/**
* @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);
}
}
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);
}
}
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;
}
/**
* @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 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;
}
