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nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
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Grape not supported anymore on Nextflow version v24.0.7.0-edge #5234

Closed VasLem closed 3 days ago

VasLem commented 3 weeks ago

Bug report

The following piece of code works in v24.06,0-edge but not in the latest version:

@Grab(group='org.apache.commons', module='commons-text', version='1.12.0')
import org.apache.commons.text.similarity.LevenshteinDistance

Program output

ERROR ~ Class definition not found: org/apache/ivy/util/MessageLogger

...
Aug-17 20:03:02.815 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NoClassDefFoundError: org/apache/ivy/util/MessageLogger
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:413)
    at java.base/java.lang.Class.forName(Class.java:404)
    at groovy.grape.Grape.getInstance(Grape.java:124)
    at groovy.grape.Grape$1.run(Grape.java:161)
    at groovy.grape.Grape$1.run(Grape.java:158)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:319)
    at groovy.grape.Grape.grab(Grape.java:158)
    at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:380)
    at org.codehaus.groovy.transform.ASTTransformationVisitor.lambda$addPhaseOperationsForGlobalTransforms$5(ASTTransformationVisitor.java:374)
    at org.codehaus.groovy.control.CompilationUnit$ISourceUnitOperation.doPhaseOperation(CompilationUnit.java:897)
    at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:692)
    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:666)
    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:373)
    at groovy.lang.GroovyClassLoader.lambda$parseClass$2(GroovyClassLoader.java:316)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
    at groovy.lang.GroovyShell.parseClass(GroovyShell.java:572)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:585)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:639)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:643)
    at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:175)
    at nextflow.script.ScriptParser.parse(ScriptParser.groovy:206)
    at nextflow.script.ScriptRunner.parseScript(ScriptRunner.groovy:229)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:136)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
    at nextflow.cli.Launcher.run(Launcher.groovy:503)
    at nextflow.cli.Launcher.main(Launcher.groovy:657)
Caused by: java.lang.ClassNotFoundException: org.apache.ivy.util.MessageLogger
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:525)
    ... 29 common frames omitted

Environment

pditommaso commented 3 weeks ago

I think it's a side effect of the new launcher distribution. https://github.com/nextflow-io/nextflow/pull/3395

However, @Grab was never expected to be supported "officially" by nextflow. It's time to sunsetting it.

VasLem commented 3 weeks ago

I see, thank you for the answer, what is an alternative? I found no documentation about adding Groovy dependencies to a process, and Grape was really that it worked out of the box.

bentsherman commented 3 weeks ago

I would try moving this code into a Groovy script in the lib directory. If that doesn't work, I think you can also include a JAR file in the lib directory and it will be added to the classpath.

bentsherman commented 3 weeks ago

Docs: https://nextflow.io/docs/latest/sharing.html#utility-code

VasLem commented 3 weeks ago

Hi Ben, thanks for the input. Doesn't Google Batch require Tower in order to have the lib directory considered? If that's not the case, then including the jar file is a good enough alternative I guess.

bentsherman commented 3 weeks ago

The lib directory should work regardless of where you run your pipeline.