galaxy-commits
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- ----- 2010 -----
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- 15302 discussions
Branch: refs/heads/martenson-patch-1
Home: https://github.com/galaxyproject/usegalaxy-playbook
1
0
30 May '17
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 1283e77813b20b31ee19271f289e01a149dc94cd
https://github.com/galaxyproject/usegalaxy-playbook/commit/1283e77813b20b31…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-25 (Thu, 25 May 2017)
Changed paths:
M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
Log Message:
-----------
give salmon 16gb and rna_Star 64
Commit: 4de1718bc260a36bc13be6d3c049a83231077e75
https://github.com/galaxyproject/usegalaxy-playbook/commit/4de1718bc260a36b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-05-30 (Tue, 30 May 2017)
Changed paths:
M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
Log Message:
-----------
Merge pull request #28 from galaxyproject/martenson-patch-1
give salmon 16gb and rna_Star 64
Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/07c13f0094d2...…
1
0
30 May '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fd2e8fe517608f506d57b2a131b520c7c720da82
https://github.com/galaxyproject/galaxy/commit/fd2e8fe517608f506d57b2a131b5…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Replacing configure_menu mako by JavaScript
Commit: 5d48e62eeae3dd7e55a0b51d64f9b71f90e50582
https://github.com/galaxyproject/galaxy/commit/5d48e62eeae3dd7e55a0b51d64f9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Removing unused code
Commit: 91d08cc746a28cc19ced4d1cdb03f54b27691d47
https://github.com/galaxyproject/galaxy/commit/91d08cc746a28cc19ced4d1cdb03…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
A static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
New file for configure workflow menu and adding check and uncheck all buttons
Commit: 64312c4331abb4b75b3b55e8366e7c1f351dca0c
https://github.com/galaxyproject/galaxy/commit/64312c4331abb4b75b3b55e8366e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/style/less/base.less
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-configure-menu.js
M static/style/blue/base.css
Log Message:
-----------
Adding styling and back button to configure workflow menu page
Commit: f0d28992a4bf47d4a3bf338696c202144e8463cb
https://github.com/galaxyproject/galaxy/commit/f0d28992a4bf47d4a3bf338696c2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/apps/panels/history-panel.js
A client/galaxy/scripts/apps/panels/tool-panel.js
R client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/grid/grid-template.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/util.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M client/webpack.config.js
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/tours/core.history.yaml
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M doc/source/admin/special_topics/webhooks.rst
M lib/galaxy/config.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/container_resolvers/explicit.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
A lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/util/repository_util.py
A static/maps/admin.toolshed.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/grid/grid-template.js.map
A static/maps/mvc/toolshed/categories-view.js.map
A static/maps/mvc/toolshed/repo-queue-view.js.map
A static/maps/mvc/toolshed/repo-status-view.js.map
A static/maps/mvc/toolshed/repositories-view.js.map
A static/maps/mvc/toolshed/repository-queue-view.js.map
A static/maps/mvc/toolshed/repository-view.js.map
A static/maps/mvc/toolshed/shed-category-view.js.map
A static/maps/mvc/toolshed/shed-list-view.js.map
A static/maps/mvc/toolshed/shed-repo-details-view.js.map
A static/maps/mvc/toolshed/shed-repo-list-view.js.map
A static/maps/mvc/toolshed/sheds-list-view.js.map
A static/maps/mvc/toolshed/toolshed-model.js.map
A static/maps/mvc/toolshed/util.js.map
A static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
A static/scripts/admin.toolshed.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/grid/grid-template.js
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repo-status-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
A static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/show_params.mako
R templates/webapps/galaxy/admin/index.mako
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/webhooks/trans_object/config/trans_object.yaml
M test/qunit/tests/page_tests.js
Log Message:
-----------
Merging with dev
Commit: b9b45870730f9cdab6b9dca343aaf86072063161
https://github.com/galaxyproject/galaxy/commit/b9b45870730f9cdab6b9dca343aa…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Replacing the centerPanel by this.page in analysis.js
Commit: 091195fa23c58fc84e51155fa2fb9dfd446a9280
https://github.com/galaxyproject/galaxy/commit/091195fa23c58fc84e51155fa2fb…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
R templates/webapps/galaxy/workflow/configure_menu.mako
Log Message:
-----------
Removing configure_menu.mako file
Commit: 35ec338d5dc039a81bc470ad3c6736ea9b84887e
https://github.com/galaxyproject/galaxy/commit/35ec338d5dc039a81bc470ad3c67…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-20 (Sat, 20 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fixing build failure comments and removing commented out lines
Commit: 358ce8013fe61901efbe6e296ae9e29f422b675c
https://github.com/galaxyproject/galaxy/commit/358ce8013fe61901efbe6e296ae9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M .gitignore
M CONTRIBUTORS.md
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
A static/scripts/bundled/admin.bundled.js
A static/scripts/bundled/admin.bundled.js.map
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merging with dev
Commit: a95a78a6c5c5aea880c1dde49e652372c11e902e
https://github.com/galaxyproject/galaxy/commit/a95a78a6c5c5aea880c1dde49e65…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Log Message:
-----------
Merge branch 'dev' of https://github.com/bgruening/galaxy into workflowexport_mako
Commit: 60cb6b4d3185233237284eed5daa01c06ea4d9ed
https://github.com/galaxyproject/galaxy/commit/60cb6b4d3185233237284eed5daa…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-configure-menu.js
Log Message:
-----------
Fixing PR review comment to split api calls into two
Commit: 8975327cfd5c2e26675dc70ad5f8425a8b085ef0
https://github.com/galaxyproject/galaxy/commit/8975327cfd5c2e26675dc70ad5f8…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Adjusting indentation
Commit: 56fcd293b5095dfa87cce8864def490d05cc0143
https://github.com/galaxyproject/galaxy/commit/56fcd293b5095dfa87cce8864def…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-configure-menu.js
Log Message:
-----------
Fixing PR review comments
Commit: 852aa51225238d2150441063932564b5562b9e35
https://github.com/galaxyproject/galaxy/commit/852aa51225238d21504410639325…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-configure-menu.js
Log Message:
-----------
Making one api url for getting and setting workflows menu
Commit: 53037f6006ec4d4306234dd05642f3a80746f49b
https://github.com/galaxyproject/galaxy/commit/53037f6006ec4d4306234dd05642…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Updating url in the comments of workflow api
Commit: 4dcc145dbf8c0122b88afa3e38b33781a71d8b06
https://github.com/galaxyproject/galaxy/commit/4dcc145dbf8c0122b88afa3e38b3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove composite api function and duplicate resource connector
Commit: 9896fc0e9f478ea47378a514e9a1fc9ef65f54e4
https://github.com/galaxyproject/galaxy/commit/9896fc0e9f478ea47378a514e9a1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-30 (Tue, 30 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
A static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/workflow/workflow-configure-menu.js
M static/style/blue/base.css
R templates/webapps/galaxy/workflow/configure_menu.mako
Log Message:
-----------
Merge pull request #4092 from bgruening/workflowexport_mako
New Configure Workflow Menu UI
Compare: https://github.com/galaxyproject/galaxy/compare/aa7d701cbc76...9896fc0e9f47
1
0
[galaxyproject/galaxy] 55336d: Fix legacy Python path for genome diversity tools ...
by GitHub 30 May '17
by GitHub 30 May '17
30 May '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 55336d2c3142051f605231e6db1cb6a45639417c
https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-28 (Sun, 28 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix legacy Python path for genome diversity tools from miller lab.
Fixes #4108.
Commit: 96e1cf58f480549cf5b39647c8772863405f582f
https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-05-29 (Mon, 29 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #4117 from jmchilton/genome_diversity_fixes
[17.01] Fix legacy Python path for genome diversity tools from miller lab.
Commit: 42e274d3342720037d441222b9fb1bbcbce2d7c1
https://github.com/galaxyproject/galaxy/commit/42e274d3342720037d441222b9fb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-30 (Tue, 30 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #4122 from galaxyproject/release_17.01
[17.05] merge Release 17.01
Compare: https://github.com/galaxyproject/galaxy/compare/3d16319a15b7...42e274d33427
1
0
[galaxyproject/galaxy] 54d6a5: Avoid locale specific string.letters for job_name
by GitHub 30 May '17
by GitHub 30 May '17
30 May '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 54d6a54367ed6a852b54a89f567d901f494e682a
https://github.com/galaxyproject/galaxy/commit/54d6a54367ed6a852b54a89f567d…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2017-05-29 (Mon, 29 May 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Avoid locale specific string.letters for job_name
The job_name sanitation can fail if the locale specific
string.letters contains unexpected characters. e.g.
Saravanaraj Ayyampalayam reported getting the following
under locale en_US.iso885915
Traceback (most recent call last):
File /.../galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 397, in <genexpr>
job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name )
UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128)
See http://dev.list.galaxyproject.org/Issue-with-job-name-UnicodeDecodeError-in…
or https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-May/025687.html
The downside of this proposed change would be to mask
reasonable non ASCII letters from the job name on a
well defined system with consistent locale settings
for both Galaxy and the Cluster. But ASCII only seems
safer.
Commit: aa7d701cbc7674a13a4db30fce333e81558b2fea
https://github.com/galaxyproject/galaxy/commit/aa7d701cbc7674a13a4db30fce33…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-29 (Mon, 29 May 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Merge pull request #4121 from peterjc/locales_string_letters
Avoid locale specific string.letters for job_name
Compare: https://github.com/galaxyproject/galaxy/compare/64d6ffd59dee...aa7d701cbc76
1
0
[galaxyproject/galaxy] 55336d: Fix legacy Python path for genome diversity tools ...
by GitHub 29 May '17
by GitHub 29 May '17
29 May '17
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 55336d2c3142051f605231e6db1cb6a45639417c
https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-28 (Sun, 28 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix legacy Python path for genome diversity tools from miller lab.
Fixes #4108.
Commit: 96e1cf58f480549cf5b39647c8772863405f582f
https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-05-29 (Mon, 29 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #4117 from jmchilton/genome_diversity_fixes
[17.01] Fix legacy Python path for genome diversity tools from miller lab.
Compare: https://github.com/galaxyproject/galaxy/compare/b7a66f182ef8...96e1cf58f480
1
0
[galaxyproject/galaxy] 68433b: Force uniqueness of preserved tags (so, don't allo...
by GitHub 27 May '17
by GitHub 27 May '17
27 May '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 68433b1eff0a93704544a49f3d8f3a912d97c285
https://github.com/galaxyproject/galaxy/commit/68433b1eff0a93704544a49f3d8f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-25 (Thu, 25 May 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one)
Commit: b6e8d3e8acd00c1a595f15f2654c1b7809ecc831
https://github.com/galaxyproject/galaxy/commit/b6e8d3e8acd00c1a595f15f2654c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-26 (Fri, 26 May 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though.
Commit: dd06a01746f2ace048b9e1e604756e648a6ef1fd
https://github.com/galaxyproject/galaxy/commit/dd06a01746f2ace048b9e1e60475…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-26 (Fri, 26 May 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Handle *both* paths for tag appending using the now-dict correctly.
Commit: 2ac04bbf095573f2621ffeea0e2fdeb59b21da53
https://github.com/galaxyproject/galaxy/commit/2ac04bbf095573f2621ffeea0e2f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-26 (Fri, 26 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hdca-li.js
Log Message:
-----------
Uniqueify hashtag display
Commit: 3d16319a15b7ac2f947eca24c36957894ae00afe
https://github.com/galaxyproject/galaxy/commit/3d16319a15b7ac2f947eca24c369…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-05-27 (Sat, 27 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hdca-li.js
Log Message:
-----------
Merge pull request #4114 from dannon/force_uniqueness_preserved_tags
[17.05] Force uniqueness of preserved tags
Compare: https://github.com/galaxyproject/galaxy/compare/18ef6a6ab0dc...3d16319a15b7
1
0
25 May '17
Branch: refs/heads/martenson-patch-1
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 1283e77813b20b31ee19271f289e01a149dc94cd
https://github.com/galaxyproject/usegalaxy-playbook/commit/1283e77813b20b31…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-25 (Thu, 25 May 2017)
Changed paths:
M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
Log Message:
-----------
give salmon 16gb and rna_Star 64
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 07c13f0094d292a15b5c8a930304bc9914fd2062
https://github.com/galaxyproject/usegalaxy-playbook/commit/07c13f0094d292a1…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-05-25 (Thu, 25 May 2017)
Changed paths:
A env/main/files/galaxy/galaxy_version.yml
Log Message:
-----------
Update Main
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6f5e76eecc52de175b4d48cb9c13c4c78eb39772
https://github.com/galaxyproject/galaxy/commit/6f5e76eecc52de175b4d48cb9c13…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix bad merge for populate model
Commit: 64d6ffd59dee8ee68b7a835b1566cca162a173db
https://github.com/galaxyproject/galaxy/commit/64d6ffd59dee8ee68b7a835b1566…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #4112 from guerler/fix_populate
Fix failed merge for populate model
Compare: https://github.com/galaxyproject/galaxy/compare/d7a0fdfaa748...64d6ffd59dee
1
0
[galaxyproject/galaxy] e0f80d: Add possibility to load collections into library
by GitHub 24 May '17
by GitHub 24 May '17
24 May '17
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: e0f80db701b2c843c78074b9957452aa2eb3fe58
https://github.com/galaxyproject/galaxy/commit/e0f80db701b2c843c78074b99574…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M test/api/test_libraries.py
Log Message:
-----------
Add possibility to load collections into library
and to conserve element_identifier.
Commit: 8906f515e1df604c62a0faf6744b309b396431d5
https://github.com/galaxyproject/galaxy/commit/8906f515e1df604c62a0faf6744b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Add first working version of js needed for collection import
Commit: 08449059f4e3c62fd281fcbeae67cdce149241c0
https://github.com/galaxyproject/galaxy/commit/08449059f4e3c62fd281fcbeae67…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M test/api/test_libraries.py
Log Message:
-----------
Test adding a single dataset to a folder and test creating library using from_hdca_id
Commit: 8b9fd288bc4a05b177a56665229cbd9b58f4de3c
https://github.com/galaxyproject/galaxy/commit/8b9fd288bc4a05b177a56665229c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M test/api/test_libraries.py
Log Message:
-----------
Test creating library datatsets fails when not owning HDA
Commit: 26050f6deafe51fc38632dc4a02c284ec0ea993d
https://github.com/galaxyproject/galaxy/commit/26050f6deafe51fc38632dc4a02c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
Log Message:
-----------
Move functionality shared between folder and library api into UsesLibraryMixinItems
Commit: e7a0c186a9494f3589364dfc5f76e25bcd97dbad
https://github.com/galaxyproject/galaxy/commit/e7a0c186a9494f3589364dfc5f76…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
Log Message:
-----------
Simplify exception handling
Commit: 46af8ba4c3007f33f68c0b0d95f2dc166e69a14f
https://github.com/galaxyproject/galaxy/commit/46af8ba4c3007f33f68c0b0d95f2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Simplify exceptions some more
Commit: 6e7d290d0c462772cf51118f83e3f6c39a170ede
https://github.com/galaxyproject/galaxy/commit/6e7d290d0c462772cf51118f83e3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
Log Message:
-----------
Remove unused rval variable
Commit: ea013fefa82ea6454168feda71be7e589e3b162d
https://github.com/galaxyproject/galaxy/commit/ea013fefa82ea6454168feda71be…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
add a task to protect the release branch in github
to the release process
should prevent https://github.com/galaxyproject/galaxy/pull/3560#issuecomment-277520315
thanks @nsoranzo
Commit: 2392bb90624273a6288b720819a6816c945a0cc1
https://github.com/galaxyproject/galaxy/commit/2392bb90624273a6288b720819a6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
A .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
A .ci/jenkins/selenium/docker-compose.yml
A .ci/jenkins/selenium/galaxy.ini
A .ci/jenkins/selenium/run_galaxy.bash
A .ci/jenkins/selenium/run_tests.sh
A .ci/jenkins/toolshed/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
A config/build_sites.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.xml
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
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M lib/tool_shed/util/workflow_util.py
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A scripts/slideshow/example.md
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M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/add_scores.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/pasteWrapper.xml
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.py
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.py
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.py
M tools/maf/vcf_to_maf_customtrack.xml
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.py
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into protect-release-branch
Commit: 9c4587969ec71a0759e9a46053ffaf13e98944da
https://github.com/galaxyproject/galaxy/commit/9c4587969ec71a0759e9a46053ff…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
typo spotted by @nsoranzo
Commit: 828422fe5e6d419ec1af28e0c62b7a8759bae9b8
https://github.com/galaxyproject/galaxy/commit/828422fe5e6d419ec1af28e0c62b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Only show items in selector if item is visible and state is ok
Commit: 75994c8816cdac0af80614db629553495dcb6bff
https://github.com/galaxyproject/galaxy/commit/75994c8816cdac0af80614db6295…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Always set new ldda's to visible
Commit: d62824892ccfbdd20b5ff6af46b8af61eca3c8b9
https://github.com/galaxyproject/galaxy/commit/d62824892ccfbdd20b5ff6af46b8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #3562 from martenson/protect-release-branch
add a task to protect the release branch in github
Commit: 900c8d2dfe5ee687b8926c55a6d1a701c5049113
https://github.com/galaxyproject/galaxy/commit/900c8d2dfe5ee687b8926c55a6d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3533 from mvdbeek/tdt_reload
Watch tool data table *.loc files, and reload if modified.
Commit: a391af968742ab616f98edf7b889fe639302cf00
https://github.com/galaxyproject/galaxy/commit/a391af968742ab616f98edf7b889…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Remove duplicated/unused display_migration_details() functions
Also fix import order.
Commit: ed98b1b75aacc676d0f43a0a3a519132756518b7
https://github.com/galaxyproject/galaxy/commit/ed98b1b75aacc676d0f43a0a3a51…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Merge pull request #3564 from nsoranzo/remove_display_migration_details
Remove duplicated/unused display_migration_details() functions
Commit: 09f9396eab2c511013c0b637997191bc4f0e74ba
https://github.com/galaxyproject/galaxy/commit/09f9396eab2c511013c0b6379971…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Use number library to identify numeric values
Commit: 440c75fe589d3c92e6837bdd244490dc29003e45
https://github.com/galaxyproject/galaxy/commit/440c75fe589d3c92e6837bdd2444…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 1bb10da295fdf25855f5140f26bc7a62b278acab
https://github.com/galaxyproject/galaxy/commit/1bb10da295fdf25855f5140f26bc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Raise message exception instead of return a dictionary
Commit: f264e91cabfd29a8f385f8fbce4c8714b088fa23
https://github.com/galaxyproject/galaxy/commit/f264e91cabfd29a8f385f8fbce4c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use update endpoint to store workflows
Commit: 6fc64f6f46f16efb45450cf4597d5e86dec865b5
https://github.com/galaxyproject/galaxy/commit/6fc64f6f46f16efb45450cf4597d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge pull request #3565 from dannon/merge_1701_dev
Merge 1701 to dev
Commit: db47be5ad91bdd9364d5f9525941fd9a7b2c57c0
https://github.com/galaxyproject/galaxy/commit/db47be5ad91bdd9364d5f9525941…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove endpoint from routing
Commit: 284000c688724f47055a46bab4e8b377224db751
https://github.com/galaxyproject/galaxy/commit/284000c688724f47055a46bab4e8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Remove unused error variable
Commit: 5b366642019b4d69d033d916b71b5a85c3767d0f
https://github.com/galaxyproject/galaxy/commit/5b366642019b4d69d033d916b71b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M static/maps/mvc/form/form-input.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Fix qunit tests
Commit: 86a7880e48b81dec9a480600da9f918f7380c3bf
https://github.com/galaxyproject/galaxy/commit/86a7880e48b81dec9a480600da9f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
Log Message:
-----------
Update Nagios check
Commit: 5657a8b809e5938d3d996a77c826811e1176c108
https://github.com/galaxyproject/galaxy/commit/5657a8b809e5938d3d996a77c826…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Display the genbank file type in upload
Commit: 0d21f657ca4115ce3e309394cff8bdb084de6ef3
https://github.com/galaxyproject/galaxy/commit/0d21f657ca4115ce3e309394cff8…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Consolidate exception logging in db migrations
Also:
- align engine_true() and engine_false() methods
- remove unused 'now' variables
Commit: cb4fbe7a1caba8195ac8ec4965c702a58378f592
https://github.com/galaxyproject/galaxy/commit/cb4fbe7a1caba8195ac8ec4965c7…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
Log Message:
-----------
Fix a bunch of database migration bugs
Commit: 3b78907fdbbf2f26ea89f4459901e59164a033b7
https://github.com/galaxyproject/galaxy/commit/3b78907fdbbf2f26ea89f4459901…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/deletable.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M test/api/test_history_contents.py
M test/unit/managers/test_HDAManager.py
Log Message:
-----------
Set 'deleted' to True when purging a history dataset association
Fix https://github.com/galaxyproject/galaxy/issues/3548
Add API and unit test cases.
Add migration to fix misaligned databases.
Commit: 6a8dc6e26cf92d0c54a35e76c978dba8d6cd9864
https://github.com/galaxyproject/galaxy/commit/6a8dc6e26cf92d0c54a35e76c978…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Evaluate cyclic workflows on the fly when loading the run workflow form
Commit: 27d871f20edc8bc45a8b7b9d54ef88e48d3cb154
https://github.com/galaxyproject/galaxy/commit/27d871f20edc8bc45a8b7b9d54ef…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #3569 from natefoo/genbank-upload
Display the genbank file type in upload
Commit: 68752b7db0c6328d1d88e657ad21b2e4312f4401
https://github.com/galaxyproject/galaxy/commit/68752b7db0c6328d1d88e657ad21…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Merge pull request #3570 from nsoranzo/database_migrations
Database migrations: improvements and fixes
Commit: afb024819917535ba4820405c31f00d16224f453
https://github.com/galaxyproject/galaxy/commit/afb024819917535ba4820405c31f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Remove blank line
Commit: 7411aa52fd9cdaa1874a773fbfd440866f909e65
https://github.com/galaxyproject/galaxy/commit/7411aa52fd9cdaa1874a773fbfd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/modules.py
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Merge pull request #3522 from guerler/store_step_json_000
Store module step states as nested dictionaries, fix export for backward compatibility
Commit: d302400b99b7ae32a2d3f09266b15380b81d83b3
https://github.com/galaxyproject/galaxy/commit/d302400b99b7ae32a2d3f09266b1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/ui/autocom_tagging.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/steps.py
M static/maps/libs/jquery/jquery.autocomplete.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/ui/autocom_tagging.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/autocom_tagging.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge pull request #3407 from guerler/fix_workflow_ui
Workflow editor UI touch up
Commit: 846e765fa93ebcf33c0acce2ba9a9a49366b6a3a
https://github.com/galaxyproject/galaxy/commit/846e765fa93ebcf33c0acce2ba9a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
Log Message:
-----------
Update Jupyter IE name to be shorter and consistent with other names. Makes menu entries look correct.
Commit: 36686199cc7111cbf17df3ec619a5097048117e3
https://github.com/galaxyproject/galaxy/commit/36686199cc7111cbf17df3ec619a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
Log Message:
-----------
Merge pull request #3576 from dannon/jupyter_naming
Update Jupyter IE name to be shorter and consistent with other names.…
Commit: 3b3bfad8e0af0d07dee1ef379560258aece3f8e6
https://github.com/galaxyproject/galaxy/commit/3b3bfad8e0af0d07dee1ef379560…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M doc/source/releases/index.rst
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/users.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: b215ea1eed127e61421cccb8ff5ddb68963e28ae
https://github.com/galaxyproject/galaxy/commit/b215ea1eed127e61421cccb8ff5d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/galaxy/api/histories.py
M test/api/test_histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Sync API history purge with hda implementation
Add API and unit test cases.
Import order and Python3 fixes.
Commit: ed3062b41de47d77974bfae97bac21b2d9806432
https://github.com/galaxyproject/galaxy/commit/ed3062b41de47d77974bfae97bac…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/managers/deletable.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/webapps/galaxy/api/histories.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge pull request #3572 from nsoranzo/fix_3548
Set 'deleted' to True when purging a history dataset association
Commit: 0815e6b8813b0ef980cc95ddf08244c44e8fb2e0
https://github.com/galaxyproject/galaxy/commit/0815e6b8813b0ef980cc95ddf082…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Add d3_hierarchy subclass
This is to support Unipept API tool and visualization: https://github.com/unipept/unipept-visualizations
The unipept visualization would only apply to the d3_hierarchy of json datasets.
Commit: 7e98cde0a9cf62f60b907ed14ee407f6183dee72
https://github.com/galaxyproject/galaxy/commit/7e98cde0a9cf62f60b907ed14ee4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Update tool XSD for (hopefully deprecated) change_format syntax.
Fixes #3552.
Commit: 139bacb7d3e507ea56b8c8997e47408db87b5fa3
https://github.com/galaxyproject/galaxy/commit/139bacb7d3e507ea56b8c8997e47…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Remove broken tour step.
This causes the Selenium tests to fail under various conditions - but legimately so. The referenced target link disappears pretty quickly after the step in the previous click. When I run them in the web browser and this step is "disconnected" and in the center of the screen and as a result it isn't clear what links are being referred to.
Commit: ca847e2d588db417bb66664a76ecfdb2105ccc41
https://github.com/galaxyproject/galaxy/commit/ca847e2d588db417bb66664a76ec…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
Log Message:
-----------
Merge pull request #3568 from natefoo/nagios
Update Nagios check
Commit: be09b7c2ccf2ef861927795c16fb1306ef37ff1a
https://github.com/galaxyproject/galaxy/commit/be09b7c2ccf2ef861927795c16fb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Merge pull request #3582 from jmchilton/selenium_fixes
Remove broken tour step.
Commit: 07a92fd3ef084a6d7cbe27199d281e534e35cec1
https://github.com/galaxyproject/galaxy/commit/07a92fd3ef084a6d7cbe27199d28…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Remove tool_model usage from client
Commit: f7092bd959cfae7f6ee0262a993a2dc5867416e4
https://github.com/galaxyproject/galaxy/commit/f7092bd959cfae7f6ee0262a993a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M .ci/jenkins/selenium/run_tests.sh
Log Message:
-----------
Clean up Selenium resources better.
Commit: 171655930aa44227d6b88709aac638dea77a6cd0
https://github.com/galaxyproject/galaxy/commit/171655930aa44227d6b88709aac6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Move populate state to parameter handling module
Commit: 3e3eb4d1397effc8b46c913bb80f3c02773ac506
https://github.com/galaxyproject/galaxy/commit/3e3eb4d1397effc8b46c913bb80f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Unify build_module handler
Commit: 62d42f711e26e0ab176041ce9a552d1af1290f1a
https://github.com/galaxyproject/galaxy/commit/62d42f711e26e0ab176041ce9a55…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Parse payload directly to from_dict handler, handle tool specific attributes in corresponding module wrapper
Commit: 7d35a029174da0e3c8f481c0662139b9a59b3051
https://github.com/galaxyproject/galaxy/commit/7d35a029174da0e3c8f481c06621…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M .ci/jenkins/selenium/run_tests.sh
Log Message:
-----------
Merge pull request #3583 from jmchilton/selenium_fixes
Clean up docker-compose resources better for Selenium tests.
Commit: f3309822c856e50c61d94c2e021859342d40c5fb
https://github.com/galaxyproject/galaxy/commit/f3309822c856e50c61d94c2e0218…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
add option to send API key in header
Commit: 812ad3af18b087372b31188ac173b7e9238d712b
https://github.com/galaxyproject/galaxy/commit/812ad3af18b087372b31188ac173…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Fix transiently failing Selenium upload test.
Commit: 6f5743d052fb4c2ee227d71bf6106f2be9f4428a
https://github.com/galaxyproject/galaxy/commit/6f5743d052fb4c2ee227d71bf610…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Merge pull request #3584 from jvolkening/http_header_api_key
add option to send API key in header
Commit: d27e0570cb0b372288114498fa1ad26a1f5df188
https://github.com/galaxyproject/galaxy/commit/d27e0570cb0b372288114498fa1a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Remove name handling field from workflow module forms
Commit: ed52230952a1411a39cff3bde7a7ed66e1344f6f
https://github.com/galaxyproject/galaxy/commit/ed52230952a1411a39cff3bde7a7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
config/datatypes_conf.xml.sample
Commit: 1922d50f903f0c6ad1440d9128a1a23d37cc529c
https://github.com/galaxyproject/galaxy/commit/1922d50f903f0c6ad1440d9128a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
M test/selenium_tests/framework.py
Log Message:
-----------
Increase patience of Galaxy tests throughout.
This should help reduce various API and Selenium transient failures.
Commit: 1858e43d46355be344c0fab9e61a2e5a57dc8947
https://github.com/galaxyproject/galaxy/commit/1858e43d46355be344c0fab9e61a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Unify handling/parsing of label and fixed module name to build title in workflow run form
Commit: d484355832a1c6518d38326ef4fbb526423c0e34
https://github.com/galaxyproject/galaxy/commit/d484355832a1c6518d38326ef4fb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Provide attributes to front-end, build title on client side
Commit: dc0e9fd79eaff575a731409ed7f1771c6cd82b93
https://github.com/galaxyproject/galaxy/commit/dc0e9fd79eaff575a731409ed7f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Avoid step duplication when ordering steps on the fly
Commit: 2ad612349683dd4ab3bde476f9153e90415f0b53
https://github.com/galaxyproject/galaxy/commit/2ad612349683dd4ab3bde476f915…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
M test/selenium_tests/framework.py
Log Message:
-----------
Merge pull request #3589 from jmchilton/test_timeout_increases
Increase patience of Galaxy tests throughout.
Commit: 66a24c8830f5a87579f5e6e4f55c8efbf9073b0f
https://github.com/galaxyproject/galaxy/commit/66a24c8830f5a87579f5e6e4f55c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Merge pull request #3587 from jmchilton/selenium_fixes
Fix transiently failing Selenium upload test.
Commit: b9f1e29eaf32cda146fea2b102157489a639ea51
https://github.com/galaxyproject/galaxy/commit/b9f1e29eaf32cda146fea2b10215…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Remove redundant label handling from subworkflows
Commit: 7ac954f757d2485ae7543db15f400dca0b94fdf3
https://github.com/galaxyproject/galaxy/commit/7ac954f757d2485ae7543db15f40…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Strip name handler
Commit: 11f9e1863f9616d58fc00a22526f71b2bca7b880
https://github.com/galaxyproject/galaxy/commit/11f9e1863f9616d58fc00a22526f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix label and annotation handling for subworkflows
Commit: c6c210a4fa47d0fc47306d30b9dbf40589f68cd8
https://github.com/galaxyproject/galaxy/commit/c6c210a4fa47d0fc47306d30b9db…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Remove uncommented code block from request builder
Commit: eb95131ab3a03a3675c3e6d6db23caca524b3da6
https://github.com/galaxyproject/galaxy/commit/eb95131ab3a03a3675c3e6d6db23…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Export label instead of name for description export
Commit: a79ae2a8c297c1c0f6c0e61271a2ca05ae0aa0f0
https://github.com/galaxyproject/galaxy/commit/a79ae2a8c297c1c0f6c0e61271a2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M CONTRIBUTING.md
M doc/source/slideshow/architecture/galaxy_architecture.md
M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
M doc/source/slideshow/architecture/images/objectstore.plantuml.svg
M doc/source/slideshow/architecture/images/plantuml_options.txt
M doc/source/slideshow/architecture/images/server_client.plantuml.svg
M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
M doc/source/slideshow/architecture/images/webapp.plantuml.svg
M doc/source/slideshow/architecture/style.css
M scripts/slideshow/slideshow_template.html
Log Message:
-----------
Align architecture slides with training-material remarkjs template.
- Copy over the training material style CSS template and add to it only what is needed.
- Cleanup style and layout handling in architecture slides markdown.
- Update generated images for white background.
- Small updates in content to architecture for recent changes (and CONTRIBUTING.md linked to from slides).
Commit: d9b36176a8181168f5c4553ead4f9e6545d7e856
https://github.com/galaxyproject/galaxy/commit/d9b36176a8181168f5c4553ead4f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-11 (Sat, 11 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #3580 from jj-umn/patch-5
Add d3_hierarchy subclass
Commit: 93453e490f2490899d818473d79eeddf9f6d0808
https://github.com/galaxyproject/galaxy/commit/93453e490f2490899d818473d79e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M templates/admin/reload_tool.mako
Log Message:
-----------
Avoid html response when reloading tool through the api
Commit: b466ff6cd8dc86c03f0d6322e26b94605087bb39
https://github.com/galaxyproject/galaxy/commit/b466ff6cd8dc86c03f0d6322e26b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix root location for tool reloader
Commit: 1aa459f19d45221957ff0be6a5f708bf6bd41a41
https://github.com/galaxyproject/galaxy/commit/1aa459f19d45221957ff0be6a5f7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Use shared modal viewer
Commit: cd52f20961fcdee3453b5c5ce28b84f25b50f3f3
https://github.com/galaxyproject/galaxy/commit/cd52f20961fcdee3453b5c5ce28b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Align code style to existing code in tool form base
Commit: 727bfbd258c548917d2025708368f73b57199648
https://github.com/galaxyproject/galaxy/commit/727bfbd258c548917d2025708368…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/tools.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix error message style, raise message exception if tool has not been found
Commit: 8e59ec1e2be863dc00cb86d1689e7169cd43b6e5
https://github.com/galaxyproject/galaxy/commit/8e59ec1e2be863dc00cb86d1689e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/tools.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Remove unused tooltips for submenu options, fix response
Commit: 10943712b829ac48760fc5ecd25405d768cc9dd4
https://github.com/galaxyproject/galaxy/commit/10943712b829ac48760fc5ecd254…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Revise dropdown item label
Commit: 9590d4551439c7b9ae13f704508bfef376ff1fc4
https://github.com/galaxyproject/galaxy/commit/9590d4551439c7b9ae13f704508b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Improve success message upon tool xml reloading
Commit: 73b8fc45aa088b17970c5309108442d968c70a7b
https://github.com/galaxyproject/galaxy/commit/73b8fc45aa088b17970c53091084…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Check once for admin operations when building dropdown list in tool form
Commit: d298c1c0da5871105898166ca72dd224f7897fc6
https://github.com/galaxyproject/galaxy/commit/d298c1c0da5871105898166ca72d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-11 (Sat, 11 Feb 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fix lint issues
Commit: 047c833db79fef8daa25ddf022f85d2ef9386d63
https://github.com/galaxyproject/galaxy/commit/047c833db79fef8daa25ddf022f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-11 (Sat, 11 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Align subworkflow handling, fix run request through input name
Commit: 823ac3cc6172db54c35fdae43553af304a6a162b
https://github.com/galaxyproject/galaxy/commit/823ac3cc6172db54c35fdae43553…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-02-11 (Sat, 11 Feb 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
M config/plugins/webhooks/demo/search/static/styles.css
Log Message:
-----------
add new Search plugin styles
Commit: 2e787394cc0b9ea1a73ba87235faa4f38c1e495e
https://github.com/galaxyproject/galaxy/commit/2e787394cc0b9ea1a73ba87235fa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-12 (Sun, 12 Feb 2017)
Changed paths:
M test/selenium_tests/test_stock_tours.py
Log Message:
-----------
Disable transiently failing tour test.
See code comment for more information - I am tracking the issue here https://github.com/galaxyproject/galaxy/issues/3598. I think it is important to resolve that test and fix the usability problems with current tours but I'd like to get the Selenium tests stable and testing against new PRs first.
Commit: 9ceaa0d41583b66efb1c228755ca4368c0bdb6af
https://github.com/galaxyproject/galaxy/commit/9ceaa0d41583b66efb1c228755ca…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-12 (Sun, 12 Feb 2017)
Changed paths:
M test/selenium_tests/test_stock_tours.py
Log Message:
-----------
Merge pull request #3599 from jmchilton/disable_galaxy_ui_test
Disable transiently failing tour test.
Commit: 9bb9feb0a8aeec36ded548aa8d28927e2b26d678
https://github.com/galaxyproject/galaxy/commit/9bb9feb0a8aeec36ded548aa8d28…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-12 (Sun, 12 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again'
Commit: fcbb7c3de17841027da5c2ec16cf11f78e709872
https://github.com/galaxyproject/galaxy/commit/fcbb7c3de17841027da5c2ec16cf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-12 (Sun, 12 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M static/maps/mvc/user/user-quotameter.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
Log Message:
-----------
Tooltips to suggest relog for quota correction.
Commit: 412d8e1bb6c82a9aa8a86971e64e4242a5341419
https://github.com/galaxyproject/galaxy/commit/412d8e1bb6c82a9aa8a86971e64e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-02-12 (Sun, 12 Feb 2017)
Changed paths:
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Adding NGL viewer for molecule representation
Commit: d066ae2223ef006a7621ddaa30ecd24ffa2942dd
https://github.com/galaxyproject/galaxy/commit/d066ae2223ef006a7621ddaa30ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M doc/source/slideshow/architecture/galaxy_architecture.md
Log Message:
-----------
Link fixes thanks to @nsoranzo.
