Workflow assigning columns on output causes "Uncaught exception in exposed API method"

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Workflow assigning columns on output causes "Uncaught exception in exposed API method"

Peter Briggs
Dear Devs

We've encountered a problem trying to run a workflow on our local Galaxy instance, which is resulting in an "uncaught exception in exposed API method" message displayed in the Galaxy window.

The most trivial workflow exhibiting the problem consists of a single 'cut' task, where the output of the task is configured to change the datatype to "interval", and to explicitly assign the chrom, start and end columns to 1,2 and 3. Attempts to run this workflow generate the API exception.

If the workflow is updated so that the column assignments are no longer attempted then the workflow is able to start without apparent problems.

Our local Galaxy instance is a bit out of data (18.09) but I have been able to reproduce this error on Galaxy main so it looks like it also affects later versions. The failing workflow can be accessed on main via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-reassign-columns-fails-with-uncaught-api-exception

The same workflow with the column assignment removed is accessible via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-no-column-reassignment

(Main offers two variants of the 'cut' tool - as far as I can tell this problem happens with both.)

Apologies if this has already been reported elsewhere - any suggestions for a workaround appreciated.

Thanks,

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: Workflow assigning columns on output causes "Uncaught exception in exposed API method"

Marius van den Beek
Hi Peter,

thanks for the report, I've opened a pull request to fix this at
https://github.com/galaxyproject/galaxy/pull/8023.
We'll backport this to 18.09 after acceptance.
As a (terrible) workaround you could download the workflow and change the
section that looks like
```
          "action_type": "ColumnSetAction",
          "output_name": "out_file1",
          "action_arguments": {
            "chromCol": 1,
            "endCol": 3,
            "startCol": 2
          }
```
to
```
          "action_type": "ColumnSetAction",
          "output_name": "out_file1",
          "action_arguments": {
            "chromCol": "1",
            "endCol": "3",
            "startCol": "2"
          }
```
(the "output_name" value may be different for each tool) and then upload it
back to the instance.

Hope that helps,
Marius

On Wed, 22 May 2019 at 10:36, Peter Briggs <[hidden email]>
wrote:

> Dear Devs
>
> We've encountered a problem trying to run a workflow on our local Galaxy
> instance, which is resulting in an "uncaught exception in exposed API
> method" message displayed in the Galaxy window.
>
> The most trivial workflow exhibiting the problem consists of a single
> 'cut' task, where the output of the task is configured to change the
> datatype to "interval", and to explicitly assign the chrom, start and end
> columns to 1,2 and 3. Attempts to run this workflow generate the API
> exception.
>
> If the workflow is updated so that the column assignments are no longer
> attempted then the workflow is able to start without apparent problems.
>
> Our local Galaxy instance is a bit out of data (18.09) but I have been
> able to reproduce this error on Galaxy main so it looks like it also
> affects later versions. The failing workflow can be accessed on main via:
>
>
> https://usegalaxy.org/u/pjbriggs/w/cut-workflow-reassign-columns-fails-with-uncaught-api-exception
>
> The same workflow with the column assignment removed is accessible via:
>
> https://usegalaxy.org/u/pjbriggs/w/cut-workflow-no-column-reassignment
>
> (Main offers two variants of the 'cut' tool - as far as I can tell this
> problem happens with both.)
>
> Apologies if this has already been reported elsewhere - any suggestions
> for a workaround appreciated.
>
> Thanks,
>
> Peter
>
> --
> Peter Briggs [hidden email]
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
>
___________________________________________________________
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Re: Workflow assigning columns on output causes "Uncaught exception in exposed API method"

Peter Briggs
Hello Marius

Thanks for looking into this - I've tried the workaround you suggested and the workflow now seems to start okay.

Thanks also for the fix in the PR, much appreciated!

Best wishes

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

________________________________
From: Marius van den Beek [[hidden email]]
Sent: Thursday, May 23, 2019 2:18 PM
To: Peter Briggs
Cc: [hidden email]; Ian Donaldson
Subject: Re: [galaxy-dev] Workflow assigning columns on output causes "Uncaught exception in exposed API method"

Hi Peter,

thanks for the report, I've opened a pull request to fix this at https://github.com/galaxyproject/galaxy/pull/8023.
We'll backport this to 18.09 after acceptance.
As a (terrible) workaround you could download the workflow and change the section that looks like
```
          "action_type": "ColumnSetAction",
          "output_name": "out_file1",
          "action_arguments": {
            "chromCol": 1,
            "endCol": 3,
            "startCol": 2
          }
```
to
```
          "action_type": "ColumnSetAction",
          "output_name": "out_file1",
          "action_arguments": {
            "chromCol": "1",
            "endCol": "3",
            "startCol": "2"
          }
```
(the "output_name" value may be different for each tool) and then upload it back to the instance.

Hope that helps,
Marius

On Wed, 22 May 2019 at 10:36, Peter Briggs <[hidden email]<mailto:[hidden email]>> wrote:
Dear Devs

We've encountered a problem trying to run a workflow on our local Galaxy instance, which is resulting in an "uncaught exception in exposed API method" message displayed in the Galaxy window.

The most trivial workflow exhibiting the problem consists of a single 'cut' task, where the output of the task is configured to change the datatype to "interval", and to explicitly assign the chrom, start and end columns to 1,2 and 3. Attempts to run this workflow generate the API exception.

If the workflow is updated so that the column assignments are no longer attempted then the workflow is able to start without apparent problems.

Our local Galaxy instance is a bit out of data (18.09) but I have been able to reproduce this error on Galaxy main so it looks like it also affects later versions. The failing workflow can be accessed on main via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-reassign-columns-fails-with-uncaught-api-exception

The same workflow with the column assignment removed is accessible via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-no-column-reassignment

(Main offers two variants of the 'cut' tool - as far as I can tell this problem happens with both.)

Apologies if this has already been reported elsewhere - any suggestions for a workaround appreciated.

Thanks,

Peter

--
Peter Briggs [hidden email]<mailto:[hidden email]>
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
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