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Add Unipept taxonomy viewer plugin #4310

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merged 10 commits into from Jul 18, 2017

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@caleb-easterly
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commented Jul 12, 2017

Adds a plugin that allows for visualization of taxonomy datasets. It is based on the visualizations at http://unipept.ugent.be, and relies on the standalone visualizations code from @unipept (at https://github.com/unipept/unipept-visualizations). The viewer appears only for the d3_hierarchy datatype (added by @jj-umn).

This is a sample screenshot from the integrated Galaxy plugin, which opens in a separate tab:
unipept_viz

The data is human gut microbiome data, Sample 7 from Verberkmoes, et al. 2009, also used on the Unipept website.

The data in json format are also attached (unipept-pept2lca.txt) - after upload, the d3_hierarchy datatype must be manually selected for the "Unipept Taxonomy Viewer" to appear in the vis drop-down menu.

@galaxybot galaxybot added the triage label Jul 12, 2017

@galaxybot galaxybot added this to the 17.09 milestone Jul 12, 2017

.gitmodules Outdated
@@ -0,0 +1,3 @@
[submodule "config/plugins/unipept"]
path = config/plugins/unipept
url = https://github.com/caleb-easterly/galaxy-plugin-unipept-visualization.git

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@jmchilton

jmchilton Jul 13, 2017

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Thanks for the contribution! Did you mean for this to be here - the project as a submodule? It looks like you tried to add it as a submodule and then just added it directly - is that correct? I'd prefer not adding vizs as submodules to Galaxy for now - they'd be better just directly inserted into Galaxy IMO - at least for now.

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caleb-easterly Jul 13, 2017

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This was my first shot at working with submodules...and I mostly just got confused. So I deleted .gitmodules and the submodule file in .git. Would that clean it up enough?

@@ -0,0 +1,21 @@
MIT License

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@bgruening

bgruening Jul 13, 2017

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@caleb-easterly are you also fine to distribute this under the same license than the Galaxy project? If so you could remove this file as well.

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caleb-easterly Jul 13, 2017

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yep, just removed the license

caleb-easterly added some commits Jul 13, 2017

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commented Jul 16, 2017

@caleb-easterly do we need the unipept-visualizations.min.js file with your latest commit?
Can you attach a simple screenshot to the PR description and maybe even an example file. I guess we will mention this addition in the Galaxy news brief and images are always great! :)

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commented Jul 17, 2017

No, I think we just need the es5.js and es5.js.map, so I removed everything else. Screenshot and example file are in the PR description!

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commented Jul 17, 2017

Awesome stuff! @guerler ready to be merged?

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commented Jul 18, 2017

Looks good to me.

@bgruening bgruening merged commit 7351252 into galaxyproject:dev Jul 18, 2017

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