Commit: d382537008da588b68a86925a42f0828a9e376d8
https://github.com/galaxyproject/galaxy/commit/d382537008da588b68a86925a42f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Merge pull request #3590 from guerler/fix_order_steps
Avoid step duplication when ordering steps on the fly
Commit: 75a17bc311662fae24b679a7b41146552f796992
https://github.com/galaxyproject/galaxy/commit/75a17bc311662fae24b679a7b411…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M CONTRIBUTING.md
M doc/source/slideshow/architecture/galaxy_architecture.md
M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
M doc/source/slideshow/architecture/images/objectstore.plantuml.svg
M doc/source/slideshow/architecture/images/plantuml_options.txt
M doc/source/slideshow/architecture/images/server_client.plantuml.svg
M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
M doc/source/slideshow/architecture/images/webapp.plantuml.svg
M doc/source/slideshow/architecture/style.css
M scripts/slideshow/slideshow_template.html
Log Message:
-----------
Merge pull request #3594 from jmchilton/architecture_touchup
Align architecture slides with training-material remarkjs template.
Commit: e06f56a61521563f1bd17c5ad09df94264d45772
https://github.com/galaxyproject/galaxy/commit/e06f56a61521563f1bd17c5ad09d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
static/maps/mvc/tool/tool-form-base.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/tool/tool-form-base.js
Commit: b4b75b276c9d41181e89322754c64abba57cd753
https://github.com/galaxyproject/galaxy/commit/b4b75b276c9d41181e89322754c6…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3579 from jmchilton/deprecated_change_format_when
Update tool XSD for (hopefully deprecated) change_format syntax.
Commit: 9f9d0cb4082b66e385bd43e31995cbaa5a2a0e09
https://github.com/galaxyproject/galaxy/commit/9f9d0cb4082b66e385bd43e31995…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 4fc0b84910adef446daa20a68cd69b0721a4d362
https://github.com/galaxyproject/galaxy/commit/4fc0b84910adef446daa20a68cd6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M templates/admin/reload_tool.mako
Log Message:
-----------
Merge remote-tracking branch 'guerler/fix_tool_reload_003' into dev
Commit: ac46305686c81a94b60a76dd6904a772a784ff24
https://github.com/galaxyproject/galaxy/commit/ac46305686c81a94b60a76dd6904…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
Minor fix of core.galaxy-ui tour in more robustly selecting first reload icon in the active history.
Commit: 9597b9b62b66d933ae5d891ff45550d23a86b6f2
https://github.com/galaxyproject/galaxy/commit/9597b9b62b66d933ae5d891ff455…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-13 (Mon, 13 Feb 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
Merge pull request #3608 from dannon/minor-tour-fix
Minor fix of core.galaxy-ui tour in more robustly selecting first rel…
Commit: dfa1ddacb93acf341b71148114450c993379adc1
https://github.com/galaxyproject/galaxy/commit/dfa1ddacb93acf341b7114811445…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Restore legacy name handling for backward compatibility
Commit: 93f190dd0518005f195960333895b645556860cd
https://github.com/galaxyproject/galaxy/commit/93f190dd0518005f195960333895…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Restore previous export behavior
Commit: c4491b2d834cdbb61cf009d57c1d3f1086bcfbdb
https://github.com/galaxyproject/galaxy/commit/c4491b2d834cdbb61cf009d57c1d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Fix quotes
Commit: 79c24066b444b7bd7a85f0ec2ccdd4b131c4da9e
https://github.com/galaxyproject/galaxy/commit/79c24066b444b7bd7a85f0ec2ccd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M CONTRIBUTING.md
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M config/datatypes_conf.xml.sample
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
M doc/source/slideshow/architecture/galaxy_architecture.md
M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
M doc/source/slideshow/architecture/images/objectstore.plantuml.svg
M doc/source/slideshow/architecture/images/plantuml_options.txt
M doc/source/slideshow/architecture/images/server_client.plantuml.svg
M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
M doc/source/slideshow/architecture/images/webapp.plantuml.svg
M doc/source/slideshow/architecture/style.css
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/workflow/steps.py
M scripts/slideshow/slideshow_template.html
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M templates/admin/reload_tool.mako
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
M test/selenium_tests/framework.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Merge branch 'dev' into unify_name_label
Commit: 3f07555173f89f39b4823767daaa25bd92ec7d68
https://github.com/galaxyproject/galaxy/commit/3f07555173f89f39b4823767daaa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M CONTRIBUTING.md
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M config/plugins/tours/core.galaxy_ui.yaml
M doc/source/slideshow/architecture/galaxy_architecture.md
M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
M doc/source/slideshow/architecture/images/objectstore.plantuml.svg
M doc/source/slideshow/architecture/images/plantuml_options.txt
M doc/source/slideshow/architecture/images/server_client.plantuml.svg
M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
M doc/source/slideshow/architecture/images/webapp.plantuml.svg
M doc/source/slideshow/architecture/style.css
M lib/galaxy/datatypes/interval.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/workflow/steps.py
M scripts/slideshow/slideshow_template.html
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M templates/admin/reload_tool.mako
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' into recalc-on-logout
Commit: df22e40522d7777cc3c82a4e32b64fe2d95d9273
https://github.com/galaxyproject/galaxy/commit/df22e40522d7777cc3c82a4e32b6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-quotameter.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
Log Message:
-----------
Merge pull request #3600 from dannon/recalc-on-logout
Recalculate user disk usage on logout.
Commit: 1cb8a5da38006cace8c48966a5326b2d3747c574
https://github.com/galaxyproject/galaxy/commit/1cb8a5da38006cace8c48966a532…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix import order
Commit: 6330f6051790b7d86bdd5674697163efc3c2a0f0
https://github.com/galaxyproject/galaxy/commit/6330f6051790b7d86bdd56746971…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-quotameter.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
Log Message:
-----------
Merge branch 'dev' into unify_name_label
Commit: 6864bc30b4a02495220d1552026c0cacb5d41af7
https://github.com/galaxyproject/galaxy/commit/6864bc30b4a02495220d1552026c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Replacing url by download_url to fetch files
Commit: 8ce1291359c88148023e5bb3f44a9eb38c78a864
https://github.com/galaxyproject/galaxy/commit/8ce1291359c88148023e5bb3f44a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: dcda376c9ca68742eb58efe6f3438d4d6c5f834f
https://github.com/galaxyproject/galaxy/commit/dcda376c9ca68742eb58efe6f343…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Restore subworkflow behavior, no need for modifications anymore
Commit: 48639028df5b59e7547a2e716b9c7e34e9743a41
https://github.com/galaxyproject/galaxy/commit/48639028df5b59e7547a2e716b9c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Removing utils.get to fetch pdb files
Commit: 452ab0d509171033e901bf65cf2556ef411e5161
https://github.com/galaxyproject/galaxy/commit/452ab0d509171033e901bf65cf25…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
Implementation of slow query logging. Disabled by default.
Commit: 78282a288bd1528dfd5222f47baaaeaaf1480f17
https://github.com/galaxyproject/galaxy/commit/78282a288bd1528dfd5222f47baa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Aarrghs spacing.
Commit: 19e18dd5719abe08e361bf4b50a7bf4bbbd554e1
https://github.com/galaxyproject/galaxy/commit/19e18dd5719abe08e361bf4b50a7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Add forgotten sample change.
Commit: c390da3cbd933c27ad0c731bc3b557ad916a72cd
https://github.com/galaxyproject/galaxy/commit/c390da3cbd933c27ad0c731bc3b5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Change default settings, avoid flickering on startup
Commit: 7810f5a8648c913045ae042a7c991642dbc045c8
https://github.com/galaxyproject/galaxy/commit/7810f5a8648c913045ae042a7c99…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super.
Commit: eb5ded2a439d1c9491700650842f9ece04cfad33
https://github.com/galaxyproject/galaxy/commit/eb5ded2a439d1c9491700650842f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Remove likely un-needed check.
Commit: da24f4c8ad03a34da9323041e634d4bbe55617b4
https://github.com/galaxyproject/galaxy/commit/da24f4c8ad03a34da9323041e634…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
Import formatting...
Commit: 149dfa007f70fe6794b8c1f37708ac8fbb7cccef
https://github.com/galaxyproject/galaxy/commit/149dfa007f70fe6794b8c1f37708…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
Merge pull request #3616 from dannon/slow_query_logging
Slow query logging
Commit: a7572145e9c0d4872cde027d547ef4c31c87af10
https://github.com/galaxyproject/galaxy/commit/a7572145e9c0d4872cde027d547e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge pull request #3618 from jmchilton/remove_unneeded_15
Remove un-needed check in histories manager code
Commit: 5cd05161413b73c5eb6ea7393b78cafd213409b9
https://github.com/galaxyproject/galaxy/commit/5cd05161413b73c5eb6ea7393b78…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge branch 'dev' into unify_name_label
Commit: 7472568fe5102a77ff69c47db0f19d7fd0a8487a
https://github.com/galaxyproject/galaxy/commit/7472568fe5102a77ff69c47db0f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Remove unused name from stage parameter
Commit: 43f2a648230b5b0ee46c124cc3df95b758e50fb2
https://github.com/galaxyproject/galaxy/commit/43f2a648230b5b0ee46c124cc3df…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
Log Message:
-----------
Merge pull request #3601 from bgruening/ngl_viewer
NGL Viewer for molecule representation
Commit: be5eaf4881b9624c67a7e3125dbb080032502477
https://github.com/galaxyproject/galaxy/commit/be5eaf4881b9624c67a7e3125dbb…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
A scripts/cookie.py
Log Message:
-----------
Util to encode or decode values
Commit: 6849752fb68b018aaf30f61d9d3c564894ed9e2b
https://github.com/galaxyproject/galaxy/commit/6849752fb68b018aaf30f61d9d3c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
R scripts/cookie.py
A scripts/secret_decoder_ring.py
Log Message:
-----------
Rename, Strip F for Folder
Commit: fb2450ff33ebdbdeb3f1205bdc58c38519921e7a
https://github.com/galaxyproject/galaxy/commit/fb2450ff33ebdbdeb3f1205bdc58…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M scripts/secret_decoder_ring.py
Log Message:
-----------
document scriptg
Commit: 89e32ee526e7f2ebc64be8bd46337a6edef78cab
https://github.com/galaxyproject/galaxy/commit/89e32ee526e7f2ebc64be8bd4633…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
A scripts/secret_decoder_ring.py
Log Message:
-----------
Merge pull request #3622 from erasche/encode-decode-util
Util to encode or decode values
Commit: 678a8627984852ea4282f6a25bf8c5176783c7c3
https://github.com/galaxyproject/galaxy/commit/678a8627984852ea4282f6a25bf8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Fix
Commit: 7ad46c22694ac7b58acdaefca59ca82cca328f25
https://github.com/galaxyproject/galaxy/commit/7ad46c22694ac7b58acdaefca59c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix subworkflow caller
Commit: c75671484058bc5c0cec8f07dda081cff7c0eb57
https://github.com/galaxyproject/galaxy/commit/c75671484058bc5c0cec8f07dda0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Properly initialize subworkflow parameter
Commit: 841cbfd9c7bf1efe2c10bbbff59da22ce67e800c
https://github.com/galaxyproject/galaxy/commit/841cbfd9c7bf1efe2c10bbbff59d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix content id parsing, through error if subworkflow could not be found
Commit: 4610da47863c9ca9c5eb092bfd031f32c6984b96
https://github.com/galaxyproject/galaxy/commit/4610da47863c9ca9c5eb092bfd03…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix style
Commit: f548af88076b11d33e3a24b50102108a076df1b4
https://github.com/galaxyproject/galaxy/commit/f548af88076b11d33e3a24b50102…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Add test case for state populating
Commit: f6649f890499a2e4569057e4b1921f0c95426e11
https://github.com/galaxyproject/galaxy/commit/f6649f890499a2e4569057e4b192…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_execution.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 2ff6f910373a2eaf547472f8b4be7f92cda495bb
https://github.com/galaxyproject/galaxy/commit/2ff6f910373a2eaf547472f8b4be…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: e5da52e388af093e432efeae9f395a7f92ce97da
https://github.com/galaxyproject/galaxy/commit/e5da52e388af093e432efeae9f39…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Fix kombu documentation link, add a tiny bit more description to handle the old TODO.
Commit: 28089a3ae1ea4eb8be62364aaaef65ae019dc127
https://github.com/galaxyproject/galaxy/commit/28089a3ae1ea4eb8be62364aaaef…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Merge pull request #3629 from dannon/kombu_url_fix
Fix kombu documentation link in galaxy.ini.sample
Commit: 430ac221baea4c18af247eee8e9106869a570390
https://github.com/galaxyproject/galaxy/commit/430ac221baea4c18af247eee8e91…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 8557c32034c9723dc110719b26082312dde1a998
https://github.com/galaxyproject/galaxy/commit/8557c32034c9723dc110719b2608…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-20 (Mon, 20 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix sanitization
Commit: cdb15f63925e9879744ae38e5e140e5eb9cc6c19
https://github.com/galaxyproject/galaxy/commit/cdb15f63925e9879744ae38e5e14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/util/workflow_util.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge pull request #3593 from guerler/unify_name_label
Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler
Commit: 24eba8c58ee9d7f8907c83f5d72ea01997d56ab4
https://github.com/galaxyproject/galaxy/commit/24eba8c58ee9d7f8907c83f5d72e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
client/galaxy/scripts/mvc/tool/tool-form-composite.js
static/maps/mvc/tool/tool-form-composite.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/tool/tool-form-composite.js
Commit: 9abe8a7b91d969a5b3af2bc026911dcde8656e24
https://github.com/galaxyproject/galaxy/commit/9abe8a7b91d969a5b3af2bc02691…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Allow composite datatypes of type auto_primary_file to automatically generate primary datatype for standard (non-upload) jobs when the tool does not already create the file.
Commit: fd082663866c06afb35a179327b1df6efd9c77c7
https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Parse name to label on module initialization
Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957
https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a01000…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use shared initialization procedure for subworkflows
Commit: fc1e0702542af846c28e2910d77cbd07f0913769
https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Hide name input fields for data input modules
Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c
https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use shared label/annotation input parameter building process
Commit: e13958ffcd14f2eb62b29f446a535487dd344904
https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a53…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Remove tool module related annotation input parameter
Commit: 92bd559c11e62ef1ab704b967621966a31f71e39
https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b967621…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Move label/annotation input parameters at top for all modules
Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426
https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-view-form.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-view-form.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-view-form.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Move workflow related tool form to workflow directory
Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464
https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
R client/galaxy/scripts/mvc/workflow/workflow-view-form.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
R static/maps/mvc/workflow/workflow-view-form.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/scripts/mvc/workflow/workflow-view-form.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Enable labels for all modules, used shared building process
Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108
https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix comments, show default wrapper first in code file
Commit: b03904b52c6064e77a378347d9213ec0b270ebb9
https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d921…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Allow input specific error handling, fix input parameter configuration
Commit: c9b765794bb14adbaee13a44290e9df242778ffe
https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix form handler
Commit: a967c088f78e39819d4cc0bd349166501e00d74e
https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd3491…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Avoid parsing default names of inputs to labels
Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a
https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Remove hidden input parameters, attempt to identify label directly from previous state
Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b
https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Move backward compatibility handling of former names out of modules to the workflow manager
Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348
https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Revise comment
Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830
https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use label to connect workflow steps
Commit: badf49daa54a660a032ac22b2e4b7c84c92284e1
https://github.com/galaxyproject/galaxy/commit/badf49daa54a660a032ac22b2e4b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #3643 from blankenberg/composite-datatype-auto-gen
Allow composite datatypes of type auto_primary_file to automatically generate dataset
Commit: 9563a691b05f65ec3bdcd9135f75878b2ec666e3
https://github.com/galaxyproject/galaxy/commit/9563a691b05f65ec3bdcd9135f75…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3641 from nsoranzo/merge_17.01
Merge 17.01 into dev
Commit: 387805fc1365dbf976e6d3e10ae4a11817e501da
https://github.com/galaxyproject/galaxy/commit/387805fc1365dbf976e6d3e10ae4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
client/galaxy/scripts/mvc/tool/tool-form-composite.js
preserved the dev version
static/maps/mvc/tool/tool-form-composite.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/tool/tool-form-composite.js
Commit: d1c9ffb94c06a7a39cff37a38e78f43fd4e0ca10
https://github.com/galaxyproject/galaxy/commit/d1c9ffb94c06a7a39cff37a38e78…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Conflicts:
client/galaxy/scripts/mvc/tool/tool-form-composite.js
preserved dev version
static/maps/mvc/tool/tool-form-composite.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/tool/tool-form-composite.js
Commit: c52715fd69fba88746181601e8210eb3cbc8b145
https://github.com/galaxyproject/galaxy/commit/c52715fd69fba88746181601e821…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: ae751adac8ae46d7f0eb2831666258143724bc0f
https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb28316662…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Adjust unit test to use labels instead of name through state
Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930
https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Use constants to filter default naming of input modules
Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97
https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b
https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Fix comment
Commit: 619bfeffd503681ab7d6072426f621fde7485fd5
https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Attempt to use fixed default name for unlabeled subworkflow inputs
Commit: 007b6599c21a4927d58629210f103829e947011f
https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f10…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix name handling in build module
Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1
https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix step title in composite tool form
Commit: 05687b8a19785c89772db499d6ede5a097ba47ce
https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M test/unit/workflows/test_modules.py
Log Message:
-----------
Strip debug output
Commit: 102fffd172963c0e97a7b469c394c3d239935e9c
https://github.com/galaxyproject/galaxy/commit/102fffd172963c0e97a7b469c394…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
When using the new slow query logger, include parameters. Originally left these out, but 1) logs are assumed to be secure, and 2) it's super useful
Commit: 2cfd833e457f513d5e83f9a7f8ca77f96741942e
https://github.com/galaxyproject/galaxy/commit/2cfd833e457f513d5e83f9a7f8ca…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Reduce indentation from 6 to 4 whitespaces
Fix a TODO
Remove funny but unused sub-sub-items.
Commit: 0da2ac78e6ac5583271881dabd4b4d0a3bcf59cd
https://github.com/galaxyproject/galaxy/commit/0da2ac78e6ac5583271881dabd4b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Rebuild client -- bad merge previously.
Commit: 8130d8b4c88343cdd44243fe700eae3fb863cc1a
https://github.com/galaxyproject/galaxy/commit/8130d8b4c88343cdd44243fe700e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Update against the latest changes in galaxy-dev.
Commit: 18e514d9b72b6efb57772009de1c0d65b791fa1b
https://github.com/galaxyproject/galaxy/commit/18e514d9b72b6efb57772009de1c…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Merge pull request #3652 from dannon/rebuild_client
Rebuild client -- bad merge previously.
Commit: 647fcad924a969ae35299b7ef6e60672ddb7a6a0
https://github.com/galaxyproject/galaxy/commit/647fcad924a969ae35299b7ef6e6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #3653 from nsoranzo/fix_bootstrap_history
Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py
Commit: d9d3b22efdf5d7e0f4c9b371b0ea74a64ab53f46
https://github.com/galaxyproject/galaxy/commit/d9d3b22efdf5d7e0f4c9b371b0ea…
Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
Update dynamic_tool_destination.py
Commit: d19a158e10ada652fb1bf1549dac4f1f3446aa5a
https://github.com/galaxyproject/galaxy/commit/d19a158e10ada652fb1bf1549dac…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
Allow nest param in the dynamic_tool rule -> argument
Commit: 99fdc37b815ab9c26f15250d722f2d30ab9691b2
https://github.com/galaxyproject/galaxy/commit/99fdc37b815ab9c26f15250d722f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #3654 from jmchilton/galaxy-lib-update
Update against the latest changes in galaxy-lib
Commit: 73c444eaf4074c98262b9de0011e686170b1b125
https://github.com/galaxyproject/galaxy/commit/73c444eaf4074c98262b9de0011e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
Merge pull request #3655 from lecorguille/patch-3
Update dynamic_tool_destination.py
Commit: b18736d82447637d7257f3fd406e1c40a02afed0
https://github.com/galaxyproject/galaxy/commit/b18736d82447637d7257f3fd406e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
M config/plugins/visualizations/charts/static/repository/registry.json
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Updating Cytoscape viewer in Viz/Charts, replacing the previous 'basic' folder name to 'viewer' and updating the wrapper.js file
Commit: 2c49779d81b8eb2eae1e9f4dd74de7e01647f675
https://github.com/galaxyproject/galaxy/commit/2c49779d81b8eb2eae1e9f4dd74d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Separate condensed user preference form into three components, improve route handling
Commit: 84f9d3c5c9dc27af1d121e9b84504109d9291ff0
https://github.com/galaxyproject/galaxy/commit/84f9d3c5c9dc27af1d121e9b8450…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix basic routing between main preference panel and individual user forms
Commit: 3c31cbd21ed222060c31400eb0e0d0ea90b33ec0
https://github.com/galaxyproject/galaxy/commit/3c31cbd21ed222060c31400eb0e0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Fix error message
Commit: 88b4b7a7182fb48904d587b7a049e099169c7ccf
https://github.com/galaxyproject/galaxy/commit/88b4b7a7182fb48904d587b7a049…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Properly handle openid redirect and sign out feature
Commit: ceb11577bde43e6ee61ee1c89e6c002037039510
https://github.com/galaxyproject/galaxy/commit/ceb11577bde43e6ee61ee1c89e6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Place row template into separate function
Commit: 365c56f77f6b57c8930641864924ec9a67fdf174
https://github.com/galaxyproject/galaxy/commit/365c56f77f6b57c8930641864924…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/web/base/controllers/admin.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Redirect admin user manager route to js-based preference forms
Commit: 99397fad74d3e47c27073f44e36300d43f48a181
https://github.com/galaxyproject/galaxy/commit/99397fad74d3e47c27073f44e363…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/proteomics.py
Log Message:
-----------
add the mzData datatype
Commit: 036df2ac2003ab378f6a0227e4642d980639a5ab
https://github.com/galaxyproject/galaxy/commit/036df2ac2003ab378f6a0227e464…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/proteomics.py
Log Message:
-----------
Fix linting
Commit: d5e4dc4753b8e6ab4a079b5fedb0ad1834bda157
https://github.com/galaxyproject/galaxy/commit/d5e4dc4753b8e6ab4a079b5fedb0…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/proteomics.py
Log Message:
-----------
Merge pull request #3661 from lecorguille/datatype_mzdata
add the mzData datatype
Commit: 585c1070f29260895497c01bc7723317e3751934
https://github.com/galaxyproject/galaxy/commit/585c1070f29260895497c01bc772…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/visualization/plugins/plugin.py
Log Message:
-----------
Display an error message when IE loading raises an exception
Commit: cbc1faf3a45d58353a9d352047fbbedb970e3215
https://github.com/galaxyproject/galaxy/commit/cbc1faf3a45d58353a9d352047fb…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/auth/providers/ldap_ad.py
Log Message:
-----------
Set LDAP options only once.
Always check option value is not empty in _get_subs()
Better log message for malformed <ldap_options>
Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8
https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack scripts
Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54
https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
M scripts/bootstrap_history.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082
https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M static/maps/mvc/tool/tool-form-composite.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/mvc/tool/tool-form-composite.js
A static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix repacked files
Commit: b4ba2768a246c3788bc9f4adc5f2741dd7ab4956
https://github.com/galaxyproject/galaxy/commit/b4ba2768a246c3788bc9f4adc5f2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Ignore Node modules installed for the IE proxy when linting
Commit: 10d0f627dcdfac2bd24085a599a7087809cec1bf
https://github.com/galaxyproject/galaxy/commit/10d0f627dcdfac2bd24085a599a7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
Log Message:
-----------
Bump Jupyter container version to 16.01.1
Commit: 77a47d2f6f947a1ec7d24d068538bbabdf5e88dd
https://github.com/galaxyproject/galaxy/commit/77a47d2f6f947a1ec7d24d068538…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
Log Message:
-----------
Merge pull request #3665 from natefoo/jupyter-16.01.1
Bump Jupyter container version to 16.01.1
Commit: 0baae35c56cfa26908ebff9a3124640489459c31
https://github.com/galaxyproject/galaxy/commit/0baae35c56cfa26908ebff9a3124…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Merge pull request #3664 from natefoo/lint-ignore-js-proxy
Ignore Node modules installed for the IE proxy when linting
Commit: efa856dbb91766dbf80c447c241dd37e1a5401ca
https://github.com/galaxyproject/galaxy/commit/efa856dbb91766dbf80c447c241d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M templates/grid_base.mako
Log Message:
-----------
Attempt to fix grid routing options
Commit: 075d53af92ea2640ba3005f36354712b966ea98e
https://github.com/galaxyproject/galaxy/commit/075d53af92ea2640ba3005f36354…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Fix for transiently failing workflow test.
The history can be complete before a workflow has fully scheduled if the workflow still has more jobs to schedule but all the current ones are complete.
Commit: a5ea10622bf2616278827221d43a4ab635932edd
https://github.com/galaxyproject/galaxy/commit/a5ea10622bf2616278827221d43a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M lib/galaxy/visualization/plugins/plugin.py
Log Message:
-----------
Merge pull request #3662 from natefoo/ie-error-message
Display an error message when IE loading raises an exception
Commit: 8a8603be7f697c065382d61fb0539552d15d1f3f
https://github.com/galaxyproject/galaxy/commit/8a8603be7f697c065382d61fb053…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-24 (Fri, 24 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
Log Message:
-----------
Enhance grid target handling for links
Commit: d3f2df57699bf6b85fdb16f85d023d562342f778
https://github.com/galaxyproject/galaxy/commit/d3f2df57699bf6b85fdb16f85d02…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-25 (Sat, 25 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
improve wording of getgalaxy in bootstrapping script for RN
Commit: c8dd5f9b25ac222ff37fe06bed5d1834f292e485
https://github.com/galaxyproject/galaxy/commit/c8dd5f9b25ac222ff37fe06bed5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-26 (Sun, 26 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #3671 from martenson/improve-bootstrapping
improve wording of getgalaxy in bootstrapping script for RN
Commit: f645259dd0633cfdac2768c7de2d1de918bc1bbe
https://github.com/galaxyproject/galaxy/commit/f645259dd0633cfdac2768c7de2d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-27 (Mon, 27 Feb 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Only keep the last path element when naming files uploaded via the URL
paste method
Commit: fb17e55a1daf90220e19980fd8fd56dd70b2cde2
https://github.com/galaxyproject/galaxy/commit/fb17e55a1daf90220e19980fd8fd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-27 (Mon, 27 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Use former version of autocomplete module for grids
Commit: 3efe748279711e89852bf7bf173612ff9cbe45de
https://github.com/galaxyproject/galaxy/commit/3efe748279711e89852bf7bf1736…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-27 (Mon, 27 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
Log Message:
-----------
Strip partially removed autocomplete feature for history names, removed in #1303
Commit: 69b9b575172086376657433ff0a066bf732d4e4d
https://github.com/galaxyproject/galaxy/commit/69b9b575172086376657433ff0a0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding basic options like layout name and curve style for cytoscape graphs
Commit: 73921a21e9164bad342269ed3fe3c347d42a5c8d
https://github.com/galaxyproject/galaxy/commit/73921a21e9164bad342269ed3fe3…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
change the tool_destinations.yml the argument rules syntax
Commit: 705eb17b02b748ce76b5644386c793a610d9ab90
https://github.com/galaxyproject/galaxy/commit/705eb17b02b748ce76b5644386c7…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
fix python syntax
Commit: d624b04f25510475bd1cb48fbcbdca471bc1a5d7
https://github.com/galaxyproject/galaxy/commit/d624b04f25510475bd1cb48fbcbd…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M config/tool_destinations.yml.sample
Log Message:
-----------
update the documentation
Commit: 194fb1eb07b627682b258d5c302aeb75b266cf89
https://github.com/galaxyproject/galaxy/commit/194fb1eb07b627682b258d5c302a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
Log Message:
-----------
Merge pull request #3676 from guerler/fix_jquery_autocomplete
Strip broken autocomplete feature, webbrowsers console error is an artifact
Commit: 33c528ee13e6c4317ac4acc9b48ba157c5976b6c
https://github.com/galaxyproject/galaxy/commit/33c528ee13e6c4317ac4acc9b48b…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Generate primary composite file after extra files collection.
Commit: 1bac3b3be81821a4cbe687165985cfafd7989b46
https://github.com/galaxyproject/galaxy/commit/1bac3b3be81821a4cbe687165985…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #3674 from natefoo/upload-drop-url-name
Only keep the last path element when naming files uploaded via the URL paste method
Commit: a505fa79ac26e2f30a4404f9a11f3b029abb5436
https://github.com/galaxyproject/galaxy/commit/a505fa79ac26e2f30a4404f9a11f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/auth/providers/ldap_ad.py
Log Message:
-----------
Merge pull request #3663 from nsoranzo/ldap_auth
Set LDAP options only once.
Commit: c80380dc57305be36e615ec13d1d17aecd285114
https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M client/galaxy/scripts/mvc/grid/grid-view.js
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M scripts/bootstrap_history.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into unify_label_name_000
Commit: 5efbab864cab6693d4bde2159661a6ff6c7caafd
https://github.com/galaxyproject/galaxy/commit/5efbab864cab6693d4bde2159661…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #3678 from blankenberg/composite-auto-after
Generate primary composite file after extra files collection.
Commit: f0a26f309dd330e49e8e7ad227db5e40507f60cc
https://github.com/galaxyproject/galaxy/commit/f0a26f309dd330e49e8e7ad227db…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-28 (Tue, 28 Feb 2017)
Changed paths:
M lib/galaxy/model/orm/engine_factory.py
Log Message:
-----------
Merge pull request #3649 from dannon/slowquery_tweak
When using the new slow query logger, include parameters.
Commit: 504f4ac670b3135b9df885d9d884d176dc494768
https://github.com/galaxyproject/galaxy/commit/504f4ac670b3135b9df885d9d884…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding min and max zoom settings for graphs
Commit: 0b4e52c8e93aa5693f97ff1fc5d0a4c272f58b18
https://github.com/galaxyproject/galaxy/commit/0b4e52c8e93aa5693f97ff1fc5d0…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
lib/galaxy/managers/workflows.py
Discarded all changes made to
lib/galaxy/managers/workflows.py
in https://github.com/galaxyproject/galaxy/pull/3681
Commit: cc6fa6a4c8607c0c2f33b2271a963da54756334f
https://github.com/galaxyproject/galaxy/commit/cc6fa6a4c8607c0c2f33b2271a96…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M client/galaxy/scripts/mvc/grid/grid-view.js
M config/datatypes_conf.xml.sample
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M doc/source/releases/17.01_announce.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M scripts/bootstrap_history.py
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
M templates/grid_base.mako
A templates/webapps/galaxy/user/manage_info.mako
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into ui_pref_routing
Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570
https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge pull request #3644 from guerler/unify_label_name_000
Introduce labels for all modules, remove name handling field for data inputs
Commit: f0b03a59b51bd02a07b591900147d0e9a79053f7
https://github.com/galaxyproject/galaxy/commit/f0b03a59b51bd02a07b591900147…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
R templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Strip old user manager mako
Commit: c281dd87ed83934ffe2654130d8c709892796142
https://github.com/galaxyproject/galaxy/commit/c281dd87ed83934ffe2654130d8c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge branch 'dev' into ui_pref_routing
Commit: 7cc25c9082de5df6ff4ed89365f34f39dbbec545
https://github.com/galaxyproject/galaxy/commit/7cc25c9082de5df6ff4ed89365f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Parse tags with datatoolparameter options
Commit: a02c1cfda10e2b600e5209db7f7be8dfb0069467
https://github.com/galaxyproject/galaxy/commit/a02c1cfda10e2b600e5209db7f7b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add tags to name
Commit: 4d5a03ba55eeb1a1f3884999f3399fb47503cbcc
https://github.com/galaxyproject/galaxy/commit/4d5a03ba55eeb1a1f3884999f339…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-01 (Wed, 01 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove brackets
Commit: 9f4764f22cc63f7a734b9ea98707bfcb842aed14
https://github.com/galaxyproject/galaxy/commit/9f4764f22cc63f7a734b9ea98707…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Preserve tags (ignoring collection handling for now) when running tools.
Commit: fa1f81cbcf5ac4c026bb624ee003f56405ef358e
https://github.com/galaxyproject/galaxy/commit/fa1f81cbcf5ac4c026bb624ee003…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Users -> user in menu/interface usage.
Commit: 42c090cb20e82bee50b8931aeeedca4e735f766b
https://github.com/galaxyproject/galaxy/commit/42c090cb20e82bee50b8931aeeed…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Update users->user in the menu as well
Commit: ca238c4323a9d8efd8bb6fca06da5dd87d86032f
https://github.com/galaxyproject/galaxy/commit/ca238c4323a9d8efd8bb6fca06da…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
Log Message:
-----------
Add tags to mock hda
Commit: 2135e63f8e144e21c926c8ea593acb5ce9615069
https://github.com/galaxyproject/galaxy/commit/2135e63f8e144e21c926c8ea593a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Filter tags regardless of given select field label
Commit: a7ec0c8579267adf6355e6f678b734e3f1b63cc9
https://github.com/galaxyproject/galaxy/commit/a7ec0c8579267adf6355e6f678b7…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Add datatypes for soon coming PlantTribes Galaxy tools.
Commit: 7e19245c8af5b203c0a76f2ab5eee5a1856fdded
https://github.com/galaxyproject/galaxy/commit/7e19245c8af5b203c0a76f2ab5ee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M test/unit/tools/test_evaluation.py
Log Message:
-----------
Fix spacing
Commit: ed95412b36a0f349951e088ad5707f5c62e5851f
https://github.com/galaxyproject/galaxy/commit/ed95412b36a0f349951e088ad570…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
Log Message:
-----------
add ethercalc interactive environment
Commit: d47f582d152d095044ddb6454e880b8dedc7cab6
https://github.com/galaxyproject/galaxy/commit/d47f582d152d095044ddb6454e88…
Author: Saskia Hiltemann <zazkia(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
Log Message:
-----------
remove commented section
Commit: a93c29fa4a438b93016cb5e31d0e4ef88ca88029
https://github.com/galaxyproject/galaxy/commit/a93c29fa4a438b93016cb5e31d0e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add tag filtering for collections
Commit: 82137b433cf00f2b83a00e08b71bdea2bfebf9bd
https://github.com/galaxyproject/galaxy/commit/82137b433cf00f2b83a00e08b71b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix append calling for collections
Commit: 31d222c91031775629896feb027e00ea535ef7d9
https://github.com/galaxyproject/galaxy/commit/31d222c91031775629896feb027e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/style/less/history.less
M static/maps/mvc/history/hda-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
M static/style/blue/base.css
Log Message:
-----------
'name' tag rendering, very basic, needs styling and loading fixes
Commit: 4fa76caf67e33ce38f2e45325d504e2f1ff824a7
https://github.com/galaxyproject/galaxy/commit/4fa76caf67e33ce38f2e45325d50…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Set $HOME to a temp directory rather than conda_prefix because
conda_prefix may not be writable either.
Commit: f6353c28f6f3a7012daf1eb95a7f7bcfd1d58d7c
https://github.com/galaxyproject/galaxy/commit/f6353c28f6f3a7012daf1eb95a7f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/style/less/history.less
M static/style/blue/base.css
Log Message:
-----------
Fix underlines in nametags
Commit: 9e5008984fc3ce1fd8359acfe502b3010ca76c1f
https://github.com/galaxyproject/galaxy/commit/9e5008984fc3ce1fd8359acfe502…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M static/maps/mvc/history/hda-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
Log Message:
-----------
nametags first, then hid+title
Commit: ef1344f03f291468b87c89d90b3a0f06ec9b0a79
https://github.com/galaxyproject/galaxy/commit/ef1344f03f291468b87c89d90b3a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/style/less/history.less
M static/style/blue/base.css
Log Message:
-----------
Adjust margins on labels
Commit: a144ce58939b122cc1bfb0575081a2082942e773
https://github.com/galaxyproject/galaxy/commit/a144ce58939b122cc1bfb0575081…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdas.py
Log Message:
-----------
Swap tags to default view for hdas -- may need to revisit this if it proves too expensive.
Commit: 4b7fea8d3fe0afa062213f81a75003cac593ad74
https://github.com/galaxyproject/galaxy/commit/4b7fea8d3fe0afa062213f81a750…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-02 (Thu, 02 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M static/maps/mvc/history/hda-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
Log Message:
-----------
Adjust positioning again for nametags, below the standard title but still visible above the fold.
Commit: 845e43c1e537f66c8208165a82583b4ca814b1f0
https://github.com/galaxyproject/galaxy/commit/845e43c1e537f66c8208165a8258…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/json.py
Log Message:
-----------
Avoid autoconversion of boolean values when calling json loads
Remove unused import
Fix
Commit: cb27f921c7e82f09c675e1e472417ad47d65bfab
https://github.com/galaxyproject/galaxy/commit/cb27f921c7e82f09c675e1e47241…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/util/json.py
Log Message:
-----------
Fix comment
Commit: bb604e65ee0f34ccce664f5798c55adbcedc9e5e
https://github.com/galaxyproject/galaxy/commit/bb604e65ee0f34ccce664f5798c5…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Merge pull request #3701 from natefoo/conda_home_temp
Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either.
