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API installation of toolshed repositories. #3626

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merged 84 commits into from May 17, 2017

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@davebx
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commented Feb 16, 2017

Repositories can be previewed and installed or added to the queue for later installation.

  • Handle cases where the workflow requires tools from multiple repositories.
  • Handle cases where a workflow uses tools from multiple toolsheds.
  • Pop up a modal with the tool form when clicking on the tool button.
  • List repositories that are an exact match for missing workflow tools.

Workflows

Screenshot

This is a refactor of #2823 using backbone. It is better in every way and should probably replace the old pull request.

davebx added some commits Aug 17, 2016

Update the display of workflows missing tools.
Thus accomodating the API changes made in the previous commit.
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commented Feb 28, 2017

@davebx this is great stuff! Thanks a bunch for working on this.

This is a quite big PR any idea how we can review this efficiently? @nsoranzo @martenson @mvdbeek ?

"seq_primer_clip",
"fastq_groomer_parallel",
"fasta_filter_by_id",
"fastq_filter_by_id",

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@jmchilton

jmchilton Mar 3, 2017

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This isn't correct - I think this is an odd merge artifact.

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@davebx

davebx Mar 6, 2017

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Good catch

define([], function() {

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jmchilton Mar 3, 2017

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This also looks incorrect.

@martenson martenson self-requested a review Mar 3, 2017

davebx and others added some commits Mar 6, 2017

@martenson martenson referenced this pull request Apr 20, 2017

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The Roadmap #1928

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@martenson martenson modified the milestones: 17.09, 17.05 Apr 27, 2017

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commented Apr 27, 2017

The plan is to merge this early in 17.09 cycle and enable it by default in config (so two options for installing tools will be available)

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commented Apr 28, 2017

@martenson Sounds good to me, that gives me more time to work out the UX issues you mentioned during the meeting and implement a few bells and whistles I had in mind.

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commented Apr 29, 2017

first portion of feedback on latest version

  1. (bug) clicking on Repository Queue (0) emit JS error Unexpected token u in JSON at position 0

  2. (ux) when searching for a repository I get a list of results such as
    screenshot 2017-04-24 14 22 37
    but when I navigate results with arrows (as suggested) the cursor is not highlighted and the name of the repository is replaced by the ID which makes the search experience really confusing.
    screenshot 2017-04-24 14 22 44

@martenson martenson merged commit b9fb2de into galaxyproject:dev May 17, 2017

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api test Test started.
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continuous-integration/travis-ci/pr The Travis CI build is in progress
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framework test Test started.
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integration test Test started.
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toolshed test Test started.
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commented May 17, 2017

Merging this early in the cycle, and enabling the config option by default, to get more testing done.

tool_model[ 'inputs' ] = []
populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] )
tool_model[ 'inputs' ] = {}
self.populate_model( request_context, self.inputs, state_inputs, tool_model[ 'inputs' ] )

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@guerler

guerler May 23, 2017

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These changes to this file break the workflow editor i.e. clicking on a tool module fails. The reason is that the model population has been tweaked since work was performed on this PR. I suggest to use the previous/most recent version of populate model (e.g. in 17.05) and move it out of the function block to redo this section. ping @davebx. Let me know if you need help with this.

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@davebx

davebx May 24, 2017

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Yes, this should be fixed. I'll be having a look at that today and tomorrow. I remember the populate_model method being an annoying source of frequent merge conflicts, so it's no surprise that one of those merges went the wrong way and broke things.

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@guerler

guerler May 25, 2017

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I cant blame you.

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