Galaxy: Error importing TRS workflow

[mvdbeek]

I guess something in the mapping isn't quite right ?
https://dockstore.org/workflows/github.com/mvdbeek/workflow-testing-repo/COVID-19%20variation%20analysis%20on%20Illumina%20metagenomic%20data:master?tab=dag looks ok

[mvdbeek]

I guess most people don't actually use whitespaces ?

[jmchilton]

It was easy to reproduce. I'll see if I can figure out the problem.

[jmchilton]

Well I get a similar problem in the UI and I don't get it for my workflows, so probably not related to the API we're using. Let me see what I can figure out:

[bgruening]

@jmchilton maybe that also helps: https://github.com/ga4gh/tool-registry-service-schemas/issues/153

[jmchilton]

I can't fork your repo @mvdbeek because I have one of the same name and I can't push to yours.

commit 48a7210dbb2113f2ad4d02bd8ba176b0219f2e9f (HEAD -> master)
Author: John Chilton <[email protected]>
Date:   Mon Oct 5 15:45:34 2020 -0400

    These need forward slashes I think, right?

diff --git a/.dockstore.yml b/.dockstore.yml
index f37de7d..8364fe3 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -1,7 +1,7 @@
 version: 1.2
 workflows:
 - name: 'COVID-19 variation analysis on Illumina metagenomic data'
-  primaryDescriptorPath: workflows/sars-cov-2-variant-calling/workflow.ga
+  primaryDescriptorPath: /workflows/sars-cov-2-variant-calling/workflow.ga
   subclass: Galaxy
   testParameterFiles:
-  - workflows/sars-cov-2-variant-calling/workflow-test.yml
+  - /workflows/sars-cov-2-variant-calling/workflow-test.yml

Is this problem this?

[mvdbeek]

The forward slashes were the problem, but that broke the tools and DAG previews in the dockstore interface, and the examples on dockstore or the GTN don't use forward slashes.

[jmchilton]

Odd - the DAG with Github Actions is working for a smaller workflow (https://github.com/jmchilton/galaxy-workflow-dockstore-example-3 | https://dockstore.org/my-workflows/github.com/jmchilton/galaxy-workflow-dockstore-example-3). I'll ping the Dockstore team and see if they have ideas.

[coverbeck]

Is the problem now with the DAG, the import, or both?

[denis-yuen]

It sounds like the question is that the DAG is functional for https://dockstore.org/workflows/github.com/jmchilton/galaxy-workflow-dockstore-example-3:version_3?tab=dagbut not for https://dockstore.org/workflows/github.com/mvdbeek/workflow-testing-repo/COVID-19%20variation%20analysis%20on%20Illumina%20metagenomic%20data:master?tab=dag

Looking superficially, it looks like part of the problem might be that there is a validation error, it seems to be parsing the test parameter file as a json when it is actually a yaml (might be an assumption since WDL and CWL use JSON) and it seems to be dragging down the rest of it.

Edit: Looks like yes
https://dockstore.org/workflows/github.com/denis-yuen/workflow-testing-repo/COVID-19%20variation%20analysis%20on%20Illumina%20metagenomic%20data:0.1?tab=dag

[mvdbeek]

Hmm, https://dockstore.org/my-workflows/github.com/jmchilton/galaxy-workflow-dockstore-example-3 also specifies test parameters as yaml, but that's interesting, I can skip the yaml file for now (and I think JSON might also work for us ?)

[denis-yuen]

Created https://github.com/dockstore/dockstore/issues/3851
I also see a validation error on 3, so there might be more than one issue going on.

[bgruening]

We have deployed a local hack at usegalaxy.eu that makes it work on Dockstore and WorkflowHub.eu. https://github.com/usegalaxy-eu/galaxy/pull/85

Of course, this is just a hack and it would be nice if both TRS servers could behave identical.

[denis-yuen]

We have deployed a local hack at usegalaxy.eu that makes it work on Dockstore and WorkflowHub.eu. usegalaxy-eu#85

Of course, this is just a hack and it would be nice if both TRS servers could behave identical.

Re-reading the beginning of https://github.com/ga4gh/tool-registry-service-schemas/issues/153
I think this is on a different issue from the beginning of the thread

My understanding is that it seems like Dockstore can either use id or name property for a tool version for input to version_id in the end point of /tools/{id}/versions/{version_id}. workflowhub.eu can only use id
Unfortunately, it seems like the TRS specification is a bit ambiguous on the meaning of name which we had interpreted as being a part of the id field.

Can I confirm?

[bgruening]

Unfortunately, it seems like the TRS specification is a bit ambiguous on the meaning of name which we had interpreted as being a part of the id field.

Yes, this is true. The spec could be more clear. BioContainers and workflowhub.eu are using the ID to my knowledge. The name seems to be not very intuitive given how arbritrary it can be.