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;
}
/**
* 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;
}
/** Creates a new instance of ImportVariables */
public ImportVariables() {
CREATE = true;
SUID = true;
try {
headers = new ArrayList<FileHeader>();
headers.add(new FileHeader("VARIABLE", "LIST", 1, '\t'));
} catch (Exception e) {
e.printStackTrace();
}
}
/** Compares all values to whats already in the database returns the number of errors found. */
private void checkCreate(
String id_or_alias,
String ind,
String variable,
String value,
String date,
String ref,
String comm,
int suid) {
// ResultSet rset;
int nrErrors = 0;
String identity = null;
try {
// First if no IDENTITY was sent, we need to get it through alias!
if (id_or_alias.equalsIgnoreCase("ALIAS")
&& (ind != null)
&& (!ind.trim().equalsIgnoreCase(""))) {
identity = db.getIdentity(ind);
} else {
identity = ind;
}
// compare to database, is this unique? (can it be inserted?)
if (!db.isPhenotypeUnique(variable, identity)) {
// the phenotype exists
String Message =
" The Phenotype [V="
+ variable
+ ", I="
+ identity
+ "] already exists, cannot be created.";
errorList.add(Message);
nrErrors++;
}
// Does the individual exist?
if (db.isIndividualUnique(identity)) {
// the Individual does not exist
String Message = " The Individual with " + id_or_alias + " " + ind + " does not exist.";
errorList.add(Message);
}
// does variable exist?
if (db.isVariableUnique(variable)) {
// the variable does not exist
String Message = " Variable " + variable + " does not exist";
errorList.add(Message);
}
} catch (Exception e) {
// Flag for error and set the errMessage if it has not been set
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);
}
}
/**
* Checks if the genotype exists, that alleles exists etc. Makes certain the genotype can be
* updated
*/
private void checkCreateOrUpdate(
String id_or_alias,
String ind,
String variable,
String value,
String date,
String ref,
String comm,
int suid,
Vector deviationMessages,
Vector databaseValues,
char delim) {
// ResultSet rset;
String identity = null;
boolean match = false;
try {
// First if no IDENTITY was sent, we need to get it through alias!
if (id_or_alias.equalsIgnoreCase("ALIAS")
&& ind != null
&& !ind.trim().equalsIgnoreCase("")) {
identity = db.getIdentity(ind);
} else identity = ind;
// compare to database, does genotype exist? can it be updated..
if (!db.isPhenotypeUnique(variable, identity)) {
// Genotype exists -- check for update
checkUpdate(
id_or_alias,
ind,
variable,
value,
date,
ref,
comm,
suid,
deviationMessages,
databaseValues,
delim);
} else {
// Genotype doesn't exist
checkCreate(id_or_alias, ind, variable, value, date, ref, comm, suid);
// checkCreate(id_or_alias, ind, variable, value, date, ref, comm, suid,
// errorMessages,warningMessages);
}
} // try
catch (Exception e) {
// Flag for error and set the errMessage if it has not been set
e.printStackTrace(System.err);
}
}
/** Creates a new instance of ImportPhenotypes */
public ImportPhenotypes() {
CREATE = true;
UPDATE = true;
CREATE_OR_UPDATE = true;
SUID = true;
LEVEL = true;
try {
headers = new ArrayList<FileHeader>();
headers.add(new FileHeader("PHENOTYPE", "LIST", 1, '\t'));
headers.add(new FileHeader("PHENOTYPE", "MATRIX", 1, '\t'));
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* @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);
}
}
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;
}
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;
}
/**
* @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;
}