/* good1() changes IO.staticReturnsTrue() to IO.staticReturnsFalse() */
private void good1() throws Throwable {
if (IO.staticReturnsFalse()) {
/* INCIDENTAL: CWE 561 Dead Code, the code below will never run */
IO.writeLine("Benign, fixed string");
} else {
BufferedReader readerBuffered = null;
InputStreamReader readerInputStream = null;
try {
readerInputStream = new InputStreamReader(System.in, "UTF-8");
readerBuffered = new BufferedReader(readerInputStream);
double num = 0;
IO.writeString("Enter double number (1e-50): ");
try {
num = Double.parseDouble(readerBuffered.readLine());
} catch (NumberFormatException exceptionNumberFormat) {
IO.writeLine("Error parsing number");
}
/* FIX: check for conversion error */
if (num > Float.MAX_VALUE || num < Float.MIN_VALUE) {
IO.writeLine("Error, cannot safely cast this number to a float!");
return;
}
IO.writeLine("" + (float) num);
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error with stream reading", exceptIO);
} finally {
try {
if (readerBuffered != null) {
readerBuffered.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing BufferedReader", exceptIO);
}
try {
if (readerInputStream != null) {
readerInputStream.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing InputStreamReader", exceptIO);
}
}
}
}
public void bad() throws Throwable {
for (int j = 0; j < 1; j++) {
BufferedReader readerBuffered = null;
InputStreamReader readerInputStream = null;
try {
/* Enter: 1e-50, result should be 0.0 (for bad case)
*
* Note: alternate input
* 999999999999999999999999999999999999999999999999999999999999999
*/
readerInputStream = new InputStreamReader(System.in, "UTF-8");
readerBuffered = new BufferedReader(readerInputStream);
double doubleNumber = 0;
IO.writeString("Enter double number (1e-50): ");
try {
doubleNumber = Double.parseDouble(readerBuffered.readLine());
} catch (NumberFormatException exceptionNumberFormat) {
IO.writeLine("Error parsing number");
}
/* FLAW: should not cast without checking if conversion is safe */
IO.writeLine("" + (float) doubleNumber);
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error with stream reading", exceptIO);
} finally {
try {
if (readerBuffered != null) {
readerBuffered.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing BufferedReader", exceptIO);
}
try {
if (readerInputStream != null) {
readerInputStream.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing InputStreamReader", exceptIO);
}
}
}
}
private void buildXmlPropertiesFile() {
System.out.println(
"\nBuilding and checking your pipeline properties file -> " + truncPipePropFile);
StringBuilder toPrint = new StringBuilder();
// walk through the prop file
String[] prop = IO.loadFileIntoStringArray(truncPipePropFile);
Pattern val = Pattern.compile("(<entry key.+>)([D|A|B].*)</entry>");
boolean missingFile = false;
for (String s : prop) {
// does it match a file needing prepending? Data/, Apps/, Bed/
Matcher mat = val.matcher(s);
if (mat.matches()) {
File test = new File(referenceDir, mat.group(2));
if (test.exists()) {
System.out.println("Found\t" + test);
toPrint.append(mat.group(1));
toPrint.append(test.toString());
toPrint.append("</entry>");
} else {
System.out.println("Misssing\t" + test);
missingFile = true;
}
}
// threads?
else if (s.contains("threads"))
toPrint.append("<entry key=\"threads\">" + threads + "</entry>");
// nope just save it and add a line return
else toPrint.append(s);
toPrint.append("\n");
}
// anything missing? if so exit
if (missingFile)
Misc.printErrAndExit(
"\nFailed to find all of the files in your properties file, see above.\n");
// OK, write it out
completePipelinePropFile = new File(outputDirectory, "pipelineProperties.xml");
if (IO.writeString(toPrint.toString(), completePipelinePropFile) == false)
Misc.printErrAndExit("Problem writing -> " + truncPipePropFile);
}
/* good1() use the GoodSinkBody in the for statement */
private void good1() throws Throwable {
for (int k = 0; k < 1; k++) {
BufferedReader readerBuffered = null;
InputStreamReader readerInputStream = null;
try {
readerInputStream = new InputStreamReader(System.in, "UTF-8");
readerBuffered = new BufferedReader(readerInputStream);
double num = 0;
IO.writeString("Enter double number (1e-50): ");
try {
num = Double.parseDouble(readerBuffered.readLine());
} catch (NumberFormatException exceptionNumberFormat) {
IO.writeLine("Error parsing number");
}
/* FIX: check for conversion error */
if (num > Float.MAX_VALUE || num < Float.MIN_VALUE) {
IO.writeLine("Error, cannot safely cast this number to a float!");
return;
}
IO.writeLine("" + (float) num);
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error with stream reading", exceptIO);
} finally {
try {
if (readerBuffered != null) {
readerBuffered.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing BufferedReader", exceptIO);
}
try {
if (readerInputStream != null) {
readerInputStream.close();
}
} catch (IOException exceptIO) {
IO.logger.log(Level.WARNING, "Error closing InputStreamReader", exceptIO);
}
}
}
}
private void executePipelineJob() {
String[] cmd = null;
try {
// write out tempTemplate
File template = new File(outputDirectory, "pipelineTemplate.xml");
if (IO.writeString(xmlTemplate, template) == false)
Misc.printErrAndExit("Problem writing -> " + template);
// build and execute cmd
cmd =
new String[] {
"java",
"-jar",
"-Xmx2G",
pJar.getCanonicalPath(),
"-props",
completePipelinePropFile.getCanonicalPath(),
template.getCanonicalPath()
};
String stringCmd = Misc.stringArrayToString(cmd, " ");
System.out.println("\nExecuting:\n" + stringCmd);
System.out.println("\nPipelineOutput:");
String[] out = IO.executeViaProcessBuilder(cmd, true);
// check output for possible errors
for (String line : out) {
String lcLine = line.toLowerCase();
// watch out for cases where error is mentioned in a warning output line.
if (lcLine.contains("error") && lcLine.startsWith("warning") == false)
Misc.printErrAndExit(
"\n\nERROR found in Pipeline.jar output, see above. Aborting!\n" + line);
}
} catch (Exception e) {
e.printStackTrace();
Misc.printErrAndExit("ERROR: executing " + Misc.stringArrayToString(cmd, " "));
}
}