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AskOmics Interactive Environment #4737

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merged 7 commits into from Nov 15, 2017

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@xgaia
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xgaia commented Oct 3, 2017

Hello everyone,

This PR add a new interactive environment to Galaxy: AskOmics

The docker used is available here

With this IE, users can upload datasets into AskOmics, then, they can launch queries on their data using the query builder of askomics, and then, send the results into the most recently used history.

Users can also save the state of a query to Galaxy, and reuse it later.

image

ping @abretaud @ofilangi

@jmchilton

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jmchilton commented Oct 3, 2017

Thanks for the contribution - this is exciting!

A couple thoughts about the license in case anyone else considers it. The AGPL is a little more copy-left than the GPL - in ways that explicitly deal with network usage.

From https://www.gnu.org/licenses/why-affero-gpl.en.html

The GNU Affero General Public License is a modified version of the ordinary GNU GPL version 3. It has one added requirement: if you run a modified program on a server and let other users communicate with it there, your server must also allow them to download the source code corresponding to the modified version running there.

We are not really running a modified version it seems and the original is clearly available - so I think it should be totally fine to run AGPL software via GIEs configurations licensed under AFL like this. I'm not trying to raise concerns - just documenting my research and thought process about why this is fine.

@galaxybot galaxybot added the triage label Oct 3, 2017

@galaxybot galaxybot added this to the 18.01 milestone Oct 3, 2017

if not additional_ids:
additional_ids = str(trans.security.encode_id( hda.id ) )
else:
additional_ids += "," + trans.security.encode_id( hda.id )

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@bgruening

bgruening Oct 3, 2017

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In case of None: Is additional_ids then None, 45

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@xgaia

xgaia Oct 5, 2017

Contributor

Thanks for your feedback @bgruening, but I don't understand what you mean here.

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@bgruening

bgruening Oct 5, 2017

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When additional_ids = trans.request.params.get('additional_dataset_ids', None) is None, what is the value of additional_ids after the if condition?

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@xgaia

xgaia Oct 6, 2017

Contributor

When the IE is lauched by clicking the visualize button of a dataset, trans.request.params.get('additional_dataset_ids', None) is None. After the condition, additional_ids is the selected dataset id.

ie_request.load_deploy_config()
# Get a random API key
askomics_api_key = ''.join([random.choice(string.ascii_letters + string.digits) for n in xrange(20)])

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@erasche

erasche Oct 4, 2017

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there's a built-in, randomly generated password available to you already via ie_request.notebook_pw

e.g. in use here.
https://github.com/galaxyproject/galaxy/blob/dev/config/plugins/interactive_environments/jupyter/templates/jupyter.mako#L15

but maybe that doesn't meet askomics requirements>?

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@xgaia

xgaia Oct 5, 2017

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fixed :-)

@dannon

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dannon commented Nov 15, 2017

Looks like it's working pretty well with the javascript fixes in xgaia#1.

Merge pull request #1 from dannon/askomics-fixes
Small javascript fixes for askomics IE integration
@dannon

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dannon commented Nov 15, 2017

@xgaia Thanks! Checking one more thing and then I'll merge this in.

@dannon dannon merged commit f34e6a1 into galaxyproject:dev Nov 15, 2017

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