Re: [scipion-users] Scipion 3.0 Issue with Commands Waiting for Eachother

[Jose M. de la R. T. <del...@gm...>]

Hi Colin,

Thanks for reaching out. Regarding your question, it is not possible to set
the waiting ID from the workflow template. The reason for this is that the
ID shown in the template .json file might change when imported into the
project (e.g other objects might already have that ID). But your goal of
launching a whole pipeline where one job waits for the other is doable via
the Python API. It might require some Python coding, but not really
complex.

You can get an idea with the following scripts that launch a workflow from
a json file (almost the same that you want  to achieve):
https://github.com/I2PC/scipion-scripts/blob/master/run_workflow.py

Please let me know if you have any questions.

Kind regards,
Jose Miguel



On Fri, Oct 2, 2020 at 9:03 AM Colin Deniston <cde...@gn...> wrote:

> Hello,
>
>
>
> First off, I’m new to Scipion and have been loving the flexibility,
> streaming, monitoring, and reporting abilities of the program! However, I’m
> currently trying to run a custom built workflow in Scipion 3.0.3 and I’m
> running into a few issues.
>
>
>
> 1) I don’t see in the actual .json.template file a line to designate what
> ID to wait for under each protocol (I want each job to wait for the prior
> job to completely finish before running). Is this something I can add? If
> so, what is the command I should use?
>
> 2) When I try and circumvent that by simply typing the ID in the GUI once
> the workflow is loaded (in the “wait for” box of each protocol), nothing
> seems to wait. They all run while the previous job is still going. Am I
> doing something wrong? I’ve been entering them as just the ID number like
> “432” but should they be entered differently? Also, I see multiple IDs for
> the same job/protocol under different menus, not sure if that is a bug or
> not or whether it is maybe related to the issue of jobs not waiting.
>
>
>
> Any feedback would be helpful, my end goal is just to make a reproducible
> workflow that can be loaded and run on multiple Appoferritin calibration
> datasets all the way to 3D refinement without any user intervention.
> However, at the moment one job will try to run too soon and fail and then
> lead to a cascade of downstream jobs failing. Thanks!
>
>
>
> *Colin Deniston*
> Principal Scientist I
>
> *GNF BIOTHERAPEUTICS & BIOTECHNOLOGY / GNF*
>
> Novartis Institutes for Biomed.Research, Inc.
>
> 10675 John Jay Hopkins Drive
>
> GNF Business
>
> San Diego, CA 92121
>
>
>
> T +1 (858) 332-4750
>
> cde...@gn...
>
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>
>
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