Use the API to install repositories instead of loading the toolshed in an iframe. #1392

davebx · 2015-12-23T15:21:12Z

There remains work to be done on this, I'm sure the javascript in preview_repository.mako could be dramatically improved, but the current code should be functional.

This will return a dict of the repository, with the repository_dependencies element containing a list of dicts with the dependency chain descending from that repository.

Optionally show list of repositories in category.

This is only for development purposes, until the UI designer fixes it.

…olshed_decouple

- Repository dependencies reflect the selected changeset - So do tool dependencies - Tool panel select field shows/hides new tool panel section input field

…olshed_decouple

Cherry-picked changes from pull request #1392.

…shed_decouple

davebx · 2016-03-09T15:24:03Z

@martenson I believe I have corrected many of the points on your checklist.

Add the virtualenv to run_tool_shed.sh

bgruening · 2016-03-10T07:06:26Z

@galaxybot test this

mvdbeek · 2016-03-11T13:50:14Z

@davebx this is amazing, I'm testing it right now, and the UI is very nice!
One thing that I would do is to throw a nicer error message if targeting an older toolshed!

If more people want to test this, feel free point your galaxy instances at https://lbcd41.snv.jussieu.fr/toolshed ... though there are just a few repos to test. But I guess you can always import capsules?!

mvdbeek · 2016-03-11T13:56:35Z

Okay, this is seriously awesome. The bedtools suite installed fine, and in three different toolpanel (one default, and 2 in 2 seperate) sections. But it does log errors when there are actually no errors:

....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,130 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_bed12tobed6/2.24.0, version: 2.24.0 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,130 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/genomeCoverageBed.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,167 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_genomecoveragebed/2.24.0, version: 2.24.0 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,167 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/spacingBed.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,197 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_spacingbed/2.24.0, version: 2.24.0 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,197 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/expandBed.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,229 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_expandbed/2.24.0, version: 2.24.0 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,229 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/bamToFastq.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,259 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0, version: 2.24.0 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,260 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/annotateBed.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,292 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_annotatebed/2.24.1, version: 2.24.1 into tool panel....
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,293 Error while loading tool lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/0cc0bc30f78c/bedtools/intersectBed.xml : 
galaxy.tools.toolbox.base DEBUG 2016-03-11 14:57:51,338 Loaded tool id: lbcd41.snv.jussieu.fr/toolshed/repos/iuc/bedtools/bedtools_intersectbed/2.24.0, version: 2.24.0 into tool panel....

mvdbeek · 2016-03-11T14:14:12Z

Okay, I see the error has nothing to do with your PR, but us running the toolshed in a subdirectory.

I can't judge the quality of the javascript / mako part, but it does seem to work well. 👍

…shed_decouple

bgruening · 2016-03-30T10:40:53Z

@davebx, @martenson can we merge this before feature-freeze. It's working for me and @mvdbeek and it does not break the old form so I consider this a save move.

davebx · 2016-03-30T13:10:05Z

@bgruening I'll update it to fix the merge conflict, in case your motion carries.

…shed_decouple

martenson · 2016-03-30T14:07:47Z

I am in favor of merging as long as it is clearly labeled (Beta) which it is and does not interfere with the current approach.
👍

bgruening · 2016-03-30T14:07:58Z

@davebx are you working on the two missing bullet-points above? Should we migrate them to an issue and track the progress there?

davebx · 2016-03-30T14:08:32Z

@bgruening Yes, an issue for cleaning up the search feature would be a good idea.

martenson · 2016-03-30T14:09:13Z

@davebx @bgruening I will implement the two search points as a part of porting toolshed.tools search here.

mvdbeek · 2016-03-30T14:15:28Z

Nice work @davebx !

bgruening · 2016-03-30T14:19:30Z

@martenson thanks!
Great work @davebx!

davebx added 25 commits August 7, 2015 10:39

Use API to initiate repository installation.

9c49f57

Fix imminent import error in travis.

849cdab

Rename API endpoint. Correct url for API endpoint.

3f766f5

Typo.

cef6ad8

Additional cleanup.

ea7ad24

Add API endpoint to show installation status.

6ce5ac5

This will return a dict of the repository, with the repository_dependencies element containing a list of dicts with the dependency chain descending from that repository.

Load toolshed categories with API.

992812e

Update category API endpoint.

72e8f73

Optionally show list of repositories in category.

