We Keep Coding

Difficulty with Octave's "javaMethod"

In this question, I was trying to import java classes into Octave. In my particular example, I was (and am) working with javaplex, a set of java tools with code for implementation in Matlab. The answer to the question shows that, whereas in Matlab you would do the following:
import edu.stanford.math.plex4.*;
api.Plex4.createExplicitSimplexStream();
The answer provided in the question showed that the way to do this in Octave is
javaMethod( 'createExplicitSimplexStream', 'edu.stanford.math.plex4.api.Plex4')
This was working excellently, but then I ran into a strange problem. There is another method called createVietorisRipsStream. In Matlab, I would run this with a line such as the following:
api.Plex4.createVietorisRipsStream(parameters);
So I would think that the equivalent command in Octave would be
javaMethod( 'createVietorisRipsStream', 'edu.stanford.math.plex4.api.Plex4')
However, when I do this, I get the following error:
error: [java] java.lang.NoSuchMethodException: createVietorisRipsStream
I'm not sure why this error is coming up, and both are in the same JAVA file ('Plex4'). I did take a look at the Plex4 file, and there are two differences between createExplicitSimplexStream and createVietorisRipsStream that I noticed:
There are two instances of createExplicitSimplexStream and six instances of createVietorisRipsStream
There is bit that says <double[]>. I don't know if that is relevant however (I haven't read or wrote much java, up to this point, I've been able to use the tutorial they provided to only use Matlab and not have to look under the hood).
Here is one example of the code from the Plex4 file for a createExplicitSimplexStream:
public static ExplicitSimplexStream createExplicitSimplexStream(double maxFiltrationValue) {
return new ExplicitSimplexStream(maxFiltrationValue);
}
Here is one example of the code from the Plex4 file for a createVietorisRipsStream:
public static VietorisRipsStream<double[]> createVietorisRipsStream(double[][] points, int maxDimension, double maxFiltrationValue, int numDivisions) {
return FilteredStreamInterface.createPlex4VietorisRipsStream(points, maxDimension, maxFiltrationValue, numDivisions);
}
Any idea of why I'm getting the error I'm getting?

Read the octave documentation for the Java section properly, it's only 4 pages, and it explains this well!
As I mentioned in the comments in the previous question, the way to call a java method with arguments is:
javamethod(
name of method as a string,
name of class fully qualified with packages as a string,
method's first argument,
method's second argument,
... etc
)
This is the only way to call 'static' methods; with normal 'instance' methods, you can either use javaMethod and replace the name of the class by the java object itself, or simply use it as you would in java, i.e. objectname.methodname(arg1, arg2, ... etc)
I have implemented here the tutorial for you to have a look at (page 14 in the pdf). (don't forget to run the modified 'load_javaplex' script first).
octave:2> max_dimension = 3;
octave:3> max_filtration_value = 4;
octave:4> num_divisions = 1000;
octave:5> point_cloud = javaMethod( 'getHouseExample', 'edu.stanford.math.plex4.examples.PointCloudExamples')
point_cloud =
<Java object: double[][]>
octave:6> stream = javaMethod( 'createVietorisRipsStream', 'edu.stanford.math.plex4.api.Plex4', point_cloud, max_dimension, max_filtration_value, num_divisions)
stream =
<Java object: edu.stanford.math.plex4.streams.impl.VietorisRipsStream>
octave:7> persistence = javaMethod( 'getModularSimplicialAlgorithm', 'edu.stanford.math.plex4.api.Plex4', max_dimension, 2)
persistence =
<Java object: edu.stanford.math.plex4.autogen.homology.IntAbsoluteHomology>
octave:8> intervals = persistence.computeIntervals(stream)
intervals =
<Java object: edu.stanford.math.plex4.homology.barcodes.BarcodeCollection>
(I have not gone further because plot_barcodes needs to be modified a bit too; it's only a couple of lines but it would be too much to post here, the reasoning is the same though).
Also, if you're not sure what is meant by class constructors, class methods, and static vs instance-specific methods, unfortunately this is more to do with java, although it should be pretty introductory stuff. It is well worth reading up a bit about it first.
Good luck!

