Merge dev and add tighter env abstraction. #3

jmchilton · 2015-05-11T13:12:28Z

There was a conflict with -dev - this merges dev and resolves that.
This moves ENV handling logic into the the ierequest object - should eliminate the necessity to have each IE do the same command-line building logic and doing string rewriting.

[Stable] Bind the IPython IE to a fixed Docker Image

Fixes regressions introduced with PR galaxyproject#110.

[STABLE] Job file API fixes

[15.05] Generate base url on client request

… (exact same functionality here, but it's less chatty this way, since it might not be bound)

… revert changes in auth_conf.xml syntax. After galaxyproject#75 , the <filter> tag of config/auth_conf.xml is broken, see galaxyproject#75 (comment) . I don't think that there is a meaningful way to filter on usernames, so I changed it to filter on email instead of login. Also: - fix AuthManager.check_registration_allowed to use both email and username since which is used for login depends on the AuthProvider used; - move ldap <authenticator> example to config/auth_conf.xml.sample .

[15.03] Check to see if toolshed install is actually bound prior to disposing (e...

Requested by @dctrud. With respect to previous implementation, email and username are passed as separate parameters.

[15.05] Create empty history if history is unavailable during api call

…or same

…andard

This is used by Bioblend, Pulsar, and Planemo and provides several benefits: - More flexibility then baking logic directly into .travis.yml - Makes the CI testing more portable - Generally leads to more parallelism on Travis - "prettier" display of results (things are broken down by the kind of test). For the last two points - compare https://travis-ci.org/galaxyproject/galaxy and https://travis-ci.org/galaxyproject/planemo. I would like to add the qunit tests to Travis and I see this a good first step toward being able to do that well.

Found bug with tox randomizing Python's hash seed.

Tests are more correct and perhaps less strong as result.

[15.05] Fix lib/galaxy/main.py for changes in starting control queue

…built-in visualizations

Testing: use unittest2 to allow 2.7 assertions

Sample files already being tracked won't be affected. If an ignored file is to be added, add it with -f.

…mplate Visualizations registry: switch to entry_point config definition for …

Ignore sample files from toolshed installed tools

Add RData and RData.gz formats

Conflicts: config/plugins/interactive_environments/ipython/config/ipython.ini.sample

hexylena · 2015-05-11T16:52:47Z

Excellent, that was definitely turning into unnecessary boilerplate pretty quickly. Thanks @jmchilton

Merge dev and add tighter env abstraction.

all data source tools go to _top

Update contact info for Marten.

Modify a few references to underscore.

PROXY_URL_WS Support and deprecation of APACHE_URLs

Retab galaxy_bootstrap/variables.less

Several fixes necessary for merging.

It's a function, not a true-y value :/

offer TS searching while browsing a category

styling changes to share and download page

Updates to current galaxy dev

Improve abstraction in webhook API tests.

Merge from upstream

Second pass after coffee break

add rna related tours

bgruening and others added 30 commits May 1, 2015 20:54

Bind the IPython IE to a fixed Docker Image

9cdd688

Merge pull request galaxyproject#201 from bgruening/couple_image_to_ie

a319329

[Stable] Bind the IPython IE to a fixed Docker Image

Workflow editor adjustments

0a506dc

Generate base url on client request

bd8ee3d

Fix flat sections

32eb1ea

Fix job files API for case when nginx upload not being used.

a594b32

Fixes regressions introduced with PR galaxyproject#110.

Merge pull request galaxyproject#213 from jmchilton/job_files_fix

d523d53

[STABLE] Job file API fixes

Merge pull request galaxyproject#203 from guerler/revise_baseurl

4154af4

[15.05] Generate base url on client request

Check to see if toolshed install is actually bound prior to disposing…

c1c8259

… (exact same functionality here, but it's less chatty this way, since it might not be bound)

Merge pull request galaxyproject#215 from dannon/release_15.03

5cf0332

[15.03] Check to see if toolshed install is actually bound prior to disposing (e...

Client libs: minor version bumps to jQuery and Raven

801adcd

Create empty history if history is unavailable during api call

62abcd0

Include hmmer3 text format

eeecf41

Move msa datatypes into separate file

7ef0d4e

Remove unnecessary lines

9ebf691

Imported stockholm from @bgruening

92ff779

Bump version of hmm format

c1840a4

Add in hmmer2 datatypes

ec363b2

Refactor count_special

5037c4d

Move ddatatypes upwards of images

d1c1af3

Filter also on username in AuthManager.active_authenticators().

f4b648d

Requested by @dctrud. With respect to previous implementation, email and username are passed as separate parameters.

Fix test cases

f0f2f39

Merge pull request galaxyproject#217 from guerler/fix_missing_history

bb75068

[15.05] Create empty history if history is unavailable during api call

Client libs: update requirejs to 2.1.17, correct bower installation f…

b18d215

…or same

Client libs: correct dependency location for requirejs from dev to st…

673aef1

…andard

Move stockholm as well

791785c

Bugfix: Make dataset naming more deterministic.

