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Rework Jupyter IE for additional_ids handling. #3980

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merged 3 commits into from May 1, 2017

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commented Apr 26, 2017

  • Add a new option use_volumes to the Docker config.
  • If using volumes, do nothing differently.
  • If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires bgruening/docker-jupyter-notebook#17).
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commented Apr 26, 2017

xref #3974 - this will require updating main's GIE configuration and rebuilding a new container.

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commented Apr 26, 2017

@jmchilton any interest in adding these changes to rstudio.mako as well? I'm happy to test.

@galaxybot galaxybot added the triage label Apr 26, 2017

@galaxybot galaxybot added this to the 17.05 milestone Apr 26, 2017

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commented Apr 27, 2017

@erasche I saw you already started work on this from the container side of things - do you want me to just make the same changes to the mako entry points then?

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commented Apr 27, 2017

@jmchilton yes, that'd be perfect!

jmchilton added some commits Apr 26, 2017

Rework Jupyter IE for additional_ids handling.
- Add a new option ``use_volumes`` to the Docker config.
- If using volumes, do nothing differently.
- If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires bgruening/docker-jupyter-notebook#17).
Update rstudio to match additional hid handling of Jupyter.
Ping @erasche - does this work? I'm not sure how rstudio handles the existing DATASET_HID.

@jmchilton jmchilton force-pushed the jmchilton:ie_for_mac_os_x_fixes branch from 3b615f8 to 9bc24ae Apr 28, 2017

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commented Apr 28, 2017

yep, perfect! Thanks.

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commented Apr 28, 2017

Tested this PR in all the configurations that I use regularly, looks good! 👍 Should this new option be documented in the individual .ini.sample config files?

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commented May 1, 2017

@erasche Good point - I've added a comment about this new option to the two most relevant GIEs.

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commented May 1, 2017

Looks good, thanks @jmchilton

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commented May 1, 2017

I'm happy to merge, but the test seems to be failing due to ConventionChecker missing? Is that safe to merge over?

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commented May 1, 2017

@erasche Yeah - that is an unrelated CI problem. I have an open PR to fix that.

@erasche erasche merged commit 0940411 into galaxyproject:dev May 1, 2017

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@martenson martenson removed the status/WIP label Jul 16, 2018

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