Example #1
0
 @Override
 public List<Assertion> getAssertions() throws SyntaxError {
   if (table.getRowCount() < 2) throw new SyntaxError("Query tables must have at least two rows.");
   assignColumns();
   Assertion make = constructFixture(getFixtureName());
   Assertion ti =
       makeAssertion(
           callFunction(getTableName(), "table", tableAsList()),
           new SilentReturnExpectation(0, 0));
   Assertion qi =
       makeAssertion(callFunction(getTableName(), "query"), new QueryTableExpectation());
   tableInstruction = ti.getInstruction().getId();
   queryId = qi.getInstruction().getId();
   // addExpectation(new QueryTableExpectation());
   return list(make, ti, qi);
 }
Example #2
0
  public boolean imp() {
    boolean res = false;

    DbVariable dbVariable = null;
    String fullFileName = "";
    String errMessage = null;
    DbImportFile dbInFile = new DbImportFile();
    try {
      dbVariable = new DbVariable();

      // Store the file on server filesystem
      fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);

      FileParser fileParser = new FileParser(fullFileName);
      fileParser.Parse(
          FileTypeDefinitionList.matchingDefinitions(
              FileTypeDefinition.VARIABLE, FileTypeDefinition.LIST));

      dbVariable.CreateVariables(fileParser, connection, sampleUnitId, Integer.parseInt(userId));

      errMessage = dbVariable.getErrorMessage();
      Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage);

      dbInFile.setStatus(conn_viss, ifid, "IMPORTED");
      // dbInFile.UpdateImportFile(connection,null,null,"Done",Integer.parseInt(ifid),Integer.parseInt(userId));

      // Add a message to the log
      dbInFile.addErrMsg(
          conn_viss,
          ifid,
          "File imported to sampling unit "
              + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
              + "Note: Markers is always imported in Create mode.");
      res = true;
    } catch (Exception e) {
      Errors.logError("ImportVariables.imp(...)" + e.getMessage());

      dbInFile.setStatus(conn_viss, ifid, "ERROR");
      // dbInFile.UpdateImportFile(connection,null,null,e.getMessage(),Integer.parseInt(ifid),Integer.parseInt(userId));

      // Add a message to the log
      dbInFile.addErrMsg(conn_viss, ifid, e.getMessage());

      e.printStackTrace(System.err);
      if (errMessage == null) {
        errMessage = e.getMessage();
      }
    } finally {
      try {
        /*
         * Delete files uploaded
         */
        File tmp = new File(fullFileName);
        tmp.delete();
      } catch (Exception ignore) {
      }
    }

    return res;
  }
Example #3
0
  private void directory_to_directory(
      String source_base_name, String destination_base_name, String directory_name)
      throws IOException, InterruptedException {
    // E.g.
    // source_base_name:        /foo/bar
    // destination_base_name:   /x/y
    // directory_name:     abc
    //
    // - Create /x/y/abc
    // - Copy /foo/bar/abc/* to /x/y/abc/*

    // Get source directory.
    String source_directory_name = Path.concatenate(source_base_name, directory_name);
    File source_directory = File.create(source_directory_name);
    Assertion.check(source_directory.isDirectory());

    // Get destination directory, creating it if
    // necessary.
    String destination_directory_name = Path.concatenate(destination_base_name, directory_name);
    File destination_directory = File.create(destination_directory_name);
    destination_directory.mkdirs();

    // Get files in source directory
    String[] source_file_names = source_directory.list();
    Vector source_files = new Vector();
    for (int i = 0; i < source_file_names.length; i++)
      source_files.addElement(File.create(source_directory_name, source_file_names[i]));

    // Copy
    to_directory(source_files, destination_directory);
  }
Example #4
0
 private void to_directory(Vector sources, File destination_directory)
     throws IOException, InterruptedException {
   Assertion.check(destination_directory.exists());
   for (Enumeration source_scan = sources.elements(); source_scan.hasMoreElements(); ) {
     File source = (File) source_scan.nextElement();
     if (source.isFile()) {
       File destination = File.create(destination_directory.getPath(), source.getName());
       file_to_file(source, destination);
     } else if (_recursive) {
       String source_base = source.getParent();
       if (source_base == null) source_base = ".";
       String destination_base = destination_directory.getCanonicalPath();
       directory_to_directory(source_base, destination_base, source.getName());
     }
   }
 }
Example #5
0
  public boolean imp() {
    boolean res = false;
    String errMessage = null;

    DbImportFile dbInFile = new DbImportFile();
    DbPhenotype dbp = new DbPhenotype();
    String fullFileName = null;

    try {
      Errors.logInfo("CheckPhenotype started");
      // connection.setAutoCommit(false);
      dbInFile.setStatus(conn_viss, ifid, "0%");

      fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);

      FileHeader header = FileParser.scanFileHeader(fullFileName);
      FileParser fileParser = new FileParser(fullFileName);

      // Set status
      dbInFile.setStatus(conn_viss, ifid, "10%");

      // Ensure file format is list or matrix
      Assertion.assertMsg(
          header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST)
              || header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX),
          "Format type name should be list or matrix "
              + "but found found "
              + header.formatTypeName());

      // If file is a list
      if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST)) {
        fileParser.Parse(
            FileTypeDefinitionList.matchingDefinitions(
                FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST));
        dbInFile.setStatus(conn_viss, ifid, "20%");

        if (updateMethod.equals("CREATE")) {
          dbp.CreatePhenotypesList(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        } else if (updateMethod.equals("UPDATE")) {
          dbp.UpdatePhenotypesList(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        } else if (updateMethod.equals("CREATE_OR_UPDATE")) {
          dbp.CreateOrUpdatePhenotypesList(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        }
      }

      // If file is a matrix
      else if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX)) {
        fileParser.Parse(
            FileTypeDefinitionList.matchingDefinitions(
                FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX));
        dbInFile.setStatus(conn_viss, ifid, "20%");

        if (updateMethod.equals("CREATE")) {
          dbp.CreatePhenotypesMatrix(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        } else if (updateMethod.equals("UPDATE")) {
          dbp.UpdatePhenotypesMatrix(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        } else if (updateMethod.equals("CREATE_OR_UPDATE")) {
          dbp.CreateOrUpdatePhenotypesMatrix(
              fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
        }
      }
      errMessage = dbp.getErrorMessage();

      Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage);

      dbInFile.setStatus(conn_viss, ifid, "IMPORTED");

      // Add a message to the log
      dbInFile.addErrMsg(
          conn_viss,
          ifid,
          "File imported for sampling unit "
              + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)));
      res = true;

      Errors.logInfo("Check Phenotype ended");
    } catch (Exception e) {
      // Flag for error and set the errMessage if it has not been set
      // isOk = false;
      dbInFile.setStatus(conn_viss, ifid, "ERROR");

      // Add a message to the log
      dbInFile.addErrMsg(conn_viss, ifid, e.getMessage());

      e.printStackTrace(System.err);
      if (errMessage == null) {
        errMessage = e.getMessage();
      }
    }

    return res;
  }