Commit: 0914c05f8823759af21b37ff0ea8a7e757c4ba3a
https://github.com/galaxyproject/galaxy/commit/0914c05f8823759af21b37ff0ea8…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
fix metadata failure for large count tables
Commit: a3ab46ef26031ba4c1fb22ebd0232bdb930651e5
https://github.com/galaxyproject/galaxy/commit/a3ab46ef26031ba4c1fb22ebd023…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M lib/galaxy/managers/hdas.py
M static/maps/mvc/history/hda-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
Log Message:
-----------
Swap to a 'nametags' field in the high level view instead of returning all tags. TODO: Optimize this
Commit: 293726c57933cb2465a650d005332241eac0f912
https://github.com/galaxyproject/galaxy/commit/293726c57933cb2465a650d00533…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Support Docker Engine swarm mode
Commit: 2ee81a3faaef38547295f9a47f9f063423b40394
https://github.com/galaxyproject/galaxy/commit/2ee81a3faaef38547295f9a47f9f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Client route priority is *last*
Commit: b00dfc8a7b7bc739a84c5a229c161a917601d68a
https://github.com/galaxyproject/galaxy/commit/b00dfc8a7b7bc739a84c5a229c16…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove extra empty line.
Commit: 0fb9fbc3885eb11b7e49f97f6a129f9c0343e780
https://github.com/galaxyproject/galaxy/commit/0fb9fbc3885eb11b7e49f97f6a12…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Merge pull request #18 from dannon/ui_pref_routing
User->Users
Commit: 5818bbcbaaeca54a85bef9acaadd41d12386a6ad
https://github.com/galaxyproject/galaxy/commit/5818bbcbaaeca54a85bef9acaadd…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Prefer versioned Conda dependencies to unversioned Galaxy ones.
Commit: 4aec70cae28f336212a6bc8f5d24a325cb851bab
https://github.com/galaxyproject/galaxy/commit/4aec70cae28f336212a6bc8f5d24…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #3666 from natefoo/docker-swarm-mode
Support Docker Engine swarm mode for Interactive Environments
Commit: fe41ec185f85cdca4e0eb4a5705b511d20f699aa
https://github.com/galaxyproject/galaxy/commit/fe41ec185f85cdca4e0eb4a5705b…
Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
fix typos
Commit: 735f56ec95dba7d58d8d1dad922a01c3074af1ce
https://github.com/galaxyproject/galaxy/commit/735f56ec95dba7d58d8d1dad922a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Concat all tags to improve front-end performance
Commit: 83df8d5c9653c8e213eed63aecb9377503eb42f2
https://github.com/galaxyproject/galaxy/commit/83df8d5c9653c8e213eed63aecb9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Attempt to prefetch tags when building active datasets list
Commit: 6b2f9be75ab16e69a8fb1c72d10d169d20ab7854
https://github.com/galaxyproject/galaxy/commit/6b2f9be75ab16e69a8fb1c72d10d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Use space instead of comma when concatenating tags
Commit: 861368ae1c7fa21f4ee7b55fbb682f78e07ece9d
https://github.com/galaxyproject/galaxy/commit/861368ae1c7fa21f4ee7b55fbb68…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-03 (Fri, 03 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdas.py
Log Message:
-----------
Remove dead code from prior work in nametag collection, change to user_tname usage.
Commit: 4120781713cc65d3c05064bee981cf826d5c4be8
https://github.com/galaxyproject/galaxy/commit/4120781713cc65d3c05064bee981…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-03-05 (Sun, 05 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M config/plugins/webhooks/demo/search/static/styles.css
Log Message:
-----------
increase contrast and improve readability
Commit: b769da1b3d67195d3a2cd908321f0f200dc2a8b0
https://github.com/galaxyproject/galaxy/commit/b769da1b3d67195d3a2cd908321f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Merge pull request #3706 from shiltemann/mothur-dataype-fix
Mothur datatypes: fix metadata failure for large count tables
Commit: 6e3a9661d45cb239e116660888834ea8037b726b
https://github.com/galaxyproject/galaxy/commit/6e3a9661d45cb239e11666088883…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3668 from jmchilton/workflow_transient_failing_test
Fix for transiently failing workflow test.
Commit: ad3025f46a00190674bbc4dbc3bfab16983f9cb4
https://github.com/galaxyproject/galaxy/commit/ad3025f46a00190674bbc4dbc3bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M run_tests.sh
M test/TESTING.md
Log Message:
-----------
Touch up Galaxy testing documentation.
Commit: 5704013301f8b185fbc55324a79ab58937a48230
https://github.com/galaxyproject/galaxy/commit/5704013301f8b185fbc55324a79a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/selenium_tests/test_collection_builders.py
Log Message:
-----------
Implement initial collection builder UX test cases.
Exercise list and paired builder's most basic functionality.
Commit: 97d6e1b6c1ca56575c1297649fd0484c85e15a7a
https://github.com/galaxyproject/galaxy/commit/97d6e1b6c1ca56575c1297649fd0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Merge branch 'filter_dataset_tags' into dev
Commit: 8800376eb41d262b41862b3a1ad160218b47d45d
https://github.com/galaxyproject/galaxy/commit/8800376eb41d262b41862b3a1ad1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Improved Selenium exception messages.
For many common waiting operations used throughout many tests:
```
TimeoutException: Message:
```
Will become something like
```
TimeoutException: Message: Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible.
```
For HID waiting I've added the state and HID as well - so something like this:
```
TimeoutException: Message: Failed waiting on history item 1 state to change to [ok] current state [failed]. Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible.
```
Commit: 179e58c8b3a7d10fa15e238ec7d2f982aa3fed00
https://github.com/galaxyproject/galaxy/commit/179e58c8b3a7d10fa15e238ec7d2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M run_tests.sh
M test/TESTING.md
Log Message:
-----------
Merge pull request #3715 from jmchilton/test_docs_0
Touch up Galaxy testing documentation.
Commit: 5055283f49d73b7eb3b420875dfe8ccc1adb85de
https://github.com/galaxyproject/galaxy/commit/5055283f49d73b7eb3b420875dfe…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/style/less/history.less
M lib/galaxy/managers/hdas.py
M lib/galaxy/tools/actions/__init__.py
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/mvc/history/hda-li.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'tags_in_history' into dev
Commit: ecaf1be02f2364a2494e7adabd3b8733e194baf7
https://github.com/galaxyproject/galaxy/commit/ecaf1be02f2364a2494e7adabd3b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/style/blue/base.css
Log Message:
-----------
Show tags in select search field
Commit: e606dbdacbbad0b604f5395c1140571d9a219984
https://github.com/galaxyproject/galaxy/commit/e606dbdacbbad0b604f5395c1140…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix style
Commit: 4c4f78857b7141227e6ac320c36aad7c3429b7b5
https://github.com/galaxyproject/galaxy/commit/4c4f78857b7141227e6ac320c36a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdas.py
Log Message:
-----------
Swap to using tag values to store name instead of child values.
Commit: 0d95bf43ad84f014b404624a8e41f69f55b2a132
https://github.com/galaxyproject/galaxy/commit/0d95bf43ad84f014b404624a8e41…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3718 from guerler/add_tags_to_label_000
Show tags in select search field
Commit: 496f476b300733d818062fcace7e8d1a61517abc
https://github.com/galaxyproject/galaxy/commit/496f476b300733d818062fcace7e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Fix tag escaping
Commit: 2e5e6bb028165a735908543a063396f03bed375e
https://github.com/galaxyproject/galaxy/commit/2e5e6bb028165a735908543a0633…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/style/blue/base.css
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into nametags_to_value
Commit: a52695dee6b179ed6cb24eaeb7146c946b28ccc9
https://github.com/galaxyproject/galaxy/commit/a52695dee6b179ed6cb24eaeb714…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Escape title for select labels
Commit: d20e19e85a11ab8cf7eaff4fd0b3ee3dee337ff2
https://github.com/galaxyproject/galaxy/commit/d20e19e85a11ab8cf7eaff4fd0b3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Include values in tags and tag selection lgoic
Commit: 942f0d98d912196e95cfbb6f390c321676c28bce
https://github.com/galaxyproject/galaxy/commit/942f0d98d912196e95cfbb6f390c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Only compose tag:value one time on the client.
Commit: e54792f4263ed5ddacc1044fe0b2182735732fdb
https://github.com/galaxyproject/galaxy/commit/e54792f4263ed5ddacc1044fe0b2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Merge pull request #3720 from guerler/escape_tags
Fix tag escaping
Commit: 278da1b35653aa1ad5835b74206bb46bb4d6373a
https://github.com/galaxyproject/galaxy/commit/278da1b35653aa1ad5835b74206b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into nametags_to_value
Commit: f8e6b84998ab13cc99037c5eda3425f81329cbe5
https://github.com/galaxyproject/galaxy/commit/f8e6b84998ab13cc99037c5eda34…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Compose tag:value serverside -- we don't benefit from having them split when shipped (yet)
Commit: 477626385c14e3df00aa654194dd8502c064c5d7
https://github.com/galaxyproject/galaxy/commit/477626385c14e3df00aa654194dd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Filter tags by query term
Commit: 192d75a4654411ad242819536a7968703697f524
https://github.com/galaxyproject/galaxy/commit/192d75a4654411ad242819536a79…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Strip hanging extra comma.
Commit: b8b7739292676ba928664417be771bd6e3f8f087
https://github.com/galaxyproject/galaxy/commit/b8b7739292676ba928664417be77…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M lib/galaxy/managers/hdas.py
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Merge pull request #3719 from dannon/nametags_to_value
Use values for 'name'tags instead of child tags.
Commit: 006801ba1aace0a58f0ae90ba6a6777dfb834b58
https://github.com/galaxyproject/galaxy/commit/006801ba1aace0a58f0ae90ba6a6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/upload/upload-ftp.js
Log Message:
-----------
Escape FTP filename. Thanks @yhoogstrate
Commit: 656a0f396ed6d64a8010d9a6a32f138539f0b296
https://github.com/galaxyproject/galaxy/commit/656a0f396ed6d64a8010d9a6a32f…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M static/maps/mvc/upload/upload-ftp.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/upload/upload-ftp.js
Log Message:
-----------
Merge pull request #3722 from dannon/escape_ftp_filename
Filename handling for FTP upload
Commit: 79945f37c31d4d42be86bee352370af11b063271
https://github.com/galaxyproject/galaxy/commit/79945f37c31d4d42be86bee35237…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Do not require stored workflow id for subworkflows
Commit: 9ccb0953ad63aa46464a0ef8ec3bb6d5d1944539
https://github.com/galaxyproject/galaxy/commit/9ccb0953ad63aa46464a0ef8ec3b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/selenium_tests/test_collection_builders.py
Log Message:
-----------
Merge pull request #3716 from jmchilton/selenium_uploads_0
Selenium Testing Improvements
Commit: 1b12259739e28bc69e68576a76aefcd61ee99358
https://github.com/galaxyproject/galaxy/commit/1b12259739e28bc69e68576a76ae…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #3698 from gregvonkuster/ptformats
Add datatypes for soon coming PlantTribes Galaxy tools.
Commit: 9aa911d509ac50f44ba4e6c5dca2cb9dba61ebbb
https://github.com/galaxyproject/galaxy/commit/9aa911d509ac50f44ba4e6c5dca2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #3723 from guerler/fix_subworkflow_id
Do not require stored workflow id for subworkflows
Commit: 0bfe9fa7ca1489d744351eecc4312838a20008eb
https://github.com/galaxyproject/galaxy/commit/0bfe9fa7ca1489d744351eecc431…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M CONTRIBUTING.md
M README.rst
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
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M static/scripts/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/admin/reload_tool.mako
M templates/grid_base.mako
A templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/simple.xml
M test/TESTING.md
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_tools.py
A test/api/test_webhooks.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/checksum.xml
A test/functional/tools/is_valid_xml.xml
A test/functional/tools/legacy_r.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/output_format_deprecated_when.xml
A test/functional/tools/param_text_option.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/galaxy_selenium/sizzle.py
M test/integration/test_resolvers.py
M test/qunit/tests/form_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_tool_deps.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_workflow_progress.py
M tools/data_source/upload.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.xml
M tools/filters/pasteWrapper.xml
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/plotting/bar_chart.xml
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tox.ini
Log Message:
-----------
Merging with dev
Commit: b9c1abd43a69241accd54d3531442b56508efc0f
https://github.com/galaxyproject/galaxy/commit/b9c1abd43a69241accd54d353144…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-07 (Tue, 07 Mar 2017)
Changed paths:
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Merge pull request #3374 from jmchilton/singleton_workflow_cycles
Fix cycle detection for single node workflows.
Commit: aa0af352cdd034872d24b3a5f497a04204c9c017
https://github.com/galaxyproject/galaxy/commit/aa0af352cdd034872d24b3a5f497…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Add a simple UI to manage tool dependencies
This page simply lists all loaded tools and their dependency status.
On the left are checkboxes to select multiple tools, and at the bottom
is a button to install the selected tool dependencies.
Commit: 818c10832a1429b79e65906d106b6fda0ed28a35
https://github.com/galaxyproject/galaxy/commit/818c10832a1429b79e65906d106b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Build the dependency status more efficiently: Pass a dictionary with ToolRequirements object as key and requirements status as value
Commit: f882a14886de65b0079d5eea72a7bea044ab4a02
https://github.com/galaxyproject/galaxy/commit/f882a14886de65b0079d5eea72a7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Add new view that primarily manages dependencies
Commit: f1bb5a6a7114f1aa4dc331622183432604e9dbc7
https://github.com/galaxyproject/galaxy/commit/f1bb5a6a7114f1aa4dc331622183…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
close opened div
Commit: 96ae2893b3610e28101445f58966cffd61f873eb
https://github.com/galaxyproject/galaxy/commit/96ae2893b3610e28101445f58966…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
improve the markup and UX a bit
Commit: 5dc73b7966d3c9e90e0a58823e34bc26663d5d71
https://github.com/galaxyproject/galaxy/commit/5dc73b7966d3c9e90e0a58823e34…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Add title and explanation for Manage Tool Dependencies
page.
Commit: 07490e428dc0a3596d7623a7a787443494626c63
https://github.com/galaxyproject/galaxy/commit/07490e428dc0a3596d7623a7a787…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M config/galaxy.ini.sample
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
A config/plugins/webhooks/demo/search/static/styles.css
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #3460 from bgruening/search_overlay
Overlay search for tools, wf, libraries and histories
Commit: 0118c57af3ea2bae8b5c8c72fa45f431afb4aa8f
https://github.com/galaxyproject/galaxy/commit/0118c57af3ea2bae8b5c8c72fa45…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Merge pull request #3479 from mvdbeek/manage_tool_dependencies
Add a simple UI to manage tool dependencies
Commit: 704e6a6676c2aa6aafe4a283f50dcfd8a646682e
https://github.com/galaxyproject/galaxy/commit/704e6a6676c2aa6aafe4a283f50d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/json.py
Log Message:
-----------
Merge pull request #3702 from guerler/fix_boolean_handling
Properly handle boolean values when parsed to a string-based/default tool parameter
Commit: 90108e450fd2d13d3010e05a2fcb1224a2549a2a
https://github.com/galaxyproject/galaxy/commit/90108e450fd2d13d3010e05a2fcb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
tool-form needs to not be required at the top level of the Galaxy webapp
Commit: 2134d6c3856edf8358c185178f9efe35a232c03b
https://github.com/galaxyproject/galaxy/commit/2134d6c3856edf8358c185178f9e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Use a redirect (which will get routed, soon) instead of instantiating a toolform within the overlay -- this is much lighter weight
Commit: da9ee941afa604586cfc6dfdacb2594284b3e6f0
https://github.com/galaxyproject/galaxy/commit/da9ee941afa604586cfc6dfdacb2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Standardize tabs/spaces in webhook overlay search
Commit: 3d33586d4a5758e566dc5d1eceda91e97cd3d73a
https://github.com/galaxyproject/galaxy/commit/3d33586d4a5758e566dc5d1eceda…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-08 (Wed, 08 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/search/static/script.js
Log Message:
-----------
Cleanup pass on formatting/unused vars in webhooks
Commit: 7bf6a581249ec409d33ccc060816b9f505185165
https://github.com/galaxyproject/galaxy/commit/7bf6a581249ec409d33ccc060816…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Remove outdated items from tool cache
Commit: 9928a74c6c1cb57edbfba4068616bd5b15f51093
https://github.com/galaxyproject/galaxy/commit/9928a74c6c1cb57edbfba4068616…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox()
It's called only once from there when app is initialised, real toolbox
reloads are performed by executing reload_toolbox() from
lib/galaxy/queue_worker.py .
Commit: a89954c8928f0997aa9a5781a39d18339914b387
https://github.com/galaxyproject/galaxy/commit/a89954c8928f0997aa9a5781a39d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Fix 2 typos
Commit: 0d80b8807a70ff94a6f8dbee6279207c53869755
https://github.com/galaxyproject/galaxy/commit/0d80b8807a70ff94a6f8dbee6279…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Remove hash when expiring tool from tool cache
and rename `clean_paths` to `paths_to_cleanup` (thx @nsoranzo).
Commit: bcc4e025c36c3ee394c73cee06a8031cec6e9354
https://github.com/galaxyproject/galaxy/commit/bcc4e025c36c3ee394c73cee06a8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Merge pull request #3732 from nsoranzo/reload_toolbox_merge
Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox()
Commit: 7b375664634075c1ad261eff42a2355637cfc363
https://github.com/galaxyproject/galaxy/commit/7b375664634075c1ad261eff42a2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Use config_filename throughout ToolCache
Commit: 33ababaeb48e8ecfad487a54e96550ce7e43bc78
https://github.com/galaxyproject/galaxy/commit/33ababaeb48e8ecfad487a54e965…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Move the user calculate_and_set_disk_usage functionality to the model instead of the queue worker.
Commit: c928f15b4d00bb798453d42a6f6a79042692edfc
https://github.com/galaxyproject/galaxy/commit/c928f15b4d00bb798453d42a6f6a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Robustify calculate_and_set_disk_usage for handling changes during the long calc
Commit: cd6e7f73d8a54698aa63d670e8aba6e45f8eef1b
https://github.com/galaxyproject/galaxy/commit/cd6e7f73d8a54698aa63d670e8ab…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Swap admin recalculate to use model-based recalc-and-set
Commit: 751182640d1a76962cbac872ae31c0ce471872dd
https://github.com/galaxyproject/galaxy/commit/751182640d1a76962cbac872ae31…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Remove now-unused import of pgcalc
Commit: 8002ef31ea6f4cb52d6e907dcdf1d002ced45eb6
https://github.com/galaxyproject/galaxy/commit/8002ef31ea6f4cb52d6e907dcdf1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Ensure there's a user before calling calculate_and_set_disk_usage
Commit: e088a48323a06e80d55e85944a4c09cf368b8391
https://github.com/galaxyproject/galaxy/commit/e088a48323a06e80d55e85944a4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Add error logging to recalculate task.
Commit: 2d964eb50c9f2f2246044a1d7b83e0f920046510
https://github.com/galaxyproject/galaxy/commit/2d964eb50c9f2f2246044a1d7b83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
I have no idea what I would be doing without Nicola.
Commit: 8911e491a56cdc3b8fb327bc702b4843d7d22a4d
https://github.com/galaxyproject/galaxy/commit/8911e491a56cdc3b8fb327bc702b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge pull request #3734 from dannon/queue_worker_trim
Quota recalculation logic consolidation
Commit: 6e32b0f7c119ca6c3d54a761e64f49fe6a7f8280
https://github.com/galaxyproject/galaxy/commit/6e32b0f7c119ca6c3d54a761e64f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Use routing helper to navigate to tool form
Commit: 5df0187d42d19c5a930bf067a52a2ef4cf9d3ec8
https://github.com/galaxyproject/galaxy/commit/5df0187d42d19c5a930bf067a52a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
A config/plugins/webhooks/demo/search/static/styles.css
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/json.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/workflow/steps.py
M run_tests.sh
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/onload.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/onload.js
M static/style/blue/base.css
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/tool_shed/repository/common.mako
M test/TESTING.md
M test/api/test_workflows.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/selenium_tests/test_collection_builders.py
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Merge branch 'dev' into ui_pref_routing
Commit: 9f498f9c4be7d1ba6cfba38a2cc8993f732c013b
https://github.com/galaxyproject/galaxy/commit/9f498f9c4be7d1ba6cfba38a2cc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Avoid reusing 'map' builtin
Commit: 3ef22d2e6728bf890f14ef6465e88f757bd88b94
https://github.com/galaxyproject/galaxy/commit/3ef22d2e6728bf890f14ef6465e8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Slightly more accurate check to verify we have a controller match
Commit: 675c375cad69affacda74521d7e88f5227160cb6
https://github.com/galaxyproject/galaxy/commit/675c375cad69affacda74521d7e8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
A try at two layer routing with failthrough to clientside routes.
Commit: 036d35ac643ace26f1bad289d1989d3db8971ff2
https://github.com/galaxyproject/galaxy/commit/036d35ac643ace26f1bad289d198…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Slight refactoring to reduce duplication in map matching
Commit: 66e6be890bedbf59f98b1d10a54146175524df8a
https://github.com/galaxyproject/galaxy/commit/66e6be890bedbf59f98b1d10a541…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
No need to check API routes against clientside mapper, catch specific exception
Commit: 5a7eab0f06b4eb9f877c8e582bb6e078622be1ad
https://github.com/galaxyproject/galaxy/commit/5a7eab0f06b4eb9f877c8e582bb6…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-09 (Thu, 09 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/search/static/script.js
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #3731 from dannon/fix_webhook_search_overlay
Fix webhook search overlay interfering with masthead load
Commit: 01e1bc6f3007aff1234e518977115c97bd20e1eb
https://github.com/galaxyproject/galaxy/commit/01e1bc6f3007aff1234e51897711…
Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Added percolator proteomics datatypes for input and output
Commit: b437be2c566c431267d814b7718380969b8bd3b7
https://github.com/galaxyproject/galaxy/commit/b437be2c566c431267d814b77183…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding SIF to JSON converter for Cytoscape viewer
Commit: bf88e891977da140d36ba9a627ffebf19178b290
https://github.com/galaxyproject/galaxy/commit/bf88e891977da140d36ba9a627ff…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Merge pull request #20 from dannon/ui_pref_routing
Ui pref routing
Commit: df73622becc820017a1873db00f64fdcbb6de27a
https://github.com/galaxyproject/galaxy/commit/df73622becc820017a1873db00f6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
Log Message:
-----------
Fix route used in admin controller
Commit: 05a689e2adf455f461556fa1aa9229cf4f0454ff
https://github.com/galaxyproject/galaxy/commit/05a689e2adf455f461556fa1aa92…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/search/static/script.js
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M static/maps/onload.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge branch 'dev' into ui_pref_routing
Commit: 20916c16a9861cf1f491173cbded2bac0b61f378
https://github.com/galaxyproject/galaxy/commit/20916c16a9861cf1f491173cbded…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/layout/menu.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove back button to simplify routing, avoid failing returns
Commit: 66a02b6af192c78f53ad2901f55515cd9f712ab7
https://github.com/galaxyproject/galaxy/commit/66a02b6af192c78f53ad2901f555…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M doc/source/admin/index.rst
A doc/source/admin/tool_panel.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
M doc/source/project/issues.rst
Log Message:
-----------
modify our docs in preparation for restructuring
start moving admin content from old wiki
Commit: 7523ff6983bd6511725509ae4f4d744b36223b97
https://github.com/galaxyproject/galaxy/commit/7523ff6983bd6511725509ae4f4d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add random identifier to request url in order to allow proper reload upon multiple navigation requests
Commit: 2275d098eeeaeb115fa69b0d1fa7856f7bfa4d18
https://github.com/galaxyproject/galaxy/commit/2275d098eeeaeb115fa69b0d1fa7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding graph resize property for window resize
Commit: f94174912a09a56eebe2e14e63238c3f3f172327
https://github.com/galaxyproject/galaxy/commit/f94174912a09a56eebe2e14e6323…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
update xsd codefile doc with info from moin
Commit: 817a9db1f7bca855fe8f35c4b188c10a5c3a6653
https://github.com/galaxyproject/galaxy/commit/817a9db1f7bca855fe8f35c4b188…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
R doc/source/admin/grt.rst
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/webhooks.rst
R doc/source/admin/webhooks.rst
M doc/source/index.rst
Log Message:
-----------
move some admin docs to separate special topics section
Commit: 45971b29bd8b93825fe48134750bd866c82f7a9f
https://github.com/galaxyproject/galaxy/commit/45971b29bd8b93825fe48134750b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M doc/source/admin/dependency_resolvers.rst
Log Message:
-----------
Update dependency resolver docs for new default order
Commit: 33ff2754cc75981796176b7e7ae75ce362db62a0
https://github.com/galaxyproject/galaxy/commit/33ff2754cc75981796176b7e7ae7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-10 (Fri, 10 Mar 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Merge pull request #3708 from natefoo/dep-resolve-order
Prefer versioned Conda dependencies to unversioned Galaxy ones
Commit: 46e452bfe820ddbb329e694d0eb2b7b755594910
https://github.com/galaxyproject/galaxy/commit/46e452bfe820ddbb329e694d0eb2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Fix typo in install_dependencies docstring
Commit: 8b5d408e438c346f04088374d70eaca65e06c292
https://github.com/galaxyproject/galaxy/commit/8b5d408e438c346f04088374d70e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add API to remove requirements installed by Conda
This is currently limited to the Conda dependency resolver, but other
resolver would only need to implement the resolver.uninstall method and
set can_uninstall_dependencies to True.
To use this endpoint, POST to
<galaxy_url>/tools/<tool_id>/uninstall_dependencies'.
Commit: 3b067ef62a4dfa8af54bc4c75c6260f98d660aeb
https://github.com/galaxyproject/galaxy/commit/3b067ef62a4dfa8af54bc4c75c62…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Return last non-zero returncode
Commit: d5b5d29137ee1e5577530ed2c56579b9394520b3
https://github.com/galaxyproject/galaxy/commit/d5b5d29137ee1e5577530ed2c565…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Change endpoint to `api/tools/<tool_id>/dependencies`
A POST will trigger installation and DELETE will trigger uninstalling
the dependencies (Thx for the suggestion @jmchilton).
Commit: 6902e62d38e3c5741a238736f640b5b847c5e8c2
https://github.com/galaxyproject/galaxy/commit/6902e62d38e3c5741a238736f640…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix uninstall when not all dependencies are resolved by all-in-one resolver
Commit: 95106ea3c9ad875ce35b16c6b9bb8556f3d82076
https://github.com/galaxyproject/galaxy/commit/95106ea3c9ad875ce35b16c6b9bb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-12 (Sun, 12 Mar 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Add UI for Conda dependency uninstall
Commit: fc1df7bad17e53c54bd57602b82bbec22cc0e074
https://github.com/galaxyproject/galaxy/commit/fc1df7bad17e53c54bd57602b82b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3725 from mvdbeek/remove_env_conda
Add API and UI to remove requirements installed by Conda
Commit: 38336e7e94b15b1580e32e4d0b4321836791db9b
https://github.com/galaxyproject/galaxy/commit/38336e7e94b15b1580e32e4d0b43…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/integration/test_resolvers.py
Log Message:
-----------
Merge branch 'dev' into ui_pref_routing
Commit: 7e1c04cc6df810ca3a4e726a85cc9566d9d1ff61
https://github.com/galaxyproject/galaxy/commit/7e1c04cc6df810ca3a4e726a85cc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3739 from martenson/update-codefile-schema
update xsd codefile doc with info from moin
Commit: 90b300cbd731df2e6005ca1dcd2f5c1c59a34e0e
https://github.com/galaxyproject/galaxy/commit/90b300cbd731df2e6005ca1dcd2f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Return empty list if resolve_all() has failed
This should solve the problems pointed out by :eyes: @nsoranzo
introduced in https://github.com/galaxyproject/galaxy/pull/3725.
This commit also clarifies this behaviour in the docstrings.
Commit: 8192d3562937d07410aa5d7dd73727efc5832634
https://github.com/galaxyproject/galaxy/commit/8192d3562937d07410aa5d7dd737…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/__init__.py
Log Message:
-----------
Add `:returns: list of resolved dependencies` to docstring of `resolve_all` method
Commit: 7d08f8f2fecf08743a58f71c431e1d71f84f0d76
https://github.com/galaxyproject/galaxy/commit/7d08f8f2fecf08743a58f71c431e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #3746 from mvdbeek/resolve_all_fix_3725
BUG: Return empty list if resolve_all() has failed
Commit: 08f66a924b8a46d673fc6237dec3a4e8fcb34f21
https://github.com/galaxyproject/galaxy/commit/08f66a924b8a46d673fc6237dec3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-13 (Mon, 13 Mar 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A config/swarm_manager_conf.yml.sample
R cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
GIE container waiting and swarm management.
1. Create a new API endpoint and client spin to wait for GIE containers to
become ready. IEs are not required to use it, but usage does require
a slight change to their `load_notebook()` functions.
2. Add a Docker swarm manager daemon that runs automatically
to add nodes when services are waiting, clean up exited services, and
remove idle nodes. Shuts down automatically when there's nothing to
do.
The format of the GIE proxy session database has changed, if GIEs are
running when you restart Galaxy, they will be interrupted. If you run
the GIE proxy separate from Galaxy, you should restart it after
upgrading.
Commit: f21f963a23427e2b5aa1f58a7d9b0fb85aed7607
https://github.com/galaxyproject/galaxy/commit/f21f963a23427e2b5aa1f58a7d9b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
Log Message:
-----------
Change API path in docstrings to correct /api/dependency_resolvers/*
Commit: e9c98e46ed580463a4f7a4ed989d11f7714ac13f
https://github.com/galaxyproject/galaxy/commit/e9c98e46ed580463a4f7a4ed989d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Don't have the clientside mapper register itself
Commit: 65e7ee0c78e5c61a6ef9d9eaa8ccd6d8666014ad
https://github.com/galaxyproject/galaxy/commit/65e7ee0c78e5c61a6ef9d9eaa8cc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
Log Message:
-----------
Merge pull request #3749 from mvdbeek/docstring_fix_api
Change API path in docstrings to correct /api/dependency_resolvers/*
Commit: 3b0be252e3485b413d7978a91b14242b589702c5
https://github.com/galaxyproject/galaxy/commit/3b0be252e3485b413d7978a91b14…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Remove old deprecated option (explicit is defined at mapper instantiation, and we wat the default
Commit: 6f8deb6f4a07bd57493d24cd90a9862dbf7e6d0c
https://github.com/galaxyproject/galaxy/commit/6f8deb6f4a07bd57493d24cd90a9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
Log Message:
-----------
move webhooks images where they belong
Commit: 4b6373f042ad98f4f3ac664911ab35611280f204
https://github.com/galaxyproject/galaxy/commit/4b6373f042ad98f4f3ac664911ab…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M doc/source/admin/index.rst
Log Message:
-----------
fix outdated links
Commit: 93c2286442bbb27e9dd3db708064e6f3deb45287
https://github.com/galaxyproject/galaxy/commit/93c2286442bbb27e9dd3db708064…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Initialize clientside_routes regexes.
Commit: 061b7d78f26d4aa1298a3a072fcc420d214d4f7b
https://github.com/galaxyproject/galaxy/commit/061b7d78f26d4aa1298a3a072fcc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Refactor failthrough mapping logic
Commit: 5e11b54da59e09f9e31b71c00f3ecaf99842a0c5
https://github.com/galaxyproject/galaxy/commit/5e11b54da59e09f9e31b71c00f3e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Add the possibility to uninstall conda environments that are not in use by Galaxy
Commit: 550bc423af0cb036d1a870c0c419533f25517bbf
https://github.com/galaxyproject/galaxy/commit/550bc423af0cb036d1a870c0c419…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Rename parameter, make it a bit more clear what this failthrough logic is doing.
Commit: 88fb8650b9699a50348ddece8d336797aacd03c5
https://github.com/galaxyproject/galaxy/commit/88fb8650b9699a50348ddece8d33…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Bump routes to 2.4.1, fix (newly?) broken archive route.
Commit: 44fd8aa9bbc77680083eb71d30840a41ce1f79ee
https://github.com/galaxyproject/galaxy/commit/44fd8aa9bbc77680083eb71d3084…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Merge pull request #21 from dannon/ui_pref_routing
Don't have the clientside mapper register itself
Commit: 6700c08a96467d322e917347a63f1ec8c932700e
https://github.com/galaxyproject/galaxy/commit/6700c08a96467d322e917347a63f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
Log Message:
-----------
Update Routes 2.4.1 hash
Commit: 1578ffe1ca5bf28a34f91a892eed286ab69a14ba
https://github.com/galaxyproject/galaxy/commit/1578ffe1ca5bf28a34f91a892eed…
Author: Clemens BlanK <blankclemens(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Add tool_list webhook plugin to create the tool list yaml file for this instance.
Commit: 90ae42c3f1d0efc4f8b461e43a158eb5b7b95d4f
https://github.com/galaxyproject/galaxy/commit/90ae42c3f1d0efc4f8b461e43a15…
Author: Clemens BlanK <blankclemens(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Reduced API calls to speed it up.
Commit: 417d1d251e7e7c735a8d4aefd53edcec941db1f4
https://github.com/galaxyproject/galaxy/commit/417d1d251e7e7c735a8d4aefd53e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
Log Message:
-----------
Initial commit to get this rolling, library-security does not exist and needs to be created, among others.
Commit: bc870cdf66ecaaf218cd20debdbcc68b20e7f959
https://github.com/galaxyproject/galaxy/commit/bc870cdf66ecaaf218cd20debdbc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Update galaxy.ini.sample and config.
Commit: 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4
https://github.com/galaxyproject/galaxy/commit/11829c4f9df12cf8e8e3e7a14dc1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/managers/configuration.py
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
Log Message:
-----------
More defaults, these should be consolidated.
Commit: d505fcf26027fd908b0a0fa1a6e1cb814c56b6ce
https://github.com/galaxyproject/galaxy/commit/d505fcf26027fd908b0a0fa1a6e1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
A doc/source/admin/authentication.md
M doc/source/admin/index.rst
Log Message:
-----------
New Authentication section of the docs.
I pulled in this doc https://galaxyproject.org/develop/authentication/ which was very dated and somewhat incorrect and I filled it out with more details, updated configuration information, and a whole new section on the authentication framework. I also pulled in this doc https://galaxyproject.org/admin/user-accounts/ which was pretty good and I left it largely unchanged.
Rebased to fix index inclusion and with edits suggested by :eagle::eyes:.
Commit: e12c07cacd12fbf4a2fb148242be5bea7c13221e
https://github.com/galaxyproject/galaxy/commit/e12c07cacd12fbf4a2fb148242be…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
Log Message:
-----------
Use config.py for defaults used in managers/configuration.
Commit: ed1d19a967989416caebd3588fe6b8b6460764e2
https://github.com/galaxyproject/galaxy/commit/ed1d19a967989416caebd3588fe6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Update reports and toolshed app configs as well.
Commit: 77b29880c8e9eddaf282e8738542aa57a189f6d2
https://github.com/galaxyproject/galaxy/commit/77b29880c8e9eddaf282e8738542…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M run_tests.sh
Log Message:
-----------
Fix run_tests.sh --dockerize for Mac OS X usage.
Without this I get the error message below and the tests do not execute.
```
./run_tests.sh: line 279: UID: readonly variable
```
This was likely broken with b75ee68d9f6305646a55d816fb1173210e36eab9.
Commit: d1eab2685f652f0b6f8c8119c51acf080c54556e
https://github.com/galaxyproject/galaxy/commit/d1eab2685f652f0b6f8c8119c51a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Provide a fallback for GALAXY_TEST_UID if manually running Docker tests.
Commit: d6654838f361a1e3064619cb059f9137579dc376
https://github.com/galaxyproject/galaxy/commit/d6654838f361a1e3064619cb059f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Fix pip install cache inside Galaxy testing container.
It is causing Jenkins to fail throughout on https://github.com/galaxyproject/galaxy/pull/3179.
Commit: b1429d4340f11591768bb853fd646508e32e0501
https://github.com/galaxyproject/galaxy/commit/b1429d4340f11591768bb853fd64…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
Log Message:
-----------
Mirror latest galaxy-lib changes for Conda and CWL improvements.
- I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50).
- I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (https://github.com/galaxyproject/galaxy-lib/commit/6d53fc7dec6c48ea8fb00fa3…)
- I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though.
- I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. https://github.com/galaxyproject/galaxy-lib/pull/53
- I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. https://github.com/galaxyproject/galaxy-lib/pull/52
There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically.
- galaxyproject/galaxy-lib@bdacc4d
- galaxyproject/galaxy-lib@1b7bca6
- galaxyproject/galaxy-lib@36b2e65
Commit: 6ece9acfde69fadd4e8b105c9c14ce572ddbfbcd
https://github.com/galaxyproject/galaxy/commit/6ece9acfde69fadd4e8b105c9c14…
Author: Clemens BlanK <blankclemens(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Fix linting.
Commit: d7cf8a4b33991c3117f725a1d418706b758703b5
https://github.com/galaxyproject/galaxy/commit/d7cf8a4b33991c3117f725a1d418…
Author: Clemens BlanK <blankclemens(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Fix Python 2.7 linting.
