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java.lang.RuntimeException: child must not be null: expression text [methylome] #502

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iromeo opened this issue Dec 15, 2022 · 0 comments
Open

java.lang.RuntimeException: child must not be null: expression text [methylome] #502

iromeo opened this issue Dec 15, 2022 · 0 comments
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@iromeo
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iromeo commented Dec 15, 2022 •
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After typed '--merged' in:

rule foo:
   #...
    shell:
        "java -Xmx{config[methtool][toNPZ][mem_gb]}g -jar {config[methtool][path]} toNPZ"
        " --cs {input.chromsizes} -r {input.twoBit}" 
        " -m {input.meth_file} --basename {params.basename}"
        " {'--merged q' if config[methylome][individual][input_methylomes][merged] else ''}"
        " {config[methtool][toNPZ][opts]} {config[methtool][toNPZ][opts_chr_names_mapping]}"
        " >{log} 2>&1"

Here injections syntax doesn't support F-String like constructions, but exception should be thrown (SnakeCharm 2022.3.771)

java.lang.RuntimeException: java.lang.RuntimeException: child must not be null: expression text [methylome]
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
	at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:562)
	at java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:591)
	at java.base/java.util.concurrent.ForkJoinTask.join(ForkJoinTask.java:672)
	at com.intellij.concurrency.JobLauncherImpl.processQueue(JobLauncherImpl.java:360)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.processInOrder(InspectionRunner.java:300)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.visitElements(InspectionRunner.java:275)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$inspect$4(InspectionRunner.java:129)
	at com.intellij.codeInspection.InspectionEngine.withSession(InspectionEngine.java:226)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.inspect(InspectionRunner.java:116)
	at com.intellij.codeInsight.daemon.impl.LocalInspectionsPass.collectInformationWithProgress(LocalInspectionsPass.java:117)
	at com.intellij.codeInsight.daemon.impl.ProgressableTextEditorHighlightingPass.doCollectInformation(ProgressableTextEditorHighlightingPass.java:97)
	at com.intellij.codeHighlighting.TextEditorHighlightingPass.collectInformation(TextEditorHighlightingPass.java:57)
	at com.intellij.codeInsight.daemon.impl.PassExecutorService$ScheduledPass.lambda$doRun$1(PassExecutorService.java:405)
	at com.intellij.openapi.application.impl.ApplicationImpl.tryRunReadAction(ApplicationImpl.java:1086)
	at com.intellij.codeInsight.daemon.impl.PassExecutorService$ScheduledPass.lambda$doRun$2(PassExecutorService.java:397)
	at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$executeProcessUnderProgress$13(CoreProgressManager.java:591)
	at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:666)
	at com.intellij.openapi.progress.impl.CoreProgressManager.computeUnderProgress(CoreProgressManager.java:622)
	at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:590)
	at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:60)
	at com.intellij.codeInsight.daemon.impl.PassExecutorService$ScheduledPass.doRun(PassExecutorService.java:396)
	at com.intellij.codeInsight.daemon.impl.PassExecutorService$ScheduledPass.lambda$run$0(PassExecutorService.java:372)
	at com.intellij.openapi.application.impl.ReadMostlyRWLock.executeByImpatientReader(ReadMostlyRWLock.java:174)
	at com.intellij.openapi.application.impl.ApplicationImpl.executeByImpatientReader(ApplicationImpl.java:182)
	at com.intellij.codeInsight.daemon.impl.PassExecutorService$ScheduledPass.run(PassExecutorService.java:370)
	at com.intellij.concurrency.JobLauncherImpl$VoidForkJoinTask$1.exec(JobLauncherImpl.java:181)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:373)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1182)
	at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1655)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1622)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:165)
Caused by: java.lang.RuntimeException: child must not be null: expression text [methylome]
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.childToPsiNotNull(PyBaseElementImpl.java:109)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionExpressionImpl.getOperand(SmkSLSubscriptionExpressionImpl.kt:90)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionIndexKeyExpressionImpl.getQualifier(SmkSLSubscriptionIndexKeyExpressionImpl.kt:46)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionIndexKeyExpressionImpl.getReference(SmkSLSubscriptionIndexKeyExpressionImpl.kt:25)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionIndexKeyExpressionImpl.getReference(SmkSLSubscriptionIndexKeyExpressionImpl.kt:43)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor$1.visitPyElement(PyUnresolvedReferencesVisitor.java:159)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyExpression(PyElementVisitor.java:174)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyReferenceExpression(PyElementVisitor.java:30)
	at com.jetbrains.python.psi.impl.PyReferenceExpressionImpl.acceptPyVisitor(PyReferenceExpressionImpl.java:86)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionIndexKeyExpressionImpl.acceptPyVisitor(SmkSLSubscriptionIndexKeyExpressionImpl.kt:39)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.psi.impl.PsiElementBase.acceptChildren(PsiElementBase.java:58)