Add API endpoint to check for updates to installed repositories.

aff62e7

Fix the update check API method.

2dca8f1

Add rudimentary mako files for the new interface.

a4bf833

This is only for development purposes, until the UI designer fixes it.

Add code to initiate repository installation.

83a9c6d

Merge in changes from api_install branch.

6e58db9

Functional installation of repository.

099f8eb

Merge branch 'dev' of https://github.com/galaxyproject/galaxy into to…

2a67128

…olshed_decouple

Separate the decoupled and iframed toolshed installations.

b55ac36

Some refinements to the beta toolshed browsing.

271c8e9

Merge branch 'dev' of https://github.com/galaxyproject/galaxy into to…

fb336b9

…olshed_decouple

Add some styling, allow selecting revision to install.

d91fff8

Merge branch 'dev' of https://github.com/galaxyproject/galaxy into to…

9206e95

…olshed_decouple

Update displayed metadata on changeset change.

4fdfc0f

More dynamic updating.

7c357d1

- Repository dependencies reflect the selected changeset - So do tool dependencies - Tool panel select field shows/hides new tool panel section input field

Fill in some gaps in the repository listing.

ba9493a

Merge branch 'dev' of https://github.com/galaxyproject/galaxy into to…

e7072c0

…olshed_decouple

Fix typo.

68cecc6

davebx added kind/enhancement status/WIP area/API area/toolshed labels Dec 23, 2015

martenson added a commit that referenced this pull request Mar 3, 2016

Merge pull request #1821 from davebx/toolshed_decouple_api

02ed07c

Cherry-picked changes from pull request #1392.

davebx added 6 commits March 3, 2016 12:21

Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

3a5584a

…shed_decouple

Update javascript with Carl's suggestions.

f44c3ae

Do not display the valid tools section if there are none.

2a91835

Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

16b179f

…shed_decouple

Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

b8fc585

…shed_decouple

Return tools in metadata when repository has no dependencies.

be2c51d

Show tool panel selector only when needed.

f60edb9

Add the virtualenv to run_tool_shed.sh

mvdbeek mentioned this pull request Mar 11, 2016

Retrieve authentification also for long urls #1912

Merged

martenson mentioned this pull request Mar 15, 2016

The Roadmap #1928

Closed

Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

96ca49b

…shed_decouple

Merge branch 'dev' of git://github.com/galaxyproject/galaxy into tool…

ef960a6

…shed_decouple

bgruening merged commit 3ad68fd into galaxyproject:dev Mar 30, 2016

davebx deleted the toolshed_decouple branch March 30, 2016 14:08

davebx mentioned this pull request Mar 31, 2016

Replace common_util.url_join with util.build_url. #2055

Merged

martenson added this to the 16.04 milestone May 12, 2016

martenson mentioned this pull request Jul 27, 2016

Install via conda #2554

Merged

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Use the API to install repositories instead of loading the toolshed in an iframe. #1392

Use the API to install repositories instead of loading the toolshed in an iframe. #1392

Uh oh!

davebx commented Dec 23, 2015

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davebx commented Mar 9, 2016

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bgruening commented Mar 10, 2016

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mvdbeek commented Mar 11, 2016

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mvdbeek commented Mar 11, 2016

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mvdbeek commented Mar 11, 2016

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bgruening commented Mar 30, 2016

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davebx commented Mar 30, 2016

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martenson commented Mar 30, 2016

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bgruening commented Mar 30, 2016

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davebx commented Mar 30, 2016

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martenson commented Mar 30, 2016

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mvdbeek commented Mar 30, 2016

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bgruening commented Mar 30, 2016

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Uh oh!

Use the API to install repositories instead of loading the toolshed in an iframe. #1392

Use the API to install repositories instead of loading the toolshed in an iframe. #1392

Uh oh!

Conversation

davebx commented Dec 23, 2015

Uh oh!

davebx commented Mar 9, 2016

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bgruening commented Mar 10, 2016

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mvdbeek commented Mar 11, 2016

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mvdbeek commented Mar 11, 2016

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mvdbeek commented Mar 11, 2016

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bgruening commented Mar 30, 2016

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davebx commented Mar 30, 2016

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martenson commented Mar 30, 2016

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bgruening commented Mar 30, 2016

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davebx commented Mar 30, 2016

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martenson commented Mar 30, 2016

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mvdbeek commented Mar 30, 2016

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bgruening commented Mar 30, 2016

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