Commit: bc203d022f92fd596514d935c0e569163e2cf4d1
https://github.com/galaxyproject/galaxy/commit/bc203d022f92fd596514d935c0e5…
Author: Clemens BlanK <blankclemens(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Speed up list creation.
Commit: 4f27240ef760446743b7b774404f159b713ae3ce
https://github.com/galaxyproject/galaxy/commit/4f27240ef760446743b7b774404f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #3737 from glormph/percolator_datatypes
Percolator out datatypes
Commit: aaa28071b3acaad514157dae856cb2f5a4895eef
https://github.com/galaxyproject/galaxy/commit/aaa28071b3acaad514157dae856c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #3752 from dannon/routes-bump
Bump routes to 2.4.1
Commit: 149bbf87e3d57ffe22c51c283a94fbec33542f05
https://github.com/galaxyproject/galaxy/commit/149bbf87e3d57ffe22c51c283a94…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A config/swarm_manager_conf.yml.sample
R cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Merge pull request #3740 from natefoo/docker-swarm-mode-wait
Interactive Environment container waiting and swarm management
Commit: 0498c7f833fad513e2ca878843938e378475202b
https://github.com/galaxyproject/galaxy/commit/0498c7f833fad513e2ca87884393…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M static/maps/layout/menu.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/user/user-preferences.js
M templates/grid_base.mako
R templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge pull request #3446 from guerler/ui_pref_routing
Improve routing for user preference views
Commit: d32317438c407799c2b33364af6e553fa03fbdfa
https://github.com/galaxyproject/galaxy/commit/d32317438c407799c2b33364af6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add build endpoints to user api
Commit: 814d58f9810283c1e851b6c6ec062ab3cb0784bf
https://github.com/galaxyproject/galaxy/commit/814d58f9810283c1e851b6c6ec06…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Remove empty lines, reduce comments
Commit: c12c2d1dff45afe1a62321f45a26e2de2d696a99
https://github.com/galaxyproject/galaxy/commit/c12c2d1dff45afe1a62321f45a26…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Add potential len files to response for now, might move to client-side further down the road
Commit: 72fb0d6f043e5085323059f80a39a9c2fab43b88
https://github.com/galaxyproject/galaxy/commit/72fb0d6f043e5085323059f80a39…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Fix error handling for build deletion
Commit: 32a8633f4e0b4fc06ba3b61027ae3127cd0c7ece
https://github.com/galaxyproject/galaxy/commit/32a8633f4e0b4fc06ba3b61027ae…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Add link to user preference page, return exception if chrom count failed
Commit: 2153ef5b76a1958c0067abb6c5492d1df6767c3c
https://github.com/galaxyproject/galaxy/commit/2153ef5b76a1958c0067abb6c549…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add route for custom builds
Commit: 56338972b9767b9e0be474d99b8f4ea915e6dd96
https://github.com/galaxyproject/galaxy/commit/56338972b9767b9e0be474d99b8f…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
Log Message:
-----------
Extending the sif to json converter to allow single nodes to be plotted
Commit: 3d092d683efef26bde2d2d453c07caa8a8c4322e
https://github.com/galaxyproject/galaxy/commit/3d092d683efef26bde2d2d453c07…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
A config/plugins/webhooks/demo/search/static/styles.css
A config/swarm_manager_conf.yml.sample
R cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/special_topics/interactive_environments.rst
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/json.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/user/user-preferences.js
M templates/grid_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/tool_shed/repository/common.mako
M test/integration/test_resolvers.py
Log Message:
-----------
Merge branch 'dev' into admin-docs-from-hub
Commit: c6bd499d001b667f20bd4caf99612a3d56b200c1
https://github.com/galaxyproject/galaxy/commit/c6bd499d001b667f20bd4caf9961…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding node text and colors for graphs
Commit: 27cb4fbedca6ab44ecc5a154e3102462bd0a09af
https://github.com/galaxyproject/galaxy/commit/27cb4fbedca6ab44ecc5a154e310…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
R doc/source/admin/webhooks.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
M doc/source/project/issues.rst
Log Message:
-----------
Merge pull request #3738 from martenson/admin-docs-from-hub
modify our docs in preparation for restructuring
Commit: 460d876fc4814ab10badb859b64a05225b04e952
https://github.com/galaxyproject/galaxy/commit/460d876fc4814ab10badb859b64a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
A doc/source/admin/authentication.md
M doc/source/admin/index.rst
Log Message:
-----------
Merge pull request #3751 from jmchilton/auth_docs
New Authentication section of the docs.
Commit: d42848ec9b73a89e1cbe20a3250481bd1b41a93a
https://github.com/galaxyproject/galaxy/commit/d42848ec9b73a89e1cbe20a32504…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
A static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Add client view for custom builds, add api endpoint for builds metadata
Commit: 0b26d561aabdb5af6e21e8d845f15325e18d8751
https://github.com/galaxyproject/galaxy/commit/0b26d561aabdb5af6e21e8d845f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/ui/ui-table.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-table.js
Log Message:
-----------
Align style of table view component to other ui views
Commit: 88d4bf204c554c95ca40aa88504198f6705aa9a1
https://github.com/galaxyproject/galaxy/commit/88d4bf204c554c95ca40aa885041…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M .ci/py3_sources.txt
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
Fix KeyError when getting request and response content-type headers
Fix https://github.com/galaxyproject/galaxy/issues/2551
Also fix Python3 compatibility, xref: #1715
Commit: 2a6391550b2256c18f2671b2260f58746b507db7
https://github.com/galaxyproject/galaxy/commit/2a6391550b2256c18f2671b2260f…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding directed/undirected attribute for graphs
Commit: 131aeb66b4884200c6c9433aef9a80aabf98d132
https://github.com/galaxyproject/galaxy/commit/131aeb66b4884200c6c9433aef9a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy/util/postfork.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Abstract uWSGI handling into new galaxy.web.stack package.
Commit: 718df44921db25eedf21f5fefb2b4a6ac7bc7792
https://github.com/galaxyproject/galaxy/commit/718df44921db25eedf21f5fefb2b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
R lib/galaxy/tags/tag_handler.py
Log Message:
-----------
Prune empty tag handler
Commit: 1b5d95a5800aeed632888a42473a7ce24b9623c5
https://github.com/galaxyproject/galaxy/commit/1b5d95a5800aeed632888a42473a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
R lib/galaxy/tags/__init__.py
Log Message:
-----------
Remove unused (and empty) tags module.
Commit: 0e7a71596d859728600bbf4569cae3bfd85574c9
https://github.com/galaxyproject/galaxy/commit/0e7a71596d859728600bbf4569ca…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M .ci/py3_sources.txt
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
Merge pull request #3757 from nsoranzo/fix_for_2551
Fix KeyError when getting request and response content-type headers
Commit: 689560d7db23240df193fc913d8165643eea8cac
https://github.com/galaxyproject/galaxy/commit/689560d7db23240df193fc913d81…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Implement and connect client add request with endpoint
Commit: 06f61927b5f9f6d35c7c0bdebdd330bae56f6710
https://github.com/galaxyproject/galaxy/commit/06f61927b5f9f6d35c7c0bdebdd3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Fix delete request, fix error triggered by attempting invalid conversions
Commit: 8b5e27aaeae1ac9b35b0959f2cccaa6988d69163
https://github.com/galaxyproject/galaxy/commit/8b5e27aaeae1ac9b35b0959f2ccc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Add name validator
Commit: d2692dc77bdd4db48cbcc77d9cd776e0cd7e8bab
https://github.com/galaxyproject/galaxy/commit/d2692dc77bdd4db48cbcc77d9cd7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/ui/ui-table.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Sort custom builds in table
Commit: b1b87358e7fdb991cf1ef1b90aabfc8d182304b1
https://github.com/galaxyproject/galaxy/commit/b1b87358e7fdb991cf1ef1b90aab…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Reset form after submission, highlight missing/failed chrom count
Commit: 72b3b8596253500cbbf54bfe7a5415b08f46b14d
https://github.com/galaxyproject/galaxy/commit/72b3b8596253500cbbf54bfe7a54…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M lib/galaxy/managers/tags.py
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Fix bug(?) that prevented associating multiple values to a tag.
Commit: 200b3837c7956e4ee5b19b01eb67e62375e58e97
https://github.com/galaxyproject/galaxy/commit/200b3837c7956e4ee5b19b01eb67…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Remove debug statements for user preferences
Commit: 977b1acc48e878fb90a7b52e973ae497052b8583
https://github.com/galaxyproject/galaxy/commit/977b1acc48e878fb90a7b52e973a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
Log Message:
-----------
Remove duplicate keys from nls locales.
Commit: d0eaeff9c4b47b922ae5c764fbe3722603ac1148
https://github.com/galaxyproject/galaxy/commit/d0eaeff9c4b47b922ae5c764fbe3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/locale.js
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/locale.js
Log Message:
-----------
Add FR localization template. Needs translation next.
Commit: 02327e7085559bd776bfda8743dc99edd2c3f14f
https://github.com/galaxyproject/galaxy/commit/02327e7085559bd776bfda8743dc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
A client/galaxy/scripts/nls/fr/locale.js
A static/maps/nls/fr/locale.js.map
A static/scripts/nls/fr/locale.js
Log Message:
-----------
Add FR localization template (the actual files). Needs translation next.
Commit: e7b1d45a3990ce6db9fcdaa92dac6a18cb605345
https://github.com/galaxyproject/galaxy/commit/e7b1d45a3990ce6db9fcdaa92dac…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Add some basic (likely awful) FR translations just to check the machinery here.
Commit: d7e4e8e162bbeb071e83d08bd22f17b8bc59602f
https://github.com/galaxyproject/galaxy/commit/d7e4e8e162bbeb071e83d08bd22f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Readability formatting for existing locales to set a standard moving forward.
Commit: d4462cb3213e81c2d25b7575ca3865c7720437fd
https://github.com/galaxyproject/galaxy/commit/d4462cb3213e81c2d25b7575ca38…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Localization support for menu.
Commit: 4f82467117d12fe6bab70fb96e769d3c89d9c212
https://github.com/galaxyproject/galaxy/commit/4f82467117d12fe6bab70fb96e76…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
FR locale masthead support.
Commit: 2ebf46effae518fc9d0dc1c574d2d5a30407b3ce
https://github.com/galaxyproject/galaxy/commit/2ebf46effae518fc9d0dc1c574d2…
Author: Bérénice Batut <berenice.batut(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Correct some translation errors
Commit: f7cb5b70fc6ba0142b88a467f8a06889a0c7911a
https://github.com/galaxyproject/galaxy/commit/f7cb5b70fc6ba0142b88a467f8a0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #10 from dannon/bebatut-patch-1
Correct some translation errors
Commit: f174358b9542610ffa4c00588096a4e80583ae0a
https://github.com/galaxyproject/galaxy/commit/f174358b9542610ffa4c00588096…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M doc/source/releases/_header.rst
Log Message:
-----------
fix link to galaxy logo
Commit: 85093dc13ad06eb8d4896f01d934846cd57c1473
https://github.com/galaxyproject/galaxy/commit/85093dc13ad06eb8d4896f01d934…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M doc/source/admin/useful_scripts.rst
Log Message:
-----------
reword topic
Commit: e02e2cb09e245ab5cbbe48d532e4f3ffe9a1612a
https://github.com/galaxyproject/galaxy/commit/e02e2cb09e245ab5cbbe48d532e4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M doc/source/index.rst
Log Message:
-----------
improve doc-build-urself docs
Commit: 9f42821f57c3126826ebc773407ac02084a965ea
https://github.com/galaxyproject/galaxy/commit/9f42821f57c3126826ebc773407a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding Breadth First Search for cytoscape graphs. Tapping any node plays BFS
Commit: 15273ad1489c9cdc216126ff36c2ec2d912e4165
https://github.com/galaxyproject/galaxy/commit/15273ad1489c9cdc216126ff36c2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Add uploader element
Commit: bb5b8cf525562e1a930ad03a4071dffd341865e5
https://github.com/galaxyproject/galaxy/commit/bb5b8cf525562e1a930ad03a4071…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Declare submit caller for upload element
Commit: 474b0c1d2ceade095fd995d19ba30334be612458
https://github.com/galaxyproject/galaxy/commit/474b0c1d2ceade095fd995d19ba3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Sort models in table, fix message parameter, properly return models with count attribute
Commit: 39c9f79970579556eac63c12d40174ee95e2c337
https://github.com/galaxyproject/galaxy/commit/39c9f79970579556eac63c12d401…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Improve error handling, add success and warning messages
Commit: 4180d2e08841628753a65966143c58d6c5630d90
https://github.com/galaxyproject/galaxy/commit/4180d2e08841628753a65966143c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Fix success message
Commit: 542a84afd5552b94bfdaff4ca8a6c0c368f1489a
https://github.com/galaxyproject/galaxy/commit/542a84afd5552b94bfdaff4ca8a6…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
first pass
Commit: c4f906cb729e08412924186726dfaba12bf2f2d8
https://github.com/galaxyproject/galaxy/commit/c4f906cb729e08412924186726df…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #11 from lecorguille/i18n
first pass
Commit: 59526d82e8c1ce8e796b461d3e69eb8c03cc3030
https://github.com/galaxyproject/galaxy/commit/59526d82e8c1ce8e796b461d3e69…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M README.rst
Log Message:
-----------
update logo URL
Commit: caf0675176ae9b8a0b578fb8de3cba97695e9ad4
https://github.com/galaxyproject/galaxy/commit/caf0675176ae9b8a0b578fb8de3c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M README.rst
Log Message:
-----------
Merge pull request #3768 from martenson/logo-url-update
update logo URL
Commit: 986134d766e69344c511e2627739a51f9d8cf044
https://github.com/galaxyproject/galaxy/commit/986134d766e69344c511e2627739…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M scripts/secret_decoder_ring.py
Log Message:
-----------
Should exit immediately to avoid index error
Commit: 90de3671f132848a9eaae9048bf091f1969d0caf
https://github.com/galaxyproject/galaxy/commit/90de3671f132848a9eaae9048bf0…
Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
pass 2
Commit: face53037d476bbc59e4674f861e903c23d52109
https://github.com/galaxyproject/galaxy/commit/face53037d476bbc59e4674f861e…
Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
pass 2 from Gildas
Commit: 6b38ccada116ce2445a9bfc6fb513b54feacb65b
https://github.com/galaxyproject/galaxy/commit/6b38ccada116ce2445a9bfc6fb51…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Uncomment and format FR localization.
Commit: 9704b73500db07fde28c778a9977c6aa22aa237a
https://github.com/galaxyproject/galaxy/commit/9704b73500db07fde28c778a9977…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Build client.
Commit: 78074243d734c81891795d3ad25dffbe70130a29
https://github.com/galaxyproject/galaxy/commit/78074243d734c81891795d3ad25d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Forgot localization for 'Login'
Commit: eaf631efbfe7dc7b0624ded57adb4410dab93f30
https://github.com/galaxyproject/galaxy/commit/eaf631efbfe7dc7b0624ded57adb…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
second pass
Commit: 4f749098d56b282125bf5644620f0bf5a273e5a3
https://github.com/galaxyproject/galaxy/commit/4f749098d56b282125bf5644620f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M scripts/secret_decoder_ring.py
Log Message:
-----------
Merge pull request #3770 from erasche/index-error
Should exit immediately to avoid index error
Commit: 6d803463318a721bab91d4458fc8b1da540cc091
https://github.com/galaxyproject/galaxy/commit/6d803463318a721bab91d4458fc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #14 from lecorguille/i18npass2
second pass
Commit: 0221bdf9c71b5567af8928a121d62970850fa8c2
https://github.com/galaxyproject/galaxy/commit/0221bdf9c71b5567af8928a121d6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
One last rebuild w/ final changes.
Commit: 11ee6ea6384e3fde47fb0eb10d466461ffc050ee
https://github.com/galaxyproject/galaxy/commit/11ee6ea6384e3fde47fb0eb10d46…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Fix 'logged in as' localization usage.
Commit: fe35ed009e72a65b0e120d4d29c8614652560db1
https://github.com/galaxyproject/galaxy/commit/fe35ed009e72a65b0e120d4d29c8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Fix localization of Preferences
Commit: 576ad4f95aa50fa80aa1de993bcbf03da5d2da98
https://github.com/galaxyproject/galaxy/commit/576ad4f95aa50fa80aa1de993bcb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Add preferences to core translations, update search datasets
Commit: af849e506257419f73dbac58d7618bc00104b60c
https://github.com/galaxyproject/galaxy/commit/af849e506257419f73dbac58d761…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
fix Yvan integration :P
Commit: dc201094aa3cf07967f1c16ae6bef88718476e37
https://github.com/galaxyproject/galaxy/commit/dc201094aa3cf07967f1c16ae6be…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Duplicated word in localization
Commit: 8aaee3d33b378a8fd9d29b90f9003b0217c7ad43
https://github.com/galaxyproject/galaxy/commit/8aaee3d33b378a8fd9d29b90f900…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #15 from lecorguille/i18npass3
Fix Yvan integration :P
Commit: cc37049af8c08e50e6ca81ce83f93f35a0711c6e
https://github.com/galaxyproject/galaxy/commit/cc37049af8c08e50e6ca81ce83f9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge branch 'i18n' of github.com:dannon/galaxy into i18n
Commit: ae049fe54068408866265ad2f040ee5b0aa8a763
https://github.com/galaxyproject/galaxy/commit/ae049fe54068408866265ad2f040…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Merge more fixes, rebuild.
Commit: f5844252ae9feee554342e69562c3ae65985bb82
https://github.com/galaxyproject/galaxy/commit/f5844252ae9feee554342e69562c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Attempt to determine line count upon file upload to allow early validation
Commit: aea96855bb5da18623c51ab6e6885f5c9acaf19e
https://github.com/galaxyproject/galaxy/commit/aea96855bb5da18623c51ab6e688…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Merge branch 'add_uploader' into remove_custom_builds_mako
Commit: a2affcc618ae5ec8d0f36e55a0f7ef15de53ef68
https://github.com/galaxyproject/galaxy/commit/a2affcc618ae5ec8d0f36e55a0f7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding Depth First Search for cytoscape graphs
Commit: e78e1607db1eacc175c8f731cdb879fe3e293476
https://github.com/galaxyproject/galaxy/commit/e78e1607db1eacc175c8f731cdb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Upload and preview file using HTML5, client-side file reader
Commit: b557e31a4c29fcab875837c1ccc3c9cd9f37f6ba
https://github.com/galaxyproject/galaxy/commit/b557e31a4c29fcab875837c1ccc3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Fix form reset, remove debug statements
Commit: abe156783a7305a8341e217ece31500c36631232
https://github.com/galaxyproject/galaxy/commit/abe156783a7305a8341e217ece31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Set default to fasta selection
Commit: d50ca25a822a48e58b08c404fca1c25dfdc2bbd3
https://github.com/galaxyproject/galaxy/commit/d50ca25a822a48e58b08c404fca1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Merge pull request #3729 from mvdbeek/cleanup_tool_cache
Remove outdated items from tool cache when reloading the toolbox
Commit: 95b6f033a447d25b5826a4e368caf2fc15201d10
https://github.com/galaxyproject/galaxy/commit/95b6f033a447d25b5826a4e368ca…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Display installed builds as searchable list
Commit: 6b2a4ebd3653f25ef01e109ac7bdad601d6959a5
https://github.com/galaxyproject/galaxy/commit/6b2a4ebd3653f25ef01e109ac7bd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Len-file hdas not needed in metadata
Commit: 72cd0ba00ad05793751105dccf434c9868791b2a
https://github.com/galaxyproject/galaxy/commit/72cd0ba00ad05793751105dccf43…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Adjust link to the new Galaxy HUB site
Commit: b4fda2ccd49fd7b406a5521bce3243ff6ffb7950
https://github.com/galaxyproject/galaxy/commit/b4fda2ccd49fd7b406a5521bce32…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Merge pull request #16 from bgruening/wf_link
/learn/advanced-workflow/variables-edit
Commit: 39c1b1b24998d9ce77d660ad5dee525f71156720
https://github.com/galaxyproject/galaxy/commit/39c1b1b24998d9ce77d660ad5dee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Render len type help section
Commit: 031ce2307367f021646c2a1640112599320076fc
https://github.com/galaxyproject/galaxy/commit/031ce2307367f021646c2a164011…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
Log Message:
-----------
Merge pull request #3742 from jmchilton/galaxy-lib-20170311
Mirror latest galaxy-lib changes for Conda and CWL improvements.
Commit: 76bcf23b434984cd45002192a72bb90d3c06ade5
https://github.com/galaxyproject/galaxy/commit/76bcf23b434984cd45002192a72b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Add help section content
Commit: ad73c7d39d93683aba1b065b6660c4b5a98554bf
https://github.com/galaxyproject/galaxy/commit/ad73c7d39d93683aba1b065b6660…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
R templates/user/dbkeys.mako
Log Message:
-----------
Remove mako
Commit: 5ee585c681326072c489f26d2d2b084a6995a349
https://github.com/galaxyproject/galaxy/commit/5ee585c681326072c489f26d2d2b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Remove controller endpoint
Commit: ff5166c2930f54a05601ab9a934319689df9c3f8
https://github.com/galaxyproject/galaxy/commit/ff5166c2930f54a05601ab9a9343…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Redirect masthead link to new custom builds ui
Commit: a89a4f726ba60110810c99b372a53b48e9152c4e
https://github.com/galaxyproject/galaxy/commit/a89a4f726ba60110810c99b372a5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Revise style
Commit: 72c96bd5c6c6c3c1dea3a662dd2fa2d802822401
https://github.com/galaxyproject/galaxy/commit/72c96bd5c6c6c3c1dea3a662dd2f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-18 (Sat, 18 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
Log Message:
-----------
Hide select field if local fields are unavailable
Commit: c658ef3c7efd56986c096dc71a73c06260351ccc
https://github.com/galaxyproject/galaxy/commit/c658ef3c7efd56986c096dc71a73…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-19 (Sun, 19 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding Kruskal algorithm for graphs and color choosing scheme for highlighted edges
Commit: 8e77fe93b8e0b1eae57d454adc13a86a376bae35
https://github.com/galaxyproject/galaxy/commit/8e77fe93b8e0b1eae57d454adc13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/managers/tags.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #3760 from dannon/nametag_fixes
Tagging tweaks
Commit: b1f12d41f66c2b07929c037363fc6d94b890b283
https://github.com/galaxyproject/galaxy/commit/b1f12d41f66c2b07929c037363fc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Simplify run_test_wrapper.sh per @natefoo comments.
https://github.com/galaxyproject/galaxy/pull/3755/files#r106182107
Commit: 024e296ea8fa6dc7c3b3da3e74ac9e520e8daf73
https://github.com/galaxyproject/galaxy/commit/024e296ea8fa6dc7c3b3da3e74ac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/managers/datasets.py
Log Message:
-----------
Re-use job.finish abstraction in dataset manager stop_creating_job.
It is used in purge a bit above and it is the better abstraction.
Commit: f153400e95ff3888fab1b6c0fb7be5686a882532
https://github.com/galaxyproject/galaxy/commit/f153400e95ff3888fab1b6c0fb7b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Rework jobs API to not use deprecated TestsDatasets mixin.
Commit: cd36aa0878aed1a604a256098241068df169e4a3
https://github.com/galaxyproject/galaxy/commit/cd36aa0878aed1a604a256098241…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M run_tests.sh
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Merge pull request #3755 from jmchilton/docker_test_fixes
Assorted Fixes for Dockerized Test Setup
Commit: d18b4d13cbc25c85005e4b19a02abedbed7aba46
https://github.com/galaxyproject/galaxy/commit/d18b4d13cbc25c85005e4b19a02a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
Log Message:
-----------
Add an exception for unsupported middleware wrapping for better failure
handling.
Commit: 0602712a35015bba52f3bc756b0ce0fa1c20728e
https://github.com/galaxyproject/galaxy/commit/0602712a35015bba52f3bc756b0c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M scripts/api/README
Log Message:
-----------
deduplicate obsolete API readme
Commit: 009e2cbf5e9592fd8af782b2cde36d8d1687c003
https://github.com/galaxyproject/galaxy/commit/009e2cbf5e9592fd8af782b2cde3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/datasets.py
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Improve interaction between job state and purged datasets.
There are two basic behavior changes here and bunch of testing to verify the new behaviors.
1) Previously purging a dataset would cause a creating job to be cancelled but all outputs would need to be "deleted" in order to cause the creating job to be cancelled. After this change the behavior is the same for both deletion and purging - the job will run until all outputs are deleted or purged.
2) Previously Galaxy jobs wouldn't attempt to cleanup purged datasets that were created by a running tool - this cleanup now occurs.
These are tackled as a pair because I assume the difference in the behaviors between deletion and purging was a hack around tools populating datasets that had been purged while running. Cancelling the job wasn't a sure fix - but it would reduce the likelihood of such problems. I think the new approach is a bit more robust and explicit.
Commit: 0d95b4e2079aa0d442a2e030fe7606c7627bd1e6
https://github.com/galaxyproject/galaxy/commit/0d95b4e2079aa0d442a2e030fe76…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding graph traversal types
Commit: cbc7dd17fcf3bfe9eecdd8a0577a6d63e565f509
https://github.com/galaxyproject/galaxy/commit/cbc7dd17fcf3bfe9eecdd8a0577a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Removing unused if else
Commit: 5440889bf6a7c5f278860760cd8c4ba18708c263
https://github.com/galaxyproject/galaxy/commit/5440889bf6a7c5f278860760cd8c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy/util/postfork.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Merge pull request #3759 from natefoo/abstract-app-stack
Abstract uWSGI handling into new galaxy.web.stack package
Commit: 18cb50ecea80b3feeac02a2ef07c4cbd816c39d4
https://github.com/galaxyproject/galaxy/commit/18cb50ecea80b3feeac02a2ef07c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Abstraction for re-use between collection creators.
The new mixin reduces the duplication between the list and list of paired collection creators.
I'd like to add functionality related to hiding the original datasets (especially useful for direct upload of collections but previously requested also) but I'd like to reduce the duplication related to doing that first. This is a start in that direction.
Commit: d9f21fd34c059d422e63d31e9fb94660e826c4ff
https://github.com/galaxyproject/galaxy/commit/d9f21fd34c059d422e63d31e9fb9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Only fail through to client mapping when it exists.
Commit: 3921aa573c0fa7b900316cdad4d06e23c02b19b2
https://github.com/galaxyproject/galaxy/commit/3921aa573c0fa7b900316cdad4d0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M scripts/api/README
Log Message:
-----------
Merge pull request #3777 from martenson/dedup-readme
deduplicate obsolete API readme
Commit: 5428d39adb6bf37c61b8c17efb1b3157e0b242d2
https://github.com/galaxyproject/galaxy/commit/5428d39adb6bf37c61b8c17efb1b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
Log Message:
-----------
Merge pull request #3753 from blankclemens/webhook_tool_list
Webhook plugin: tool_list
Commit: 61677d2026f155868ad57a1289609c1aad1044e6
https://github.com/galaxyproject/galaxy/commit/61677d2026f155868ad57a128960…
Author: nekrut <anton(a)nekrut.org>
Date: 2017-03-20 (Mon, 20 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
made collection ops help sections slightly more readable
Commit: 9ecb71ecf76df08fee7829e28db081ec2dc3fb0a
https://github.com/galaxyproject/galaxy/commit/9ecb71ecf76df08fee7829e28db0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/views.py
Log Message:
-----------
Build toolbox_requirements_status only once (thanks for the review @nsoranzo)
Commit: 69e2af50317abefa98748b8fc84db2870552b589
https://github.com/galaxyproject/galaxy/commit/69e2af50317abefa98748b8fc84d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Restore render_tool_centric_table function
Commit: a5b0e760503dc09ac99d47bbcde1524c7f3e37a4
https://github.com/galaxyproject/galaxy/commit/a5b0e760503dc09ac99d47bbcde1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Merge pull request #3781 from jmchilton/collection-builders
Abstraction for re-use between collection creators.
Commit: 7a6579878a09862e1cd5919ba7d94c527f3b0e56
https://github.com/galaxyproject/galaxy/commit/7a6579878a09862e1cd5919ba7d9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
fix markup and add a stylistic space
Commit: a8d0c46ee97b37df20ac2022af4309890ca0c6e0
https://github.com/galaxyproject/galaxy/commit/a8d0c46ee97b37df20ac2022af43…
Author: Anton Nekrutenko <anekrut(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/unzip_collection.xml
Log Message:
-----------
Update unzip_collection.xml
fixed typos identified by @mvdbeek
Commit: 234361253a168eaf4b4c86fe4a1963a511271c86
https://github.com/galaxyproject/galaxy/commit/234361253a168eaf4b4c86fe4a19…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M CONTRIBUTING.md
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
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M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/user/user-quotameter.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/maps/ui/autocom_tagging.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
M static/scripts/libs/jquery/jquery.autocomplete.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/autocom_tagging.js
M static/style/blue/base.css
M templates/admin/reload_tool.mako
M templates/grid_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/TESTING.md
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/mulled_example_multi_incomplete.xml
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/integration/test_resolvers.py
M test/qunit/tests/form_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_uploads.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_execution.py
M test/unit/workflows/test_modules.py
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into add_hdca_to_library
Commit: 3dcd174f2b2f0e78d58b3e9d7e19103bd299b128
https://github.com/galaxyproject/galaxy/commit/3dcd174f2b2f0e78d58b3e9d7e19…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
repack
Commit: eadbb16462f2bd6f6f8f8cf71d992f0c5389c80f
https://github.com/galaxyproject/galaxy/commit/eadbb16462f2bd6f6f8f8cf71d99…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
Log Message:
-----------
Merge pull request #3784 from nekrut/collection_ops_help_fixes
made collection ops help sections slightly more readable
Commit: 279548574136817c226fad61c52168cfab199fb8
https://github.com/galaxyproject/galaxy/commit/279548574136817c226fad61c521…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-foldertoolbar-view.js
M test/api/test_libraries.py
Log Message:
-----------
Merge pull request #3559 from mvdbeek/add_hdca_to_library
Add possibility to load collection into library
Commit: 7873aac2edb003fa073efc1249884d7b25c9028f
https://github.com/galaxyproject/galaxy/commit/7873aac2edb003fa073efc124988…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M .ci/py3_sources.txt
M README.rst
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
R doc/source/admin/webhooks.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
M doc/source/project/issues.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
R lib/galaxy/util/postfork.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run_tests.sh
M scripts/api/README
M scripts/secret_decoder_ring.py
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M test/api/test_libraries.py
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Merge branch 'dev' into remove_custom_builds_mako
Commit: 2872a31881f2f404b2962464ffb734065e96d1b3
https://github.com/galaxyproject/galaxy/commit/2872a31881f2f404b2962464ffb7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
M static/style/blue/base.css
Log Message:
-----------
Move styles out of code file
Commit: 79b26d2273d46250b55f04eb6c1e0a0c03bf65bf
https://github.com/galaxyproject/galaxy/commit/79b26d2273d46250b55f04eb6c1e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
M test/base/populators.py
Log Message:
-----------
Fix collection operations not having a history.
Fixes #3437.
Commit: 269aac614b5d19ffbfc3ec1ad7e4330ba9c0b847
https://github.com/galaxyproject/galaxy/commit/269aac614b5d19ffbfc3ec1ad7e4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Apply some suggested FR localization wording changes.
Commit: 3036df35f0f5089cfbfc69ecdc46dcf057a3d6bf
https://github.com/galaxyproject/galaxy/commit/3036df35f0f5089cfbfc69ecdc46…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Avoid potential inconsistencies between differently stored labels
Commit: 54af1979676c817b00044e645383e638b86fdcfa
https://github.com/galaxyproject/galaxy/commit/54af1979676c817b00044e645383…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Add more translation points for localization.
Commit: 8eb40ae7fb9d59586e40a7a85abdf5e222c903bd
https://github.com/galaxyproject/galaxy/commit/8eb40ae7fb9d59586e40a7a85abd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Correct 'Get Data' usage, since we won't be translating that in the first pass
Commit: 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9
https://github.com/galaxyproject/galaxy/commit/3ed60db5ce9bf2acb954c843c14f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
lib/galaxy/tools/deps/container_resolvers/__init__.py
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
Commit: 10ddd3d3bdb238f1ff0de26326fcaca07c81a316
https://github.com/galaxyproject/galaxy/commit/10ddd3d3bdb238f1ff0de26326fc…
Author: lecorguille <lecorguille(a)users.noreply.github.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
new points
Commit: 2eefe8571a00497c6faefff64cf86224bae05825
https://github.com/galaxyproject/galaxy/commit/2eefe8571a00497c6faefff64cf8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Fix usage of _.extend in joint collection builder templates.
Fixes bug introduced in #3781. #minor
Commit: 390adffb988ff4f1c6b723e4f5776ed5186c26bb
https://github.com/galaxyproject/galaxy/commit/390adffb988ff4f1c6b723e4f577…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #17 from lecorguille/i18n_history_options
new points history options
Commit: f8950feb30ca3caa94d48f487d9d7079839143a0
https://github.com/galaxyproject/galaxy/commit/f8950feb30ca3caa94d48f487d9d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
Log Message:
-----------
Merge pull request #3799 from jmchilton/fix_extend_usage
Fix usage of _.extend in joint collection builder templates.
Commit: c58fa9a349ce4432f1febd5f530fc4afdd4893bd
https://github.com/galaxyproject/galaxy/commit/c58fa9a349ce4432f1febd5f530f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M .ci/py3_sources.txt
M README.rst
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M config/datatypes_conf.xml.sample
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/zip_collection.xml
R lib/galaxy/util/postfork.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run_tests.sh
M scripts/api/README
M scripts/secret_decoder_ring.py
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/nls/fr/locale.js
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/api/test_libraries.py
M test/docker/base/run_test_wrapper.sh
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Rebuild client and merge from upstream.
Commit: 9d736dd42eba2e8bd116d575c7d1278e15183ba3
https://github.com/galaxyproject/galaxy/commit/9d736dd42eba2e8bd116d575c7d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
Log Message:
-----------
Fix container resolution.
Without these decorators swapped - resolving containers results in the following Exception:
```
TypeError: unbound method __str__() must be called with ContainerResolver instance as first argument (got nothing instead)
```
I think this recent merge commit 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 introduced this problem as it merged the two decorators together.
Commit: 2fc18675dbfd66a296006bb4ef90d57bdde4d5dc
https://github.com/galaxyproject/galaxy/commit/2fc18675dbfd66a296006bb4ef90…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Debug
Commit: 8a033b720b370a7e7e9049fa22a5c7a78f0d5a85
https://github.com/galaxyproject/galaxy/commit/8a033b720b370a7e7e9049fa22a5…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/__init__.py
Log Message:
-----------
Merge pull request #3805 from jmchilton/container_resolution_fix
Fix container resolution.
Commit: 71b09b49a7541789909b1617e661e0252573453a
https://github.com/galaxyproject/galaxy/commit/71b09b49a7541789909b1617e661…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Fix label, fix dataset id parsing
Commit: ef2353a1423586845da9d19c5780f298db742b1c
https://github.com/galaxyproject/galaxy/commit/ef2353a1423586845da9d19c5780…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Add len id for converted datasets to dbkey attributes
Commit: afbb3b5a1e26a0a3e9698cec71ed5d733189d451
https://github.com/galaxyproject/galaxy/commit/afbb3b5a1e26a0a3e9698cec71ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Add additional error message for fasta conversions
Commit: 368b276ded599e7f0c206b852cdd901199b16b7e
https://github.com/galaxyproject/galaxy/commit/368b276ded599e7f0c206b852cdd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Parse correct dataset id
Commit: 50283125ea37f313afdfd0d69b92a0380fc77e17
https://github.com/galaxyproject/galaxy/commit/50283125ea37f313afdfd0d69b92…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message:
-----------
Merge branch 'dev' into remove_custom_builds_mako
Commit: 76bd515879d4353bff066d0b2526d68d86cdff56
https://github.com/galaxyproject/galaxy/commit/76bd515879d4353bff066d0b2526…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix lint
Commit: b0325cef02f995a589dc14425d1ae73d7ef4cfee
https://github.com/galaxyproject/galaxy/commit/b0325cef02f995a589dc14425d1a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Post determine fasta results
Commit: 7457b7611513159551a604afe13927a1a50dc6da
https://github.com/galaxyproject/galaxy/commit/7457b7611513159551a604afe139…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Merge pull request #3807 from galaxyproject/release_17.01
Merge Release 17.01 in Dev
Commit: 9e807dab3f7b98e77ca2358e1204a6220879764c
https://github.com/galaxyproject/galaxy/commit/9e807dab3f7b98e77ca2358e1204…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M static/maps/layout/menu.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
Log Message:
-----------
Merge pull request #3762 from dannon/i18n
i18n improvements and French localization
Commit: 7fdb4064c6194534cb654f1afd5d9b5e9dd98ef3
https://github.com/galaxyproject/galaxy/commit/7fdb4064c6194534cb654f1afd5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Trim down one translation, thanks @mvdbeek
Commit: 3a52d07a900f4d4fa9933bbccce1efe76708988d
https://github.com/galaxyproject/galaxy/commit/3a52d07a900f4d4fa9933bbccce1…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #3809 from dannon/minor_wording_tweak
One minor translation followup tweak to French Localization
Commit: a3b16bf69a4d6f09b9693ffbc6a54ed0910918e9
https://github.com/galaxyproject/galaxy/commit/a3b16bf69a4d6f09b9693ffbc6a5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M run_tests.sh
M test/qunit/package.json
Log Message:
-----------
Small improvements to Qunit tests.
