Example #1
0
  public boolean check() {
    Errors.logDebug("CheckVariables started");
    boolean res = false;
    DbImportFile dbInFile = new DbImportFile();
    String fullFileName = "";
    String checkFileName = "";
    String errMessage = null;

    try {
      // Create the variable
      DbVariable dbVariable = new DbVariable();

      dbInFile.setStatus(conn_viss, ifid, "0%");

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

      FileHeader header = FileParser.scanFileHeader(fullFileName);
      String type = header.formatTypeName().toUpperCase();
      char delimiter = header.delimiter().charValue();

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

      // Write out the result to a new file
      FileWriter fileOut = new FileWriter(checkFileName);
      fileOut.write(
          header.objectTypeName()
              + "/"
              + header.formatTypeName()
              + "/"
              + header.version()
              + "/"
              + header.delimiter()
              + "\n");

      String titles[] = fileParser.columnTitles();
      for (int j = 0; j < titles.length; j++) {
        fileOut.write(titles[j] + delimiter);
      }
      fileOut.write("\n");

      String errorMsg = "";
      errorMsg = checkList(fileParser, fileOut, delimiter);
      fileOut.close();

      /*
       * Save the file to database
       */
      dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName);

      if (errorMsg.startsWith("ERROR:")) {
        res = false;
        dbInFile.setStatus(conn_viss, ifid, "ERROR");

        // Add a message to the log
        dbInFile.addErrMsg(
            conn_viss,
            ifid,
            "File checked failed for sampling unit "
                + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
                + ". <br>"
                + errorMsg);
        Errors.logDebug("ErrorMsg=" + errorMsg);
      } else if (errorMsg.startsWith("WARNING:")) {
        dbInFile.setStatus(conn_viss, ifid, "WARNING");
        res = true;

        // Add a message to the log
        dbInFile.addErrMsg(conn_viss, ifid, "Warnings exists: " + errorMsg);
      } else {
        dbInFile.setStatus(conn_viss, ifid, "CHECKED");
        res = true;

        // Add a message to the log
        dbInFile.addErrMsg(
            conn_viss,
            ifid,
            "File checked for sampling unit "
                + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
                + ".<br>"
                + errorMsg);
      }

      /*
      if (errorMsg.length()>0)
      {
          res = false;
          dbInFile.setStatus(conn_viss,ifid,"ERROR");
          // Add a message to the log
          dbInFile.addErrMsg(conn_viss,ifid,"File failed the check for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg);
      }
      else
      {
          res = true;
          dbInFile.setStatus(conn_viss,ifid,"CHECKED");
          // Add a message to the log
          dbInFile.addErrMsg(conn_viss,ifid,"File checked for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg);
      }*/
    } catch (Exception e) {
      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();
      }
    } finally {
      try {
        /*
         * Delete files uploaded
         */
        File tmp = new File(checkFileName);
        tmp.delete();

        tmp = new File(fullFileName);
        tmp.delete();
      } catch (Exception ignore) {
      }
    }

    Errors.logDebug("CheckVariables completed");
    return res;
  }
Example #2
0
  public String checkMatrix(
      FileParser fp, Vector fatalErrors, FileWriter fileOut, char delimiter, String indId) {

    String errMsg = "";
    // String ind, marker = "", allele1 = "", allele2 = ""; //, raw1, raw2; //, //ref; //, comm;
    String ind = "", variable = "", value = "";
    // String alleles[];

    int nrErrors = 0;
    int nrWarnings = 0;
    int nrDeviations = 0;

    /*
    Vector errorMessages = new Vector();
    Vector warningMessages = new Vector();
    Vector deviationMessages = new Vector();
    Vector databaseValues = new Vector();
    */

    DbImportFile dbInFile = new DbImportFile();
    String statusStr;
    double status;
    double status_last = 0.0;

    int dataRows = fp.dataRows();
    String titles[] = fp.columnTitles();
    String variables[] = new String[titles.length - 1];
    for (int i = 0; i < variables.length; i++) variables[i] = titles[i + 1];

    Vector deviationMessages = null;
    Vector databaseValues = null;
    Vector newAlleles = null;
    Vector values = null;

    warningList = new ArrayList();
    errorList = new ArrayList();

    for (int row = 0; row < fp.dataRows(); row++) {
      deviationMessages = new Vector();
      databaseValues = new Vector();
      values = new Vector();

      ind = fp.getValue(indId, row);

      // newAlleles = new Vector();

      // check the whole row
      for (int mNum = 0; mNum < variables.length; mNum++) {
        // String old_alleles[]=null;
        variable = variables[mNum];
        value = fp.getValue(variable, row);

        // Add the values for error writing
        values.add(value);

