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Add DTD to Galaxy #2579

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merged 8 commits into from Jul 21, 2016

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@ericenns
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commented Jun 29, 2016

This merges DTD upstream into Galaxy.

https://github.com/phac-nml/dynamic-tool-destination

WIP until all tests have been moved over and reviewed fully.

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commented Jun 30, 2016

Great poster, great idea, I like it much and I think it is a nice addition to the dynamic tool destinations.
Thanks @ericenns!

@erasche erasche added kind/feature area/jobs and removed triage labels Jun 30, 2016

ericenns added some commits Jul 4, 2016

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commented Jul 4, 2016

I think WIP label can be removed, I have added all our tests in and they pass!

@bgruening bgruening removed the status/WIP label Jul 4, 2016

# Galaxy's history panel).


tools:

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Should this be commented out?

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Do you mean should the whole file be commented out? If so yes, is that what is done with out sample config files?

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commented Jul 4, 2016

@ericenns do you think we should keep the configuration under config or is this something really specific to the dynamic-job-destination and should be next to the job-destination to not pollute the config dir?

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commented Jul 4, 2016

The config file is specific to dtd, one benefit to keeping it in config is that it gives visibility to it. I guess I could add it as an example to job_conf.xml.sample_advanced

@galaxybot galaxybot added the status/WIP label Jul 4, 2016

@ericenns ericenns changed the title [WIP] Add DTD to Galaxy Add DTD to Galaxy Jul 5, 2016

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commented Jul 5, 2016

Guess I have to remove WIP from the title or galaxybot will keep adding the label back.

@bgruening bgruening removed the status/WIP label Jul 5, 2016

@galaxybot galaxybot added this to the 16.07 milestone Jul 5, 2016

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commented Jul 20, 2016

@galaxybot test this

jmchilton added a commit to jmchilton/starforge that referenced this pull request Jul 20, 2016

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commented Jul 20, 2016

Really nifty - I ❤️ the tests and focus on validation - this great.

I created galaxyproject/starforge#100 so the wheel for testfixtures can be placed on wheels.galaxyproject.org.

I'm going to open a counter-PR to make the config handling more Galaxy-ish.

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commented Jul 20, 2016

The upstream project has a different copyright statement and license than Galaxy and it is featured prominently in README - given that I just wanted to make sure that you are explicitly granting the Galaxy project permission to redistribute this code with our license and copyright.

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commented Jul 20, 2016

Yes I am granting the Galaxy project permission to redistribute this code with their license and copyright.

jmchilton added some commits Jul 20, 2016

Ease configuration and add documentation for using DTD syntax for des…
…tinations.

Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly.
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commented Jul 20, 2016

Thanks @ericenns!

I have two commits I'd like to discuss but Github isn't letting me open a PR against your repo and I don't understand why. Any chance you can review them, test them, and cherry-pick them into your branch if they look good?

They are from my branch here - https://github.com/jmchilton/galaxy/tree/add-dtd-to-galaxy.

jmchilton@ed48c6c Makes the config handling more like traditional Galaxy - navigating the Galaxy config object to find that YAML file.
jmchilton@d87957e Re-imagines how this would be used a bit - it makes this a special "type" of dynamic destination (there were already some others) so details such as the function name don't need to be exposed. It also adds some documentation to job_conf.xml.sample_advanced about how to use it.

Any problems with these changes?

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commented Jul 20, 2016

Thanks @jmchilton, the changes look good to me. I will merge them and retest.

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commented Jul 20, 2016

@jmchilton everything looks good, a revised test location and updated the sample config with a little more information on how to validate your config.

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commented Jul 20, 2016

@galaxybot test this

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commented Jul 20, 2016

Hmm looks like there is a problem with running the following command:

 bash -c '. .venv/bin/activate; python lib/galaxy/jobs/dynamic_tool_destination.py -c config/tool_destinations.yml.sample'

I am looking into it right now

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commented Jul 20, 2016

Ok everything should be good to go now

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commented Jul 20, 2016

@galaxybot test this

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commented Jul 21, 2016

Very nice @ericenns - thanks a bunch for this contribution!

@jmchilton jmchilton merged commit f67d3cb into galaxyproject:dev Jul 21, 2016

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commented Jul 21, 2016

And of course I merged this without waiting for my own starforge PR (galaxyproject/starforge#100) 😠.

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commented Jul 21, 2016

🎉 This is awesome! Next GCC presentation in Galaxy main! Thanks a lot @ericenns!

jmchilton added a commit to jmchilton/starforge that referenced this pull request Jul 21, 2016

natefoo added a commit to galaxyproject/starforge that referenced this pull request Aug 4, 2016

jxtx added a commit to jxtx/starforge that referenced this pull request Oct 10, 2016

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