- Drop explicit requirement on phantomjs since we are moving away from explicit phantomjs testing (it is still pulled in by QUnit which is fine).
- If ``npm install .`` has previously been executed from the ``test/qunit``, don't require globally available grunt to run the tests via ``run_tests.sh -q``.
Commit: ca36c0dbfd438708e35e18d06c603f2cc2ce7047
https://github.com/galaxyproject/galaxy/commit/ca36c0dbfd438708e35e18d06c60…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Have tool-search listen to change as well as keyup
Commit: 0ced044897bc40f28b758e53b1019c422ea0410a
https://github.com/galaxyproject/galaxy/commit/0ced044897bc40f28b758e53b101…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Flush out upload tests for Selenium.
- Use newer abstraction in the simplest upload test - verify the default extension (auto -> sam) and dbkey (?) also.
- Add a test case that explicitly sets the extension of an upload and verifies.
- Add a test case that explicitly sets a genome and verifies.
- Add a test case that tests setting ext for all uploads and verifies.
- Add a test case that tests setting genome for all uploads and verifies.
Commit: 9e61aff69314606bff4ad16d502295cfdcb0ed07
https://github.com/galaxyproject/galaxy/commit/9e61aff69314606bff4ad16d5022…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M run_tests.sh
M test/qunit/package.json
Log Message:
-----------
Merge pull request #3810 from jmchilton/qunit_touchup
Small improvements for driving Qunit tests.
Commit: 3b7d44e6f7b773218fad0820464efa4610130938
https://github.com/galaxyproject/galaxy/commit/3b7d44e6f7b773218fad0820464e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix message margin in left column
Commit: 4a0f00fc1e3f383450968a9732edb479378f82ac
https://github.com/galaxyproject/galaxy/commit/4a0f00fc1e3f383450968a9732ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/users.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Trigger jobs when custom build has been added, check for linecount file on reload
Commit: 95be12787ace869bf01f6c30e4b62ba7a4739c96
https://github.com/galaxyproject/galaxy/commit/95be12787ace869bf01f6c30e4b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M lib/galaxy/jobs/runners/__init__.py
M run_tests.sh
M static/maps/layout/menu.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M test/qunit/package.json
Log Message:
-----------
Merge branch 'dev' into remove_custom_builds_mako
Commit: fbd8507e3a34e8f46545c1bf4869f179e03dde4e
https://github.com/galaxyproject/galaxy/commit/fbd8507e3a34e8f46545c1bf4869…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #3793 from guerler/store_label_in_step
Avoid potential inconsistencies between differently stored labels
Commit: b82d7311c1034afa32a5ce3caa8aaa44b63d4bb9
https://github.com/galaxyproject/galaxy/commit/b82d7311c1034afa32a5ce3caa8a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
M test/base/populators.py
Log Message:
-----------
Merge pull request #3786 from jmchilton/zip_edit
Fix collection operations not having a history.
Commit: 5e97c017b980cb7d478b5d17837f7438727e7551
https://github.com/galaxyproject/galaxy/commit/5e97c017b980cb7d478b5d17837f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Merge pull request #3811 from jmchilton/upload_tests
Implement more upload testing in Selenium.
Commit: 18a26c5f376b9c7be07f0998e817ef6262fc22c2
https://github.com/galaxyproject/galaxy/commit/18a26c5f376b9c7be07f0998e817…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
Log Message:
-----------
Merge pull request #3699 from shiltemann/ethercalc
Ethercalc Interactive Environment
Commit: d270a21908a8b1d203ac653d96177ae921cb5a5d
https://github.com/galaxyproject/galaxy/commit/d270a21908a8b1d203ac653d9617…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/history/history-view-edit.js
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
M test/selenium_tests/test_collection_builders.py
Log Message:
-----------
Allow non-ready jobs in collection builder.
This includes two parallel changes to the Selenium tests.
- It adds a decorator to allow retrying certain atomic actions that may occur during jQuery transitions automatically.
- It refactors things to allow waiting on HIDs to become visible instead of just green.
Commit: 3d13a2bb4f75f2224f24511aa96c9f97d8ff3e44
https://github.com/galaxyproject/galaxy/commit/3d13a2bb4f75f2224f24511aa96c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Fix transiently failing Selenium test of tool form re-running.
Reworks addition of staleness checkers introduced in #3780.
Commit: c9d06aeb41d9e15c07dddf4fff67630f2ee2237d
https://github.com/galaxyproject/galaxy/commit/c9d06aeb41d9e15c07dddf4fff67…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M test/api/test_history_contents.py
Log Message:
-----------
Allow collection creation API to hide original datasets during creation.
Commit: 5fa546749bcc7b5a8c2579c46a1360217d4883c8
https://github.com/galaxyproject/galaxy/commit/5fa546749bcc7b5a8c2579c46a13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/style/less/ui/paired-collection-creator.less
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-contents.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-contents.js
M static/style/blue/base.css
Log Message:
-----------
Allow collection builders to hide original datasets.
Commit: 82ca6931c02b1a4b13fe9dc4e86c7ace6029f5d5
https://github.com/galaxyproject/galaxy/commit/82ca6931c02b1a4b13fe9dc4e86c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
Log Message:
-----------
More test cases for collection builders.
- Add test case for building paired lists.
- Add tests for new hide original datasets functionality for lists and paired lists.
Commit: ad68b154d4cbecdbc2e96e58d9d3c4153e014eeb
https://github.com/galaxyproject/galaxy/commit/ad68b154d4cbecdbc2e96e58d9d3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Make ToolConfWatcher watch ToolCache
If any item in the tool cache has changed (local tool update, repository
update, tool deleted) the toolbox will be reloaded and any tool changes are
applied.
Should fix https://github.com/galaxyproject/galaxy/issues/3813.
Commit: c91c988c852e5a30e1c7c69168b5df770933dcd5
https://github.com/galaxyproject/galaxy/commit/c91c988c852e5a30e1c7c69168b5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M test/unit/tools/test_watcher.py
Log Message:
-----------
Fix ToolConfWatcher test: can only watch existing files
Commit: 5be7ebe780b487175563eb4661955a07df1d30cd
https://github.com/galaxyproject/galaxy/commit/5be7ebe780b487175563eb466195…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Only call tool_cache.cleanup if tool_cache exists
Commit: 4d9cf642a80025e28ea0276f8c41fcd9d9a53903
https://github.com/galaxyproject/galaxy/commit/4d9cf642a80025e28ea0276f8c41…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix toolshed startup by setting tool_cache to `None` (the toolshed loads an empty toolbox)
Commit: 0bf2493233fd0afbc07da6620740536938d8d059
https://github.com/galaxyproject/galaxy/commit/0bf2493233fd0afbc07da6620740…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Wrap tool_cache cleanup in try/except clause
Commit: 50417de1b4971db4fe42b1c797024081c66deef5
https://github.com/galaxyproject/galaxy/commit/50417de1b4971db4fe42b1c79702…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-24 (Fri, 24 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding A* search algorithm for finding shortest distance between root and destination
Commit: 197aa402d72895d370307ce9724c86b892cded96
https://github.com/galaxyproject/galaxy/commit/197aa402d72895d370307ce9724c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-25 (Sat, 25 Mar 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Improve ToolCache cleanup logic
Pull `removed_tool_ids` out of try/except, so that we can return
`removed_tool_ids` even if an exception occured. Fix a typo in the
`_should_cleanup` docstring. Many thanks for the suggestions @nsoranzo.
Commit: a47828bf892f8e1627bcb5f00ae63be56c9b6fcf
https://github.com/galaxyproject/galaxy/commit/a47828bf892f8e1627bcb5f00ae6…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-25 (Sat, 25 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
Log Message:
-----------
Merge pull request #3814 from mvdbeek/repository_updates
Awesome, thanks @mvdbeek !
Commit: 50a51575f1d4f0a7ccc8c476ab0ad7de2ffca3c8
https://github.com/galaxyproject/galaxy/commit/50a51575f1d4f0a7ccc8c476ab0a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-26 (Sun, 26 Mar 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/py3_sources.txt
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
A config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/swarm_manager_conf.yml.sample
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
M doc/source/admin/dependency_resolvers.rst
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
R doc/source/admin/webhooks.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
M doc/source/project/issues.rst
M doc/source/releases/17.01_announce.rst
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tools/zip_collection.xml
M lib/galaxy/util/json.py
R lib/galaxy/util/postfork.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run_tests.sh
M scripts/api/README
M scripts/bootstrap_history.py
M scripts/secret_decoder_ring.py
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/user/user-preferences.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/grid_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/tool_shed/repository/common.mako
M test/TESTING.md
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/integration/test_resolvers.py
M test/qunit/package.json
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/workflows/test_modules.py
M tools/data_source/upload.py
Log Message:
-----------
Merging with dev
Commit: 086dfd71ca4b82a7aeb2421cb2a08e76975639b3
https://github.com/galaxyproject/galaxy/commit/086dfd71ca4b82a7aeb2421cb2a0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-26 (Sun, 26 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Removing tabs and updating time out for path animation
Commit: 371d277c5514d0e7d033c8724f8d5cc58878f6bc
https://github.com/galaxyproject/galaxy/commit/371d277c5514d0e7d033c8724f8d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-26 (Sun, 26 Mar 2017)
Changed paths:
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Disable tool shed test function that fails frequently on Jenkins.
Commit: c8573888232f15ef3641bfeb2f0d92a7aa80387f
https://github.com/galaxyproject/galaxy/commit/c8573888232f15ef3641bfeb2f0d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge ToolConfWatchers and separate from Toolbox
This should avoid some complexities associated with managing threads.
I would also like to eliminate the separate reload_tool_data_tables
and reload_data_managers callbacks and do this when reloading the
toolbox, but every tool data table reload triggers twice the download of
http://igv.broadinstitute.org/genomes/genomes.txt, which each time takes
2 seconds.
Commit: 04941d0aea0be51fd169cb332070f6a420b71d0c
https://github.com/galaxyproject/galaxy/commit/04941d0aea0be51fd169cb332070…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Fixing review comments- removing sliders for colors and zoom and adding color pickers, updating values for min and max zoom and replacing logo of the plugin
Commit: f1206a8e352b9ef4288aa08bd18ac6b3387c790e
https://github.com/galaxyproject/galaxy/commit/f1206a8e352b9ef4288aa08bd18a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
Log Message:
-----------
Updating library files
Commit: 229c0a2339b38f6481a489e5a8454018458297d2
https://github.com/galaxyproject/galaxy/commit/229c0a2339b38f6481a489e5a845…
Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update __init__.py
using the lagacy python environemnt is also required for "CONVERTER_bed_to_fli_0" when displaying a bed file in trackster
Commit: 37fd039bd5bf0ca2beda8183e298cd1454b16544
https://github.com/galaxyproject/galaxy/commit/37fd039bd5bf0ca2beda8183e298…
Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update __init__.py
Commit: a6240c4b8c7477d2aca39ef97217139962fd5848
https://github.com/galaxyproject/galaxy/commit/a6240c4b8c7477d2aca39ef97217…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3822 from hrhotz/patch-1
fix bedfile display in trackster
Commit: 21e5731355ebcbba2bb4280844091576c7700abf
https://github.com/galaxyproject/galaxy/commit/21e5731355ebcbba2bb428084409…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
Log Message:
-----------
Fix for EtherCalc IE image specification.
Will allow EtherCalc to work in 17.05.
Commit: b4feb85f11280935b0ce13ea5d3693122f4319e8
https://github.com/galaxyproject/galaxy/commit/b4feb85f11280935b0ce13ea5d36…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/ts_api_doc.rst
Log Message:
-----------
improve accessibility of API docs
for both Galaxy and TS
Commit: bdcf4807ce5f2d3c1f12cd23120f4f5ec55f0067
https://github.com/galaxyproject/galaxy/commit/bdcf4807ce5f2d3c1f12cd23120f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
Log Message:
-----------
add basic Reports documentation
Commit: 1c716eb9da355864bd0116ce2579be3f03482e7c
https://github.com/galaxyproject/galaxy/commit/1c716eb9da355864bd0116ce2579…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Merge pull request #3808 from dannon/trigger-search-input
Have tool-search listen to change as well as keyup
Commit: 90c534570876c0f76a02458433960d9923a96ec3
https://github.com/galaxyproject/galaxy/commit/90c534570876c0f76a0245843396…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Fixing an issue with JSON data 'elements' attribute
Commit: 967d0b6c0aef6fe331c4e9c92bc1b902363e660a
https://github.com/galaxyproject/galaxy/commit/967d0b6c0aef6fe331c4e9c92bc1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/datasets.py
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3619 from jmchilton/purge_jobs_rework
Improve interaction between job state and purged datasets.
Commit: 810a96caef678462369604afd2a52b5c25c9268c
https://github.com/galaxyproject/galaxy/commit/810a96caef678462369604afd2a5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
Log Message:
-----------
Merge branch 'dev' into collection_builder_enhancements
Commit: db09acb0263751560714c74d9f7c9ea6fed649ae
https://github.com/galaxyproject/galaxy/commit/db09acb0263751560714c74d9f7c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-27 (Mon, 27 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/style/less/ui/paired-collection-creator.less
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/style/blue/base.css
M test/api/test_history_contents.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #3806 from jmchilton/collection_builder_enhancements
Small enhancements for collection builders
Commit: 7964c7d1d0564422131760d1c6a1b9334954ca48
https://github.com/galaxyproject/galaxy/commit/7964c7d1d0564422131760d1c6a1…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
Log Message:
-----------
Adding styles for selected nodes and updating default colors for nodes, edges and higlighted elements
Commit: 0809c19c36cf5f73f60928bd11c6a091c96e06b2
https://github.com/galaxyproject/galaxy/commit/0809c19c36cf5f73f60928bd11c6…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/ui/paired-collection-creator.less
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/tools/__init__.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merging with dev
Commit: cfd8ec776e692fe2706c1bd7cc40dcf1a8c56832
https://github.com/galaxyproject/galaxy/commit/cfd8ec776e692fe2706c1bd7cc40…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge pull request #3817 from bgruening/cytoscape
Cytoscape as the Galaxy charts plugin
Commit: c24ed4f8fa2f277757eccb8e5cdb7d324a3a3521
https://github.com/galaxyproject/galaxy/commit/c24ed4f8fa2f277757eccb8e5cdb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
M doc/source/admin/useful_scripts.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
Log Message:
-----------
Merge pull request #3812 from martenson/admin-docs-imp
api & reports documentation improvements
Commit: 2839153eb4b08f0b9a536059912d39fd3ee902a0
https://github.com/galaxyproject/galaxy/commit/2839153eb4b08f0b9a536059912d…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Adding Phylocanvas visualization for the Galaxy charts
Commit: 606c32998f94a5e94921315a1be66d570e68c63d
https://github.com/galaxyproject/galaxy/commit/606c32998f94a5e94921315a1be6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Allow upload to collections.
- New upload tab for "Collections".
- This has a new option to select "Collection Type" in footer.
- Collection upload geared toward homogeneous datasets - must specify genome and file format for all files.
- New button "Build" after all individual datasets have finished their upload to the server.
- Clicking "Build" launches the appropriate collection builder for selected collection type.
- By default, uploading a collection hides the original uploaded datasets (can be unchecked).
Implement tests for all uploaded collection types.
Commit: 07be669ed0d392fde70a79aa442bae028cfe3fcd
https://github.com/galaxyproject/galaxy/commit/07be669ed0d392fde70a79aa442b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
Log Message:
-----------
Merge pull request #3825 from blankenberg/ethercalc
Fix for EtherCalc IE image specification.
Commit: 66ca698f5aa4e897a792fe47f81526ed703bc154
https://github.com/galaxyproject/galaxy/commit/66ca698f5aa4e897a792fe47f815…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M display_applications/igv/bigwig.xml
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3829 from galaxyproject/release_17.01
Merge Release 17.01
Commit: 876c7a2d3df70b1c4edcf4fe738eb51c6e76bcfa
https://github.com/galaxyproject/galaxy/commit/876c7a2d3df70b1c4edcf4fe738e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
Log Message:
-----------
Adding more features like colors, collapse, prune and resize of the tree
Commit: 8e1d761beccfc301129070f2c5c0a79939d290a0
https://github.com/galaxyproject/galaxy/commit/8e1d761beccfc301129070f2c5c0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M display_applications/igv/bigwig.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
M doc/source/admin/useful_scripts.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merging with dev
Commit: f88d893562112223553ba069eff2a1f42fe7d69b
https://github.com/galaxyproject/galaxy/commit/f88d893562112223553ba069eff2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/tags.py
Log Message:
-----------
Add HistoryDatasetCollectionAssociation as a possible tagged item in the galaxy tag manager. Should refactor this down the road, feels weird to register everything here in the manager.
Commit: 73bfb57abf5ba728e4145731f91d0b222d74f5df
https://github.com/galaxyproject/galaxy/commit/73bfb57abf5ba728e4145731f91d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Use the correct tag manager instance from the Collections manager.
Commit: 64f8e1cf3c27d86f625736ecd0438df7d329ca2d
https://github.com/galaxyproject/galaxy/commit/64f8e1cf3c27d86f625736ecd043…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
Log Message:
-----------
Stricter checks for GFF/GFF3/GTF sniffing
Check frame column in Gff.sniff() and Gtf.sniff() .
Parse attributes column in Gff3.sniff() with a specific function to prevent
non-compliant GTF files being recognised as GFF3.
Commit: 32e8a2023deef55db60c61910321e366f40396d6
https://github.com/galaxyproject/galaxy/commit/32e8a2023deef55db60c61910321…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/util/gff_util.py
Log Message:
-----------
Fix import order for lib/galaxy/datatypes/util/gff_util.py
Commit: 5ceca34344b92d6bfa63ad1eb433a1cdea893f4f
https://github.com/galaxyproject/galaxy/commit/5ceca34344b92d6bfa63ad1eb433…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M lib/galaxy/managers/collections.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
Log Message:
-----------
Add basic tag rendering to expanded collection
Commit: 821ee5bbcbfdd9a79c52ac60a20a51e20898b573
https://github.com/galaxyproject/galaxy/commit/821ee5bbcbfdd9a79c52ac60a20a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/collection-view-edit.js
Log Message:
-----------
Simplify tags usage, since this editor's display is static.
Commit: 4a45c9097e5c7d19977196d3ade1cd949af5af03
https://github.com/galaxyproject/galaxy/commit/4a45c9097e5c7d19977196d3ade1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M client/package.json
M client/webpack.config.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Add babel loader.
Commit: 2a86f8e54c95da45b59fe166d515fc40b06f3c26
https://github.com/galaxyproject/galaxy/commit/2a86f8e54c95da45b59fe166d515…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdcas.py
Log Message:
-----------
Add tags to hdca serializer. TODO: Details only.
Commit: 225393a30006ca0313585de1a4bd93b3f0d88566
https://github.com/galaxyproject/galaxy/commit/225393a30006ca0313585de1a4bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M lib/galaxy/managers/hdcas.py
Log Message:
-----------
Add nametags to dataset collection serializer
Commit: 2f66d4563e02e8b585e5c1529b4e414117846858
https://github.com/galaxyproject/galaxy/commit/2f66d4563e02e8b585e5c1529b4e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-28 (Tue, 28 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
Log Message:
-----------
Adding shapes for leaves of phylogenetic tree
Commit: f369ab0668fcedf572346553d3e0b70564f81796
https://github.com/galaxyproject/galaxy/commit/f369ab0668fcedf572346553d3e0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add login redirect for backbone router
Commit: e431af074f4bb8a0d70f6a387af2654bfa21790b
https://github.com/galaxyproject/galaxy/commit/e431af074f4bb8a0d70f6a387af2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Redirect through push
Commit: 81824fa0446a6f4f5c372961528609d362e5fbfa
https://github.com/galaxyproject/galaxy/commit/81824fa0446a6f4f5c3729615286…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/ui/paired-collection-creator.less
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M display_applications/igv/bigwig.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
M doc/source/admin/useful_scripts.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_tools.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
Log Message:
-----------
Merge branch 'dev' into remove_custom_builds_mako
Commit: 11860d55fb7a51985d4027e35b6a6ead78748cfa
https://github.com/galaxyproject/galaxy/commit/11860d55fb7a51985d4027e35b6a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test.
- When registering, put a little pause in after clicking to ensure the browser has a chance to submit the request before continuing to check if indeed the user is logged in.
- If the user doesn't appear to be logged in, dump the contents of the user menu out so we can see if a different user is logged in or if there is no log in.
- Attempt to be more robust about conditions being waited on when clicking history option menu - in case clicks were being fired during jQuery transitions or something.
xref #3838
Commit: ab11adfa501ababc2d1f20e731727b8df787b803
https://github.com/galaxyproject/galaxy/commit/ab11adfa501ababc2d1f20e73172…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Merge pull request #3819 from jmchilton/disable_pesky_ts_test
Disable tool shed test function that fails frequently on Jenkins.
Commit: 790a35ea2e605c3b15e3e59df07f3febc9688f8d
https://github.com/galaxyproject/galaxy/commit/790a35ea2e605c3b15e3e59df07f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Properly handle multiple hidden datasets when populating data select options
Commit: a0b4ab63d288d04ddd7b4372090c1e956653f4e6
https://github.com/galaxyproject/galaxy/commit/a0b4ab63d288d04ddd7b4372090c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #3842 from guerler/fix_hidden_datasets
Properly handle multiple hidden datasets when populating data select options
Commit: 777db9829b41a0ffde892ac9fe11846f5af93b91
https://github.com/galaxyproject/galaxy/commit/777db9829b41a0ffde892ac9fe11…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Merge pull request #3696 from jmchilton/upload_collection
Allow uploading to collections.
Commit: 10e89cfc851526973b8234257ba9039b5961160f
https://github.com/galaxyproject/galaxy/commit/10e89cfc851526973b8234257ba9…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge pull request #3841 from jmchilton/selenium_fixes_7
Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test.
Commit: 9aa02339e730988cc1174103e3091690f3c8a42d
https://github.com/galaxyproject/galaxy/commit/9aa02339e730988cc1174103e309…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
Log Message:
-----------
Fix for direct message routing using a 'real' exchange like rabbitmq -- this worked with local/database connections already, if accidentally. I want to do more refactoring of how these are configured, but am deferring that for now as it's not a priority.
Commit: 452683998293d525e4c999d6ebf6f5eb85adca2e
https://github.com/galaxyproject/galaxy/commit/452683998293d525e4c999d6ebf6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Annotate new api endpoints
Commit: 31a8ebe9d5e6595ea0299546b59c07ce32931ac0
https://github.com/galaxyproject/galaxy/commit/31a8ebe9d5e6595ea0299546b59c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Merge branch 'dev' into remove_custom_builds_mako
Commit: 185aa3968bd38cfe021f7bcec9bae02c12ae4c0b
https://github.com/galaxyproject/galaxy/commit/185aa3968bd38cfe021f7bcec9ba…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Log when workflow scheduling is delayed about why.
Currently the logs contain fairly uninformative step delayed messages that don't allow admins to understand why parts of the workflow are being delayed during scheduling.
Here are some examples of before and after.
When running the test:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_pause
```
Before these lines would show up:
```
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,327 Workflow step 2 of invocation 1 invoked (174.149 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,347 Workflow step 3 of invocation 1 invoked (19.355 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:23:47,364 Workflow step 4 of invocation 1 delayed (16.262 ms)
```
Now these same lines are as follows:
```
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,601 Workflow step 2 of invocation 1 invoked (172.849 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,619 Marking step 3 outputs delayed (executing pause step)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,620 Workflow step 3 of invocation 1 invoked (17.999 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:19:28,633 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (13.398 ms)
```
Also, when running the test:
```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections_3
```
Before these lines would be printed:
```
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,910 Workflow step 4 of invocation 1 invoked (281.479 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,937 Workflow step 5 of invocation 1 delayed (25.904 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:25:35,970 Workflow step 6 of invocation 1 delayed (32.597 ms)
```
Now these same lines are as follows:
```
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,270 Workflow step 4 of invocation 1 invoked (295.826 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,315 Workflow step 5 of invocation 1 delayed (dependent collection [1] not yet populated with datasets) (44.581 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:27:54,326 Workflow step 6 of invocation 1 delayed (dependent step [5] delayed, so this step must be delayed) (10.804 ms)
```
When running workflows with steps that depend explicitly on other steps (instead of implicitly between dataset connections), lines such as:
```
galaxy.workflow.run DEBUG 2017-03-30 09:33:52,966 Marking step 3 outputs delayed (workflow paused at this step waiting for review)
galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (0.157 ms)
galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 5 of invocation 1 delayed (depends on step [4] but that step has not been invoked yet) (0.084 ms)
```
and
```
galaxy.workflow.run DEBUG 2017-03-30 09:33:57,090 Workflow step 5 of invocation 1 delayed (depends on step [4] but one or more jobs created from that step have not finished yet) (0.144 ms)
```
now may appear.
Commit: c4fd96092bcabd869f8c4a4427489d0b2c6209a3
https://github.com/galaxyproject/galaxy/commit/c4fd96092bcabd869f8c4a442748…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Make TagEditor label optional.
Commit: e67dc45c26e77d3f2b85ac7e2ab80ac5fdab0cf9
https://github.com/galaxyproject/galaxy/commit/e67dc45c26e77d3f2b85ac7e2ab8…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/upload.less
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/bgruening/galaxy into phylocanvas
Commit: b8692309484c3a671145684277201ed7aaf444dd
https://github.com/galaxyproject/galaxy/commit/b8692309484c3a67114568427720…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M lib/galaxy/workflow/run.py
Log Message:
-----------
Re-arrange workflow scheduling logic according to @nsoranzo's suggestions.
Commit: 94c357f608f93ccf9c0494e07599cae85c15782d
https://github.com/galaxyproject/galaxy/commit/94c357f608f93ccf9c0494e07599…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/__init__.py
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/data/test_workflow_pause.ga
M test/base/populators.py
A test/integration/test_maximum_worklfow_invocation_duration.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 3d2833fdb72b9d967d4ec05581c7e0c1aa3a81a1
https://github.com/galaxyproject/galaxy/commit/3d2833fdb72b9d967d4ec05581c7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
Log Message:
-----------
Merge pull request #3750 from mvdbeek/remove_unused_envs
Add the possibility to uninstall conda environments that are not in u…
Commit: 90ac2f43566220cd82a771afd2040a1410addb4a
https://github.com/galaxyproject/galaxy/commit/90ac2f43566220cd82a771afd204…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
Log Message:
-----------
Merge pull request #3832 from nsoranzo/gff_sniff_fix
Stricter checks for GFF/GFF3/GTF sniffing
Commit: 200e475bc7cd340401f46028fc234a1e7c2ad87c
https://github.com/galaxyproject/galaxy/commit/200e475bc7cd340401f46028fc23…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3849 from jmchilton/improved_scheduling_delay_logging
Log reason when workflow scheduling of a step is delayed.
Commit: c51adf781a1a711c4e54d89fbdca7ea9d3331f08
https://github.com/galaxyproject/galaxy/commit/c51adf781a1a711c4e54d89fbdca…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-options.js
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-options.js
Log Message:
-----------
Insert update caller/helper for options
Commit: fa086edf22c725b8a98cff92ac6ca6a4ab210237
https://github.com/galaxyproject/galaxy/commit/fa086edf22c725b8a98cff92ac6c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
Log Message:
-----------
Adding support for .nhx files (Newick) and removing txt files support
Commit: c9f602d434104423078d2f0661e6acd8aa5c359b
https://github.com/galaxyproject/galaxy/commit/c9f602d434104423078d2f0661e6…
Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Update datatypes_conf.xml.sample
Oups, I did it again :)
Just add the sniffer for the mzData datatype
Commit: dfbb80dd8b21f87af217fce49d14df396517c6d9
https://github.com/galaxyproject/galaxy/commit/dfbb80dd8b21f87af217fce49d14…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #3852 from lecorguille/patch-1
Update datatypes_conf.xml.sample
Commit: 190d1901a43a284c478876d2ec3567a1cc1af5a5
https://github.com/galaxyproject/galaxy/commit/190d1901a43a284c478876d2ec35…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into dev
Commit: ad2e6473bc07a5b229d50f85c28cad0363a40f11
https://github.com/galaxyproject/galaxy/commit/ad2e6473bc07a5b229d50f85c28c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M test/api/test_workflows.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into dev
Commit: c8eb2c186def4b505143a5a6b0d971549b15d19a
https://github.com/galaxyproject/galaxy/commit/c8eb2c186def4b505143a5a6b0d9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-options.js
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-options.js
Log Message:
-----------
Merge pull request #3851 from guerler/add_lost_update_caller
[17.01] Fix update caller/helper for options
Commit: c452af01bd16cf85e7459f767ee77c381e527a9a
https://github.com/galaxyproject/galaxy/commit/c452af01bd16cf85e7459f767ee7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li.js
M static/maps/mvc/history/hdca-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hdca-li.js
Log Message:
-----------
Render 'nametags' for hdcas
Commit: 2f4aa1a763146e980f9c1c929f07ffd4b7bf7ff3
https://github.com/galaxyproject/galaxy/commit/2f4aa1a763146e980f9c1c929f07…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/collection-view-edit.js
Log Message:
-----------
Toggle tags prompt on collection view
Commit: 01655895174eb14530d27452789682335b2f7197
https://github.com/galaxyproject/galaxy/commit/01655895174eb14530d274527896…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view.js
M static/maps/mvc/collection/collection-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/collection-view.js
Log Message:
-----------
Tags editor location/styling fix for collection view.
Commit: 5dcc0ed04376d08deb960f309e21fc14a6d29ce8
https://github.com/galaxyproject/galaxy/commit/5dcc0ed04376d08deb960f309e21…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M test/api/test_users.py
Log Message:
-----------
Clean up old TODO into history tests.
We upgraded the module a long time ago now that was referenced in the Trello card.
Commit: 99c8f2c9fc6f335863f134a5b8b4055d5079cfe1
https://github.com/galaxyproject/galaxy/commit/99c8f2c9fc6f335863f134a5b8b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Fix setting UUID on steps when copying steps from another workflow.
It seems like the client is correctly setting the UUID to None, but the backend is treating the None as a UUID because it was (incorrectly IMO) making a distinction between ``uuid`` being absent and being set to ``None``.
Fixes #3845.
Commit: 6af5334f125461fba1ea1735bf06eed516bd6754
https://github.com/galaxyproject/galaxy/commit/6af5334f125461fba1ea1735bf06…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M test/api/test_users.py
Log Message:
-----------
Merge pull request #3855 from jmchilton/user_api_tests
Clean up old TODO into history tests.
Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e
https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-01 (Sat, 01 Apr 2017)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Small changes to links and add gitter
Commit: ffce14e65d70441827086c1eccdae46a28819df3
https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccda…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
change devteam to iuc
Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40
https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
fix contribute pdf link
Commit: 5169fbe917c90ee6b13a345e869bf88bf51f6512
https://github.com/galaxyproject/galaxy/commit/5169fbe917c90ee6b13a345e869b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-31 (Fri, 31 Mar 2017)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Merge pull request #3861 from galaxyproject/contrib_changes
Small changes to links and add gitter
Commit: 1a5e337420e4832593b6e30089c0022291fd6078
https://github.com/galaxyproject/galaxy/commit/1a5e337420e4832593b6e30089c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Move ConfigWatchers into galaxy.webapps.galaxy.config_watchers
Commit: 268aac29526b3526a42457576e8de7867c2bfe1f
https://github.com/galaxyproject/galaxy/commit/268aac29526b3526a42457576e8d…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #3856 from jmchilton/1701_uuid_on_copy_fix
[17.01] Fix setting UUID on steps when copying steps from another workflow.
Commit: f79fb9075a4f724d5bad95163a6450c9ffb89b84
https://github.com/galaxyproject/galaxy/commit/f79fb9075a4f724d5bad95163a64…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Move ToolWatcher from Toolbox to ConfigWatchers class
Commit: 63f1efd15a6903526406ff8d643fb3d6f4a5e678
https://github.com/galaxyproject/galaxy/commit/63f1efd15a6903526406ff8d643f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix toolshed startup
Commit: c4e6671ce50a64ba561a3ef815816426183adf4d
https://github.com/galaxyproject/galaxy/commit/c4e6671ce50a64ba561a3ef81581…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Fix import order in config_watchers.py
Commit: 0c3f7989bb913842e28a8fbb267d1280420caa92
https://github.com/galaxyproject/galaxy/commit/0c3f7989bb913842e28a8fbb267d…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/data/test_workflow_pause.ga
M test/base/populators.py
A test/integration/test_maximum_worklfow_invocation_duration.py
Log Message:
-----------
Merging wtih dev
Commit: b037332e943edbf9cf65f4799a1226bf53e8476a
https://github.com/galaxyproject/galaxy/commit/b037332e943edbf9cf65f4799a12…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/config_watchers.py
Log Message:
-----------
Avoid race-condition between multiple instances of ToolConfWatchers
Commit: 2c7089df46fa0a5178a1e0f72cc87514e8a97142
https://github.com/galaxyproject/galaxy/commit/2c7089df46fa0a5178a1e0f72cc8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix TS tests
Commit: 5b46c431b416e619a7ac5467527ab30743eabd33
https://github.com/galaxyproject/galaxy/commit/5b46c431b416e619a7ac5467527a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Fix certain aspects of dataset reductions in conditionals/repeats.
For instance, fixes #3859 restoring the correct ``element_identifier`` for reduces collections in conditionals. Add tests for combinations of repeats and conditionals.
Commit: 1e70211fa4827badf4bd3fe1f1703004d369afec
https://github.com/galaxyproject/galaxy/commit/1e70211fa4827badf4bd3fe1f170…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M test/api/test_libraries.py
Log Message:
-----------
Touch up #3559 based on post-merge discussions.
Commit: 3c080cae96aadccd824aa7cf6fda9c4b5bf7471a
https://github.com/galaxyproject/galaxy/commit/3c080cae96aadccd824aa7cf6fda…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M test/api/test_tools.py
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3864 from jmchilton/fix_identifiers_in_conditionals
[17.01] Fix certain aspects of collection reductions in conditionals/repeats.
Commit: 8e0be5089c63d94b841babfffcd70f2d8ab9b27c
https://github.com/galaxyproject/galaxy/commit/8e0be5089c63d94b841babfffcd7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-03 (Mon, 03 Apr 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M test/api/test_workflows.py
Log Message:
-----------
[17.01] Fix collection operations in workflows.
Due to a couple bugs things weren't being delayed correctly for some of these tools in some workflows.
Commit: 339566bc03f1a51c7a4c60c2d6a100f43e1d3c15
https://github.com/galaxyproject/galaxy/commit/339566bc03f1a51c7a4c60c2d6a1…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M CONTRIBUTING.md
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
M test/api/test_users.py
M test/api/test_workflows.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
Log Message:
-----------
Merging with dev
Commit: 6f4e242b16487b6032347dad3f60fef00f60464f
https://github.com/galaxyproject/galaxy/commit/6f4e242b16487b6032347dad3f60…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
Log Message:
-----------
Merge pull request #3850 from bgruening/phylocanvas
Phylocanvas as a BioJS component for the Galaxy charts
Commit: 5d810d5908ac851e398ebc7fcd7d54c5a892fd04
https://github.com/galaxyproject/galaxy/commit/5d810d5908ac851e398ebc7fcd7d…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M test/api/test_libraries.py
Log Message:
-----------
Merge pull request #3857 from jmchilton/3559_touchups
Touch up #3559 based on post-merge discussions.
Commit: 29331b36cf4ad350d4919679deeca6f342b1e182
https://github.com/galaxyproject/galaxy/commit/29331b36cf4ad350d4919679deec…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
A config/containers_conf.yml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
R lib/galaxy/container/__init__.py
R lib/galaxy/container/docker_swarm.py
A lib/galaxy/containers/__init__.py
A lib/galaxy/containers/docker.py
A lib/galaxy/containers/docker_decorators.py
A lib/galaxy/containers/docker_model.py
A lib/galaxy/containers/docker_swarm.py
A lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/util/submodules.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
Log Message:
-----------
Container interface abstraction. Support Docker and Docker Swarm mode
(>1.12 SwarmKit). Container interface configuration is performed via the
containers_conf.yml config file, for which a documented sample is
provided.
The GIE launcher has been modified to use the container interface if the
`enable_beta_containers_interface` option is set in galaxy.ini. This
removes some of the previous GIE-specific swarm mode work that was done.
The Galaxy docker swarm manager also uses the container interface now.
TODO: The API docker interfaces should be done fairly soon before we
have many consumers of the docker model objects, because they'll
probably be changed to more closely reflect their API representations.
