Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 35a716b8549bd575c96ef9cafe0e78a7e2048139
https://github.com/galaxyproject/galaxy/commit/35a716b8549bd575c96ef9cafe0e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Not all objects added to the runner work queue are
JobWrappers/TaskWrappers as claimed in the comment.
AsynchronousJobStates could also be added, and if the fail method was
called this would result in the AttributeError of attempting to access
an AJS' non-existent `get_id_tag` being logged in job.exeception as a
red herring.
Commit: 38209bbbac705612c11f7f3083e357e046cb5c64
https://github.com/galaxyproject/galaxy/commit/38209bbbac705612c11f7f3083e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-14 (Sat, 14 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Merge pull request #2350 from natefoo/fix-ajs-red-herring
[16.04] Properly handle AsynchronousJobState objects in the job runner work queue
Compare: https://github.com/galaxyproject/galaxy/compare/e28d305f3cda...38209bbbac70
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 86050f2b67e84c3322363d67ef457e5303ce52c9
https://github.com/galaxyproject/galaxy/commit/86050f2b67e84c3322363d67ef45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/style/less/base.less
M static/maps/mvc/tool/tool-form.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/tool/tool-form.js
M static/style/blue/base.css
Log Message:
-----------
Build job success messages within tool form view
Commit: b5ea024cd17ba60cbf96eec0cd6ba0d84e1db208
https://github.com/galaxyproject/galaxy/commit/b5ea024cd17ba60cbf96eec0cd6b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-14 (Sat, 14 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/style/less/base.less
M static/maps/mvc/tool/tool-form.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/tool/tool-form.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #2355 from guerler/revise_template_001
Build job success messages within tool form view
Compare: https://github.com/galaxyproject/galaxy/compare/db8afda49d59...b5ea024cd17b
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 364ce6ed84c15a09a008b2bdcafb4aa192c4b842
https://github.com/galaxyproject/infrastructure-playbook/commit/364ce6ed84c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-13 (Fri, 13 May 2016)
Changed paths:
M jetstreamiuenv/group_vars/galaxynodes.yml
M jetstreamtaccenv/group_vars/galaxynodes.yml
M taccenv/group_vars/galaxynodes.yml
Log Message:
-----------
Install LZO on execution hosts now that we don't ship it (formerly an
egg)
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8255e722cd21bb1cee594db3212657c6a22aa730
https://github.com/galaxyproject/galaxy/commit/8255e722cd21bb1cee594db32126…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Do not pollute param_dict with a non JSONifiable dict
When running a data manager with a dataset parameter, the job fails
with the following backtrace:
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job
job_wrapper.prepare()
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare
tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment
self.tool.exec_before_job( self.app, inp_data, out_data, param_dict )
File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job
out.write( json.dumps( (json_params) ).encode('utf8') )
File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps
return _default_encoder.encode(obj)
File "/usr/lib/python2.7/json/encoder.py", line 207, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode
return _iterencode(o, 0)
TypeError: keys must be a string
The bug was introduced in PR #2029.
Commit: e28d305f3cda4377325190363057431f1f4f4d46
https://github.com/galaxyproject/galaxy/commit/e28d305f3cda4377325190363057…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029
[16.04] Do not pollute param_dict with a non JSONifiable dict
Commit: bf7996087e8b3da9c40f7cd575691cf7123d760d
https://github.com/galaxyproject/galaxy/commit/bf7996087e8b3da9c40f7cd57569…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/366056c0b70a...bf7996087e8b
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 8255e722cd21bb1cee594db3212657c6a22aa730
https://github.com/galaxyproject/galaxy/commit/8255e722cd21bb1cee594db32126…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Do not pollute param_dict with a non JSONifiable dict
When running a data manager with a dataset parameter, the job fails
with the following backtrace:
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job
job_wrapper.prepare()
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare
tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment
self.tool.exec_before_job( self.app, inp_data, out_data, param_dict )
File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job
out.write( json.dumps( (json_params) ).encode('utf8') )
File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps
return _default_encoder.encode(obj)
File "/usr/lib/python2.7/json/encoder.py", line 207, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode
return _iterencode(o, 0)
TypeError: keys must be a string
The bug was introduced in PR #2029.
