IllegalModelAccessError when trying to run workflow

[fac2003]

I moved some of the samples into a writeable model and adjusted to run. The model includes a logger I found in the sample.
jetbrains.mps.smodel.IllegalModelAccessError: You can write model only inside write actions
at jetbrains.mps.smodel.ModelAccess.checkWriteAccess(ModelAccess.java:115)
at jetbrains.mps.smodel.ModelAccessBase.checkWriteAccess(ModelAccessBase.java:48)
at jetbrains.mps.smodel.AttachedNodeOwner.assertLegalChange(AttachedNodeOwner.java:81)
at jetbrains.mps.smodel.SNode.assertCanChange(SNode.java:109)
at jetbrains.mps.smodel.SNode.insertChildBefore(SNode.java:751)
at jetbrains.mps.smodel.SNode.addChild(SNode.java:799)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList$ChildrenSNodesList.doAddReference(AbstractSNodeList.java:163)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList.addReference(AbstractSNodeList.java:38)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList.add(AbstractSNodeList.java:140)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList$ChildrenSNodesList.add(AbstractSNodeList.java:150)
at jetbrains.mps.internal.collections.runtime.AbstractCollectionSequence.addElement(AbstractCollectionSequence.java:20)
at org.campagnelab.logger.behavior.Logger__BehaviorDescriptor.add_id1EUvP1fLbE6(Unknown Source)
at org.campagnelab.logger.behavior.Logger__BehaviorDescriptor.invokeSpecial0(Unknown Source)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeSpecial(BaseBHDescriptor.java:346)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtualCommon(BaseBHDescriptor.java:294)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtual(BaseBHDescriptor.java:270)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invoke(BaseBHDescriptor.java:231)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke0(SMethodImpl.java:151)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke(SMethodImpl.java:126)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.log(ExecuteDockerCommands.java:655)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.executeLsWithCache(ExecuteDockerCommands.java:731)
at org.campagnelab.docker.bash.behavior.DockerPath__BehaviorDescriptor.doesPathExist_id2h_fDmyfOCy(DockerPath__BehaviorDescriptor.java:126)
at org.campagnelab.docker.bash.behavior.DockerPath__BehaviorDescriptor.invokeSpecial0(DockerPath__BehaviorDescriptor.java:194)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeSpecial(BaseBHDescriptor.java:346)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeVirtual(BaseBHDescriptor.java:305)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invoke(BaseBHDescriptor.java:229)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke0(SMethodImpl.java:151)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke(SMethodImpl.java:126)
at org.campagnelab.docker.bash.typesystem.FileDoesNotExist_NonTypesystemRule.applyRule(FileDoesNotExist_NonTypesystemRule.java:21)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.applyRuleToNode(IncrementalTypechecking.java:151)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$3.run(NonTypeSystemComponent.java:343)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.runApplyRulesTo(IncrementalTypechecking.java:163)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyNonTypesystemRulesToNode(NonTypeSystemComponent.java:323)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyRulesToRoot(NonTypeSystemComponent.java:312)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.access$000(NonTypeSystemComponent.java:41)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$2.compute(NonTypeSystemComponent.java:295)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$2.compute(NonTypeSystemComponent.java:292)
at jetbrains.mps.languageScope.LanguageScopeExecutor.execWithModelScope(LanguageScopeExecutor.java:35)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyNonTypeSystemRulesToRoot(NonTypeSystemComponent.java:292)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.applyNonTypesystemRulesToRoot(IncrementalTypechecking.java:231)
at jetbrains.mps.newTypesystem.context.typechecking.BaseTypechecking.applyNonTypesystemRulesToRoot(BaseTypechecking.java:140)
