Unable to execute klarigi

[NuriaQueralt]

Hi!

I read your preprint and I was trying to play with klarigi, but I cannot run it due to some errors that arise. I tried two different ways:

1 GitHub

I cloned your repo, and executed:

groovy klarigi/src/main/groovy/klarigi/Klarigi.groovy --data data/eg_data.tsv --ontology ontology/hp.owl  --group OMIM:604271

and got the error:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass (file:/usr/share/groovy/lib/groovy-2.4.17.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/home/nur/workspace/klarigi/klarigi/src/main/groovy/klarigi/Klarigi.groovy: 17: unable to resolve class org.apache.log4j.Level
@ line 17, column 1.
import org.apache.log4j.Level;
^

/home/nur/workspace/klarigi/klarigi/src/main/groovy/klarigi/Klarigi.groovy: 18: unable to resolve class org.apache.log4j.Logger
@ line 18, column 1.
import org.apache.log4j.Logger;
^

/home/nur/workspace/klarigi/klarigi/src/main/groovy/klarigi/Klarigi.groovy: 19: unable to resolve class org.apache.log4j.LogManager
@ line 19, column 1.
import org.apache.log4j.LogManager;
^

/home/nur/workspace/klarigi/klarigi/src/main/groovy/klarigi/Klarigi.groovy: 50: unable to resolve class Scorer
@ line 50, column 19.
this.scorer = new Scorer(ontoHelper, coefficients, data, excludeClasses, threads)
^
and continues to 11 errors in total.

2 Tutorial on colab

I downloaded and executed klarigi like:

mkdir tutorial | cd tutorial
!wget https://lokero.xyz/klarigi-0.0.12-SNAPSHOT.tar
!tar -xvf klarigi-0.0.12-SNAPSHOT.tar
!mv klarigi-0.0.12-SNAPSHOT klarigi

./klarigi/bin/klarigi --data ../data/eg_data.tsv --ontolohy ../ontology/hp.owl --group OMIM:604271

and got the error:

Exception in thread "main" groovy.lang.GroovyRuntimeException: Could not find matching constructor for: java.io.File(Boolean)
at groovy.lang.MetaClassImpl.invokeConstructor(MetaClassImpl.java:1845)
at groovy.lang.MetaClassImpl.invokeConstructor(MetaClassImpl.java:1615)
at org.codehaus.groovy.runtime.callsite.MetaClassConstructorSite.callConstructor(MetaClassConstructorSite.java:46)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:263)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:277)
at klarigi.Klarigi.loadOntology(Klarigi.groovy:129)
at klarigi.Klarigi$loadOntology$0.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
at klarigi.Klarigi.(Klarigi.groovy:36)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:72)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:263)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:277)
at klarigi.App.main(App.groovy:82)

I presume that I am missing some Groovy configuration since I usually don't code/execute scripts in Groovy. Could you shed light on this?

Thank you very much!
Kind regards,
Núria

[reality]

Hi,

Sorry you had trouble running the program. Currently, the error reporting is not very good at all - I am working to improve that.

Issue 1:

Klarigi requires a compiled version to use. The easiest way to do that is to download the latest release here: https://github.com/reality/klarigi/releases/tag/0.0.12 and run that (in a similar way to that described in your part two, and in the colab notebooks)

(( there is also this release https://github.com/reality/klarigi/releases/tag/0.0.13-SNAPSHOT-2 , which has improved metrics/permutation testing etc, but is less stable, and new features aren't all yet documented. I plan on finishing the 0.0.13 full release very soon to co-incide with final submission of the paper/update of preprint/documentation ))

Issue 2:

It looks like you mistyped the '--ontology' argument, so the command should be

./klarigi/bin/klarigi --data ../data/eg_data.tsv --ontology ../ontology/hp.owl --group OMIM:604271

It complains about a 'false' value being passed to java File because there is no '--ontology' argument, which it needs to execute the program. It should check the necessary arguments and give a helpful message, not just try to run with no value... I will keep this issue open so that I remember to fix the parameter checking before the release of the next version

Hope that helps!