Commit: 41a88de7527c4e5f38070fe31e0dfe78ad817603
https://github.com/galaxyproject/galaxy/commit/41a88de7527c4e5f38070fe31e0d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-options.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-options.js
M test/api/test_tools.py
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
Commit: c9bbaa30f7400f547e8549ae8d0d3bed5ccbf0c5
https://github.com/galaxyproject/galaxy/commit/c9bbaa30f7400f547e8549ae8d0d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M CONTRIBUTING.md
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-options.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M display_applications/igv/bigwig.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
M doc/source/admin/useful_scripts.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-options.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-options.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api_asserts.py
M test/base/data/test_workflow_pause.ga
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into tags_improvements
Commit: d1974a42e5787ef06d4c4d25dbe7178eb26284d5
https://github.com/galaxyproject/galaxy/commit/d1974a42e5787ef06d4c4d25dbe7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
Log Message:
-----------
Use detect_errors="exit_code" in Trim tool
Prevent job failures due to spurious messages on stderr from the cluster
scheduler.
Commit: 405dbd3b7f3022332fb6c660f88e67361fbb5429
https://github.com/galaxyproject/galaxy/commit/405dbd3b7f3022332fb6c660f88e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/user/user-custom-builds.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-custom-builds.js
Log Message:
-----------
Move custom build metadata endpoint to histories
Commit: a16c5320fd647b45dbad197714fc52d2a5254548
https://github.com/galaxyproject/galaxy/commit/a16c5320fd647b45dbad197714fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/api/histories.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Wait for history panel, workaround until overall ui has been visited
Commit: 439444e65ad9c79a0a2553a5eb916405b1910e93
https://github.com/galaxyproject/galaxy/commit/439444e65ad9c79a0a2553a5eb91…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Preserve tags for collection outputs. This is one step forward, also need to address non-output handled collectinos, like those automatically created in workflow execution with collection inputs.
Commit: bfbca68b4e70cc380398e364dd8abdd5ac1a360e
https://github.com/galaxyproject/galaxy/commit/bfbca68b4e70cc380398e364dd8a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Don't wrap tags up in element_kwds -- this prevents them being sent to non-hda collections.
Commit: 6ce47ddbf4ed0046f52cd6c7d4f140c893d9b1e3
https://github.com/galaxyproject/galaxy/commit/6ce47ddbf4ed0046f52cd6c7d4f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Also include implicit_collection_info in collection tag creation logic.
Commit: 5937a677d57e6180aaeabcd737e70aac0809fbd5
https://github.com/galaxyproject/galaxy/commit/5937a677d57e6180aaeabcd737e7…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
Log Message:
-----------
Merge pull request #3869 from nsoranzo/trimmer
Use detect_errors="exit_code" in Trim tool
Commit: 2b0ac9a098b7ca2c207c3d00be698a993e4130ff
https://github.com/galaxyproject/galaxy/commit/2b0ac9a098b7ca2c207c3d00be69…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M static/maps/mvc/history/history-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
Log Message:
-----------
Enable drag drop for history items
Commit: 97d5a86a585b2c9ac159c9db255dd0389f83ab3b
https://github.com/galaxyproject/galaxy/commit/97d5a86a585b2c9ac159c9db255d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Catch drag and drop basic event handlers for content selector
Commit: aa7bed3b7270db18505e1dc7a8f84600482114cb
https://github.com/galaxyproject/galaxy/commit/aa7bed3b7270db18505e1dc7a8f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Add basic styles to highlight drop area on drag over
Commit: f56651b9ea8b20e34d1cb0604888d3de2e49e2c4
https://github.com/galaxyproject/galaxy/commit/f56651b9ea8b20e34d1cb0604888…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Access drop data
Commit: 642002854c2abd312e917632191c7db638234ad7
https://github.com/galaxyproject/galaxy/commit/642002854c2abd312e917632191c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Move drop handler, support datasets and collections
Commit: 5bbc91289b0d5cd69a00a487751f4782f298932a
https://github.com/galaxyproject/galaxy/commit/5bbc91289b0d5cd69a00a487751f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Display success and error colors
Commit: 039f706bd7395f8b0350453936f2e82f98fa4e93
https://github.com/galaxyproject/galaxy/commit/039f706bd7395f8b0350453936f2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix style color on inital dragover
Commit: af066197b9b9a4ff6f804fe4cc588611eab0ddd9
https://github.com/galaxyproject/galaxy/commit/af066197b9b9a4ff6f804fe4cc58…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Improve validation
Commit: da0d53728be70d26123a748546a8c0d6cb8d67c3
https://github.com/galaxyproject/galaxy/commit/da0d53728be70d26123a748546a8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Move delay timer value to attributes, rename status handler
Commit: e05036a6a02c396c207c9ea80dc056a58c9f7f08
https://github.com/galaxyproject/galaxy/commit/e05036a6a02c396c207c9ea80dc0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Avoid flickering due to bubbling events from children without masking div
Commit: 5c85fe1c9821a12caaef30df37eeac3c1fcb2a66
https://github.com/galaxyproject/galaxy/commit/5c85fe1c9821a12caaef30df37ee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Remove unused default behavior blockers
Commit: 2c3cdfb6d0355667909a40a79c8e02a76b6dca97
https://github.com/galaxyproject/galaxy/commit/2c3cdfb6d0355667909a40a79c8e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Fix code style, improve readability
Commit: 071186d520fdd0069b182dd77aeaad4bddd1e323
https://github.com/galaxyproject/galaxy/commit/071186d520fdd0069b182dd77aea…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Improve support for multiple dataset selector
Commit: 383db9bb3bedef57f490dff4feb1bd74188c798b
https://github.com/galaxyproject/galaxy/commit/383db9bb3bedef57f490dff4feb1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Trigger change to update current selection if value has not actually changed
Commit: ab1f7eae4d0f1836dad4e52a75dbc18f9bd20336
https://github.com/galaxyproject/galaxy/commit/ab1f7eae4d0f1836dad4e52a75db…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
Log Message:
-----------
synchronise against latest UCSC versions
Commit: 9234420cd770661b58ee91051015e9580505ca47
https://github.com/galaxyproject/galaxy/commit/9234420cd770661b58ee91051015…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Fix multiple collection reductions on multiple data parameters.
Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended.
This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225.
Commit: 6251b51aebc8719b64122e1311175e683e55bbb3
https://github.com/galaxyproject/galaxy/commit/6251b51aebc8719b64122e131117…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3871 from guerler/history_drag_drop
Allows to drag-and-drop history items into the content selector
Commit: 200994536e6110fffb586a968edf7edd3c04e4f2
https://github.com/galaxyproject/galaxy/commit/200994536e6110fffb586a968edf…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Revert "Allows to drag-and-drop history items into the content selector"
Commit: c27dac65c882906aa87c364961ac7783f1babd17
https://github.com/galaxyproject/galaxy/commit/c27dac65c882906aa87c364961ac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Merge pull request #3783 from dannon/routing_bug_exception_propagation
Layered routing fix for when controller route fails and client route does not exist.
Commit: 8bbd423909d7ed524b2f73cdc7f7bf42b49c43f2
https://github.com/galaxyproject/galaxy/commit/8bbd423909d7ed524b2f73cdc7f7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3877 from galaxyproject/revert-3871-history_drag_drop
Revert "Allows to drag-and-drop history items into the content selector"
Commit: d607c7e0b134ac81faf0648af6e8a48d8941c938
https://github.com/galaxyproject/galaxy/commit/d607c7e0b134ac81faf0648af6e8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
R templates/user/dbkeys.mako
Log Message:
-----------
Merge remote-tracking branch 'guerler/remove_custom_builds_mako' into dev
Commit: 676b5cb2779eda3f87d62d2ee5dd74244aaa8071
https://github.com/galaxyproject/galaxy/commit/676b5cb2779eda3f87d62d2ee5dd…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Fix inability to raise errors if OS in non en_US
Commit: bdcc474d3666fd08f0032629e1882a4441b35244
https://github.com/galaxyproject/galaxy/commit/bdcc474d3666fd08f0032629e188…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
R templates/user/dbkeys.mako
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into tags_improvements
Commit: 82fe4262148ae462eb4fe5012e4c7c03ec9be7b8
https://github.com/galaxyproject/galaxy/commit/82fe4262148ae462eb4fe5012e4c…
Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Hardklor and kronik datatypes for proteomics
Commit: c10a23b924983f11565c6a8976b80f6c65b97955
https://github.com/galaxyproject/galaxy/commit/c10a23b924983f11565c6a8976b8…
Author: Jorrit Boekel <jorrit.boekel(a)scilifelab.se>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
More recognizable naming for datatype extensions
Commit: 54b7c32bd2913c236c4eacfaf45bdef3ba4c2e7d
https://github.com/galaxyproject/galaxy/commit/54b7c32bd2913c236c4eacfaf45b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
Log Message:
-----------
Render nametags from core tag data instead of a different field. This actually should be somewhat faster, along with being easier to track/update.
Commit: 74f97a8942cd13572293ff79aec600fcdab4ed88
https://github.com/galaxyproject/galaxy/commit/74f97a8942cd13572293ff79aec6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Fix for dropping into run workflow iframe
Commit: 7304d5bdc4997da727747f86cf7049bb2452050a
https://github.com/galaxyproject/galaxy/commit/7304d5bdc4997da727747f86cf70…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/ui.less
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
R templates/user/dbkeys.mako
Log Message:
-----------
Merge branch 'dev' into history_drag_drop_000
Commit: ba91462362c59a1a0dbbfdc80920642de10dbd20
https://github.com/galaxyproject/galaxy/commit/ba91462362c59a1a0dbbfdc80920…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Add delay attribute to time success/error highlighting
Commit: 37b6d907cbc338793f950d33904421faf376f2c3
https://github.com/galaxyproject/galaxy/commit/37b6d907cbc338793f950d339044…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Remove unused cursor style
Commit: d9d4ce0ad349d506eb8e902f079453dd4cf9ba16
https://github.com/galaxyproject/galaxy/commit/d9d4ce0ad349d506eb8e902f0794…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/histories.py
Log Message:
-----------
Looks like this was always using trans.hsitory instead of the id that was passed to the endpoint.
Commit: c9863b251ee831f0a7f97935f86e3d46f692ae9f
https://github.com/galaxyproject/galaxy/commit/c9863b251ee831f0a7f97935f86e…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/histories.py
Log Message:
-----------
Merge pull request #3887 from dannon/fix_broken_jenkins
Fix new history endpoint providing custom builds metadata
Commit: 6f95ba9c2c7637fef29d639b19cde81cc3f0ec74
https://github.com/galaxyproject/galaxy/commit/6f95ba9c2c7637fef29d639b19cd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/histories.py
Log Message:
-----------
Merge branch 'dev' into history_drag_drop_000
Commit: 2215869f2d68c1839091dc23cf303bf43fa29078
https://github.com/galaxyproject/galaxy/commit/2215869f2d68c1839091dc23cf30…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Listen to tag change events, rerender list item for nametags.
Commit: d9bb8a7d300c723a172ecc288e332c2a2763f872
https://github.com/galaxyproject/galaxy/commit/d9bb8a7d300c723a172ecc288e33…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Remove unused model import from users api
Commit: c6ce56dd0a2ddb7b5e4760b3bab7be80ef367ba3
https://github.com/galaxyproject/galaxy/commit/c6ce56dd0a2ddb7b5e4760b3bab7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Merge pull request #3888 from guerler/remove_unused_model
Remove unused model import from users api
Commit: 5a513b20bbc371cf9a51483b1cf468d9126a45fe
https://github.com/galaxyproject/galaxy/commit/5a513b20bbc371cf9a51483b1cf4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Remove (previously) never-invoked change code which now double-invokes. Parents will handle this.
Commit: d2205c4167aa543be633721b6650098bca6835b4
https://github.com/galaxyproject/galaxy/commit/d2205c4167aa543be633721b6650…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/users.py
Log Message:
-----------
Merge branch 'dev' into history_drag_drop_000
Commit: 72a3fea37f3cb622f0b509a72921ad11ecabf99f
https://github.com/galaxyproject/galaxy/commit/72a3fea37f3cb622f0b509a72921…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Unused glob in buildapp
Commit: 5055172e64bb48ec0eb6d3e4b4ec6461cbc19162
https://github.com/galaxyproject/galaxy/commit/5055172e64bb48ec0eb6d3e4b4ec…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #3889 from dannon/unused_glob
Unused glob in buildapp
Commit: 6a625b2c6116992bd475cffe4f11a8ced41110fe
https://github.com/galaxyproject/galaxy/commit/6a625b2c6116992bd475cffe4f11…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge branch 'dev' into history_drag_drop_000
Commit: d41a4efd8822c46aa9f236937d4fc74678ba0dfd
https://github.com/galaxyproject/galaxy/commit/d41a4efd8822c46aa9f236937d4f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
For datasets, only rerender title bar if tags have changed (for nametags)
Commit: 2ab68fea8b20c256c30afd7e18bcf2647c978396
https://github.com/galaxyproject/galaxy/commit/2ab68fea8b20c256c30afd7e18bc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-li.js
M static/maps/mvc/history/hda-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/hda-li.js
Log Message:
-----------
Remove redundant listener, handled in parent.
Commit: 9e9a2d8312990c11ff7d9df6e71927bdc3210514
https://github.com/galaxyproject/galaxy/commit/9e9a2d8312990c11ff7d9df6e719…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Rerender specifically subtitle iff it's the only changed attribute.
Commit: bcd24e845477d72761072baf014119b3dda2372d
https://github.com/galaxyproject/galaxy/commit/bcd24e845477d72761072baf0141…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3886 from guerler/history_drag_drop_000
History drag-and-drop feature with iframe support for run workflow form
Commit: af37dd55de283602338f07452c92224eb0490fa6
https://github.com/galaxyproject/galaxy/commit/af37dd55de283602338f07452c92…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M config/tool_destinations.yml.sample
M lib/galaxy/jobs/dynamic_tool_destination.py
Log Message:
-----------
Merge pull request #3657 from lecorguille/dynamic_tool_nest_param
Allow nest param in the dynamic_tool rule -> argument
Commit: eb0ff254a59196499e7c714b4fc8d744ef463df9
https://github.com/galaxyproject/galaxy/commit/eb0ff254a59196499e7c714b4fc8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M run_tests.sh
Log Message:
-----------
Update to a new Docker test image to fix dependency bugs.
Hopefully this will fix tests for #3179.
Commit: 232e8096925dd7739b98120c172b5cb092192f3e
https://github.com/galaxyproject/galaxy/commit/232e8096925dd7739b98120c172b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Python3: Use shlex_quote() from six.moves instead of pipes.quote()
Commit: 334f4d7a19882ad97aec75f50b61fda5eb807974
https://github.com/galaxyproject/galaxy/commit/334f4d7a19882ad97aec75f50b61…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/search.py
Log Message:
-----------
Remove old, unused search controller. This would be implemented as a clientside route if we ever pursued development.
Commit: e085f8cb41a00668efa6108b3caf9e7dbbc712f2
https://github.com/galaxyproject/galaxy/commit/e085f8cb41a00668efa6108b3caf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Routes cleanup -- this adjust_hidden route is unnecessary and is handled by the normal controller logic.
Commit: a2a64821b4511db810865e75e991e19fc365f6f9
https://github.com/galaxyproject/galaxy/commit/a2a64821b4511db810865e75e991…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
This login route is also unnecessary
Commit: d19be8bf46c41d12e0a4d6c34454cc150cc06378
https://github.com/galaxyproject/galaxy/commit/d19be8bf46c41d12e0a4d6c34454…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Merge pull request #3891 from nsoranzo/python3
Python3: Use shlex_quote() from six.moves instead of pipes.quote()
Commit: dc80d8c7dcb194300b622d8cfc9fd2dd5d11a811
https://github.com/galaxyproject/galaxy/commit/dc80d8c7dcb194300b622d8cfc9f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M run_tests.sh
Log Message:
-----------
Merge pull request #3890 from jmchilton/fix_docker_testing
Update to a new Docker test image to fix dependency bugs.
Commit: 69ff6ab906d94fdb4da3bd0b858fce2de3b349fa
https://github.com/galaxyproject/galaxy/commit/69ff6ab906d94fdb4da3bd0b858f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/search.py
Log Message:
-----------
Merge pull request #3894 from dannon/search_controller_removal
Remove old, unused search controller.
Commit: cad62b1f8b5d289dc27ec88303118dadddbbbc52
https://github.com/galaxyproject/galaxy/commit/cad62b1f8b5d289dc27ec8830311…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/style/less/ui.less
M config/tool_destinations.yml.sample
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M run_tests.sh
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/ui/ui-select-content.js
M static/style/blue/base.css
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into tags_improvements
Commit: 1a5d570704da50bdca0ca3194f5549f1338f2c6b
https://github.com/galaxyproject/galaxy/commit/1a5d570704da50bdca0ca3194f55…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M static/maps/mvc/collection/collection-view-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Remove comment, rebuild.
Commit: 95fd21230b7f73434a4af60b6624b499efcaa1af
https://github.com/galaxyproject/galaxy/commit/95fd21230b7f73434a4af60b6624…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
Log Message:
-----------
Adding bug fix for SIF files
Commit: ee66994c44cda791ab4c0d5c8fe72dff4edd2710
https://github.com/galaxyproject/galaxy/commit/ee66994c44cda791ab4c0d5c8fe7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/buildapp.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M run_tests.sh
Log Message:
-----------
Merge branch 'dev' of https://github.com/bgruening/galaxy into bugfix_cytoscape
Commit: 483f25c5c2c8d375d6096d9ca239618e413dde45
https://github.com/galaxyproject/galaxy/commit/483f25c5c2c8d375d6096d9ca239…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
Log Message:
-----------
Merge pull request #3896 from bgruening/bugfix_cytoscape
Cytoscape bugfix for SIF files
Commit: 2b4b431d0a4f300c1af3d9ac4a105e7887ec09c6
https://github.com/galaxyproject/galaxy/commit/2b4b431d0a4f300c1af3d9ac4a10…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Add missing trigger event to drop handler in content selector
Commit: 8ea4cf29f812d8ce29b31efa18495aad5d5fca44
https://github.com/galaxyproject/galaxy/commit/8ea4cf29f812d8ce29b31efa1849…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M client/package.json
M client/webpack.config.js
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Merge pull request #3868 from dannon/tags_improvements
Adding tagging to collections.
Commit: ea17f2dacf8b00e579741676deb33a98d0c234ef
https://github.com/galaxyproject/galaxy/commit/ea17f2dacf8b00e579741676deb3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-06 (Thu, 06 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tag.js
M client/package.json
M client/webpack.config.js
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/tools/actions/__init__.py
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tag.js
Log Message:
-----------
Merge branch 'dev' into fix_refresh_trigger
Commit: cac9c980dfce7e22d076cec4032facd1c011d33f
https://github.com/galaxyproject/galaxy/commit/cac9c980dfce7e22d076cec4032f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
Log Message:
-----------
remove obsolete line
Commit: 5b880697c23e2cdf1c4339976db2bf7d6a9a1c62
https://github.com/galaxyproject/galaxy/commit/5b880697c23e2cdf1c4339976db2…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
Log Message:
-----------
Merge pull request #3874 from bgruening/new_ucsc
synchronise against latest UCSC versions
Commit: 408906efb118dc4f36d134c632667101d34a666e
https://github.com/galaxyproject/galaxy/commit/408906efb118dc4f36d134c63266…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #3895 from dannon/routes_cleanup
Routes cleanup
Commit: f5ade2b5daab6fbf3fa924cbda89fbf21e7373a9
https://github.com/galaxyproject/galaxy/commit/f5ade2b5daab6fbf3fa924cbda89…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Merge pull request #3897 from guerler/fix_refresh_trigger
Add missing trigger event to drop handler in content selector
Commit: b5323e7147266ccd14728e5b4783350c7704be30
https://github.com/galaxyproject/galaxy/commit/b5323e7147266ccd14728e5b4783…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #3884 from glormph/kronik_proteomics_datatype
Hardklor and kronik datatypes for proteomics
Commit: e7a4ae5c154e5a9a9d2767c76ea043c5fd846fe8
https://github.com/galaxyproject/galaxy/commit/e7a4ae5c154e5a9a9d2767c76ea0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #3821 from mvdbeek/repository_updates
Merge ToolConfWatchers and separate from Toolbox
Commit: c4cf4164b31249457a4cdb92405006136193b1bb
https://github.com/galaxyproject/galaxy/commit/c4cf4164b31249457a4cdb924050…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
A lib/galaxy/util/handlers.py
M lib/galaxy/workflow/scheduling_manager.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
Log Message:
-----------
Allow explicit workflow scheduler handler process configuration.
Refactor job handler stuff to allow this with re-use.
Commit: fd216163aec719314fb328b87e5bea6f871a3b0a
https://github.com/galaxyproject/galaxy/commit/fd216163aec719314fb328b87e5b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-07 (Fri, 07 Apr 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/util/handlers.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Initial workflow scheduling handler fixes caught by :eagle::eyes:.
Commit: cda2b32ebeb9a02c44377ded8b1727d3bd2a394d
https://github.com/galaxyproject/galaxy/commit/cda2b32ebeb9a02c44377ded8b17…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-08 (Sat, 08 Apr 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Fix Instance is not bound to a Session
by refreshing the tool_version_cache, just like we do when we reload the
toolbox.
Commit: 2396befa02df1083da56357b9210e9d62fdb4266
https://github.com/galaxyproject/galaxy/commit/2396befa02df1083da56357b9210…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-09 (Sun, 09 Apr 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
Log Message:
-----------
Merge pull request #3846 from dannon/mq_routing_fix
[17.01] Fix for direct message routing using a 'real' exchange like rabbitmq
Commit: 93b366d75a99b3335a92be792c89443487bfd49d
https://github.com/galaxyproject/galaxy/commit/93b366d75a99b3335a92be792c89…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-09 (Sun, 09 Apr 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Merge pull request #3904 from mvdbeek/fix_instance_not_bound
[17.01] Fix Instance is not bound to a Session
Commit: 414abb00d1e5b25516d9ad714575b591ea503c2c
https://github.com/galaxyproject/galaxy/commit/414abb00d1e5b25516d9ad714575…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Add a validator that ensures a dataset's extra_files_path directory exists and is non-empty
Commit: 6c82cf3c22445e97621429591e72951a0941104e
https://github.com/galaxyproject/galaxy/commit/6c82cf3c22445e97621429591e72…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M templates/user/logout.mako
Log Message:
-----------
Remove logout hack -- logout should always be a redirect or full page action, leaving it free of any JS side-effects this would be necessary for.
Commit: c134dac9d5f2ec86f0194d114d42c4742f63e6b9
https://github.com/galaxyproject/galaxy/commit/c134dac9d5f2ec86f0194d114d42…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Identify and handle runtime values when generating displayed text
Commit: 7439d03bafe6fad42db950e85c0e329a8f0c8bff
https://github.com/galaxyproject/galaxy/commit/7439d03bafe6fad42db950e85c0e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove optional app parameter for text conversion caller
Commit: 278030638c50e51e18f712d19a2b8e71c2efc4a1
https://github.com/galaxyproject/galaxy/commit/278030638c50e51e18f712d19a2b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Use new runtime value identifier for select field context values
Commit: 18b006cb75ba8f8c088e17ebc7adc52a7b0e11f8
https://github.com/galaxyproject/galaxy/commit/18b006cb75ba8f8c088e17ebc7ad…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Remove app parameter from text conversion caller
Commit: 8ef55bca36673a79974f9f2579543ed6cd15ef3d
https://github.com/galaxyproject/galaxy/commit/8ef55bca36673a79974f9f257954…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Remove app parameter from callers used in makos
Commit: 9c9a7b97c557444e564c2de6669c28c02226f857
https://github.com/galaxyproject/galaxy/commit/9c9a7b97c557444e564c2de6669c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Remove parsing of app parameter from select field wrapper
Commit: 7f111eea528b0be4ad6dfd59bb69076c899ce6aa
https://github.com/galaxyproject/galaxy/commit/7f111eea528b0be4ad6dfd59bb69…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add missing spaces
Commit: 735e38d1a3c582727476f8223cdd7c4606e5b413
https://github.com/galaxyproject/galaxy/commit/735e38d1a3c582727476f8223cdd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-11 (Tue, 11 Apr 2017)
Changed paths:
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Adjust unit test cases
Commit: 3e191c7ff4457ce4723c914d3ae9ad8157beecb5
https://github.com/galaxyproject/galaxy/commit/3e191c7ff4457ce4723c914d3ae9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-12 (Wed, 12 Apr 2017)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into dev
Commit: 4f4efe6405b866c419760af465500458d8dafdba
https://github.com/galaxyproject/galaxy/commit/4f4efe6405b866c419760af46550…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-12 (Wed, 12 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix library parameter style width to avoid second line
Commit: 33d6628dabdf75c27979925cb45b94e7ab59d725
https://github.com/galaxyproject/galaxy/commit/33d6628dabdf75c27979925cb45b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment.
Commit: 23895e9ef0a001d4dafdedc8aee4846f8c7505d7
https://github.com/galaxyproject/galaxy/commit/23895e9ef0a001d4dafdedc8aee4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #3926 from guerler/fix_library_parameter_style
Fix library parameter style width to avoid second line
Commit: d6336b712592809aabef507802d7ce8179a9d2d7
https://github.com/galaxyproject/galaxy/commit/d6336b712592809aabef507802d7…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Remove unnecessary print
Commit: d21c8dc8f11c2d4c40967ab9f532a5ce6364f2ea
https://github.com/galaxyproject/galaxy/commit/d21c8dc8f11c2d4c40967ab9f532…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Merge pull request #3881 from erasche/unicode-viz-errors
Fix inability for viz to raise loading with non-ascii messages
Commit: 8599dff7a0098e121ddb244345a1c478f0a05cee
https://github.com/galaxyproject/galaxy/commit/8599dff7a0098e121ddb244345a1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Standardize usage of log.exception in datatypes registry.
Commit: d303cf5ffbea29ad9d0d96b167f20606a022a488
https://github.com/galaxyproject/galaxy/commit/d303cf5ffbea29ad9d0d96b167f2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Strip exception strings from being included in log.exception statements across the project.
Commit: c46e36bdee354a879d2770b0ec9e22b00ec1c104
https://github.com/galaxyproject/galaxy/commit/c46e36bdee354a879d2770b0ec9e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Overhaul string templating in log.exception statements -- should apply to all logs, eventually.
Commit: 1fe9c4d066e11b61767e22475a1392e0bbacf196
https://github.com/galaxyproject/galaxy/commit/1fe9c4d066e11b61767e22475a13…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3931 from jmchilton/maf_fix_47
[17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment.
Commit: 55c4d52455763f516aed03795b4a6550ae5744c6
https://github.com/galaxyproject/galaxy/commit/55c4d52455763f516aed03795b4a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/wrappers.py
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Merge pull request #3920 from guerler/fix_display_to_text_for_runtime_values
Identify and handle runtime values when generating displayed text
Commit: 040635d3dcee4c13960170010c8a7c10319c4fd5
https://github.com/galaxyproject/galaxy/commit/040635d3dcee4c13960170010c8a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
A lib/galaxy/util/handlers.py
M lib/galaxy/workflow/scheduling_manager.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
Log Message:
-----------
Merge pull request #3844 from jmchilton/dev_workflow_conf
Allow explicit configuration of handlers for workflow scheduling.
Commit: 695293f01563f56637ee6b63db2c96bfd0204f9f
https://github.com/galaxyproject/galaxy/commit/695293f01563f56637ee6b63db2c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
A config/containers_conf.yml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
R lib/galaxy/container/__init__.py
R lib/galaxy/container/docker_swarm.py
A lib/galaxy/containers/__init__.py
A lib/galaxy/containers/docker.py
A lib/galaxy/containers/docker_decorators.py
A lib/galaxy/containers/docker_model.py
A lib/galaxy/containers/docker_swarm.py
A lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/util/submodules.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
Log Message:
-----------
Merge pull request #3863 from natefoo/containers-abstraction
Container interface abstraction
Commit: f3aee70c9547c349061cbf22760d604f5f30c821
https://github.com/galaxyproject/galaxy/commit/f3aee70c9547c349061cbf22760d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
More careful inspection of fixes for MAF tools requiring Galaxy.
Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934.
Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff
https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_1.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Start work on a relabelling collection operation.
I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:
- Validate uniqueness of identifiers and provide nice messages if they are not unique.
- Validate that at least the required number of lines are present in the file and provide a nice message if not.
- Add strict mode to ensure exactly the correct number of lines is added.
- Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
- Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
- Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331
https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e987…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_2.txt
Log Message:
-----------
Add possibility to rename collection items from a tabular file
Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8
https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/relabel_from_file.xml
Log Message:
-----------
Fix failing test case in relable_from_file based on comment from @mvdbeek.
Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47
https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_bad_1.txt
Log Message:
-----------
Various improvements to relabel from file collection operation.
- Better error handling (check for bad characters when creating collections).
- Implement a strict mode parameter to do even more validation.
- Rework tabular vs txt mode to be explicit user choice.
- Mirror fix in release_17.01 for datasets not having a history,
Commit: d43d7aa140f399fbaa65308fe842c9afba8c44a3
https://github.com/galaxyproject/galaxy/commit/d43d7aa140f399fbaa65308fe842…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-14 (Fri, 14 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Fix E241, F841 from exception refactoring.
Commit: 77caed9861d3666150c49442df9374b63660c2e5
https://github.com/galaxyproject/galaxy/commit/77caed9861d3666150c49442df93…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Update text.py Add interaction annotations to SnpEffDb metadata
Interaction annotations are now included in SnpEff v4.3
Commit: e9011488f2f5bfe91f542d173a9f7b3132e414ad
https://github.com/galaxyproject/galaxy/commit/e9011488f2f5bfe91f542d173a9f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #3938 from jj-umn/patch-6
Update text.py Add interaction annotations to SnpEffDb metadata
Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8
https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_bad_2.txt
Log Message:
-----------
Fix relabel_from_file collection operation error handling if duplicate identifiers.
Commit: abe6434916812a8236052560d58ab184b98b3ccb
https://github.com/galaxyproject/galaxy/commit/abe6434916812a8236052560d58a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
Log Message:
-----------
Update ethercalc GIE for readiness checking
Commit: a2b8b43179cbf880f1e16ab43172545e4309c058
https://github.com/galaxyproject/galaxy/commit/a2b8b43179cbf880f1e16ab43172…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/common/templates/ie.mako
Log Message:
-----------
Generate proper url for readiness endpoint
Commit: 154530994f979070fe8c94c7730a99d11164c7fc
https://github.com/galaxyproject/galaxy/commit/154530994f979070fe8c94c7730a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Error handling for GIE container readiness check
Commit: 1e536e4ec7325b8d61394ea4091d8285eff24315
https://github.com/galaxyproject/galaxy/commit/1e536e4ec7325b8d61394ea4091d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M config/containers_conf.yml.sample
M lib/galaxy/containers/docker_swarm.py
Log Message:
-----------
Add an ignore_volumes option for swarm_mode containers
Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e
https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/relabel_from_file.xml
A test-data/filter_labels_1.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement collection operation for filtering lists from a file.
Commit: c0fd3c7c6ddef01b0546b485a1a4e88d215042e2
https://github.com/galaxyproject/galaxy/commit/c0fd3c7c6ddef01b0546b485a1a4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-19 (Wed, 19 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Display input parameters default value for runtime values
Commit: fba860f689d1af5e6727a946e20e1521f83620ed
https://github.com/galaxyproject/galaxy/commit/fba860f689d1af5e6727a946e20e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-19 (Wed, 19 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Use local flag to handle runtime values
Commit: 989b6be3390e35d896122ef044ffe114f8959949
https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-19 (Wed, 19 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively.
Commit: 9f4fd7c449646f8c3da9ba90d642a99b9cec386c
https://github.com/galaxyproject/galaxy/commit/9f4fd7c449646f8c3da9ba90d642…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/containers_conf.yml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M lib/galaxy/containers/docker_swarm.py
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Merge pull request #3941 from natefoo/containers-bugfixes
Containers interface and GIE bugfixes
Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0
https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eec…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_from_file.xml
A lib/galaxy/tools/relabel_from_file.xml
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3940 from jmchilton/collection_op_filter_from_file
Collection Operation - Filtering from a File
Commit: 4adda20b0b75ba68ebc69b4aefc86adea68299d4
https://github.com/galaxyproject/galaxy/commit/4adda20b0b75ba68ebc69b4aefc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths:
M config/openid_conf.xml.sample
R openid/google.xml
Log Message:
-----------
Remove Google from OpenID providers in the sample. Google dropped OpenID support a while back.
Commit: 386afbb4f6ac703c60d2ffd975a1c3740f67457b
https://github.com/galaxyproject/galaxy/commit/386afbb4f6ac703c60d2ffd975a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Merge pull request #3933 from dannon/exception_logging_fixes
Standardize usage of log.exception
Commit: 0bc8d1f4ceb8bf3a212c5d17ddc2a1aa3e096191
https://github.com/galaxyproject/galaxy/commit/0bc8d1f4ceb8bf3a212c5d17ddc2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M config/openid_conf.xml.sample
Log Message:
-----------
move genomespace as the first shown provider in selection
Commit: e04ac61003787ea7c99bc524017ae8afaec1decf
https://github.com/galaxyproject/galaxy/commit/e04ac61003787ea7c99bc524017a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M config/openid_conf.xml.sample
R openid/google.xml
Log Message:
-----------
Merge pull request #3953 from dannon/openid_sample_nogoogle
Remove Google from OpenID providers in the sample.
Commit: 0fc0a49b4bb7de0f95bdd8f594a22515243cd4a7
https://github.com/galaxyproject/galaxy/commit/0fc0a49b4bb7de0f95bdd8f594a2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
change 'user' menu to login or register for anons
Commit: 1fa8c837accda3d8120538da98ef200ab0250453
https://github.com/galaxyproject/galaxy/commit/1fa8c837accda3d8120538da98ef…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
improve french localization of the new menu item
Commit: 439579298acbe2f85d79dd484ba1dca9cb15eee3
https://github.com/galaxyproject/galaxy/commit/439579298acbe2f85d79dd484ba1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3956 from galaxyproject/release_17.01
merge Release 17.01
Commit: 9c44ae01cd99e8d23335bbf5846d1a777b777969
https://github.com/galaxyproject/galaxy/commit/9c44ae01cd99e8d23335bbf5846d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_registry.py
Log Message:
-----------
Followup to exception refactoring, fixes a few issues @nsoranzo noticed with my semiautomatic refactorings.
Commit: 0bd59518a6411858a44f1fe5a4bd8082df74353d
https://github.com/galaxyproject/galaxy/commit/0bd59518a6411858a44f1fe5a4bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
Unused exception, templates.
Commit: e842a265875909a0bead4e6e3e9f8006170067c3
https://github.com/galaxyproject/galaxy/commit/e842a265875909a0bead4e6e3e9f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Merge pull request #3955 from martenson/user-menu-ux
change 'user' menu to login or register for anons
Commit: eb6ebc72ea6abd0cc2f497d57872b261456b9e4b
https://github.com/galaxyproject/galaxy/commit/eb6ebc72ea6abd0cc2f497d57872…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix JJ's column_join tool depending on Galaxy at runtime.
https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=e752a5a291d2…
Commit: 60e00088c8b27c04734c7f7adb3cdae6a9a9580f
https://github.com/galaxyproject/galaxy/commit/60e00088c8b27c04734c7f7adb3c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Fix edge case for workflow mapping handling when tools not available.
Fixes #3960.
Commit: aa024f6d23389dd8868ce85f7544f1c7b3f58a8e
https://github.com/galaxyproject/galaxy/commit/aa024f6d23389dd8868ce85f7544…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_registry.py
Log Message:
-----------
Merge pull request #3959 from dannon/exception_refactor_tweaks
Followup to exception refactoring
Commit: c9087fe21e650892af647940915f3bcfbac693cc
https://github.com/galaxyproject/galaxy/commit/c9087fe21e650892af647940915f…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Graphite support
Commit: d41ad577617da2577b5dabadb47cb37a7edc5cb1
https://github.com/galaxyproject/galaxy/commit/d41ad577617da2577b5dabadb47c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix margin style values for color picker element
Commit: 352a4920a93f6c92c4713e6f0b118f3ffe31997e
https://github.com/galaxyproject/galaxy/commit/352a4920a93f6c92c4713e6f0b11…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3961 from jmchilton/another_legacy_fix
[17.01] Fix JJ's column_join tool depending on Galaxy at runtime.
Commit: a6a920cb5ebb71a8f0349e733b31ffdd70ffab27
https://github.com/galaxyproject/galaxy/commit/a6a920cb5ebb71a8f0349e733b31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-color-picker.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-color-picker.js
M static/style/blue/base.css
Log Message:
-----------
Remove unused label attribute, fix styles within color selector, remove encoded style attributes
Commit: 9aa7c6d2e905fc83bb9aee2c06f85f6aa7e1ad8c
https://github.com/galaxyproject/galaxy/commit/9aa7c6d2e905fc83bb9aee2c06f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_registry.py
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Merge branch 'dev' into fix_color_input_style
Commit: 26c06880c2d49bda0c03c0ec11f39e6a529a962b
https://github.com/galaxyproject/galaxy/commit/26c06880c2d49bda0c03c0ec11f3…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M lib/galaxy/dependencies/__init__.py
Log Message:
-----------
flake8
Commit: e9eba8625d7922a9e7e7f759fc797d4fab8ddb7d
https://github.com/galaxyproject/galaxy/commit/e9eba8625d7922a9e7e7f759fc79…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Small selenium hack.