In the startup scripts generated by gradle's application plugin, how can I have the program name passed in to the application?

Executing the gradle application plugin's installDist task creates a directory build/install/my-application-name/bin that contains wrapper scripts, my-application-name and my-application-name.bat. Running either of these scripts runs the application, and arguments passed to these scripts are passed to the underlying application.
In UNIX shell scripts you can access the name that was used to execute the program as $0. In fact, the UNIX version of the gradle-generated startup script uses $0 several times.
How can I configure the gradle application plugin such that these scripts will pass the value of $0 (and whatever the Windows equivalent is on Windows) into the underlying application, perhaps as a Java system property?

Since parameter for obtaining the name of the script being run is referenced differently in Linux($0) and in Windows(%0), the most straightforward way to generate custom scripts would be to use separate custom templates for the respective start script generators:
startScripts {
unixStartScriptGenerator.template = resources.text.fromFile('unixStartScript.txt')
windowsStartScriptGenerator.template = resources.text.fromFile('windowsStartScript.txt')
}
The default templates are easy to obtain invoking e.g. unixStartScriptGenerator.template.asString()
Documentation on customizing the start scripts can be found here.

This is what I ended up doing, based on jihor's answer. I'm posting it here just so that there's a working answer for anyone else interested:
startScripts {
def gen = unixStartScriptGenerator
gen.template = resources.text.fromString(
gen.template.asString().replaceFirst('(?=\nDEFAULT_JVM_OPTS=.*?\n)') {
'\nJAVA_OPTS="\\$JAVA_OPTS "\'"-Dprogname=\\$0"\''
})
// TODO: do something similar for windowsStartScriptGenerator
}
This uses replaceFirst is instead of replace so we can match a pattern. This is a little less brittle, and also lets us use lookahead so we don't have to actually replace what we're looking for. (This is groovy's variant of replaceFirst that takes a closure, by the way. This requires far less escaping than the version that takes a replacement string in this case.)
Also, instead of:
JAVA_OPTS="$JAVA_OPTS -Dprogname=$0"
we actually need something like:
JAVA_OPTS="$JAVA_OPTS "'"-Dprogname=$0"'
This is because $0 may contains special character (like spaces), and the startup script removes one level of quoting in the value of $JAVA_OPTS using eval set --.
(If anyone knows how to make this work on Windows, pleas feel free to update this answer.)

I took an alternative approach. According to the documentation, as far back as Gradle 2.4 and all the way through Gradle 4.8, we should be able to set the following properties within the startScripts task:
applicationName
optsEnvironmentVar
exitEnvironmentVar
mainClassName
executableDir
defaultJvmOpts
appNameSystemProperty
appHomeRelativePath
classpath
Unfortunately, this is not true for the following properties, which seem to have never been exposed:
appNameSystemProperty
appHomeRelativePath
If appNameSystemProperty were exposed as the documentation describes, then we should be able to simply do the following:
startScripts {
applicationName = 'foo'
appNameSystemProperty = 'appName'
}
This would then result in the addition of -DappName=foo to the Java command constructed within both of the start scripts.
Since this is not the case, I took the following approach, which is a bit more verbose than the earlier solution to this question, but is perhaps less brittle because it does not rely on tweaking the out-of-box templates. Instead, it results in the documented behavior.
startScripts {
mainClassName = '...'
applicationName = 'foo'
unixStartScriptGenerator =
new CustomStartScriptGenerator(generator: unixStartScriptGenerator)
windowsStartScriptGenerator =
new CustomStartScriptGenerator(generator: windowsStartScriptGenerator)
}
class CustomStartScriptGenerator implements ScriptGenerator {
#Delegate
ScriptGenerator generator
void generateScript(JavaAppStartScriptGenerationDetails details,
Writer destination) {
details = new CustomDetails(details: details)
this.generator.generateScript(details, destination)
}
static class CustomDetails implements JavaAppStartScriptGenerationDetails {
#Delegate
JavaAppStartScriptGenerationDetails details
#Override
String getAppNameSystemProperty() { 'appName' }
}
}

