Nextflow keeps throwing a 'Plugin system was already setup' exception for all versions after 22.06.0

[UmmulkiramR]

Bug report

I recently upgraded the version of the nextflow.io library to version 22.10.7 in our spring boot app and since then my code has started breaking. My app calls the run() method of the K8SDriverLauncher class to create workflow pods.
Now, after the upgrade each time I run my workflows it runs perfectly fine for the 1st time but for all the subsequent runs it gives me this - IllegalArgumentException("Plugin system was already setup")

Expected behavior and actual behavior

Upon further investigation what I found is that as a part of the 22.06.0-edge release the following 2 changes were introduced in the library's code.

1. In the K8SDriverLauncher class, in the loadConfig() method there is an additional call made to the Plugins.init()
2. In the PluginsFacade class the setup() method is changed to init() and an if statement is added that throws the IllegalArgumentException

What is happening is that the init() method of the PluginsFacade class looks for the presence of the plugins manager on this line -> if( manager ) every time. For the 1st run it does not find a manager so it creates one. For the 2nd, 3rd, 4th... runs it finds the manager it created during the 1st run and that's when it throws the exception.

Here is the code snippet

void init(boolean embedded=false) {
        if( manager )
            throw new IllegalArgumentException("Plugin system was already setup")

        log.debug "Setting up plugin manager > mode=${mode}; embedded=$embedded; plugins-dir=$root; core-plugins: ${defaultPlugins.toSortedString()}"
        // make sure plugins dir exists
        if( mode!=DEV_MODE && !FilesEx.mkdirs(root) )
            throw new IOException("Unable to create plugins dir: $root")

        this.manager = createManager(root)
        this.updater = createUpdater(root, manager)
        manager.loadPlugins()
        if( embedded ) {
            manager.startPlugins()
            this.embedded = embedded
        }
    }

Why have the IllegalArgumentException thrown when it does find the plugins manager? What is wrong with one being there already?

Program output

Here's the stack trace of the exception I see.

java.lang.IllegalArgumentException: Plugin system was already setup
	at nextflow.plugin.PluginsFacade.init(PluginsFacade.groovy:190) ~[nf-commons-22.10.7.jar!/:na]
	at nextflow.plugin.Plugins.init(Plugins.groovy:41) ~[nf-commons-22.10.7.jar!/:na]
	at nextflow.plugin.Plugins.init(Plugins.groovy) ~[nf-commons-22.10.7.jar!/:na]
	at nextflow.plugin.Plugins$init.call(Unknown Source) ~[na:na]
	at nextflow.k8s.K8sDriverLauncher.loadConfig(K8sDriverLauncher.groovy:268) ~[nextflow-22.10.7.jar!/:na]
	at nextflow.k8s.K8sDriverLauncher.makeConfig(K8sDriverLauncher.groovy:299) ~[nextflow-22.10.7.jar!/:na]
	at nextflow.k8s.K8sDriverLauncher.run(K8sDriverLauncher.groovy:142) ~[nextflow-22.10.7.jar!/:na]

Environment

• Nextflow version: 22.06.0-edge onward
• Operating system: Linux, MacOs

[UmmulkiramR]

Hi Team, is there an update on this?

[Buwujiu]

Hi, is there any updates on this? This is blocking our projects, please take a look when you have chance.

[azulverdosa]

We’re seeing the same issue here.

[pditommaso]

Dear community, open-source is meant to allow everybody to access the code, debug it and contribute back improvements and bug fixes. This is not a support forum.