberOfItemsFound();
 170           resultSetCount = resultList.getSearchSummary() == null ? 0
 171                   : resultList.getSearchSummary().size();
 172           String result = (resultSetCount > 0)
 173                   ? MessageManager.getString("label.results")
 174                   : MessageManager.getString("label.result");
 175
 176           if (isPaginationEnabled() && resultSetCount > 0)
 177           {
 178             String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
 179             String f2 = totalNumberformatter
 180                     .format(Integer.valueOf(offSet + resultSetCount));
 181             String f3 = totalNumberformatter
 182                     .format(Integer.valueOf(totalResultSetCount));
 183             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 184                     + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
 185                     + (endTime - startTime) + " milli secs)");
 186           }
 187           else
 188           {
 189             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 190                     + resultSetCount + " " + result + " ("
 191                     + (endTime - startTime) + " milli secs)");
 192           }
 193
 194           setSearchInProgress(false);
 195           refreshPaginatorState();
 196           updateSummaryTableSelections();
 197         }
 198         txt_search.updateCache();
 199       }
 200     }.start();
 201   }
 202
 203   @Override
 204   public void okAction()
 205   {
 206     // mainFrame.dispose();
 207     disableActionButtons();
 208     StringBuilder selectedIds = new StringBuilder();
 209     HashSet<String> selectedIdsSet = new HashSet<>();
 210     int primaryKeyColIndex = 0;
 211     try
 212     {
 213       primaryKeyColIndex = getFTSRestClient()
 214               .getPrimaryKeyColumIndex(wantedFields, false);
 215     } catch (Exception e)
 216     {
 217       e.printStackTrace();
 218     }
 219     int[] selectedRows = getResultTable().getSelectedRows();
 220     String searchTerm = getTypedText();
 221     for (int summaryRow : selectedRows)
 222     {
 223       String idStr = getResultTable()
 224               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 225       selectedIdsSet.add(searchTerm);
 226     }
 227
 228     for (String idStr : paginatorCart)
 229     {
 230       selectedIdsSet.add(searchTerm);
 231     }
 232
 233     for (String selectedId : selectedIdsSet)
 234     {
 235       selectedIds.append(selectedId).append(";");
 236     }
 237
 238     String ids = selectedIds.toString();
 239     seqFetcher.setQuery(ids);
 240     Thread worker = new Thread(seqFetcher);
 241     worker.start();
 242     delayAndEnableActionButtons();
 243   }
 244
 245   @Override
 246   public FTSRestClientI getFTSRestClient()
 247   {
 248     return TDBeaconsFTSRestClient.getInstance();
 249   }
 250
 251   @Override
 252   public String getFTSFrameTitle()
 253   {
 254     return defaultFTSFrameTitle;
 255   }
 256
 257   @Override
 258   public boolean isPaginationEnabled()
 259   {
 260     return true;
 261   }
 262
 263   @Override
 264   public Map<String, Integer> getTempUserPrefs()
 265   {
 266     return tempUserPrefs;
 267   }
 268
 269   @Override
 270   public String getCacheKey()
 271   {
 272     return THREEDB_FTS_CACHE_KEY;
 273   }
 274
 275   @Override
 276   public String getAutosearchPreference()
 277   {
 278     return THREEDB_AUTOSEARCH;
 279   }
 280
 281   @Override
 282   protected void showHelp()
 283   {
 284     System.out.println("No help implemented yet.");
 285
 286   }
 287
 288   public static String decodeSearchTerm(String enteredText) {
 289     // no multiple query support yet
 290     return enteredText;
 291   }
 292 }