Mute Stanford coreNLP logging

First of all, Java is not my usual language, so I'm quite basic at it. I need to use it for this particular project, so please be patient, and if I have omitted any relevant information, please ask for it, I will be happy to provide it.
I have been able to implement coreNLP, and, seemingly, have it working right, but is generating lots of messages like:
ene 20, 2017 10:38:42 AM edu.stanford.nlp.process.PTBLexer next
ADVERTENCIA: Untokenizable: 【 (U+3010, decimal: 12304)
After some research (documentation, google, other threads here), I think (sorry, I don't know how I can tell for sure) coreNLP is finding the slf4j-api.jar in my classpath, and logging through it.
Which properties of the JVM can I use to set logging level of the messages that will be printed out?
Also, in which .properties file I could set them? (I already have a commons-logging.properties, a simplelog.properties and a StanfordCoreNLP.properties in my project's resource folder to set properties for other packages).

Om’s answer is good, but two other possibly useful approaches:
If it is just these warnings from the tokenizer that are annoying you, you can (in code or in StanfordCoreNLP.properties) set a property so they disappear: props.setProperty("tokenize.options", "untokenizable=NoneKeep");.
If slf4j is on the classpath, then, by default, our own Redwoods logger will indeed log through slf4j. So, you can also set the logging level using slf4j.

If I understand your problem, you want to disable all StanfordNLP logging message while the program is executing.
You can disable the logging message. Redwood logging framework is used as logging framework in Stanford NLP. First, clear the Redwood's default configuration(to display log message) then create StanfordNLP pipeline.
import edu.stanford.nlp.util.logging.RedwoodConfiguration;
RedwoodConfiguration.current().clear().apply();
StanfordCoreNLP pipeline = new StanfordCoreNLP(props);
Hope it helps.

In accordance with Christopher Manning's suggestion, I followed this link
How to configure slf4j-simple
I created a file src/simplelogger.properties with the line org.slf4j.simpleLogger.defaultLogLevel=warn.

I am able to solve it by setting a blank output stream to system error stream.
System.setErr(new PrintStream(new BlankOutputStream())); // set blank error stream
// ... Add annotators ...
System.setErr(System.err); // Reset to default
Accompanying class is
public class BlankOutputStream extends OutputStream {
#Override
public void write(int b) throws IOException {
// Do nothing
}
}

Om's answer disables all logging. However, if you wish to still log errors then use:
RedwoodConfiguration.errorLevel().apply();
I also use jdk logging instead of slf4j logging to avoid loading slfj dependencies as follows:
RedwoodConfiguration.javaUtilLogging().apply();
Both options can be used together and in any order. Required import is:
import edu.stanford.nlp.util.logging.RedwoodConfiguration;

Getting qualified method name by the line number

This question is Java and Maven specific. Please note the additional constraints below as they are different from other questions.
I have several Maven (Java) projects to analyze. What I have is:
the source code
maven-compiled Jave code with binaries in target/ folder
The question is:
Given one source code file (.java) and a line number there, how can I get the fully qualified name of the method that spans over that line? If the line is not in a method then just output null. Acceptable languages to implement this are: Java, ruby, or python.
Could you please answer the question in one of the following two ways?
use the binary and extract qualified method name of that line. (This might involve weave in debug info, but that is fine.)
directly use the source file given, try to parse it and use the AST.
Using specific libraries (like BCEL) or any 3rd party ones (as long as they are well documented and usable) are OK, too.
Many many thanks for the huge help!