Commit: 388bb42ba067a1464c1393208c3d6eea7eff0315
https://github.com/galaxyproject/galaxy/commit/388bb42ba067a1464c1393208c3d…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
A doc/source/admin/special_topics/grafana.png
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/performance_tracking.rst
Log Message:
-----------
Stats docs
Commit: 060dc7379e4a74c33a19e82c6a160f97bab1cf9e
https://github.com/galaxyproject/galaxy/commit/060dc7379e4a74c33a19e82c6a16…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: ade550f9527fd1651d79a9d01f1a4dc798585bcf
https://github.com/galaxyproject/galaxy/commit/ade550f9527fd1651d79a9d01f1a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Fix some selectors in tours
Commit: 898f22c75d5a0afeeb30df113f304e66a5b4c70b
https://github.com/galaxyproject/galaxy/commit/898f22c75d5a0afeeb30df113f30…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
More fixes for History Intro tour
- Remove unnecessary quotes that end up in the pop-up
- Fix one pop-up title
- Remove one step that is broken if the user is already logged-in
Commit: feb31685f63f6805d2e5953697b9ed531a44379d
https://github.com/galaxyproject/galaxy/commit/feb31685f63f6805d2e5953697b9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
Do not click on the section name, it is already expanded
Introduced in commit ca36c0dbfd438708e35e18d06c603f2cc2ce7047 .
Commit: 2b05fd050a3e1b517ca992a37f5d574521a37dd2
https://github.com/galaxyproject/galaxy/commit/2b05fd050a3e1b517ca992a37f5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Merge pull request #3970 from nsoranzo/tour_fixes
Tour fixes
Commit: 908dd2d342bbd5467b52211ba6fcbf02788d2371
https://github.com/galaxyproject/galaxy/commit/908dd2d342bbd5467b52211ba6fc…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Fix some typos in config/galaxy.ini.sample
Commit: 57c4020518f05221c118c9254111f789f4fe2116
https://github.com/galaxyproject/galaxy/commit/57c4020518f05221c118c9254111…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Merge pull request #3971 from nsoranzo/galaxy.ini_typos
Fix some typos in config/galaxy.ini.sample
Commit: 722c294165eb40aad9d8f4a3d02e383563064b3e
https://github.com/galaxyproject/galaxy/commit/722c294165eb40aad9d8f4a3d02e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Use first/last child selector
Commit: 6c51f5232a7af4b0a73d803b4a3e7c64b23ec9c7
https://github.com/galaxyproject/galaxy/commit/6c51f5232a7af4b0a73d803b4a3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M static/maps/mvc/ui/ui-color-picker.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-color-picker.js
Log Message:
-----------
Remove unused classes from code file
Commit: 779156111a117f5513ae10af04d0b12052627a32
https://github.com/galaxyproject/galaxy/commit/779156111a117f5513ae10af04d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
add two tools from str_fm repository to galaxy module whitelist
we broke them so we are fixing it
Commit: b9effa4a2b7ccad8e210243853d0e9429b3b034d
https://github.com/galaxyproject/galaxy/commit/b9effa4a2b7ccad8e210243853d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #3964 from erasche/graphite
Graphite support
Commit: 45e40a184a416e28d771c3cca4f487b06b6e284e
https://github.com/galaxyproject/galaxy/commit/45e40a184a416e28d771c3cca4f4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
A doc/source/admin/special_topics/grafana.png
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/performance_tracking.rst
Log Message:
-----------
Merge pull request #3968 from erasche/stats-docs
Stats docs
Commit: 7e4f805d479acc8f362ed651330f91fb8e2c9c40
https://github.com/galaxyproject/galaxy/commit/7e4f805d479acc8f362ed651330f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M test/api/test_workflows.py
Log Message:
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Merge pull request #3848 from jmchilton/collection_operation_check_inputs_bug
[17.01] Fix collection operations in workflows.
Commit: 02bdc7495d80d4fb085de26e07e200a95a20ec56
https://github.com/galaxyproject/galaxy/commit/02bdc7495d80d4fb085de26e07e2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/qunit/tests/ui_tests.js
Log Message:
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Merge pull request #3875 from jmchilton/fix_multi_collection_multi_data_param_reductions
[17.01] Fix multiple collection reductions on multiple data parameters.
Commit: 399c7f061ceff36c355536abd499362edc6f90d5
https://github.com/galaxyproject/galaxy/commit/399c7f061ceff36c355536abd499…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-color-picker.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-color-picker.js
M static/style/blue/base.css
Log Message:
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Merge pull request #3965 from guerler/fix_color_input_style
Fix margin style values for color picker element
Commit: 1d0ace1452aa9d5e334ee89aca07fa401db37806
https://github.com/galaxyproject/galaxy/commit/1d0ace1452aa9d5e334ee89aca07…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3973 from martenson/strfm-fix
[17.01] add two tools from str_fm repository to galaxy module whitelist
Commit: 2f518e5ee4444e3a95b6f4967366a1b38b1ca3b4
https://github.com/galaxyproject/galaxy/commit/2f518e5ee4444e3a95b6f4967366…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge pull request #3967 from jmchilton/selenium_fixes_8
Small selenium hack to fix occasionally failing collection upload tests.
Commit: 80324d08a5270b4961f706b1951c3b0f8c7ffe57
https://github.com/galaxyproject/galaxy/commit/80324d08a5270b4961f706b1951c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
17.01 version of rstudio
Commit: b1c6d3363d6bccbc53c689543efa4460d796c814
https://github.com/galaxyproject/galaxy/commit/b1c6d3363d6bccbc53c689543efa…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
Log Message:
-----------
remove old versions
Commit: 60a05c1811c3716e47c28ecec6f2ab25d3b56d97
https://github.com/galaxyproject/galaxy/commit/60a05c1811c3716e47c28ecec6f2…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
Log Message:
-----------
more touch-ups and easier vimdiffing with jupyter configs
Commit: f75a72aee80680537dad802944585d6007d237c9
https://github.com/galaxyproject/galaxy/commit/f75a72aee80680537dad80294458…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Rework logic for remote_user/session handling. This should fix issues @erasche reported regarding (null)(a)example.org users.
Commit: 09ba27543b8726fb61cd998bf9614018a9ba7316
https://github.com/galaxyproject/galaxy/commit/09ba27543b8726fb61cd998bf961…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Slightly adjust logic for discarding headers; this shouldn't try to throw away empty headers anymore.
Commit: b779977cdc31d50183e7b0f356e9489a43eb755d
https://github.com/galaxyproject/galaxy/commit/b779977cdc31d50183e7b0f356e9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Slightly improve error message under remote auth with anon session attempt.
Commit: eb9a940a2dd69574b5fbaca06ffdc9beea4d4153
https://github.com/galaxyproject/galaxy/commit/eb9a940a2dd69574b5fbaca06ffd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-25 (Tue, 25 Apr 2017)
Changed paths:
M templates/user/logout.mako
Log Message:
-----------
Put back old hack; necessary for now.
Commit: 42734350d2e44fce1b2e699f643d755e7e4441be
https://github.com/galaxyproject/galaxy/commit/42734350d2e44fce1b2e699f643d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Use container-based infrastructure (sudo: false) in TravisCI
Commit: f3c8edea83e537281e830fe8fa6d9de3da836489
https://github.com/galaxyproject/galaxy/commit/f3c8edea83e537281e830fe8fa6d…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Use abstract dataset functions for testing
Commit: ec22b1d3ecd85cff65d232d0997703ee096d5ce1
https://github.com/galaxyproject/galaxy/commit/ec22b1d3ecd85cff65d232d09977…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/js/package.json
Log Message:
-----------
Fixes to get IEs working on Mac OS X.
- Fix logic error related to config parsing (OS non-specific).
- Don't trust GatewayAddress from Docker if on Mac OS X - it is probably a Docker host VM specific address.
- Update sqlite dependency for the newest version of Node available from Mac OS X Homebrew.
- Add a little blurb about how to configure galaxy_infrastructure_url in this case.
Commit: d082f1c334f3079249ed4d2404c52ac96850dc4b
https://github.com/galaxyproject/galaxy/commit/d082f1c334f3079249ed4d2404c5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Purely clientside implementation of hashtag shortcut for nametags. These are translated to 'name:nametag_value' prior to saving and are persisted in that form.
Commit: f3dbf55aad06c64e26fd7dd44db9a87c73835153
https://github.com/galaxyproject/galaxy/commit/f3dbf55aad06c64e26fd7dd44db9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Render 'name:' as hashtags. I personally like the display better and
it'll nudge people towards using them I think, while still giving us the
'real' tagging hierarchy to work with.
Commit: 4a5c8823173a125fd3eade1693a23ba6e6b73aa5
https://github.com/galaxyproject/galaxy/commit/4a5c8823173a125fd3eade1693a2…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Remove unused import
Commit: 910c22b7a1c759a651186f13e6c6707d91becfec
https://github.com/galaxyproject/galaxy/commit/910c22b7a1c759a651186f13e6c6…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/js/package.json
Log Message:
-----------
Merge pull request #3978 from jmchilton/ie_for_mac_os_x_fixes
Fixes to get GIEs working on Mac OS X.
Commit: c84b5725e63a3b93b5c798d23b277df27d63cd6f
https://github.com/galaxyproject/galaxy/commit/c84b5725e63a3b93b5c798d23b27…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .travis.yml
Log Message:
-----------
Merge pull request #3977 from nsoranzo/travis
Use container-based infrastructure (sudo: false) in TravisCI
Commit: 740d85a6a6f8b3877faf75fa3488a1a1d2a10c1e
https://github.com/galaxyproject/galaxy/commit/740d85a6a6f8b3877faf75fa3488…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #3975 from erasche/17.05-gie-fixes
17.05 rstudio fixes / one small gie fix
Commit: f3c134abcb04ee2885f247ba79e95a354e4bb32b
https://github.com/galaxyproject/galaxy/commit/f3c134abcb04ee2885f247ba79e9…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Merge pull request #3976 from dannon/fix_logout
[17.01] Remote user logout fixes, rework header handling a bit.
Commit: d398c90dbd70fff91a672935997bc21e949e8767
https://github.com/galaxyproject/galaxy/commit/d398c90dbd70fff91a672935997b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/api/test_workflows.py
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
static/maps/mvc/ui/ui-select-content.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/ui/ui-select-content.js
Commit: 647b4901c30d356f13f851a76c2a7c7ed8bfd808
https://github.com/galaxyproject/galaxy/commit/647b4901c30d356f13f851a76c2a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M Makefile
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
move reqs to dev-requirements and touch makefile
Commit: d42fc9ae71b26caed30d6b904681a6b2065febbc
https://github.com/galaxyproject/galaxy/commit/d42fc9ae71b26caed30d6b904681…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
A .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
A .ci/jenkins/selenium/docker-compose.yml
A .ci/jenkins/selenium/galaxy.ini
A .ci/jenkins/selenium/run_galaxy.bash
A .ci/jenkins/selenium/run_tests.sh
A .ci/jenkins/toolshed/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTING.md
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
A client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
A client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/package.json
M client/webpack.config.js
A config/build_sites.yml.sample
A config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/openid_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.xml
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
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A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
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M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
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R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/explicit.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dependencies.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
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M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/errors.py
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A lib/galaxy/tools/filter_from_file.xml
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M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
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M lib/galaxy/tools/loader_directory.py
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A lib/galaxy/tools/locations/dockstore.py
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A lib/galaxy/tools/locations/http.py
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M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
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M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
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M lib/galaxy/tools/test.py
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M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
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M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/asserts/text.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
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M lib/galaxy/util/__init__.py
M lib/galaxy/util/aliaspickler.py
A lib/galaxy/util/compression_utils.py
M lib/galaxy/util/dbkeys.py
A lib/galaxy/util/handlers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
A lib/galaxy/util/oset.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
R lib/galaxy/util/postfork.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/submodules.py
M lib/galaxy/version.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/Dockerfile
M lib/galaxy/web/proxy/js/lib/mapper.js
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
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M lib/galaxy/webapps/galaxy/controllers/root.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
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R lib/galaxy_utils/sequence/__init__.py
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R lib/galaxy_utils/sequence/fastq.py
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R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
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M lib/tool_shed/util/repository_util.py
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M lib/tool_shed/util/web_util.py
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M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/pasteWrapper.xml
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.py
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.py
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.py
M tools/maf/vcf_to_maf_customtrack.xml
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into fix_documentation_build
Commit: be7d1294fd69618cbd415df4c562ce2c4ef88808
https://github.com/galaxyproject/galaxy/commit/be7d1294fd69618cbd415df4c562…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M tox.ini
Log Message:
-----------
Fix Travix builds which use flake8-docstrings
flake8-docstrings is broken due to the release of pydocstyle 2.0.0 (see
https://gitlab.com/pycqa/flake8-docstrings/issues/19 ), so temporarily add
an extra dep in tox.ini to pin it.
Commit: 9f36bea7f1aa25bc193ec1bcc243d303cbfff1bc
https://github.com/galaxyproject/galaxy/commit/9f36bea7f1aa25bc193ec1bcc243…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Slight refactoring, also name->hash for recommended tags.
Commit: a2b8a7d26ab748d7565ef9245a678bc2740d1bdd
https://github.com/galaxyproject/galaxy/commit/a2b8a7d26ab748d7565ef9245a67…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .travis.yml
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M config/galaxy.ini.sample
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/js/package.json
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
M test/api/test_workflows.py
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into hashtags
Commit: 7edfe39f20024f161a30be14406c0baa2a9807bf
https://github.com/galaxyproject/galaxy/commit/7edfe39f20024f161a30be14406c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M Makefile
Log Message:
-----------
fix makefile help for docs
thanks nsoranzo
Commit: b7a8bea3cd67b8e889f44fd88b8529e47fe53cbc
https://github.com/galaxyproject/galaxy/commit/b7a8bea3cd67b8e889f44fd88b85…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M tox.ini
Log Message:
-----------
Merge pull request #3981 from nsoranzo/fix_py27-lint_build
Fix Travix builds which use flake8-docstrings
Commit: ea3796152a01aad87f0585bf83ceb661392ba4d4
https://github.com/galaxyproject/galaxy/commit/ea3796152a01aad87f0585bf83ce…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Replace wiki.galaxyproject.org links in /lib
Commit: 04a32064f1d553c01828092b445175a9c7d8a53d
https://github.com/galaxyproject/galaxy/commit/04a32064f1d553c01828092b4451…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/viz/phyloviz.js
M static/maps/mvc/citation/citation-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/viz/phyloviz.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/viz/phyloviz.js
Log Message:
-----------
Update wiki.galaxyproject.org links in client
Commit: a5143ce7a86cb64c81b0ffa36a90742b872cec15
https://github.com/galaxyproject/galaxy/commit/a5143ce7a86cb64c81b0ffa36a90…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/data_manager/index.mako
Log Message:
-----------
Convert wiki.galaxyproject.org links in templates
Commit: 29aa00e42129bec564a9f1009547e3b740b29709
https://github.com/galaxyproject/galaxy/commit/29aa00e42129bec564a9f1009547…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M CONTRIBUTING.md
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/package.json
M client/webpack.config.js
A config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/openid_conf.xml.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/swarm_manager_conf.yml.sample
M config/tool_conf.xml.sample
M config/tool_destinations.yml.sample
R cron/clean_docker_swarm_mode_services.sh
M display_applications/igv/bigwig.xml
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
M doc/source/admin/framework_dependencies.rst
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/reports.md
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A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grafana.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
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A doc/source/admin/special_topics/index.rst
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A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/performance_tracking.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
M doc/source/admin/useful_scripts.rst
R doc/source/admin/webhooks.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/project/issues.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/containers/__init__.py
A lib/galaxy/containers/docker.py
A lib/galaxy/containers/docker_decorators.py
A lib/galaxy/containers/docker_model.py
A lib/galaxy/containers/docker_swarm.py
A lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/external_service_types.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/filter_failed_collection.xml
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
A lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/zip_collection.xml
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/handlers.py
R lib/galaxy/util/postfork.py
M lib/galaxy/util/submodules.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
A lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
M lib/galaxy/web/proxy/js/package.json
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
R openid/google.xml
M run_tests.sh
M scripts/api/README
M scripts/secret_decoder_ring.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/grid_base.mako
M templates/show_params.mako
R templates/user/dbkeys.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/galaxy/workflow/display.mako
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api_asserts.py
M test/base/data/test_workflow_pause.ga
M test/base/driver_util.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/qunit/package.json
M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/ui_tests.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into wiki-to-hub
Commit: 0dd75e6cdd985ec3711987ef8adb3fe6365b8501
https://github.com/galaxyproject/galaxy/commit/0dd75e6cdd985ec3711987ef8adb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
A templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Attempt to rectify bad merge.
Commit: 05e81192bd91559876da1a82b734c7e49e15f43e
https://github.com/galaxyproject/galaxy/commit/05e81192bd91559876da1a82b734…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M test/qunit/tests/form_tests.js
Log Message:
-----------
Update tool form qunit test text.
Commit: 291426a5dcd7941e1d6711b5926418bf0dab0c4c
https://github.com/galaxyproject/galaxy/commit/291426a5dcd7941e1d6711b59264…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Merge pull request #3943 from guerler/show_default_value_for_runtime_values
Show default value for runtime values
Commit: 92d93c7ef96452ba343a43502fe519e0dea3f8bf
https://github.com/galaxyproject/galaxy/commit/92d93c7ef96452ba343a43502fe5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M lib/galaxy/objectstore/azure_blob.py
Log Message:
-----------
Merge pull request #3263 from zfrenchee/patch-1
Azure - Leasing container sometimes breaks things in docker galaxy
Commit: 78c263ac7c6beb1b93269f252897b0dd6336b450
https://github.com/galaxyproject/galaxy/commit/78c263ac7c6beb1b93269f252897…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Udpate Babel to a version compat. with sphinx.
Commit: 3e14cd532074d190def283ed2cce61ae22c0eee9
https://github.com/galaxyproject/galaxy/commit/3e14cd532074d190def283ed2cce…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #3986 from jmchilton/babel_update
Udpate Babel to a version compat. with sphinx.
Commit: 3fcd78564630fae9c4670cfbe198572f94f688c0
https://github.com/galaxyproject/galaxy/commit/3fcd78564630fae9c4670cfbe198…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Merge pull request #3962 from jmchilton/workflow_editor_mapping_test
[17.01] Fix edge case for workflow mapping handling when tools not available.
Commit: b12b951e91e6b8472f81d73f184c40aac7f9aad8
https://github.com/galaxyproject/galaxy/commit/b12b951e91e6b8472f81d73f184c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Attempted fix for transiently failing API test_jobs introduced in #3619.
A couple things need to occur while the jobs are "running" and it seems that 60 seconds wasn't enough time to sleep for all that to happen on Jenkins.
I checked the timing in the raw logs (they are for some reasons being filtered out in the Jenkins display of the XUnit) - and indeed the jobs are properly sleeping the correct amount of time but the client API calls need some more time it seems. My initial thought was maybe the jobs were being interrupted or something - and that does not appear to be the case.
Commit: 26afd36a4d1336825fa47e2e8f3921c4ee8e1486
https://github.com/galaxyproject/galaxy/commit/26afd36a4d1336825fa47e2e8f39…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge remote-tracking branch 'guerler/login_routes' into dev
Commit: 54b9d7ac10535e56caf9389da00125664a9a779e
https://github.com/galaxyproject/galaxy/commit/54b9d7ac10535e56caf9389da001…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Use the configured tool_path when loading data managers.
Commit: 7ba3662d29f0f8d9c6a24ea3fa66eee421f6059d
https://github.com/galaxyproject/galaxy/commit/7ba3662d29f0f8d9c6a24ea3fa66…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M Makefile
M lib/galaxy/dependencies/dev-requirements.txt
Log Message:
-----------
Merge pull request #3104 from athos-ribeiro/fix_documentation_build
Add missing imports for documentation builds
Commit: 92f3841bee3a473b85661779790a40f773b0f86d
https://github.com/galaxyproject/galaxy/commit/92f3841bee3a473b85661779790a…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-27 (Thu, 27 Apr 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Remove dev remnant.
Commit: 8b21e651969fff8cff41f736c47312f099cc5ee9
https://github.com/galaxyproject/galaxy/commit/8b21e651969fff8cff41f736c473…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Improve implicit workflow connection test case.
I think https://jenkins.galaxyproject.org/job/docker-api/7316/testReport/junit/api.… may be the first time I have seen it fail - but still it has some other problems.
- Eliminate the sleep - instead wait on explicitly on the desired condition (first two jobs are complete and the workflow is ready for unpause). This is likely why the test case failed.
- Improve the other assertions to provide more details in the test case ever fails again.
Commit: 1d9b7d592b131b69b91c40eeed3e844df65f67e4
https://github.com/galaxyproject/galaxy/commit/1d9b7d592b131b69b91c40eeed3e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into hashtags
Commit: 6e1daab992c27fa22b7682bcf5609fcea75aa800
https://github.com/galaxyproject/galaxy/commit/6e1daab992c27fa22b7682bcf560…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Fix errors discovered by Nicola.
Commit: 89e692d980965f5a1963818180ccaf62ae2c207f
https://github.com/galaxyproject/galaxy/commit/89e692d980965f5a1963818180cc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M config/galaxy.ini.sample
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/workflow/workflow-forms.js
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
Log Message:
-----------
Tweaks for @nsoranzo.
Commit: 5fe7b7208c8668b7d4dd9dc31568c77a0a8c2562
https://github.com/galaxyproject/galaxy/commit/5fe7b7208c8668b7d4dd9dc31568…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Fix support link
Commit: a26991b2a8bea94a98eae38bdacc4739a818f57a
https://github.com/galaxyproject/galaxy/commit/a26991b2a8bea94a98eae38bdacc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Selenium workflow run test case fix.
The ``with self.main_panel():`` construct wasn't cleaning up properly - I've fixed this and eliminated the terrible workarounds in the execution test case that I guess I had added trying to figure out how to make things work. It should be more stable now. (This test case has been failing 1 out 9 times I'd say.)
Commit: 760160a02cd925168eefb0b05a4471bd5dbc7b61
https://github.com/galaxyproject/galaxy/commit/760160a02cd925168eefb0b05a44…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #3991 from jmchilton/workflow_connection_test_case_improvement
Improve implicit workflow connection test case.
Commit: 85a9b37d80fcc503d674e4f3322b9e618f5e87c5
https://github.com/galaxyproject/galaxy/commit/85a9b37d80fcc503d674e4f3322b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M .ci/jenkins/selenium/run_tests.sh
M run_tests.sh
M test/selenium_tests/framework.py
Log Message:
-----------
Setup framework for retrying failed Selenium tests.
- By default this won't occur locally, but you can set GALAXY_TEST_SELENIUM_RETRIES to a non-zero number to enable auto retrying tests that many times.
- Capture the stack trace in the Selenium test error report directory - this will be useful for debugging problems that may fail once but pass on a subsequence attempt. Jenkins now captures these directories and includes their content in the test reports.
- Document the Selenium test error report directory in run_tests.sh as well as this new retry variable.
- Update the Jenkins test script to set this new variable to 1 so transient failures break the build much less frequently.
Commit: 5fd7f8bdf728356ee1aeafb36996392dd91b9e46
https://github.com/galaxyproject/galaxy/commit/5fd7f8bdf728356ee1aeafb36996…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Explicit is better than implicit.
Commit: f0740136831623adf8b2c1fe9ed17dbf4327ebc4
https://github.com/galaxyproject/galaxy/commit/f0740136831623adf8b2c1fe9ed1…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M config/galaxy.ini.sample
Log Message:
-----------
Small tweaks for data-libraries URLS
Commit: dab18fb2387d737f859637bbd37d9b0ce3ec658c
https://github.com/galaxyproject/galaxy/commit/dab18fb2387d737f859637bbd37d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/viz/phyloviz.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M static/maps/mvc/citation/citation-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/viz/phyloviz.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/viz/phyloviz.js
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge branch 'wiki-to-hub' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
Commit: 5a6e53f728858d14064c984956c5c24666395da3
https://github.com/galaxyproject/galaxy/commit/5a6e53f728858d14064c984956c5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Rework Jupyter IE for additional_ids handling.
- Add a new option ``use_volumes`` to the Docker config.
- If using volumes, do nothing differently.
- If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires https://github.com/bgruening/docker-jupyter-notebook/pull/17)
Commit: 9bc24aeef06b3536a6f69ddc23ac1ede4fb9b7a0
https://github.com/galaxyproject/galaxy/commit/9bc24aeef06b3536a6f69ddc23ac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
Log Message:
-----------
Update rstudio to match additional hid handling of Jupyter.
Ping @erasche - does this work? I'm not sure how rstudio handles the existing DATASET_HID.
Commit: 5b9bc76cac7f8ad4dd859af97e9ae1199cf6e62a
https://github.com/galaxyproject/galaxy/commit/5b9bc76cac7f8ad4dd859af97e9a…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Change validator name
Commit: 2b09fe149dc7b65718f4a74f288cfe27cf6fcf82
https://github.com/galaxyproject/galaxy/commit/2b09fe149dc7b65718f4a74f288c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Merge pull request #3989 from davebx/fix_managers
Use the configured tool_path when loading data managers
Commit: a32e78585c843517d5ae091ce03e08427214f2ff
https://github.com/galaxyproject/galaxy/commit/a32e78585c843517d5ae091ce03e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Merge pull request #3918 from gregvonkuster/fpv
Add a validator that ensures a dataset's extra_files_path
Commit: c93afcec64d5f4036bf75011c35b4c8497068238
https://github.com/galaxyproject/galaxy/commit/c93afcec64d5f4036bf75011c35b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M .ci/jenkins/selenium/run_tests.sh
M run_tests.sh
M test/selenium_tests/framework.py
Log Message:
-----------
Merge pull request #3993 from jmchilton/selenium_fixes_10
Setup framework for retrying failed Selenium tests.
Commit: ffed281c33be5bcb1006cd3e94055fa01e5c3d18
https://github.com/galaxyproject/galaxy/commit/ffed281c33be5bcb1006cd3e9405…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-30 (Sun, 30 Apr 2017)
Changed paths:
M test/api/test_jobs.py
Log Message:
-----------
Merge pull request #3988 from jmchilton/job_test_timing_improvements
Attempted fix for transiently failing API test_jobs introduced in #3619.
Commit: 7b385c2b849fc091a477b75a9194a99934454f8e
https://github.com/galaxyproject/galaxy/commit/7b385c2b849fc091a477b75a9194…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_workflow_run.py
Log Message:
-----------
Merge pull request #3992 from jmchilton/selenium_fixes_9
Fixes for Selenium workflow run test case.
Commit: 313a006ae3ea9d383ad102ceda17f657275ff5bf
https://github.com/galaxyproject/galaxy/commit/313a006ae3ea9d383ad102ceda17…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Add entry for empty_extra_files_path validator
Commit: 41cbe242991eb69bc821a9f2d0b8ab599b73aa9a
https://github.com/galaxyproject/galaxy/commit/41cbe242991eb69bc821a9f2d0b8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Use floating point to log toolox reload times
Commit: 4d1cae41cb7ce0d3aa10d413de8ec4000e50444a
https://github.com/galaxyproject/galaxy/commit/4d1cae41cb7ce0d3aa10d413de8e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Add timing information for Data Manager reload
Commit: c06b4c92658563fda4efe8b1dcf6045113b664fd
https://github.com/galaxyproject/galaxy/commit/c06b4c92658563fda4efe8b1dcf6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/toolbox/cache.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Add a short-lived (1s) ToolShedRepositoryCache
This will speed up repeated ToolShedRepositories lookups, like when
building the Toolbox for the first time, or when loading a
shed_tool_conf.xml file with many deactivated tools.
Commit: 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227
https://github.com/galaxyproject/galaxy/commit/43c9c287a9a3520d77cc9235dfbf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Speed up tool-data table reloads by doing a os.walk and caching the result for 1s instead of repeatedly calling os.path.exists.
Commit: 34ed9b48ddc2fdd0e2456b959fed5eedec9b92c1
https://github.com/galaxyproject/galaxy/commit/34ed9b48ddc2fdd0e2456b959fed…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/cache.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Only index changed tools when re-indexing the toolbox
This speeds up repeated toolbox reloads enourmously (from 1 second on my
test-instance to 0.1 seconds).
Commit: c6429bff1c38b2196fece8155449ba62723242ee
https://github.com/galaxyproject/galaxy/commit/c6429bff1c38b2196fece8155449…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Always use cache to fetch tool_version objects
Commit: 96cb87431402454fa52db35547fb3028c5aae807
https://github.com/galaxyproject/galaxy/commit/96cb87431402454fa52db35547fb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Use cElementTree for light xml parsing speedup
Commit: 2906f0c0857fc958f7e9049e2e7134065908852f
https://github.com/galaxyproject/galaxy/commit/2906f0c0857fc958f7e9049e2e71…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
Log Message:
-----------
Update ToolVersionCache when adding a new ToolShedLineage
Commit: 6c22726db082cedee9884bde9aa913bbb93dea05
https://github.com/galaxyproject/galaxy/commit/6c22726db082cedee9884bde9aa9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Move tool_cache.reset_status() calls to reload toolbox/data managers, so that we can use information about whether tools are new during reloads
Commit: 431a4824abf91b7a10e5417d63a990ba0a5f916d
https://github.com/galaxyproject/galaxy/commit/431a4824abf91b7a10e5417d63a9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Make sure re-indexing the toolbox occurs on the new toolbox
Commit: ea9ecdf57150e800115ae28f6e80d80a7bfef249
https://github.com/galaxyproject/galaxy/commit/ea9ecdf57150e800115ae28f6e80…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Remove `replace_existing` option for data managers
If a data manager is defined twice for the same data manager id in the
shed_tool_conf.xml the first data manager will be loaded. This is not a
problem when updating a data manager through the toolshed, because the
outdated data manager will be removed from the tool cache and a new
toolbox is being built.
Commit: db910f4f81771f91f9a5b96bfc5fb9bd6d506e2b
https://github.com/galaxyproject/galaxy/commit/db910f4f81771f91f9a5b96bfc5f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
Log Message:
-----------
Reset the tool cache once all tools are loaded after starting up galaxy
Commit: 9aa5556dedb35b748ed17b20fd26348fdcdea829
https://github.com/galaxyproject/galaxy/commit/9aa5556dedb35b748ed17b20fd26…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Reduce logging during toolbox reloads
We don't log loading of tools that have not changed when reloading the
toolbox.
Commit: 475b8866bad2a58b314354ae73ee1e5ccd94b8cb
https://github.com/galaxyproject/galaxy/commit/475b8866bad2a58b314354ae73ee…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Fix unittests that access app.tool_cache
Commit: beae93bf766fc48a3a2f2edcd275d13ae0fe8ba2
https://github.com/galaxyproject/galaxy/commit/beae93bf766fc48a3a2f2edcd275…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Re-use ExecutionTimer abstractions for consistent log patterns.
Commit: a83ef0b86c0acbfb7c0bf1b40579e5102c78ad29
https://github.com/galaxyproject/galaxy/commit/a83ef0b86c0acbfb7c0bf1b40579…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
Log Message:
-----------
Log startup time
Commit: 3ff2a7832a949d300d9cddab0fea05fa74b1a403
https://github.com/galaxyproject/galaxy/commit/3ff2a7832a949d300d9cddab0fea…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Fix cElementTree imports
Commit: c905c4217b0397f92b2eb1019308851da043682f
https://github.com/galaxyproject/galaxy/commit/c905c4217b0397f92b2eb1019308…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Fix import order in lib/galaxy/tools/data/__init__.py
Commit: b72994fe0294326f99df880e3ba7e248f1ffe145
https://github.com/galaxyproject/galaxy/commit/b72994fe0294326f99df880e3ba7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Add possibility explicitly rebuild ToolShedRepositoryCache
Commit: 84c1559d473f7d9234173aeb802f30067fe0ffe6
https://github.com/galaxyproject/galaxy/commit/84c1559d473f7d9234173aeb802f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Fix path checking for files that are not in the tool_data_path directory
Commit: 0504dcd2997bc4673ded5c7fdc1e2b28a85dcb18
https://github.com/galaxyproject/galaxy/commit/0504dcd2997bc4673ded5c7fdc1e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Use generator instead of list comprehenesion followed converting it to a set. (Thanks @nsoranzo)
Commit: cbed78fbfbcb1c381af5be9442c8ce6af1a3a554
https://github.com/galaxyproject/galaxy/commit/cbed78fbfbcb1c381af5be9442c8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Don't return toolbox (thx @nsoranzo)
Commit: 4dd49c938d2c7bcfac37fe475eccb1e32653b6b4
https://github.com/galaxyproject/galaxy/commit/4dd49c938d2c7bcfac37fe475ecc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
Log Message:
-----------
Use ExecutionTimer abstraction to report startup time
Commit: dc1617596e47c384b8a88de395fe41a681145ffd
https://github.com/galaxyproject/galaxy/commit/dc1617596e47c384b8a88de395fe…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Remove unused time import
Commit: 4c44338144763819f78f99b84d5816ded18de372
https://github.com/galaxyproject/galaxy/commit/4c44338144763819f78f99b84d58…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Be more defesive when accessing app.tool_cache
Commit: 5069815c0eba0a7c4c406ec0f781f138f7aee291
https://github.com/galaxyproject/galaxy/commit/5069815c0eba0a7c4c406ec0f781…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Rebuild repo cache when deciding if repository should be created.
Commit: d15813cb2a489e1de8771886e9df8ebb69fc079e
https://github.com/galaxyproject/galaxy/commit/d15813cb2a489e1de8771886e9df…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Avoid having tools in tool_cache marked as new when they have rapidly shifted from new to expired.
Commit: 586f49486cf4c1f4597237d3df95562bb477c6f8
https://github.com/galaxyproject/galaxy/commit/586f49486cf4c1f4597237d3df95…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
Don't crash if a tool has not been added to the cache properly
Commit: 3d6bc1d56372b5853fdddd08362d8f57b4026adb
https://github.com/galaxyproject/galaxy/commit/3d6bc1d56372b5853fdddd08362d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Refresh tool_data_path_files if we know that a new table has been written
Commit: 07da123e9d311e5ec453399024ef992859770234
https://github.com/galaxyproject/galaxy/commit/07da123e9d311e5ec453399024ef…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Reference old_toolbox earlier, since reloading can happen in a different thread, which will lead to a hang when waiting for another toolbox reload
Commit: 677d98622dfa30a65d8a8fc392c25077abdcc0e9
https://github.com/galaxyproject/galaxy/commit/677d98622dfa30a65d8a8fc392c2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Always refresh tool_shed_repository_cache before fetching repositories by ids (since that is only called from admin_toolshed.py and installed_repository_metadata_manager.py)
Commit: f940c797ff981c3f0a12b6a3abeee61e05ff2436
https://github.com/galaxyproject/galaxy/commit/f940c797ff981c3f0a12b6a3abee…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Fix import order in lib/galaxy/config.py
Commit: 89f57f2aa753f5de9673cd3dcf5c13ca3d3f6639
https://github.com/galaxyproject/galaxy/commit/89f57f2aa753f5de9673cd3dcf5c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Allow looking up repositories by repository_id via ToolShedRepositoryCache
Commit: 456d1b47b62d05d3fc5180d4f9da525317efc28c
https://github.com/galaxyproject/galaxy/commit/456d1b47b62d05d3fc5180d4f9da…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/util/tool_dependency_util.py
Log Message:
-----------
Refresh TSR cache when needed
Commit: 8411b0253adc947838af760e4614611ac8183464
https://github.com/galaxyproject/galaxy/commit/8411b0253adc947838af760e4614…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Restore deactivate/activate functionality
Commit: 15e2c9b61aae9476b519a8c2e1c233e134e3ebbc
https://github.com/galaxyproject/galaxy/commit/15e2c9b61aae9476b519a8c2e1c2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Revert "Fix cElementTree imports"
This reverts commit 6d365f03e888ef12527105119f0a7adebae23b95.
Commit: 7e61f8c047ce3cb29f5d9999a93b2c7bd0ee1cde
https://github.com/galaxyproject/galaxy/commit/7e61f8c047ce3cb29f5d9999a93b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Revert "Use cElementTree for light xml parsing speedup"
This reverts commit 556469f5171ef9897a5c40de9d661d2d4f4deb86.