	at com.jetbrains.python.psi.PyRecursiveElementVisitor.visitElement(PyRecursiveElementVisitor.java:12)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyElement(PyElementVisitor.java:26)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor$1.visitPyElement(PyUnresolvedReferencesVisitor.java:156)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.acceptPyVisitor(PyBaseElementImpl.java:69)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionExpressionImpl.acceptPyVisitor(SmkSLSubscriptionExpressionImpl.kt:104)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.psi.impl.PsiElementBase.acceptChildren(PsiElementBase.java:58)
	at com.jetbrains.python.psi.PyRecursiveElementVisitor.visitElement(PyRecursiveElementVisitor.java:12)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyElement(PyElementVisitor.java:26)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor$1.visitPyElement(PyUnresolvedReferencesVisitor.java:156)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.acceptPyVisitor(PyBaseElementImpl.java:69)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionExpressionImpl.acceptPyVisitor(SmkSLSubscriptionExpressionImpl.kt:104)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.psi.impl.PsiElementBase.acceptChildren(PsiElementBase.java:58)
	at com.jetbrains.python.psi.PyRecursiveElementVisitor.visitElement(PyRecursiveElementVisitor.java:12)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyElement(PyElementVisitor.java:26)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor$1.visitPyElement(PyUnresolvedReferencesVisitor.java:156)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.acceptPyVisitor(PyBaseElementImpl.java:69)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionExpressionImpl.acceptPyVisitor(SmkSLSubscriptionExpressionImpl.kt:104)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.psi.impl.PsiElementBase.acceptChildren(PsiElementBase.java:58)
	at com.jetbrains.python.psi.PyRecursiveElementVisitor.visitElement(PyRecursiveElementVisitor.java:12)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyElement(PyElementVisitor.java:26)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor$1.visitPyElement(PyUnresolvedReferencesVisitor.java:156)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.acceptPyVisitor(PyBaseElementImpl.java:69)
	at com.jetbrains.snakecharm.stringLanguage.lang.psi.SmkSLSubscriptionExpressionImpl.acceptPyVisitor(SmkSLSubscriptionExpressionImpl.kt:104)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.psi.impl.source.tree.SharedImplUtil.acceptChildren(SharedImplUtil.java:185)
	at com.intellij.psi.impl.source.PsiFileImpl.acceptChildren(PsiFileImpl.java:754)
	at com.jetbrains.python.psi.PyRecursiveElementVisitor.visitElement(PyRecursiveElementVisitor.java:12)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor.processInjection(PyUnresolvedReferencesVisitor.java:163)
	at com.jetbrains.python.inspections.unresolvedReference.PyUnresolvedReferencesVisitor.visitPyElement(PyUnresolvedReferencesVisitor.java:140)
	at com.jetbrains.python.psi.PyElementVisitor.visitPyStringLiteralExpression(PyElementVisitor.java:218)
	at com.jetbrains.python.psi.impl.PyStringLiteralExpressionImpl.acceptPyVisitor(PyStringLiteralExpressionImpl.java:43)
	at com.jetbrains.python.psi.impl.PyBaseElementImpl.accept(PyBaseElementImpl.java:61)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$processInOrder$9(InspectionRunner.java:324)
	at com.intellij.openapi.application.impl.ApplicationImpl.tryRunReadAction(ApplicationImpl.java:1086)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$processInOrder$10(InspectionRunner.java:332)
	at com.intellij.openapi.application.impl.ReadMostlyRWLock.executeByImpatientReader(ReadMostlyRWLock.java:174)
	at com.intellij.openapi.application.impl.ApplicationImpl.executeByImpatientReader(ApplicationImpl.java:182)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$processInOrder$11(InspectionRunner.java:338)
	at com.intellij.util.AstLoadingFilter.forceAllowTreeLoading(AstLoadingFilter.java:159)
	at com.intellij.util.AstLoadingFilter.forceAllowTreeLoading(AstLoadingFilter.java:151)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$processInOrder$12(InspectionRunner.java:301)
	at com.intellij.util.AstLoadingFilter.disallowTreeLoading(AstLoadingFilter.java:130)
	at com.intellij.util.AstLoadingFilter.disallowTreeLoading(AstLoadingFilter.java:119)
	at com.intellij.codeInsight.daemon.impl.InspectionRunner.lambda$processInOrder$13(InspectionRunner.java:301)
	at com.intellij.concurrency.JobLauncherImpl$1MyProcessQueueTask.lambda$call$0(JobLauncherImpl.java:299)
	at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$executeProcessUnderProgress$13(CoreProgressManager.java:591)
	at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:666)
	at com.intellij.openapi.progress.impl.CoreProgressManager.computeUnderProgress(CoreProgressManager.java:622)
	at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:590)
	at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:60)
	at com.intellij.concurrency.JobLauncherImpl$1MyProcessQueueTask.call(JobLauncherImpl.java:284)
	at com.intellij.concurrency.JobLauncherImpl$1MyProcessQueueTask.call(JobLauncherImpl.java:272)
	at java.base/java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1428)
	... 5 more
@iromeo iromeo added the bug Something isn't working label Dec 15, 2022
@iromeo iromeo added this to the next release milestone Dec 15, 2022
@iromeo iromeo self-assigned this Dec 15, 2022
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