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; }