Unfortunately, your question is full of drawbacks:
You could, of corse, parse the input source (through an Javacc or ANTLR parser) until you reach the desired line. But it seems a waste of effort to parse the same source since you already have the .class files.
So, it seems better to analyze the .class file. But unfortunately, you have no gurantee that this is the class where your line spawns at, because there can be more than one class defined in the same source file.
Augh! That leads me to a kind of complicated solution:
I'll declare a class which will contain all the login:
public class SourceMethodsIndexer
{
private final SortedMap<Integer, List<Method>> indexOfMethodsByFirstLineNumber;
}
The constructor will be like this:
public SourceMethodsIndexer(File sourceFile)
... and should do these tasks:
1.Browse the class directory related to the target package.
File targetPackageDir=getTargetPackageDir(sourceFile);
File[] classFiles=targetPackageDir.listFiles(new FileFilter(){
public boolean accept(File dir, String name){
return name.endsWith(".class");
}
});
2.Use Apache BCEL to collect all the non public classes belonging to your input source file (you can invoke JavaClass.getSourceFileName() to filter classes), plus the public class corresponding to the name of your input source file.
Collection<JavaClass> targetClasses=getNonPublicClasses(classFiles, sourceFile.getName());
targetClasses.add(publicClass);
3.Collect then all the methods in each class.
Set<Method> targetMethods=new HashSet<Method>(1024);
for (JavaClass javaClass:targetClasses)
{
targetMethods.addAll(Arrays.asList(javaClass.getMethods()));
}
4.Now you can either search directly your line number, or index first the methods by line number to access them later more quickly: JavaClass.getMethods()[n].getLineNumberTable().getSourceLine(0) (take care that there could be repeated values).
this.indexOfMethodsByFirstLineNumber=new TreeMap<Integer, List<Method>>((int)(1.7d*methods.size()));
for (Method method: methods)
{
// Note: The -1 in this line stands to make the SortedMap work properly when searching for ranges.
int firstLine=getLineNumberTable().getSourceLine(0)-1;
List<Method> methodsInTheSameLine=indexOfMethodsByFirstLineNumber.get(firstLine);
if (methodsInTheSameLine==null)
{
methodsInTheSameLine=new ArrayList<Method>();
indexOfMethodsByFirstLineNumber.put(firstLine,methodsInTheSameLine);
}
methodsInTheSameLine.add(method);
}
5.Public a method to do the search:
public Method getMethodByLine(int lineNumber)
{
Set<Method> methodsInTheSameLine=this.indexOfMethodsByFirstLineNumber.headMap(lineNumber).lastKey();
if (methodsInTheSameLine.size()==0)
{
// There are no methods method in that line: Absurd.
}
else if (methodsInTheSameLine.size()>1)
{
// There are more than one method in that line. Hardly probable, but possible.
}
else
{
// There is one method in that line:
return methods.get(0);
}
}

There are a number of open source Maven plugins which analyse source code, and report on a per-method basis. A careful study of some of those may be your best bet.
Examples include Checkstyle, FindBugs, PMD, JDepend, JavaNCSS.
Also take a look at SonarQube.

How to write caller location information in a log file using Java, without hurting performance?

How can I write caller location information (Java source file and line), in a log file using Java and log4j, but without hurting performance?
log4j allow you to write such information in the log file, but it uses the stack trace to get that it information, every time a log statement is issued, what causes performance degradation.
I'm looking for a performance friendly alternative, like getting the location information at compile time instead at runtime. It is possible to use annotations to accomplish that? Or maybe some other technique?

How about making it part of the build process to replace certain placeholders, like $filename$ and $linenumber$ in this snippet.
logger.info("The original message... $filename$ $linenumber$");
To replace the filename, it may suffice to have keyword substitution with your revision control system. Disclaimer: this is just from the top of my head, I never tried it myself.

I agree with Rob that it is generally unnecessary. Usually there's some distinct string in a log message, searching for it will get to the source. With a good IDE this is really fast.
Now, given the question as is, this is a possible solution:
Class Foo
void bar()
new Logger(){} . warn("blah");
for each log action at runtime, a new object is created - that's not a problem.
for each line of source containing such log statement, a new class is created. that can be too many.
here's how the magic works:
abstract public class Logger
static Map<Class, String> sourceInfo = new ...
public Logger()
Class thisClass = this.getClass();
String info = sourceInfo.get(thisClass);
if(info==null)
info = ... // init from stack trace
sourceInfo.put(thisClass,info)
this.info = info
public void warn(msg)
log(WARN, this.info,msg)