Groovy 1.6.4 + IntelliJ8 + Groovy Plugin - nullpointer

For soem reason I keep get nullpointer exception with IntelliJ, which have nothing todo with my code.
They only happen if I execute the project from intelliJ out.

example for this would be:


src/example/dsl/quant.dsl
Caught: java.lang.NullPointerException
java.lang.NullPointerException
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:39)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:40)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.QuantificatorDSL.run(QuantificatorDSL.groovy:45)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.QuantificatorDSL$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:40)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.QuantificatorDSL.main(QuantificatorDSL.groovy:33)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:592)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:234)
at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1296)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:719)
at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:262)
at groovy.lang.GroovyShell.run(GroovyShell.java:218)
at groovy.lang.GroovyShell.run(GroovyShell.java:147)
at groovy.ui.GroovyMain.processOnce(GroovyMain.java:493)
at groovy.ui.GroovyMain.run(GroovyMain.java:308)
at groovy.ui.GroovyMain.process(GroovyMain.java:294)
at groovy.ui.GroovyMain.processArgs(GroovyMain.java:111)
at groovy.ui.GroovyMain.main(GroovyMain.java:92)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:592)
at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:108)
at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)


Now this exception does not occur, if I make a complete rebuild.

For some reason it is not able to initialize a class if it defined in another source file. More about this is written here

groovy 1.5.6 and delegates

while trying to write a DSL I discovered an annoying bug in groovy 1.5.6, I guess. Basically if I define a delegate for a closure it has to be in the same file as the closure. If i define it in another file I always get a nullpointer exception...


example:



class MyDelegate {
def test() {
println "tada"
}
}

static ExpandoMetaClass createEMC(Class clazz, Closure cl) {
ExpandoMetaClass emc = new ExpandoMetaClass(clazz, false)

cl(emc)

emc.initialize()
return emc
}

Script dslScript = new GroovyShell().parse("test{\ntest()\n}")

dslScript.metaClass = createEMC(dslScript.class, {
ExpandoMetaClass emc ->

emc.test = {

Closure closure ->
closure.delegate = new MyDelegate()
closure.resolveStrategy = Closure.DELEGATE_FIRST

try {
closure()
}
catch (Exception e) {
e.printStackTrace()
}
}
})
dslScript.run()



this works fine. Now if I move the class 'MyDelegate' to it's own file I end up with the following exception.


java.lang.NullPointerException
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.getDelegateMethod(ClosureMetaClass.java:207)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:78)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrent0(ScriptBytecodeAdapter.java:112)
at Script1$_run_closure1.doCall(Script1.groovy:2)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:248)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:78)
at Script1$_run_closure1.doCall(Script1.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:248)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:756)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:778)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:758)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:170)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeClosure(ScriptBytecodeAdapter.java:605)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.Tester$_run_closure1_closure2.doCall(Tester.groovy:38)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:248)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:756)
at groovy.lang.Closure.call(Closure.java:292)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:72)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:912)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:946)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:78)
at Script1.run(Script1.groovy:1)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:912)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:946)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:756)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:778)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:758)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:170)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethod0(ScriptBytecodeAdapter.java:198)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.Tester.run(Tester.groovy:45)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:912)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:756)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:778)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:758)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:401)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1105)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:749)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:170)
at edu.ucdavis.genomics.metabolomics.binbase.quantificator.dsl.Tester.main(Tester.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1105)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:749)
at groovy.lang.GroovyShell.runMainOrTestOrRunnable(GroovyShell.java:244)
at groovy.lang.GroovyShell.run(GroovyShell.java:218)
at groovy.lang.GroovyShell.run(GroovyShell.java:147)
at groovy.ui.GroovyMain.processOnce(GroovyMain.java:493)
at groovy.ui.GroovyMain.run(GroovyMain.java:308)
at groovy.ui.GroovyMain.process(GroovyMain.java:294)
at groovy.ui.GroovyMain.processArgs(GroovyMain.java:111)
at groovy.ui.GroovyMain.main(GroovyMain.java:92)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:101)
at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)


time to give groovy 1.6.4 a try and maybe migrate my project over to it.

DSL - love or hate?

recently I started to work more with DSL's (domain specific language) since I wanted to go away from doing everything in XML.

The approach of XML is great, but I'm not a big fan of the overhead with it.

So the first approach was to create a DSL for the BinBase system, precisely to provide the user with a really simple way of calculating an experiment.

It should look something like this:


/**
* our quantification dsl
*/
quantify {

//define the name of the setup
name "quantification for ${new Date()}"

//define the samples for the calculations
sample "sample 1"
sample "sample 2"
sample "sample 3"
sample "sample 4"
sample "sample 5"
sample "sample 6"
sample "sample 7"
sample "sample 8"
sample "sample 9"
sample "sample 10"

//defines the bins in the table
bin 321, 22.0
bin 322
bin 323
bin 324
bin 325, 22.0

//report definition
report {

sizeDown 50

format "xls"

replace true
}
}


And the result should calculate the data, send them to the cluster and generates a quantification report. If this all works out the way we want it. We will than adapt it to schedule BinBase experiment's this way.

My current fazit is that I love the idea of DSL's, but hate the implementations of it.

jboss - binding to all registered network cards

The JBoss Application server binds only to the local interface '127.0.0.1' since the version 4.0

Since this is not desired in a production system you can override this feature with the '-b' command.

An example to start jboss in the all configuration and bound to all registered interfaces would be


sh run.sh -b 0.0.0.0 -c all


creating a project with maven2

it is kinda pathetic I'm using maven since several years now and just can't remember this one command.


mvn archetype:create -DgroupId=myGroup -DartifactId=myArtifact


so I write it down here to make it easier for me to lookup.

osx - set disk as startup disk via terminal

to set a disk as startup disk is quite simple just execute:


sudo bless -mount /Volumes/"name of your startup disk" -setBoot


run-app vs run-war

the main differences between these two commands is that:

run-app runs a grails applications and allows the reloading from resources
run-war generates a war file and runs the war file, so no reloading of resources.

Short during development you want to use run-app.