public void process(JSONRequestContext jsonRequestContext) {
ResourceDAO resourceDAO = DAOFactory.getInstance().getResourceDAO();
ResourceCategoryDAO resourceCategoryDAO = DAOFactory.getInstance().getResourceCategoryDAO();
WorkResourceDAO workResourceDAO = DAOFactory.getInstance().getWorkResourceDAO();
TagDAO tagDAO = DAOFactory.getInstance().getTagDAO();
String name = jsonRequestContext.getRequest().getParameter("name");
Long resourceId =
NumberUtils.createLong(jsonRequestContext.getRequest().getParameter("resource"));
Double hourlyCost =
NumberUtils.createDouble(jsonRequestContext.getRequest().getParameter("hourlyCost"));
Double costPerUse =
NumberUtils.createDouble(jsonRequestContext.getRequest().getParameter("costPerUse"));
Long version = NumberUtils.createLong(jsonRequestContext.getRequest().getParameter("version"));
String tagsText = jsonRequestContext.getString("tags");
Set<Tag> tagEntities = new HashSet<Tag>();
if (!StringUtils.isBlank(tagsText)) {
List<String> tags = Arrays.asList(tagsText.split("[\\ ,]"));
for (String tag : tags) {
if (!StringUtils.isBlank(tag)) {
Tag tagEntity = tagDAO.findByText(tag.trim());
if (tagEntity == null) tagEntity = tagDAO.create(tag);
tagEntities.add(tagEntity);
}
}
}
WorkResource workResource = workResourceDAO.findById(resourceId);
if (!version.equals(workResource.getVersion()))
throw new SmvcRuntimeException(
PyramusStatusCode.CONCURRENT_MODIFICATION,
Messages.getInstance()
.getText(
jsonRequestContext.getRequest().getLocale(),
"generic.errors.concurrentModification"));
ResourceCategory resourceCategory =
resourceCategoryDAO.findById(
NumberUtils.createLong(jsonRequestContext.getRequest().getParameter("category")));
workResourceDAO.update(workResource, name, resourceCategory, costPerUse, hourlyCost);
resourceDAO.setResourceTags(workResource, tagEntities);
jsonRequestContext.setRedirectURL(jsonRequestContext.getReferer(true));
}
/**
* Returns the value as a {@link Double} value. The returned value will be <code>0</code> or
* <code>1</code> if the {@link #value} is a boolean value. If {@link #value} can not be converted
* into a number, a {@link NumberFormatException} is thrown.
*
* @return {@link #value} as {@link Double}
*/
public double getValueAsDouble() {
if (NumberUtils.isNumber(value)) {
return NumberUtils.createDouble(value);
}
if (isBooleanValue(value)) {
return BooleanUtils.toBoolean(value) ? 1 : 0;
}
throw new NumberFormatException();
}
// For example, here is a line from the 5kb chr1 MAPQGE30 raw observed contact matrix
// (GM12878_combined/5kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_5kb.RAWobserved):
// 40000000 40100000 59.0
private static void processRawContactInformation(
String fileToRead,
double minValue,
ArrayList<DesiredChrContact> contactsToCheck,
boolean intra)
throws IOException {
// Check if sorted version is available
// If not make sorted available.
if (!Gpio.exists(fileToRead + ".sorted")) {
if (intra) {
umcg.genetica.io.chrContacts.SortIntraChrContacts.readNonSortedWriteSorted(
fileToRead, fileToRead + ".sorted");
} else {
umcg.genetica.io.chrContacts.SortInterChrContacts.readNonSortedWriteSorted(
fileToRead, fileToRead + ".sorted");
}
}
int numberToBeMatched = 0;
LineIterator it = FileUtils.lineIterator(new File(fileToRead + ".sorted"), "UTF-8");
try {
while (it.hasNext()) {
String[] parts = StringUtils.split(it.nextLine(), '\t');
int posChr1 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[0]);
int posChr2 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[1]);
while (numberToBeMatched < contactsToCheck.size()) {
if (posChr1 < contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
break;
} else if (posChr1 == contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
if (posChr2 < contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
break;
}
if (posChr2 == contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
double contact = org.apache.commons.lang.math.NumberUtils.createDouble(parts[2]);
if (contact >= minValue) {
contactsToCheck.get(numberToBeMatched).setContact();
numberToBeMatched++;
} else {
numberToBeMatched++;
}
} else if (posChr2 > contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
numberToBeMatched++;
}
} else if (posChr1 > contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
numberToBeMatched++;
}
}
}
} finally {
LineIterator.closeQuietly(it);
}
}
/**
* Turns a string value into a java.lang.Number.
