/** 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);
}
}
/** Check if object support this format. If a match is found return true else return false */
public boolean supportFormat(FileHeader hdr) {
boolean out = false;
try {
for (int i = 0; i < headers.size(); i++) {
if ((headers.get(i).formatTypeName().equals(hdr.formatTypeName()))
&& (headers.get(i).objectTypeName().equals(hdr.objectTypeName()))
&& (headers.get(i).version() == hdr.version())) {
return true;
}
}
} catch (Exception e) {
e.printStackTrace();
}
return false;
}
private boolean checkValues(
String identity, String variable, String value, String date, String ref, String comm) {
boolean ret = true;
if (identity == null || identity.trim().equals("")) {
errorList.add("Unable to read Identity/Alias.");
ret = false;
} else if (identity.length() > 11) {
errorList.add("Identity/Alias [" + identity + "] exceeds 11 characters.");
ret = false;
}
if (variable == null || variable.trim().equals("")) {
errorList.add("Unable to read variable.");
ret = false;
} else if (variable.length() > 20) {
errorList.add("Variable [" + variable + "] exceeds 20 characters.");
ret = false;
}
if (value == null || value.trim().equals("")) {
errorList.add("Unable to read value.");
ret = false;
}
if (value != null && value.length() > 20) {
errorList.add("Value [" + value + "] exceeds 20 characters.");
ret = false;
}
if (!(date == null || date.trim().equals(""))) {
try {
java.util.Date temp = java.sql.Date.valueOf(date);
} catch (Exception e) {
errorList.add("Date not in the format 'YYYY-MM-DD'");
ret = false;
}
}
if (ref != null && ref.length() > 32) {
errorList.add("Reference [" + ref + "] exceeds 32 characters.");
ret = false;
}
if (comm != null && comm.length() > 256) {
errorList.add("Comment exceeds 256 characters.");
ret = false;
}
return ret;
}
/** Checks if the phenotype exists Makes certain the genotype can be updated */
private void checkUpdate(
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)) {
String Message = "The Phenotype does not exist, cannot be updated.";
errorList.add(Message);
}
// rset.close();
} // try
catch (Exception e) {
// Flag for error and set the errMessage if it has not been set
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;
}
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 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;
}