Galaxy: workflow editor js Uncaught ANY_COLLECTION_TYPE_DESCRIPTION

[mmiladi]

Adding a 'filter failed' step to a workflow then saved it. Now the workflow editor is halted: Browser console reports: Uncaught Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION
Galaxy version is 17.09

[dannon]

@mmiladi I'll take a look, thanks! (I fixed this being undefined in 30bada4c4a9, but it looks like the behavior still wasn't quite right)

[mmiladi]

@dannon This happened in our Freiburg Galaxy server. Probably it's not been updated within these days. @erasche what would you think?

[dannon]

@mmiladi Can you show me the other steps? Is it just an input dataset and a filter failed step? I'm not seeing the error on 17.09 either. (I don't think the change I made mentioned above would necessarily fix the problem you're having)

[hexylena]

@mmiladi we're on the latest 17.09, I'm not seeing any commits that we are currently missing.

[dannon]

@mmiladi Is that input dataset actually attached to the filter? I am only able to attach it to an input dataset collection.

[mmiladi]

@dannon I was waiting for the latest docker build of dev to test. Here is the scenario:

If it helps, I can send you the workflow file via Gitter.

[mmiladi]

@erasche thanks for the info. The problem is persistent with 17.09 and also dev branch.

[mmiladi]

@dannon An update on tracking the issue: I could reproduce the error without having the wf-editor halted. Same exception arises while trying to build the wf from scratch on cmsearch output. Exception is thrown by trying to connect and drag the cmsearch output :

Please note that the data collection input for cmsearch is dynamic, hidden by default and pops-up by selecting "Covariance model from your history"

[mmiladi]

@dannon Have you had time to check the workflow?

[dannon]

@mmiladi Yep, sure have, and I have reproduced it locally. Working on a fix.

[mmiladi]

Many thanks @dannon !

[dannon]

I reproduced this locally and then handed off to @guerler. Did you make any progress on the right fix for this one Sam?

[mvdbeek]

@mmiladi Is this still an issue ? I tried a couple of things that seemed to have worked

[guerler]

I have not looked into this in detail yet but can do so if the issue still exists.

[mmiladi]

@mvdbeek I checked now. It's still an issue, on usegalaxy.eu at least. This occurs most probably due to the dynamic input port. Do you agree @dannon ?

Please note that the data collection input for cmsearch is dynamic, hidden by default and pops-up by selecting "Covariance model from your history"

[dannon]

@mmiladi @guerler Yes, it's still an issue (18.05), and yes it seems related to the dynamic toggling of the I/O types related to collections. My guess was the toggling doesn't reinitialize the connectors correctly or something along those lines.

[guerler]

I have trouble reproducing this. This seems to work for me.

[mmiladi]

Thanks much for looking into it @guerler . Could you please try to see if it works to connect the cmsearch outfile to another tool?

[guerler]

Thanks @mmiladi for reporting this issue. It can be reproduced by using built-in collection tools. Clicking the output terminal of the ZIP collection tool triggers the exception.

The problem is that the filter failed, filter list and relabeling tools for collections do not specify a fixed collection output type i.e. they rely on the input type source. Adding subsequent steps in the workflow editor leaves the collection types undetermined. A possible fix is to allow appending to the generic type descriptor as in https://github.com/galaxyproject/galaxy/compare/dev...guerler:terminals. An alternative might be to validate otherMapOver.canMapOver(otherCollectionType) before appending https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/workflow/workflow-terminals.js#L359. ping @jmchilton.

[mvdbeek]

This is related to https://github.com/galaxyproject/galaxy/issues/6514, I'm working on propagating the correct collection_type on the backend and front-end