        // check that values exist, have correct length etc
        checkValues(ind, variable, value, null, null, null);

        if (updateMethod.equals("CREATE"))
          checkCreate(titles[0], ind, variable, value, null, null, null, sampleUnitId);
        else if (updateMethod.equals("UPDATE"))
          checkUpdate(
              titles[0],
              ind,
              variable,
              value,
              null,
              null,
              null,
              sampleUnitId,
              deviationMessages,
              databaseValues,
              delimiter);
        else if (updateMethod.equals("CREATE_OR_UPDATE"))
          checkCreateOrUpdate(
              titles[0],
              ind,
              variable,
              value,
              null,
              null,
              null,
              sampleUnitId,
              deviationMessages,
              databaseValues,
              delimiter);
      } // for markers

      nrErrors += errorList.size();
      nrDeviations += deviationMessages.size();
      nrWarnings += warningList.size();

      writeMatrixErrors(
          fileOut, deviationMessages, databaseValues, values, ind, delimiter, variable, value);

      /*
      //newAlleles= new Vector();
      databaseValues = new Vector();
      errorMessages=new Vector();
      warningMessages=new Vector();
      deviationMessages=new Vector();
      */
      /*
       * Set the status of the import, visible to the user
       */
      status = (new Double(row * 100 / (1.0 * dataRows))).doubleValue();
      if (status_last + 5 < status) {
        status_last = status;
        statusStr = Integer.toString((new Double(status)).intValue()) + "%";
        dbInFile.setStatus(conn_viss, ifid, statusStr);
      }
      errorList.clear();
      warningList.clear();
    } // for rows

    if (nrErrors > 0) errMsg = "ERROR: Import of the genotypes failed.";
    else if (nrWarnings > 0) errMsg = "WARNING: Some warnings exist in the import file";
    else errMsg = "Genotype file is correct";
    errMsg += "\nDeviations:" + nrDeviations + "\nWarnings:" + nrWarnings + "\nErrors:" + nrErrors;

    return errMsg;
  }
Example #3
0
  public boolean check() {
    Errors.logDebug("CheckPhenotype started");

    boolean res = false;

    String errMessage = null;
    FileWriter fileOut = null;
    DbImportFile dbInFile = new DbImportFile();

    String fullFileName = "";
    String checkFileName = "";
    try {
      dbInFile.setStatus(conn_viss, ifid, "0%");

      fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);
      checkFileName = fullFileName + "_checked";

      // Create the Phenotype
      DbPhenotype dbPhenotype = new DbPhenotype();

      FileHeader header = FileParser.scanFileHeader(fullFileName);
      String type = header.formatTypeName().toUpperCase();
      char delimiter = header.delimiter().charValue();

      // AbstractValueFileParser fp = null;
      FileParser fp = null;

      if (type.equals("LIST")) {
        fp = new FileParser(fullFileName);
        fp.Parse(
            FileTypeDefinitionList.matchingDefinitions(
                FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST));
      } else if (type.equals("MATRIX")) {
        fp = new FileParser(fullFileName);
        fp.Parse(
            FileTypeDefinitionList.matchingDefinitions(
                FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX));
      }

      // Write out the result to a new file
      fileOut = new FileWriter(checkFileName);
      fileOut.write(
          header.objectTypeName()
              + "/"
              + header.formatTypeName()
              + "/"
              + header.version()
              + "/"
              + header.delimiter()
              + "\n");

      String titles[] = fp.columnTitles();
      for (int j = 0; j < titles.length; j++) {
        fileOut.write(titles[j] + delimiter);
      }
      fileOut.write("\n");

      // Garbage collect the unused variables
      header = null;
      // fullFileName = null;
      // checkFileName = null;

      // Fix to upper case
      updateMethod = updateMethod.toUpperCase();

      Vector fatalErrors = new Vector();

      if (type.equals("LIST")) checkListTitles(titles, fatalErrors);
      else checkMatrixTitles(titles, fatalErrors);

      writeTitleErrors(fileOut, fatalErrors);

      String indId;

      if (titles[0].equals("IDENTITY")) indId = "IDENTITY";
      else indId = "Alias";

      String errMsg = "";
      if (type.equals("LIST")) errMsg = checkList((FileParser) fp, fileOut, delimiter, indId);
      // errMsg = checkList((FileParser)fp, fatalErrors,fileOut,delimiter,indId);
      else if (type.equals("MATRIX"))
        errMsg = checkMatrix((FileParser) fp, fatalErrors, fileOut, delimiter, indId);

      // Close the file
      fileOut.close();

      /*
       * Save the file to database
       */
      dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName);

