Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 05176dabbe30ba9565c4f5a6865c012aada9e047
https://github.com/galaxyproject/galaxy/commit/05176dabbe30ba9565c4f5a6865c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M test/selenium_tests/test_library_to_collections.py
Log Message:
-----------
Restructure and mark as flakey problematic library collection Selenium test.
Needs to be restructured for flakey to work, several other PRs attempted to address or clarify this but have failed.
Commit: d1489ca57ce80b7fc85f59cf2158cc041898c101
https://github.com/galaxyproject/galaxy/commit/d1489ca57ce80b7fc85f59cf2158…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-20 (Tue, 20 Mar 2018)
Changed paths:
M test/selenium_tests/test_library_to_collections.py
Log Message:
-----------
Merge pull request #5714 from jmchilton/defeated_by_selenium
Restructure and mark as flakey problematic library collection Selenium test.
Compare: https://github.com/galaxyproject/galaxy/compare/40e87162597d...d1489ca57ce8
Branch: refs/heads/usegalaxy
Home: https://github.com/galaxyproject/galaxy
Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4
https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Minor cleanup in galaxy.tools.actions
Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf
https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Fix a few mutable default params in workflow/run_request.
Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5
https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/managers/libraries.py
Log Message:
-----------
replace incorrect list add syntax
Commit: 332d79eb72c4bae90c911707d4db9285556c59b1
https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Fix 'uknown' typo in model exceptions
Commit: 6b9afb6b360108b194c03ca262a20013b444ece9
https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/managers/libraries.py
Log Message:
-----------
rmeove overly zealous syntax fix
thanks to dannon
Commit: 04404f915c70b90a9d4a56dbeb030748163dce16
https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Support re-execution of immediate PJAs when requing jobs
Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4
https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Ship context along with PJA execution when remapping workflow immediate actions
Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818
https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Instead of denoting unused var from items(), just use values()
Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64
https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Test rename PJA when resuming a failed job
Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5
https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #26 from mvdbeek/workflow-resume-pjas
Test rename PJA when resuming a failed job
Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a
https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M lib/galaxy/managers/libraries.py
Log Message:
-----------
Merge pull request #5676 from martenson/fix-library-add
[18.01] replace incorrect list add syntax
Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e
https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/workflow/run_request.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #5678 from dannon/workflow-resume-pjas
[18.01] Support re-execution of immediate PJAs when re-queing jobs
Commit: 31cb24e4229767425a72d6981bcb359b15792254
https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/grid/grid-shared.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/hdca-li-edit.js.map
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tool-genomespace.js.map
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/onload.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/utils/config.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/slotting.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.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/form/form-parameters.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-genomespace.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/onload.js
M static/scripts/ui/loading-indicator.js
M static/scripts/utils/config.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
Log Message:
-----------
add built client with maps for 18.01 tagging
Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3
https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 18.01
Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e
https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
add security announcement to the rn
Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e
https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e57…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
Merge pull request #5688 from martenson/security-rn
[18.01] backport add security announcement to the release notes
Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754
https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc…
Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior
Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999
https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type
[18.01] Fix/default role type on auto created roles
Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55
https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/admin/nginx.md
Log Message:
-----------
Clarfify that nginx-extras needs to be install for the upload_store directive to work
Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e
https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/admin/nginx.md
Log Message:
-----------
Merge pull request #5717 from mvdbeek/nginx_doc_update
[18.01] Clarify that nginx-extras needs to be install for the upload_store d…
Commit: 3b87dac78028846a803e33ae13199535c70f567d
https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae1319…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
Log Message:
-----------
Add Galaxy `lib` directory to Python path for 2 scripts
Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e .
Fix https://github.com/galaxyproject/galaxy/issues/5722 .
Commit: ef45ae3752a4ea4da73719e2917a064c8e239ab3
https://github.com/galaxyproject/galaxy/commit/ef45ae3752a4ea4da73719e2917a…
Author: pvanheus <pvh(a)webbedfeet.co.za>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Upgrade clone failure logging to error
When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'.
Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009
https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bf…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
Log Message:
-----------
Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts
[17.09] Add Galaxy `lib` directory to Python path for 2 scripts
Commit: 50035b184e0ceba61f21f223e5f701710dd86d19
https://github.com/galaxyproject/galaxy/commit/50035b184e0ceba61f21f223e5f7…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
improve update commands in RN, clarify uwsgi config changes
Commit: 74d0bcb353b4824d4d4af9ffe6bd909924feca62
https://github.com/galaxyproject/galaxy/commit/74d0bcb353b4824d4d4af9ffe6bd…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
Log Message:
-----------
Merge branch 'release_17.09' into release_18.01
Commit: 924eecc67a3155578aea6a484d9bfd86d0cc5aba
https://github.com/galaxyproject/galaxy/commit/924eecc67a3155578aea6a484d9b…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
Add missing `.`
Commit: 3699e9e4919dcb727af3ff0e7457794642973dfa
https://github.com/galaxyproject/galaxy/commit/3699e9e4919dcb727af3ff0e7457…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
re-add the motivation for uwsgi switch
Commit: 240f14d62fb6bdbf02f51ff1af19602494560880
https://github.com/galaxyproject/galaxy/commit/240f14d62fb6bdbf02f51ff1af19…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
Log Message:
-----------
Merge pull request #5730 from martenson/bootstrap
[18.01] improve update commands in RN, clarify uwsgi config changes
Commit: a73a1d6250373cd1e6bb1255052ee7cb541e4569
https://github.com/galaxyproject/galaxy/commit/a73a1d6250373cd1e6bb1255052e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Merge pull request #5728 from mvdbeek/backport_logging_level_change
[18.01] Backport 5724: upgrade clone failure logging to error
Commit: 7c962975750c9747b12413309ac0c546fe8a9046
https://github.com/galaxyproject/galaxy/commit/7c962975750c9747b12413309ac0…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-03-20 (Tue, 20 Mar 2018)
Changed paths:
M doc/source/admin/nginx.md
M doc/source/releases/18.01_announce.rst
M lib/galaxy/managers/libraries.py
M lib/galaxy/model/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/version.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/util/hg_util.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/grid/grid-shared.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/hdca-li-edit.js.map
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tool-genomespace.js.map
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/onload.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/utils/config.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/slotting.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/extended.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/form/form-parameters.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-genomespace.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/onload.js
M static/scripts/ui/loading-indicator.js
M static/scripts/utils/config.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
M test/api/test_workflows.py
Log Message:
-----------
Merge remote-tracking branch 'origin/release_18.01' into usegalaxy
Compare: https://github.com/galaxyproject/galaxy/compare/e12e773eddca...7c962975750c