Commit: 141f15256e8ef39baf457be1e8ef1cdf5414f5aa
https://github.com/galaxyproject/galaxy/commit/141f15256e8ef39baf457be1e8ef…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Use ExecutionTimer
Commit: 73c7c364a25caf519dfd4cfea17b500077510a74
https://github.com/galaxyproject/galaxy/commit/73c7c364a25caf519dfd4cfea17b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Use tool_shed_repository_cache in populate_tool_shed_info
Commit: 869d7bf481e77aca420cc3970844650f7ad6ff20
https://github.com/galaxyproject/galaxy/commit/869d7bf481e77aca420cc3970844…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/auth/__init__.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/util/plugin_config.py
Log Message:
-----------
Replace getchildren(), which has been deprecated (https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.Elem…)
Commit: 3079d0c239bf7c46d872e65d107eaab4b3741b46
https://github.com/galaxyproject/galaxy/commit/3079d0c239bf7c46d872e65d107e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Write out the datatype registry only once
Commit: f88304b65b430da0a3db67e25e457044c373bf99
https://github.com/galaxyproject/galaxy/commit/f88304b65b430da0a3db67e25e45…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
Build toolbox search in a local control task
Commit: 5e7da2c910e28e13b5a79c3ad794d6f40446694a
https://github.com/galaxyproject/galaxy/commit/5e7da2c910e28e13b5a79c3ad794…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
M test/base/driver_util.py
Log Message:
-----------
Don't fail tests without internet connectivity
Commit: 5a26896745c16e25ce951ee3a85bdc2cd81087e1
https://github.com/galaxyproject/galaxy/commit/5a26896745c16e25ce951ee3a85b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/parser/xml.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Write out datatype registry when loading set_metadata tool
Commit: f199d5b434da500330520f891a3188ee69eccce4
https://github.com/galaxyproject/galaxy/commit/f199d5b434da500330520f891a31…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Keep cache thread-local
Commit: b4e4f3ce7a9bc6ef06b4191bf8f8f2fef493d844
https://github.com/galaxyproject/galaxy/commit/b4e4f3ce7a9bc6ef06b4191bf8f8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Use current session
Commit: ff1b66afb325ebe68a2d174503980b03100ca6d4
https://github.com/galaxyproject/galaxy/commit/ff1b66afb325ebe68a2d17450398…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Fix thread local cache use
Commit: 84351de20bef488022cf82ac2610e2e5c0b369cd
https://github.com/galaxyproject/galaxy/commit/84351de20bef488022cf82ac2610…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Send control task as postfork function
Commit: b666649c8159316eaa22bc4c89575fda38e9838d
https://github.com/galaxyproject/galaxy/commit/b666649c8159316eaa22bc4c8957…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Work around InstanceDetached errors
Commit: 86684df5ef235b6390f0cfa838927cf6e5b67330
https://github.com/galaxyproject/galaxy/commit/86684df5ef235b6390f0cfa83892…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Skip time-based reloading, rely on detecting DetachedInstanceErrors to trigger cache rebuild
Commit: cdad5bee9b1f9761a5b3ab56cbdc3c3eb6e63e14
https://github.com/galaxyproject/galaxy/commit/cdad5bee9b1f9761a5b3ab56cbdc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
Log Message:
-----------
Attempt to speedup proprietary datatype loading
Commit: 2587ab55b8743ae626f977961e4f3c8e7cb0eb05
https://github.com/galaxyproject/galaxy/commit/2587ab55b8743ae626f977961e4f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Remove operations from custom_datatype_manager
Updating the upload file formats is handled when loading the datatype
into the registry, and reloading the upload tool seems unnecessary and
insufficient, since this would only affect the current web handler. In
any case removed and added datatypes are immediately propagated to the
upload tool.
Commit: af156a8f7496dc9a9e70d3992f227c626aec7fa2
https://github.com/galaxyproject/galaxy/commit/af156a8f7496dc9a9e70d3992f22…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/search/__init__.py
Log Message:
-----------
Build search index at startup, rebuild repository cache during toolbox or datamanager reload
Commit: 4c1f9c8f0d8ea2a58264fdbcb53accf3f7b52dac
https://github.com/galaxyproject/galaxy/commit/4c1f9c8f0d8ea2a58264fdbcb53a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3994 from gregvonkuster/xsd
Add entry for empty_extra_files_path validator
Commit: 7a6961e30d013d5c3bfa53118e6fb2cc1fd1d35f
https://github.com/galaxyproject/galaxy/commit/7a6961e30d013d5c3bfa53118e6f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Undo dataset renaming
Commit: 2586df45637d794c63252838573b2d1e6d692243
https://github.com/galaxyproject/galaxy/commit/2586df45637d794c63252838573b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M .ci/flake8_wrapper_docstrings.sh
M setup.cfg
M tox.ini
Log Message:
-----------
Remove pydocstyle pins - there was an update to flake8-docstrings.
Commit: 6201c61d72df9b3b0a1af454d52e4462c02fc587
https://github.com/galaxyproject/galaxy/commit/6201c61d72df9b3b0a1af454d52e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
Log Message:
-----------
Add a note about use_volumes to Jupyter and RStudio GIEs.
Commit: 09404117b9d45e73650665a612fa7001ce5006f2
https://github.com/galaxyproject/galaxy/commit/09404117b9d45e73650665a612fa…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes
Rework Jupyter IE for additional_ids handling.
Commit: 37c7425eae98c8cc39b7a0d9ca6b8cf5c4e0cbcd
https://github.com/galaxyproject/galaxy/commit/37c7425eae98c8cc39b7a0d9ca6b…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M .ci/flake8_wrapper_docstrings.sh
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #3995 from jmchilton/flake8fixes
Remove pydocstyle pins - there was an update to flake8-docstrings.
Commit: d638e377054893554e31f93d009c3bb153c6ddf5
https://github.com/galaxyproject/galaxy/commit/d638e377054893554e31f93d009c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Quick fix for displaying a message instead of just redirecting on clientside routes when login is required. TODO: refactor both message display and the decoration of routes.
Commit: edff1e65b9bd08b09ac864c93cbec867be23b444
https://github.com/galaxyproject/galaxy/commit/edff1e65b9bd08b09ac864c93cbe…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge pull request #4000 from dannon/error_message_for_login_required
Displaying a message instead of just redirecting
Commit: 7b50ae39b0d4ad5208e97f86c60e16bfa9fcfbff
https://github.com/galaxyproject/galaxy/commit/7b50ae39b0d4ad5208e97f86c60e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M .ci/flake8_wrapper_docstrings.sh
M .ci/jenkins/selenium/run_tests.sh
M CITATION
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/viz/phyloviz.js
M config/galaxy.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M run_tests.sh
M setup.cfg
M static/maps/mvc/citation/citation-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/viz/phyloviz.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/viz/phyloviz.js
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
M test/api/test_jobs.py
M test/api/test_workflows.py
M test/galaxy_selenium/navigates_galaxy.py
M test/qunit/tests/form_tests.js
M test/selenium_tests/framework.py
M test/selenium_tests/test_workflow_run.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into hashtags
Commit: 06e2e67872b8de486c189fd513ac5458c91dc2e5
https://github.com/galaxyproject/galaxy/commit/06e2e67872b8de486c189fd513ac…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/tag.js
M static/maps/mvc/tag.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tag.js
Log Message:
-----------
Merge pull request #3979 from dannon/hashtags
Hashtags
Commit: 86ebe28667008d65f0c4223e22df1e74837baf11
https://github.com/galaxyproject/galaxy/commit/86ebe28667008d65f0c4223e22df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Enhance filenames with collection context when downloading datasets from GUI.
- Reduce duplication related to calculating filename.
- Formalized pattern for normal dataset download using string.Tempalte - "Galaxy${hid}-[${name}].${ext}".
- In the context of collections, hid and name of the datasets are pretty worthless so I used a second pattern for collections based on where it is in the current GUI frame. The new pattern is "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}".
- The patterns make this a little more tweakable - for people who want something different it should be pretty straight forward to make these patterns configurable.
Fixes #2140 I think.
Commit: ef92904afaa0222e66e0861dbb37fdf07e541a88
https://github.com/galaxyproject/galaxy/commit/ef92904afaa0222e66e0861dbb37…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-01 (Mon, 01 May 2017)
Changed paths:
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/dataset/dataset-model.js
Log Message:
-----------
Repack client.
Commit: 4b7d5e32d4a0cd6ffa72e6551b57022a4d2dc6d2
https://github.com/galaxyproject/galaxy/commit/4b7d5e32d4a0cd6ffa72e6551b57…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M lib/galaxy/datatypes/data.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/dataset/dataset-model.js
Log Message:
-----------
Merge pull request #3985 from jmchilton/fix_collection_download_name
Enhance filenames with collection context when downloading datasets from GUI.
Commit: a6415b25fdb9661504505ba9c5016f7645720d30
https://github.com/galaxyproject/galaxy/commit/a6415b25fdb9661504505ba9c501…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M test/base/driver_util.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #3909 from mvdbeek/speedup_toolbox
Speedup startup and toolbox operations
Commit: de46a0edba4c49bafa061a08fc49c5d7f72cbd30
https://github.com/galaxyproject/galaxy/commit/de46a0edba4c49bafa061a08fc49…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3935 from jmchilton/more_maf_fixes
[17.01] More careful inspection of fixes for MAF tools requiring Galaxy.
Commit: 1c8370cf33a0bba05019397677c2b0a386b5136b
https://github.com/galaxyproject/galaxy/commit/1c8370cf33a0bba05019397677c2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Restore line accidentally removed as part of #3985.
Commit: 1a733864842ba8c1af3591b4d1aaa85fb3152a9a
https://github.com/galaxyproject/galaxy/commit/1a733864842ba8c1af3591b4d1aa…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #3996 from guerler/undo_url_upload_renaming
Undo dataset renaming for URL uploads
Commit: 0680a29a7992de0e606ec7047da845d5686d8029
https://github.com/galaxyproject/galaxy/commit/0680a29a7992de0e606ec7047da8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge pull request #4004 from jmchilton/filename_fixup
Restore line accidentally removed as part of #3985.
Commit: d224bedd3992e413363f345d64488e13d63518fe
https://github.com/galaxyproject/galaxy/commit/d224bedd3992e413363f345d6448…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Implicitly set use_volumes = False if using Docker swarm
Commit: 4b3a361a887d02e1944fd092b1c3a84b7da13f95
https://github.com/galaxyproject/galaxy/commit/4b3a361a887d02e1944fd092b1c3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
Log Message:
-----------
Update Jupyter image to 17.05
Commit: afc4fbcc38292c90641dcac737fd08ad0c253201
https://github.com/galaxyproject/galaxy/commit/afc4fbcc38292c90641dcac737fd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
Log Message:
-----------
Merge pull request #4007 from natefoo/jupyer-17.05
Update Jupyter image to 17.05
Commit: ecf634a619e93ffe98b5b785e3de10125940adce
https://github.com/galaxyproject/galaxy/commit/ecf634a619e93ffe98b5b785e3de…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #4006 from natefoo/implicit-use-volumes
Implicitly set use_volumes = False if using Docker swarm
Commit: 06d0e4fce57fa29e6d7fb02c455b77f6855f783c
https://github.com/galaxyproject/galaxy/commit/06d0e4fce57fa29e6d7fb02c455b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into dev
Commit: 8db51db70258463df762e6ed70f621f56d1a8d74
https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 17.05.rc1
Commit: 609842e558da5f60eef94809204b48204fc8158a
https://github.com/galaxyproject/galaxy/commit/609842e558da5f60eef94809204b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M tox.ini
Log Message:
-----------
[17.05] Pin dependencies for linting Galaxy.
Commit: aeed375c0286315c2b893d7b807d3522c5c21a36
https://github.com/galaxyproject/galaxy/commit/aeed375c0286315c2b893d7b807d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M tox.ini
Log Message:
-----------
Merge pull request #4012 from jmchilton/17.05_pin_release_linting
[17.05] Pin dependencies for linting Galaxy.
Commit: ce8f0dec0532266bff5d277f8acc50a4c6a9b2b5
https://github.com/galaxyproject/galaxy/commit/ce8f0dec0532266bff5d277f8acc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-02 (Tue, 02 May 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Merge pull request #4009 from jmchilton/version-17.05
[17.05] Update version to 17.05.rc1
Commit: 460d1737beb5d6e3e966c33998a7d5d046ac3e87
https://github.com/galaxyproject/galaxy/commit/460d1737beb5d6e3e966c33998a7…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-05-03 (Wed, 03 May 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
typo
Commit: 8dd5b153ed728591d3e44acb4271afc0210981f2
https://github.com/galaxyproject/galaxy/commit/8dd5b153ed728591d3e44acb4271…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-03 (Wed, 03 May 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Pass hdca and element_identifier to _serve_raw
This is necessary for getting the new filenames introduced in #3985 if
downloading tabular datatypes. Closes #4016.
Commit: 99317c77557ed4daec4c36619ec90a45a51e35eb
https://github.com/galaxyproject/galaxy/commit/99317c77557ed4daec4c36619ec9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-03 (Wed, 03 May 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
Log Message:
-----------
Merge pull request #4017 from mvdbeek/fix_new_download_names_tabular
Pass hdca and element_identifier to _serve_raw
Commit: 6ef7b9977a3ed936c02b3e7fadfd105bbaea9595
https://github.com/galaxyproject/galaxy/commit/6ef7b9977a3ed936c02b3e7fadfd…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-03 (Wed, 03 May 2017)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Merge pull request #4015 from erasche/remote-user-bug
[17.05] Typo in remote user / user preferences exception
Commit: 3332dfb6717e9bd368341e0bc0aa51d3b53fa861
https://github.com/galaxyproject/galaxy/commit/3332dfb6717e9bd368341e0bc0aa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-04 (Thu, 04 May 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/explicit.py
M lib/galaxy/util/plugin_config.py
Log Message:
-----------
[17.05] Fix setting up explicit container resolution from a container resolution config file.
Commit: f26e358321481500d0f993e0d7b2be9bdd1047b8
https://github.com/galaxyproject/galaxy/commit/f26e358321481500d0f993e0d7b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Fix docker_dispatch dynamic destination rule for container resolvers.
Commit: a9faa4873e4509a60822019afe3faa4cab3f8336
https://github.com/galaxyproject/galaxy/commit/a9faa4873e4509a60822019afe3f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Do not attempt to use mulled containers if tool requires legacy Galaxy environment.
Commit: be7dea47d556823abfab7a369b3ac466f6dea494
https://github.com/galaxyproject/galaxy/commit/be7dea47d556823abfab7a369b3a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Sanitize container names sending to Kubernetes.
Commit: a0c59d8f05c011f6c7b002599ed09c3fe091c340
https://github.com/galaxyproject/galaxy/commit/a0c59d8f05c011f6c7b002599ed0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Try activating conda environment again if previous activation failed
Commit: c38c0276afb88ed5b1403ede53ae35247307890d
https://github.com/galaxyproject/galaxy/commit/c38c0276afb88ed5b1403ede53ae…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-07 (Sun, 07 May 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Exit with error message when conda environemnt could not be activated (thx @nsoranzo).
Commit: 9e6c1529929132414e240e306d2b244ef6853944
https://github.com/galaxyproject/galaxy/commit/9e6c1529929132414e240e306d2b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-08 (Mon, 08 May 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4035 from mvdbeek/retry_conda_activation
[17.05] Try activating conda environment again if previous activation failed
Commit: ced568a9e5974d0a4944abce99a64f1b8eb6e6f6
https://github.com/galaxyproject/galaxy/commit/ced568a9e5974d0a4944abce99a6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-10 (Wed, 10 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Fix destructive tag rerender to be a simple replacement. Left the original template/render in place, we could refactor as this becomes more standardized.
Commit: 650691c943c096ee15233c61e4459982b2c6928d
https://github.com/galaxyproject/galaxy/commit/650691c943c096ee15233c61e445…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Merge pull request #4052 from dannon/1705_fix_tag_drag
[17.05] Fix destructive tag rerender to be a simpler, more precise html replacement.
Commit: 3e079a9f2c908e53413df0c4d77363995df8425f
https://github.com/galaxyproject/galaxy/commit/3e079a9f2c908e53413df0c4d773…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M lib/galaxy/objectstore/s3.py
Log Message:
-----------
Fix for s3objectstore _clean_cache method, thanks to @zzsoni and @nsoranzo
Commit: b7a66f182ef8607835665035e547e389d93237de
https://github.com/galaxyproject/galaxy/commit/b7a66f182ef8607835665035e547…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M lib/galaxy/objectstore/s3.py
Log Message:
-----------
Merge pull request #4055 from dannon/s3_objs_fix
[17.01] Fix for s3objectstore _clean_cache method
Commit: 9940ae70309a56013200d3e30ced5bf9437c75c7
https://github.com/galaxyproject/galaxy/commit/9940ae70309a56013200d3e30ced…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M lib/galaxy/objectstore/s3.py
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Commit: 04bb1e85cd16a04d6968c8d10755bd5e142831b1
https://github.com/galaxyproject/galaxy/commit/04bb1e85cd16a04d6968c8d10755…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M static/maps/mvc/upload/collection/collection-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/upload/collection/collection-view.js
Log Message:
-----------
[17.05] Fix FTP upload of multiple files in collection uploader.
Commit: aa1e4cea148ba6a1683d905704191e64ee64a46c
https://github.com/galaxyproject/galaxy/commit/aa1e4cea148ba6a1683d90570419…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-11 (Thu, 11 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M static/maps/mvc/upload/collection/collection-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/upload/collection/collection-view.js
Log Message:
-----------
Merge pull request #4058 from jmchilton/upload_ftp_fix
[17.05] Fix FTP upload of multiple files in collection uploader.
Commit: 0bafd683f152f28a193ee39a415018e4a8952767
https://github.com/galaxyproject/galaxy/commit/0bafd683f152f28a193ee39a4150…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-12 (Fri, 12 May 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/explicit.py
M lib/galaxy/util/plugin_config.py
Log Message:
-----------
Merge pull request #4020 from jmchilton/fix_explicit_container_resolver_from_config
[17.05] Fix setting up explicit container resolution...
Commit: 185c76605f2d0da1d8e261b9b3b3a626b8ba6226
https://github.com/galaxyproject/galaxy/commit/185c76605f2d0da1d8e261b9b3b3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-12 (Fri, 12 May 2017)
Changed paths:
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Merge pull request #4033 from jmchilton/dispatch_fix
[17.05] Fixes for containerized job executions.
Commit: 5e880815ade8756964017a446c6ceaa5cbb72f1a
https://github.com/galaxyproject/galaxy/commit/5e880815ade8756964017a446c6c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-05-14 (Sun, 14 May 2017)
Changed paths:
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M test/functional/webhooks/trans_object/config/trans_object.yaml
Log Message:
-----------
Use galaxy.root by default
Commit: 88c0635ef70d8054b50dcbfae2788a9cfa7bd973
https://github.com/galaxyproject/galaxy/commit/88c0635ef70d8054b50dcbfae278…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-05-14 (Sun, 14 May 2017)
Changed paths:
M doc/source/admin/special_topics/webhooks.rst
Log Message:
-----------
Link has already rotted
Commit: 6dd145ed1a97263eb9cca42f26613e28b22f177d
https://github.com/galaxyproject/galaxy/commit/6dd145ed1a97263eb9cca42f2661…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-05-14 (Sun, 14 May 2017)
Changed paths:
M doc/source/admin/special_topics/webhooks.rst
Log Message:
-----------
Try and document a bit
Commit: bd83608a2fb9ac6e8ec0391ab803f569e134d4fa
https://github.com/galaxyproject/galaxy/commit/bd83608a2fb9ac6e8ec0391ab803…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M static/maps/mvc/grid/grid-template.js.map
M static/scripts/mvc/grid/grid-template.js
Log Message:
-----------
Fix global grid action events
Commit: d3427a1344d165cf6b76b3e2ef4c2113f5ea1916
https://github.com/galaxyproject/galaxy/commit/d3427a1344d165cf6b76b3e2ef4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Rebuild
Commit: 6614e94a4953a8352515edded517d060cd6265c7
https://github.com/galaxyproject/galaxy/commit/6614e94a4953a8352515edded517…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-15 (Mon, 15 May 2017)
Changed paths:
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M doc/source/admin/special_topics/webhooks.rst
M test/functional/webhooks/trans_object/config/trans_object.yaml
Log Message:
-----------
Merge pull request #4065 from erasche/fix-4064
[17.05] Correct webhooks to use Galaxy.root and be compatible with proxy_prefix
Commit: 8c126a87579f89a3689cdcacf467ee01bbe6793a
https://github.com/galaxyproject/galaxy/commit/8c126a87579f89a3689cdcacf467…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-16 (Tue, 16 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Update contributors, diff of 17.01->17.05.
Commit: 3807b5d3037d569138366c44659d9ee955a5590f
https://github.com/galaxyproject/galaxy/commit/3807b5d3037d569138366c44659d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-16 (Tue, 16 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
16.10 -> 17.01 contributor diff.
Commit: b88097ae395968d562c1847189fae0b129f6ce4b
https://github.com/galaxyproject/galaxy/commit/b88097ae395968d562c1847189fa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-16 (Tue, 16 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
16.07 -> 16.10 contributors update.
Commit: 5b27ad4cb47b5b250db3cf0cf2624b09a05b40ed
https://github.com/galaxyproject/galaxy/commit/5b27ad4cb47b5b250db3cf0cf262…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-16 (Tue, 16 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
CONTRIBUTORS update 16.04 -> 16.07
Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7
https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
Log Message:
-----------
initial version of RN
Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5
https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/index.rst
Log Message:
-----------
add 17.05 to the release list
Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b
https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/_thanks.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
fix links to wiki/hub
Commit: 56874e163086b89d97dae17d59afa004777936bd
https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
rn improvements
Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966
https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new options from galaxy.ini diff
Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89
https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
link to proper release-bound sample config
Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b
https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new datatypes section to the announce
Commit: 4125f79161e584aa98098016e6a540111c7b5e2a
https://github.com/galaxyproject/galaxy/commit/4125f79161e584aa98098016e6a5…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M lib/galaxy/jobs/runners/kubernetes.py
Log Message:
-----------
Merge pull request #4034 from jmchilton/k8_name_fixed
[17.05] Sanitize container names sending to Kubernetes.
Commit: 3d6dfa4f60741743507c259da6d5610ab6fa14ff
https://github.com/galaxyproject/galaxy/commit/3d6dfa4f60741743507c259da6d5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
For people without a commit-signing email, just use the github username (for now -- they can of course change this via PR)
Commit: b1e9552e1b13c36c8d9ec7343e2f4cd11817cbef
https://github.com/galaxyproject/galaxy/commit/b1e9552e1b13c36c8d9ec7343e2f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Merge pull request #4070 from dannon/contrib_update
[17.05] CONTRIBUTORS update
Commit: f1d4ceeb304783801b96a579900e3b0e5da4010d
https://github.com/galaxyproject/galaxy/commit/f1d4ceeb304783801b96a579900e…
Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Update CONTRIBUTORS.md
completing the email address
Commit: 73bf5b4f7502e8e8f4d7701bd9ab77770968d396
https://github.com/galaxyproject/galaxy/commit/73bf5b4f7502e8e8f4d7701bd9ab…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Merge pull request #4086 from hrhotz/patch-1
Update CONTRIBUTORS.md
Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b
https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Do not modify self.app.config.tool_data_path
and self.app.config.tool_data_table_config_path during metadata setting.
xref https://github.com/galaxyproject/tools-iuc/issues/1315.
I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0
https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-05-21 (Sun, 21 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
update openbabel to version 2.4.1
Commit: d5f298baa59c05015fa19967443915e1c4faf595
https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa199674439…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
add Thoba's email
Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00
https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Merge pull request #4095 from martenson/contrib-email
[17.05] add Thoba's email to contributors
Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950
https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
polish release notes, add links to tutorials
Commit: 15556c0a71eb7bbdf33f35158239b4a243441510
https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
Merge pull request #4075 from martenson/17.05_release_notes
[17.05] release notes
Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf
https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d71313…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
listify new contributors
Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415
https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
Merge pull request #4094 from bgruening/openbabel_update
[17.05] Open Babel update for datatype converters
Commit: 9ebc464ba3f4d78822603638df00331864a1acf9
https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df00…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
Merge pull request #4100 from martenson/17.05_release_notes
[17.05] release notes- listify new contributors
Commit: 6f8472e525345b74fb6818bd2d89cd486435c822
https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fixes repeat handling in workflow editor, store values as passed from ui
Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25
https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #4104 from dannon/tags_continued
[17.05] Change to only inheriting 'name' tags
Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb
https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4089 from mvdbeek/no_global_changes
[17.05] Do not modify self.app.config.tool_data_path
Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7
https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Merge pull request #4107 from guerler/fix_repeats_in_workflows
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
Commit: 31015a83af9b3622498dd63276ffe93c45f5d6c6
https://github.com/galaxyproject/galaxy/commit/31015a83af9b3622498dd63276ff…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Remove residual comment
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
Commit: 4294663d5379555c8c6ab12eb520430379941701
https://github.com/galaxyproject/galaxy/commit/4294663d5379555c8c6ab12eb520…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
Log Message:
-----------
Improve 17.05 release notes
Also add 4 pull requests merged in the last few days.
Commit: d8c21e1fd9a1c9058ffa9efa9db2984c807e84af
https://github.com/galaxyproject/galaxy/commit/d8c21e1fd9a1c9058ffa9efa9db2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4110 from nsoranzo/release_17.05
[17.05] Improve 17.05 release notes
Commit: 18ef6a6ab0dcba1a1254a9d9f4273c346fdd1478
https://github.com/galaxyproject/galaxy/commit/18ef6a6ab0dcba1a1254a9d9f427…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 17.05
Commit: 796168bfa76b5fdb627f44c8cac4e3a137ce2690
https://github.com/galaxyproject/galaxy/commit/796168bfa76b5fdb627f44c8cac4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper_docstrings.sh
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M .travis.yml
M CITATION
M CONTRIBUTING.md
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/citation/citation-view.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
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M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/external_service_types.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/explicit.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/fetcher.py
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
A lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/compression_utils.py
A lib/galaxy/util/handlers.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/plugin_config.py
R lib/galaxy/util/postfork.py
M lib/galaxy/util/submodules.py
M lib/galaxy/version.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
A lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
M lib/galaxy/web/proxy/js/package.json
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/util.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
R openid/google.xml
M run.sh
M run_tests.sh
M scripts/api/README
M scripts/bootstrap_history.py
M scripts/common_startup.sh
A scripts/secret_decoder_ring.py
M scripts/slideshow/slideshow_template.html
M setup.cfg
A static/GruntFile.js
A static/GruntFile.js.map
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
M static/maps/libs/jquery/jquery.autocomplete.js.map
M static/maps/mvc/citation/citation-view.js.map
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-canvas.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/maps/ui/autocom_tagging.js.map
M static/maps/viz/phyloviz.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
M static/scripts/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/citation/citation-view.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/viz/phyloviz.js
M static/style/blue/base.css
M templates/admin/reload_tool.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/grid_base.mako
M templates/show_params.mako
R templates/user/dbkeys.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/galaxy.masthead.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/galaxy/workflow/display.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/TESTING.md
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_webhooks.py
M test/api/test_workflows.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/checksum.xml
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/output_format_deprecated_when.xml
A test/functional/tools/param_text_option.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/galaxy_selenium/sizzle.py
M test/integration/test_resolvers.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/qunit/package.json
M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_workflow_progress.py
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.xml
M tools/filters/pasteWrapper.xml
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tox.ini
Log Message:
-----------
Merge branch 'release_17.05'
Compare: https://github.com/galaxyproject/galaxy/compare/7e64fa395c6c...796168bfa76b
1
0
Branch: refs/tags/v17.05
Home: https://github.com/galaxyproject/galaxy
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 31015a83af9b3622498dd63276ffe93c45f5d6c6
https://github.com/galaxyproject/galaxy/commit/31015a83af9b3622498dd63276ff…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Remove residual comment
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
Commit: 4294663d5379555c8c6ab12eb520430379941701
https://github.com/galaxyproject/galaxy/commit/4294663d5379555c8c6ab12eb520…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
Log Message:
-----------
Improve 17.05 release notes
Also add 4 pull requests merged in the last few days.
Commit: d8c21e1fd9a1c9058ffa9efa9db2984c807e84af
https://github.com/galaxyproject/galaxy/commit/d8c21e1fd9a1c9058ffa9efa9db2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4110 from nsoranzo/release_17.05
[17.05] Improve 17.05 release notes
Commit: e50c787aa77c154e9098cba184e14feeed72fbfe
https://github.com/galaxyproject/galaxy/commit/e50c787aa77c154e9098cba184e1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge branch 'release_17.05' into dev
Commit: 18ef6a6ab0dcba1a1254a9d9f4273c346fdd1478
https://github.com/galaxyproject/galaxy/commit/18ef6a6ab0dcba1a1254a9d9f427…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 17.05
Commit: d7a0fdfaa748ca427dda1cef74b81e253f1921d5
https://github.com/galaxyproject/galaxy/commit/d7a0fdfaa748ca427dda1cef74b8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Log Message:
-----------
Merge branch 'release_17.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/e0c01115249a...d7a0fdfaa748
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 18ef6a6ab0dcba1a1254a9d9f4273c346fdd1478
https://github.com/galaxyproject/galaxy/commit/18ef6a6ab0dcba1a1254a9d9f427…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 17.05
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 31015a83af9b3622498dd63276ffe93c45f5d6c6
https://github.com/galaxyproject/galaxy/commit/31015a83af9b3622498dd63276ff…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Remove residual comment
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
Commit: 4294663d5379555c8c6ab12eb520430379941701
https://github.com/galaxyproject/galaxy/commit/4294663d5379555c8c6ab12eb520…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
Log Message:
-----------
Improve 17.05 release notes
Also add 4 pull requests merged in the last few days.
Commit: d8c21e1fd9a1c9058ffa9efa9db2984c807e84af
https://github.com/galaxyproject/galaxy/commit/d8c21e1fd9a1c9058ffa9efa9db2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4110 from nsoranzo/release_17.05
[17.05] Improve 17.05 release notes
Compare: https://github.com/galaxyproject/galaxy/compare/0268f5078c28...d8c21e1fd9a1
1
0
[galaxyproject/galaxy] 989b6b: Change to only inheriting 'name' tags -- we may wa...
by GitHub 24 May '17
by GitHub 24 May '17
24 May '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 989b6be3390e35d896122ef044ffe114f8959949
https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-19 (Wed, 19 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively.
Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7
https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
Log Message:
-----------
initial version of RN
Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5
https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/index.rst
Log Message:
-----------
add 17.05 to the release list
Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b
https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/_thanks.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
fix links to wiki/hub
Commit: 56874e163086b89d97dae17d59afa004777936bd
https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
rn improvements
Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966
https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new options from galaxy.ini diff
Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89
https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
link to proper release-bound sample config
Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b
https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new datatypes section to the announce
Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b
https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Do not modify self.app.config.tool_data_path
and self.app.config.tool_data_table_config_path during metadata setting.
xref https://github.com/galaxyproject/tools-iuc/issues/1315.
I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0
https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-05-21 (Sun, 21 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
update openbabel to version 2.4.1
Commit: d5f298baa59c05015fa19967443915e1c4faf595
https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa199674439…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
add Thoba's email
Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00
https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Merge pull request #4095 from martenson/contrib-email
[17.05] add Thoba's email to contributors
Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950
https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
polish release notes, add links to tutorials
Commit: 15556c0a71eb7bbdf33f35158239b4a243441510
https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
Merge pull request #4075 from martenson/17.05_release_notes
[17.05] release notes
Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf
https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d71313…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
listify new contributors
Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415
https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
Merge pull request #4094 from bgruening/openbabel_update
[17.05] Open Babel update for datatype converters
Commit: 9ebc464ba3f4d78822603638df00331864a1acf9
https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df00…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
Merge pull request #4100 from martenson/17.05_release_notes
[17.05] release notes- listify new contributors
Commit: 6f8472e525345b74fb6818bd2d89cd486435c822
https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fixes repeat handling in workflow editor, store values as passed from ui
Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25
https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #4104 from dannon/tags_continued
[17.05] Change to only inheriting 'name' tags
Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb
https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4089 from mvdbeek/no_global_changes
[17.05] Do not modify self.app.config.tool_data_path
Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7
https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Merge pull request #4107 from guerler/fix_repeats_in_workflows
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
Commit: e0c01115249a68abbd96fbc2f4e991578f5a5433
https://github.com/galaxyproject/galaxy/commit/e0c01115249a68abbd96fbc2f4e9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M CONTRIBUTORS.md
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M doc/source/releases/older_releases.rst
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge branch 'release_17.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/2aec5dda9ad7...e0c01115249a
1
0
[galaxyproject/galaxy] 6f8472: Fixes repeat handling in workflow editor, store va...
by GitHub 23 May '17
by GitHub 23 May '17
23 May '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 6f8472e525345b74fb6818bd2d89cd486435c822
https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fixes repeat handling in workflow editor, store values as passed from ui
Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7
https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Merge pull request #4107 from guerler/fix_repeats_in_workflows
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
Compare: https://github.com/galaxyproject/galaxy/compare/3d1da8e11d5a...0268f5078c28
1
0
23 May '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b
https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-05-19 (Fri, 19 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Do not modify self.app.config.tool_data_path
and self.app.config.tool_data_table_config_path during metadata setting.
xref https://github.com/galaxyproject/tools-iuc/issues/1315.
I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb
https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Merge pull request #4089 from mvdbeek/no_global_changes
[17.05] Do not modify self.app.config.tool_data_path
Compare: https://github.com/galaxyproject/galaxy/compare/aa8aafb10958...3d1da8e11d5a
1
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[galaxyproject/galaxy] 989b6b: Change to only inheriting 'name' tags -- we may wa...
by GitHub 23 May '17
by GitHub 23 May '17
23 May '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 989b6be3390e35d896122ef044ffe114f8959949
https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ff…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-19 (Wed, 19 Apr 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively.
Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25
https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #4104 from dannon/tags_continued
[17.05] Change to only inheriting 'name' tags
Compare: https://github.com/galaxyproject/galaxy/compare/9ebc464ba3f4...aa8aafb10958
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 47339bf1f33b52fade0db00a1af23eba34648da5
https://github.com/galaxyproject/galaxy/commit/47339bf1f33b52fade0db00a1af2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Catch specific exception type
Also remove unused variable
Commit: a033a5821ad11fbe0465b01984c97e591785623c
https://github.com/galaxyproject/galaxy/commit/a033a5821ad11fbe0465b01984c9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Allow empty <environment_variable>
Presently trying to install a ToolShed tool dependency defined as
<tool_dependency>
<set_environment version="1.0">
<environment_variable name="MYVAR" action="set_to"></environment_variable>
</set_environment>
</tool_dependency>
results in EnvManager.create_env_var_dict() returning None, which in turn
causes the dependency silently not being installed with this error in the
logs:
tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler DEBUG 2017-05-23 10:08:23,798 Error setting environment for tool dependency: local variable 'tool_dependency' referenced before assignment
Commit: e4de203c7da50aee3a95edacaf7f00d79b1ac416
https://github.com/galaxyproject/galaxy/commit/e4de203c7da50aee3a95edacaf7f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Raise an exception if name or action are not defined
instead of silently skipping the <environment_variable> tool dependency
Commit: 2aec5dda9ad7b66b0da6de08873b919d472b0309
https://github.com/galaxyproject/galaxy/commit/2aec5dda9ad7b66b0da6de08873b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Merge pull request #4105 from nsoranzo/ts_tool_dep_install_fixes
ToolShed tool dependency install fixes
Compare: https://github.com/galaxyproject/galaxy/compare/1bc8ea69c950...2aec5dda9ad7
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf
https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d71313…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
listify new contributors
Commit: 9ebc464ba3f4d78822603638df00331864a1acf9
https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df00…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
Merge pull request #4100 from martenson/17.05_release_notes
[17.05] release notes- listify new contributors
Compare: https://github.com/galaxyproject/galaxy/compare/0b3e29199f33...9ebc464ba3f4
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0
https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-05-21 (Sun, 21 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
update openbabel to version 2.4.1
Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415
https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
Merge pull request #4094 from bgruening/openbabel_update
[17.05] Open Babel update for datatype converters
Compare: https://github.com/galaxyproject/galaxy/compare/15556c0a71eb...0b3e29199f33
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7
https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
Log Message:
-----------
initial version of RN
Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5
https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/index.rst
Log Message:
-----------
add 17.05 to the release list
Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b
https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/_thanks.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
fix links to wiki/hub
Commit: 56874e163086b89d97dae17d59afa004777936bd
https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
rn improvements
Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966
https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new options from galaxy.ini diff
Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89
https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
link to proper release-bound sample config
Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b
https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new datatypes section to the announce
Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950
https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
polish release notes, add links to tutorials
Commit: 15556c0a71eb7bbdf33f35158239b4a243441510
https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
Merge pull request #4075 from martenson/17.05_release_notes
[17.05] release notes
Compare: https://github.com/galaxyproject/galaxy/compare/f94fa8edbe12...15556c0a71eb
1
0
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: d5f298baa59c05015fa19967443915e1c4faf595
https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa199674439…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
add Thoba's email
Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00
https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Merge pull request #4095 from martenson/contrib-email
[17.05] add Thoba's email to contributors
Compare: https://github.com/galaxyproject/galaxy/compare/73bf5b4f7502...f94fa8edbe12
1
0
20 May '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a2ed7f2fc83dfbbe3bd32b7da7a0957a4c552864
https://github.com/galaxyproject/galaxy/commit/a2ed7f2fc83dfbbe3bd32b7da7a0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-20 (Sat, 20 May 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
More workflow test case fixes for #4047.
I think previously this button would be there on page load and now it is loaded after the page in JS.
Commit: 1bc8ea69c950eeb9525b393c86bf92b93e2efcfc
https://github.com/galaxyproject/galaxy/commit/1bc8ea69c950eeb9525b393c86bf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-20 (Sat, 20 May 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge pull request #4093 from jmchilton/selenium_fixes_14
More workflow test case fixes for #4047.
Compare: https://github.com/galaxyproject/galaxy/compare/3f4d820b466d...1bc8ea69c950
1
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