      // Get the error message from the database object. If it is set an
      // error occured during the operation so an error is thrown.
      // errMessage = dbIndividual.getErrorMessage();
      // Assertion.assertMsg(errMessage == null ||
      //                     errMessage.trim().equals(""), errMessage);

      if (errMsg.startsWith("ERROR:")) {
        dbInFile.setStatus(conn_viss, ifid, "ERROR");
        res = false;
      } else if (errMsg.startsWith("WARNING:")) {
        dbInFile.setStatus(conn_viss, ifid, "WARNING");
        res = true;
      } else {
        dbInFile.setStatus(conn_viss, ifid, "CHECKED");
        res = true;
      }

      // Add a message to the log
      dbInFile.addErrMsg(
          conn_viss,
          ifid,
          "File checked for sampling unit "
              + DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
              + "<br>\n"
              + errMsg);

    } catch (Exception e) {
      // Flag for error and set the errMessage if it has not been set
      // isOk = false;
      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 temporary file
         */
        File tmp = new File(fullFileName);
        tmp.delete();
        tmp = null;

        tmp = new File(checkFileName);
        tmp.delete();
        tmp = null;
      } catch (Exception ignore) {
      }
    }

    Errors.logDebug("CheckPhenotype completed");

    return res;
  }
Example #4
0
  // public String checkList(FileParser fp, Vector errorMessages, FileWriter fileOut, char
  // delimiter, String indId)
  public String checkList(FileParser fp, FileWriter fileOut, char delimiter, String indId) {
    // String ind, marker, allele1, allele2, raw1, raw2, ref, comm;
    String ind, variable, value, date, ref, comm;

    String errMsg = "";

    int nrErrors = 0;
    int nrWarnings = 0;
    int nrDeviations = 0;

    int dataRows = fp.dataRows();
    String titles[] = fp.columnTitles();

    DbImportFile dbInFile = new DbImportFile();
    String statusStr;
    double status;
    double status_last = 0.0;

    warningList = new ArrayList();
    errorList = new ArrayList();

    for (int i = 0; i < dataRows; i++) {
      //  Vector errorMessages = new Vector();
      //      Vector warningMessages = new Vector();
      Vector deviationMessages = new Vector();
      Vector databaseValues = new Vector();

      ind = ((FileParser) fp).getValue(indId, i).trim();
      variable = ((FileParser) fp).getValue("VARIABLE", i).trim();
      value = ((FileParser) fp).getValue("VALUE", i).trim();
      date = ((FileParser) fp).getValue("DATE", i).trim();
      ref = ((FileParser) fp).getValue("REF", i).trim();
      comm = ((FileParser) fp).getValue("COMMENT", i).trim();

      // Check for valid data values.
      // Check for length, remove null and so on.
      // Syntax check.

      checkValues(ind, variable, value, date, ref, comm);
      //  checkValues(ind, variable, value, date, ref, comm, fatalErrors);

      // If create updateMethod
      if (updateMethod == null || updateMethod.equals("CREATE"))
        checkCreate(titles[0], ind, variable, value, date, ref, comm, sampleUnitId);

      // If update updateMethod
      else if (updateMethod.equals("UPDATE"))
        checkUpdate(
            titles[0],
            ind,
            variable,
            value,
            date,
            ref,
            comm,
            sampleUnitId,
            deviationMessages,
            databaseValues,
            delimiter);

      // if both update and add
      else if (updateMethod.equals("CREATE_OR_UPDATE"))
        checkCreateOrUpdate(
            titles[0],
            ind,
            variable,
            value,
            date,
            ref,
            comm,
            sampleUnitId,
            deviationMessages,
            databaseValues,
            delimiter);

      nrErrors += errorList.size();
      nrDeviations += deviationMessages.size();
      nrWarnings += warningList.size();

      // write row + all errors encountered to file

      writeListErrors(
          fileOut,
          deviationMessages,
          databaseValues,
          ind,
          delimiter,
          variable,
          value,
          date,
          ref,
          comm);

      /*
       * Set the status of the import, visible to the user
       */
      status = (new Double(i * 100 / (1.0 * dataRows))).doubleValue();
      if (status_last + 5 < status) {
        status_last = status;
        statusStr = Integer.toString((new Double(status)).intValue()) + "%";
        dbInFile.setStatus(conn_viss, ifid, statusStr);
      }

      errorList.clear();
      warningList.clear();
    }

    if (nrErrors > 0) errMsg = "ERROR: Import of the Phenotypes failed.";
    else if (nrWarnings > 0) errMsg = "WARNING: Some warnings exist in the import file";
    else errMsg = "Phenotype file is correct";
    errMsg += "\nDeviations:" + nrDeviations + "\nWarnings:" + nrWarnings + "\nErrors:" + nrErrors;

    return errMsg;
  }