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

[Colin D. <ckd...@gm...>]

Sure, I'd be happy to give it a whirl. Thanks!

On Fri, Oct 2, 2020 at 11:43 PM <pc...@cn...> wrote:

> I think we have implemented that functionality. Once reviewed and approved
> we will release a new version with it.
>
> If you want to test it before that I can give you the command to install
> the patch
>
> El 2 oct. 2020 23:20, Colin Deniston <ckd...@gm...> escribió:
>
> Thanks for the info. Integrating the wait command in the templates somehow
> would definitely be useful. I'll take a better look at the python script
> but I'm not much of a coder and at first glance that script doesn't appear
> to have a way to sequentially run the protocols. Not sure how to implement
> that in the script myself. Also, my colors appear different from what
> you've mentioned, maybe because I'm using Scipion 3.0? Peach is scheduled
> for me, orange is running, and green is finished. Thanks for all the help!
>
> On Fri, Oct 2, 2020 at 12:58 AM Pablo Conesa <pc...@cn...> wrote:
>
> Thanks Colin, see anwser in line.
> On 1/10/20 23:49, Colin Deniston 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?
>
> Certainly something to Implement. Jose Miguel is right about the ids
> potentially been changes, but I think we can update the "wait for"
> attribute too (and export it/import it). I've created and issue
> <https://github.com/scipion-em/scipion-pyworkflow/issues/151> and will
> look at it:
>
> 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.
>
> The expected behavior is all should be "scheduled" (orange). This does not
> mean they are running, but they are actively checking is they can start
> once all validation passes (wait for should be part of the validation)
>
> Do the box with the "wait for" turns orange (scheduled,this would be
> correct) or green (running, thus 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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> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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