*
* <p>First, the value is examined for a type qualifier on the end (<code>'f','F','d','D','l','L'
* </code>). If it is found, it starts trying to create successively larger types from the type
* specified until one is found that can represent the value.
*
* <p>If a type specifier is not found, it will check for a decimal point and then try
* successively larger types from <code>Integer</code> to <code>BigInteger</code> and from <code>
* Float</code> to <code>BigDecimal</code>.
*
* <p>If the string starts with <code>0x</code> or <code>-0x</code>, it will be interpreted as a
* hexadecimal integer. Values with leading <code>0</code>'s will not be interpreted as octal.
*
* <p>Returns <code>null</code> if the string is <code>null</code>.
*
* <p>This method does not trim the input string, i.e., strings with leading or trailing spaces
* will generate NumberFormatExceptions.
*
* @param str String containing a number, may be null
* @return Number created from the string
* @throws NumberFormatException if the value cannot be converted
*/
public static Number createNumber(String str) throws NumberFormatException {
if (str == null) {
return null;
}
if (StringUtils.isBlank(str)) {
throw new NumberFormatException("A blank string is not a valid number");
}
if (str.startsWith("--")) {
// this is protection for poorness in java.lang.BigDecimal.
// it accepts this as a legal value, but it does not appear
// to be in specification of class. OS X Java parses it to
// a wrong value.
return null;
}
if (str.startsWith("0x") || str.startsWith("-0x")) {
return createInteger(str);
}
char lastChar = str.charAt(str.length() - 1);
String mant;
String dec;
String exp;
int decPos = str.indexOf('.');
int expPos = str.indexOf('e') + str.indexOf('E') + 1;
if (decPos > -1) {
if (expPos > -1) {
if (expPos < decPos) {
throw new NumberFormatException(str + " is not a valid number.");
}
dec = str.substring(decPos + 1, expPos);
} else {
dec = str.substring(decPos + 1);
}
mant = str.substring(0, decPos);
} else {
if (expPos > -1) {
mant = str.substring(0, expPos);
} else {
mant = str;
}
dec = null;
}
if (!Character.isDigit(lastChar)) {
if (expPos > -1 && expPos < str.length() - 1) {
exp = str.substring(expPos + 1, str.length() - 1);
} else {
exp = null;
}
// Requesting a specific type..
String numeric = str.substring(0, str.length() - 1);
boolean allZeros = isAllZeros(mant) && isAllZeros(exp);
switch (lastChar) {
case 'l':
case 'L':
if (dec == null
&& exp == null
&& (numeric.charAt(0) == '-' && isDigits(numeric.substring(1))
|| isDigits(numeric))) {
try {
return createLong(numeric);
} catch (NumberFormatException nfe) {
// Too big for a long
}
return createBigInteger(numeric);
}
throw new NumberFormatException(str + " is not a valid number.");
case 'f':
case 'F':
try {
Float f = NumberUtils.createFloat(numeric);
if (!(f.isInfinite() || (f.floatValue() == 0.0F && !allZeros))) {
// If it's too big for a float or the float value = 0 and the string
// has non-zeros in it, then float does not have the precision we want
return f;
}
} catch (NumberFormatException nfe) {
// ignore the bad number
}
// Fall through
case 'd':
case 'D':
try {
Double d = NumberUtils.createDouble(numeric);
if (!(d.isInfinite() || (d.floatValue() == 0.0D && !allZeros))) {
return d;
}
} catch (NumberFormatException nfe) {
// ignore the bad number
}
try {
return createBigDecimal(numeric);
} catch (NumberFormatException e) {
// ignore the bad number
}
// Fall through
default:
throw new NumberFormatException(str + " is not a valid number.");
}
} else {
// User doesn't have a preference on the return type, so let's start
// small and go from there...
