/** * Check the headers of the Phenotype matrix file * * @param titles * @param errorMessages * @param suid * @return */ private boolean checkMatrixTitles(String[] titles, Vector errorMessages) { boolean errorFound = false; String errorStr = null; try { if (titles.length < 2) errorFound = true; else if (!(titles[0].equals("IDENTITY") || titles[0].equals("ALIAS"))) { errorFound = true; } if (errorFound) { errorStr = " Illegal headers.\n" + "# Required file headers: IDENTITY/ALIAS VARIABLE1 VARIABLE2 ...\n" + "# Headers found in file: "; for (int j = 0; j < titles.length; j++) { errorStr = errorStr + " " + titles[j]; } errorMessages.addElement(errorStr); } // now we check that the variables in header exists for (int i = 1; i < titles.length; i++) { if (db.isVariableUnique(titles[i])) { errorFound = true; errorStr = "Variable " + titles[i] + " does not exist."; errorMessages.addElement(errorStr); } } } catch (Exception e) { e.printStackTrace(System.err); } return errorFound; }
/** * @param fileOut * @param errorMessages * @param warningMessages * @param deviationMessages * @param databaseValues * @param ind * @param delimeter * @param marker * @param allele1 * @param allele2 * @param raw1 * @param raw2 * @param ref * @param comm */ private void writeTitleErrors(FileWriter fileOut, Vector titleError) { try { if (titleError.size() > 0) { fileOut.write("#--------------------------------------------------\n"); for (int i = 0; i < titleError.size(); i++) { fileOut.write("#" + (String) titleError.elementAt(i) + "\n"); } fileOut.write("#--------------------------------------------------\n"); } } catch (Exception e) { e.printStackTrace(System.err); } }
/** * Check the titles if they are valid. * * <p>There should be 8 columns { {IDENTITY | ALIAS} , VARIABLE , VALUE, DATE, REFERENCE, COMMIT } * * @param titles * @param errorMessages * @return */ private boolean checkListTitles(String[] titles, Vector errorMessages) { // Check the file header boolean errorFound = false; String errorStr = null; if (titles.length != 6) // 8 errorFound = true; else if (!(titles[0].equals("IDENTITY") || titles[0].equals("ALIAS")) || !titles[1].equals("VARIABLE") || !titles[2].equals("VALUE") || !titles[3].equals("DATE") || !titles[4].equals("REFERENCE") || !titles[5].equals("COMMENT")) errorFound = true; // ref=6, comm=7 if (errorFound) { errorStr = " Illegal headers.\n" + // <BR> "# Required file headers: IDENTITY/ALIAS VARIABLE VALUE DATE REFERENCE COMMENT \n" + "# Headers found in file: "; for (int j = 0; j < titles.length; j++) { errorStr = errorStr + " " + titles[j]; } errorMessages.addElement(errorStr); } return errorFound; }
private void writeListErrors( FileWriter fileOut, Vector deviationMessages, Vector databaseValues, String ind, char delimeter, String variable, String value, String date, String ref, String comm) { try { if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) { fileOut.write("#--------------------------------------------------\n"); } if (errorList.size() > 0) { for (int i = 0; i < errorList.size(); i++) { fileOut.write("#" + (String) errorList.get(i) + "\n"); } } if (warningList.size() > 0) { for (int i = 0; i < warningList.size(); i++) { fileOut.write("#" + (String) warningList.get(i) + "\n"); } } if (deviationMessages.size() > 0) { for (int i = 0; i < deviationMessages.size(); i++) { fileOut.write("#" + (String) deviationMessages.elementAt(i) + "\n"); } // write old values fileOut.write("#" + databaseValues.elementAt(0) + "\n"); } // if there are errors, the string is "Outcommented" if (errorList.size() > 0) { fileOut.write("#"); } // write original string fileOut.write( ind + delimeter + variable + delimeter + value + delimeter + date + delimeter + ref + delimeter + comm + "\n"); if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) { fileOut.write("#--------------------------------------------------\n"); } } // try catch (Exception e) { e.printStackTrace(System.err); } }
/** * @param fileOut * @param errorMessages * @param warningMessages * @param deviationMessages * @param databaseValues * @param newAlleles * @param ind * @param delim * @param marker * @param allele1 * @param allele2 */ private void writeMatrixErrors( FileWriter fileOut, Vector deviationMessages, Vector databaseValues, Vector values, String ind, char delim, String variable, String value) { try { // if row contains comments if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) { fileOut.write("#--------------------------------------------------------\n"); } if (errorList.size() > 0) { for (int i = 0; i < errorList.size(); i++) { fileOut.write("#" + (String) errorList.get(i) + "\n"); } } if (warningList.size() > 0) { for (int i = 0; i < warningList.size(); i++) { fileOut.write("#" + (String) warningList.get(i) + "\n"); } } if (deviationMessages.size() > 0) { for (int i = 0; i < deviationMessages.size(); i++) { fileOut.write("#" + (String) deviationMessages.elementAt(i) + "\n"); } // write database values fileOut.write("#" + ind); for (int i = 0; i < databaseValues.size(); i++) { fileOut.write(delim + (String) databaseValues.elementAt(i)); } fileOut.write("\n"); } // write row from file: if (errorList.size() > 0) { fileOut.write("#"); } fileOut.write(ind); for (int i = 0; i < values.size(); i++) { fileOut.write(delim + (String) values.elementAt(i)); } fileOut.write("\n"); /* for (int i=0;i<newAlleles.size();i++) { fileOut.write(delim+(String)newAlleles.elementAt(i)); } fileOut.write("\n"); */ // fileOut.write(delim+allele1); // fileOut.write(delim+allele2); // fileOut.write("\n"); if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) { fileOut.write("#--------------------------------------------------------\n"); } } // try catch (Exception e) { e.printStackTrace(System.err); } }
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; }
// 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; }