5711b45

Found bug with tox randomizing Python's hash seed.

Fix some doctests that were assuming fixed Python hashing.

5ddc493

Tests are more correct and perhaps less strong as result.

natefoo and others added 12 commits May 7, 2015 15:04

Fix lib/galaxy/main.py for changes in starting control queue.

e6b75a1

Merge pull request galaxyproject#242 from natefoo/release_15.05

1709b7f

[15.05] Fix lib/galaxy/main.py for changes in starting control queue

Merge remote-tracking branch 'upstream/release_15.05' into dev

d62b1d3

Visualizations registry: switch to entry_point config definition for …

11b2fbc

…built-in visualizations

Testing: use unittest2 to allow 2.7 assertions

d675a6a

Merge pull request galaxyproject#246 from carlfeberhard/testing.fix-26

10927bf

Testing: use unittest2 to allow 2.7 assertions

Ignore sample files from toolshed installed tools

028d1b0

Sample files already being tracked won't be affected. If an ignored file is to be added, add it with -f.

Merge pull request galaxyproject#243 from carlfeberhard/vis.remove-te…

a85eadf

…mplate Visualizations registry: switch to entry_point config definition for …

Merge pull request galaxyproject#248 from Unode/patch-1

f20c961

Ignore sample files from toolshed installed tools

Merge pull request galaxyproject#239 from erasche/rdata2

f7af19b

Add RData and RData.gz formats

Merge remote-tracking branch 'erasche/ie-updates2' into pr229

eb2034a

Conflicts: config/plugins/interactive_environments/ipython/config/ipython.ini.sample

Eliminate potential boilerplate code in new IE env stuff.

f3e81f1

hexylena added a commit that referenced this pull request May 11, 2015

Merge pull request #3 from jmchilton/pr229

7851c7e

Merge dev and add tighter env abstraction.

hexylena merged commit 7851c7e into hexylena:ie-updates2 May 11, 2015

jmchilton added a commit that referenced this pull request May 15, 2015

Merge pull request #3 from blankenberg/patch-1

cd75d6b

all data source tools go to _top

hexylena pushed a commit that referenced this pull request Jun 18, 2015

Merge pull request #3 from martenson/patch-1

5e2d615

Update contact info for Marten.

hexylena pushed a commit that referenced this pull request Jun 30, 2015

Merge pull request #3 from jmchilton/workflow_form_002_tests2

07a0ae0

Modify a few references to underscore.

bgruening added a commit that referenced this pull request Jul 16, 2015

Merge pull request #3 from erasche/ws_support

a0f045c

PROXY_URL_WS Support and deprecation of APACHE_URLs

hexylena pushed a commit that referenced this pull request Aug 5, 2015

Merge pull request #3 from dannon/style-colors

87a58e2

Retab galaxy_bootstrap/variables.less

hexylena pushed a commit that referenced this pull request Aug 19, 2015

Merge pull request #3 from dannon/Airistotal-Reports_homepage

e3b1302

Several fixes necessary for merging.

hexylena pushed a commit that referenced this pull request Mar 22, 2016

Merge pull request #3 from dannon/history-grid-state-optimization

38d7bbb

It's a function, not a true-y value :/

jmchilton pushed a commit that referenced this pull request Apr 4, 2016

Merge pull request #3 from martenson/decouple-polish

1b78b86

offer TS searching while browsing a category

jmchilton pushed a commit that referenced this pull request Apr 4, 2016

Merge pull request #3 from martenson/workflow_changes

a3a2e0d

styling changes to share and download page

hexylena pushed a commit that referenced this pull request Jun 6, 2016

Merge pull request #3 from galaxyproject/dev

c0b4119

Updates to current galaxy dev

hexylena pushed a commit that referenced this pull request Jan 12, 2017

wrong import name (#3)

b327523

hexylena pushed a commit that referenced this pull request Feb 1, 2017

Merge pull request #3 from jmchilton/webhooks_reorg

a9ba71c

Improve abstraction in webhook API tests.

hexylena pushed a commit that referenced this pull request Jul 2, 2017

Merge pull request #3 from galaxyproject/dev

7dab2aa

Merge from upstream

hexylena pushed a commit that referenced this pull request Jan 22, 2018

Merge pull request #3 from yvanlebras/patch-5

b346a02

Second pass after coffee break

hexylena added a commit that referenced this pull request Feb 1, 2019

Merge pull request #3 from pavanvidem/rna_tours

2cb9e51

add rna related tours

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Merge dev and add tighter env abstraction. #3

Merge dev and add tighter env abstraction. #3

jmchilton commented May 11, 2015

hexylena commented May 11, 2015

Merge dev and add tighter env abstraction. #3

Merge dev and add tighter env abstraction. #3

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jmchilton commented May 11, 2015

hexylena commented May 11, 2015