Path existance check assumes "definisions" in schema

[mateuszpawlik]

I have a simple schema with three parameters. One of them is a required path. I used the nf-core schema build which generated that schema. Since I have only three parameters, I didn't think about grouping them. The "exists" key wouldn't work. It took me some time to figure out that collecting parameters with "exists" key set assumes "definitions" key in the schema:

https://github.com/nextflow-io/nf-validation/blob/26f56310c397ca987ba9510abbddcc3d77abf0c6/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy#L306

Once I grouped my parameters in "definitions" the existence check was triggered.

Are group "definitions" mandatory?

[nvnieuwk]

Hi, thanks for reporting! This should not happen. We'll fix this once we find some time, can you just add the definitions there in the meantime?

[mateuszpawlik]

Yes, I solved it for myself by adding the "definitions". For me it doesn't matter.

I hope I linked the right source code lines. Let me know if you need more information. I used the latest plugin version and the latest Nextflow.

[nvnieuwk]

Hi this should be solved in version 2.0 of nf-validation. I'm not sure when it will come out because it's a big change overall, but keep an eye on it :p

[nvnieuwk]

Hi @mateuszpawlik we just released the new version of nf-validation with improved JSON schema validation. Can you please retry with version 2.0.0? (Please keep in mind that we changed some stuff in this update. You can see the full migration guide here)

[mateuszpawlik]

I first tried to update the plugin to the new version but got an error:

Feb-20 19:26:28.010 [main] INFO  nextflow.cli.CmdRun - Launching `main.nf` [big_hoover] DSL2 - revision: 1c103ce112
Feb-20 19:26:28.010 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[[email protected]]
Feb-20 19:26:28.011 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-20 19:26:28.011 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected]]
Feb-20 19:26:28.011 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 2.0.0
Feb-20 19:26:28.014 [main] INFO  nextflow.plugin.PluginUpdater - Downloading plugin [email protected]
Feb-20 19:26:28.600 [main] ERROR nextflow.cli.Launcher - @unknown
org.pf4j.PluginRuntimeException: Plugin nf-validation with version @2.0.0 does not exist in the repository

Nextflow version 23.10.1

Shall I wait a bit longer?

[nvnieuwk]

We sadly had to revert the update for now because a lot of pipelines were breaking (because they didn't pin the plugin version). We'll need to update those pipelines first before re-releasing the update. Sorry, but I hope the new version will be out soon

[nvnieuwk]

nf-schema has now been released, this contains all improvements + more from nf-validation v2.0. Can you try again with the new plugin?