if (expPos > -1 && expPos < str.length() - 1) {
exp = str.substring(expPos + 1, str.length());
} else {
exp = null;
}
if (dec == null && exp == null) {
// Must be an int,long,bigint
try {
return createInteger(str);
} catch (NumberFormatException nfe) {
// ignore the bad number
}
try {
return createLong(str);
} catch (NumberFormatException nfe) {
// ignore the bad number
}
return createBigInteger(str);
} else {
// Must be a float,double,BigDec
boolean allZeros = isAllZeros(mant) && isAllZeros(exp);
try {
Float f = createFloat(str);
if (!(f.isInfinite() || (f.floatValue() == 0.0F && !allZeros))) {
return f;
}
} catch (NumberFormatException nfe) {
// ignore the bad number
}
try {
Double d = createDouble(str);
if (!(d.isInfinite() || (d.doubleValue() == 0.0D && !allZeros))) {
return d;
}
} catch (NumberFormatException nfe) {
// ignore the bad number
}
return createBigDecimal(str);
}
}
}
private static void processNormalizedIntraContactInformation(
String fileToRead,
String baseName,
String normMethod,
String chrSmaller,
ArrayList<DesiredChrContact> contactsToCheck,
String resolution,
double minValue,
TextFile outWriter)
throws IOException {
// ReadIn normalization chr1
TextFile inputNormChr1 =
new TextFile(
baseName + "\\chr" + chrSmaller + "_" + resolution + "." + normMethod, TextFile.R);
ArrayList<String> normFactorSmallerChr = inputNormChr1.readAsArrayList();
inputNormChr1.close();
// System.out.println("Done reading norm factor 1");
if (!Gpio.exists(fileToRead + ".sorted")) {
umcg.genetica.io.chrContacts.SortIntraChrContacts.readNonSortedWriteSorted(
fileToRead, fileToRead + ".sorted");
}
int numberToBeMatched = 0;
LineIterator it = FileUtils.lineIterator(new File(fileToRead + ".sorted"), "UTF-8");
try {
while (it.hasNext()) {
String[] parts = StringUtils.split(it.nextLine(), '\t');
int posChr1 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[0]);
int posChr2 = org.apache.commons.lang.math.NumberUtils.createInteger(parts[1]);
while (numberToBeMatched < contactsToCheck.size()) {
if (posChr1 < contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
break;
} else if (posChr1 == contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
if (posChr2 < contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
break;
}
if (posChr2 == contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
String factor1Base =
normFactorSmallerChr.get((posChr1 / getNumericResolution(resolution)) + 1);
String factor2Base =
normFactorSmallerChr.get((posChr2 / getNumericResolution(resolution)) + 1);
double factor1;
double factor2;
if (StringUtils.isNumeric(factor1Base) && StringUtils.isNumeric(factor2Base)) {
factor1 = org.apache.commons.lang.math.NumberUtils.createDouble(factor1Base);
factor2 = org.apache.commons.lang.math.NumberUtils.createDouble(factor2Base);
double contact =
org.apache.commons.lang.math.NumberUtils.createDouble(parts[2])
/ (factor1 * factor2);
if (contact >= minValue) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\tContact\t"
+ contact
+ "\t"
+ org.apache.commons.lang.math.NumberUtils.createDouble(parts[2]));
numberToBeMatched++;
} else {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
} else {
System.out.println("Error in files.");
numberToBeMatched++;
}
} else if (posChr2 > contactsToCheck.get(numberToBeMatched).getChrLocationLarger()) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
} else if (posChr1 > contactsToCheck.get(numberToBeMatched).getChrLocationSmaller()) {
outWriter.writeln(
contactsToCheck.get(numberToBeMatched).getSnpName()
+ "\t"
+ contactsToCheck.get(numberToBeMatched).getProbeName()
+ "\t"
+ posChr1
+ "\t"
+ posChr2
+ "\t-\t-\t-");
numberToBeMatched++;
}
}
}
} finally {
LineIterator.closeQuietly(it);
}
}