at jetbrains.mps.newTypesystem.context.IncrementalTypecheckingContext.applyNonTypesystemRules(IncrementalTypecheckingContext.java:197)
at jetbrains.mps.newTypesystem.context.SimpleTypecheckingContext.checkRootAndGetErrors(SimpleTypecheckingContext.java:261)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker$1.run(TypesystemChecker.java:34)
at jetbrains.mps.typesystem.inference.TypeContextManager$Executor.doExecute(TypeContextManager.java:266)
at jetbrains.mps.typesystem.inference.TypeContextManager$Executor.execute(TypeContextManager.java:243)
at jetbrains.mps.typesystem.inference.TypeContextManager.runTypeCheckingAction(TypeContextManager.java:118)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.getErrors(TypesystemChecker.java:32)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.check(TypesystemChecker.java:45)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.check(TypesystemChecker.java:26)
at jetbrains.mps.checkers.IteratingChecker.check(IteratingChecker.java:86)
at jetbrains.mps.checkers.IChecker$AbstractModelChecker$2.check(IChecker.java:63)
at jetbrains.mps.checkers.IChecker$AbstractModelChecker$2.check(IChecker.java:53)
at jetbrains.mps.checkers.CategoryShowingChecker.check(CategoryShowingChecker.java:39)
at jetbrains.mps.checkers.FilteringChecker.check(FilteringChecker.java:27)
at jetbrains.mps.checkers.CatchingChecker.check(CatchingChecker.java:25)
at jetbrains.mps.checkers.AggregatingChecker.check(AggregatingChecker.java:26)
at jetbrains.mps.checkers.SkippingChecker.check(SkippingChecker.java:21)
at jetbrains.mps.checkers.ModelCheckerBuilder$1.check(ModelCheckerBuilder.java:142)
at jetbrains.mps.checkers.ModelCheckerBuilder$1.check(ModelCheckerBuilder.java:114)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder$1.compute(ModelCheckerIssueFinder.java:62)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder$1.compute(ModelCheckerIssueFinder.java:54)
at jetbrains.mps.util.ComputeRunnable.compute(ComputeRunnable.java:32)
at jetbrains.mps.util.AbstractComputeRunnable.run(AbstractComputeRunnable.java:27)
at jetbrains.mps.smodel.WorkbenchModelAccess.lambda$runReadAction$0(WorkbenchModelAccess.java:77)
at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:902)
at jetbrains.mps.smodel.WorkbenchModelAccess.runReadAction(WorkbenchModelAccess.java:74)
at jetbrains.mps.smodel.ModelAccessBase.runReadAction(ModelAccessBase.java:53)
at jetbrains.mps.smodel.ModelAccessHelper.runReadAction(ModelAccessHelper.java:44)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder.execute(ModelCheckerIssueFinder.java:54)
at jetbrains.mps.ide.findusages.view.UsagesView$RerunAction$1.run(UsagesView.java:332)
at com.intellij.openapi.progress.impl.CoreProgressManager$TaskRunnable.run(CoreProgressManager.java:750)
at com.intellij.openapi.progress.impl.CoreProgressManager$5.run(CoreProgressManager.java:434)
at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$1(CoreProgressManager.java:157)
at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:580)
at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:525)
at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:85)
at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:144)
at com.intellij.openapi.application.impl.ApplicationImpl.lambda$null$10(ApplicationImpl.java:565)
at com.intellij.openapi.application.impl.ApplicationImpl$1.run(ApplicationImpl.java:305)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

[fac2003]

Used logger plugin I got from Manuele:
Version 3.2
This plugin provides the org.campagnelab.logger language that provides a way to log from behavior methods into a Logger root node in a sandbox. Build number: 0

[manuelesimi]

The problem was due to some broken references in the Logger node. It has been cleaned.

[manuelesimi]

Few more fixes have been needed in order to run the embedded nextflow executable from the plugin. The new preview of the plugin is available on Dropbox and will be released soon.

[manuelesimi]

I tried to reproduce what was described in this issue: moving some processes/workflows from the plugin to a writable model in a new project and run them.

It worked (see the screen shot below). For this specific execution, Docker must be configured with at 10 GB of memory.