Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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: 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: 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: 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
Compare: https://github.com/galaxyproject/galaxy/compare/a7572145e9c0...43f2a648230b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b
https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Fix workflow save-as url not using galaxy's prefix.
Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665
https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #3610 from dannon/fix-editor-save-as-url
[17.01] Fix workflow save-as url not using galaxy's prefix.
Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c
https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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: 43d80a0b6052b59f8be768ad810fee952a436ce3
https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f…
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 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: 966d578b47f4999ba0f8db874bf927e5f4246d7f
https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here.
Commit: 944feb2411d1381b1743f3365b6380e883c9cccb
https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63…
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 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:
-----------
Minor tooltip tweaks.
Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48
https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33…
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 #3614 from dannon/logout-recalc-backport
[17.01] Logout recalc backport and additional logic
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
Compare: https://github.com/galaxyproject/galaxy/compare/df22e40522d7...8ce1291359c8
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c
https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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: 43d80a0b6052b59f8be768ad810fee952a436ce3
https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f…
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 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: 966d578b47f4999ba0f8db874bf927e5f4246d7f
https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here.
Commit: 944feb2411d1381b1743f3365b6380e883c9cccb
https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63…
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 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:
-----------
Minor tooltip tweaks.
Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48
https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33…
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 #3614 from dannon/logout-recalc-backport
[17.01] Logout recalc backport and additional logic
Compare: https://github.com/galaxyproject/galaxy/compare/c86d2ee8bcbd...c82530fd2384
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
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: 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.
Compare: https://github.com/galaxyproject/galaxy/compare/9597b9b62b66...df22e40522d7
Branch: refs/heads/revert-3572-fix_3548
Home: https://github.com/galaxyproject/galaxy
Commit: 4f80b11e9c513b4ca1a9442fbf955a3116c07436
https://github.com/galaxyproject/galaxy/commit/4f80b11e9c513b4ca1a9442fbf95…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/managers/deletable.py
R 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:
-----------
Revert "Set 'deleted' to True when purging a history dataset association"
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b
https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Fix workflow save-as url not using galaxy's prefix.
Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665
https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-14 (Tue, 14 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/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #3610 from dannon/fix-editor-save-as-url
[17.01] Fix workflow save-as url not using galaxy's prefix.
Compare: https://github.com/galaxyproject/galaxy/compare/5db0b7681bb6...c86d2ee8bcbd