Commit: e28d305f3cda4377325190363057431f1f4f4d46
https://github.com/galaxyproject/galaxy/commit/e28d305f3cda4377325190363057…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029
[16.04] Do not pollute param_dict with a non JSONifiable dict
Compare: https://github.com/galaxyproject/galaxy/compare/013813691ac1...e28d305f3cda
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 19a1679c94ca0a571da0453022aae15a0fce2b44
https://github.com/galaxyproject/galaxy/commit/19a1679c94ca0a571da0453022aa…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
Log Message:
-----------
UI: minor updates to libraries
Commit: bab9e44db17ff8871567b6d1933d1990ee7f1af9
https://github.com/galaxyproject/galaxy/commit/bab9e44db17ff8871567b6d1933d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
M static/maps/libs/bootstrap-tour.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/d3.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
Log Message:
-----------
(re-build client)
Commit: af15f55ea9c0e511c10e1e3b0bb45c90741c3ecf
https://github.com/galaxyproject/galaxy/commit/af15f55ea9c0e511c10e1e3b0bb4…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
M client/bower.json
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/underscore.js
M static/maps/libs/backbone.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/underscore.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/libs/backbone.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/underscore.js
Log Message:
-----------
UI: major library updates
jquery 1.12.3
jquery-migrate 1.4.0
ravenjs 3.0.3
requirejs 2.2.0
tracekit 0.4.3
underscore 1.8.3
backbone 1.3.3
bootstrap-tour 0.10.3
d3 3.5.17
Commit: 7afb7616ff4ec362b34978352ac50c132f530c56
https://github.com/galaxyproject/galaxy/commit/7afb7616ff4ec362b34978352ac5…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
M test/qunit/tests/form_tests.js
Log Message:
-----------
Tests: send empty obj to qunit/form_tests
`null` caused a script error in require.
Commit: 0844852388a16f737557ae58b7a7dd66f43656f0
https://github.com/galaxyproject/galaxy/commit/0844852388a16f737557ae58b7a7…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
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 client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.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/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.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
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
Log Message:
-----------
UI: remove deprecated jQuery.size()
(from selected scripts)
Commit: 54f25f262cdd2242e61342521c5643af037149c7
https://github.com/galaxyproject/galaxy/commit/54f25f262cdd2242e61342521c56…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M Makefile
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
Log Message:
-----------
(merge conflicts)
Commit: ecfbf53e6600c8590d3e9fcec9022bf540339985
https://github.com/galaxyproject/galaxy/commit/ecfbf53e6600c8590d3e9fcec902…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M static/maps/mvc/history/history-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.map
M static/scripts/mvc/history/history-model.js
Log Message:
-----------
(merge conflicts)
Commit: ab05091379463cf6e3d9c416cd601051aacceabd
https://github.com/galaxyproject/galaxy/commit/ab05091379463cf6e3d9c416cd60…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-12 (Thu, 12 May 2016)
Changed paths:
M client/bower.json
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.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/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M static/maps/libs/backbone.js.map
M static/maps/libs/bootstrap-tour.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/libs/underscore.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/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.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/backbone.js
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/d3.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/libs/underscore.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/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge pull request #2328 from carlfeberhard/client.libs-update
Client library updates
Compare: https://github.com/galaxyproject/galaxy/compare/09e8f0ab9b83...ab0509137946
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7e63ae66cd93d2cf046484cfa07cf6453656d8c1
https://github.com/galaxyproject/galaxy/commit/7e63ae66cd93d2cf046484cfa07c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M client/galaxy/scripts/utils/metrics-logger.js
M static/maps/utils/metrics-logger.js.map
M static/scripts/utils/metrics-logger.js
M test/qunit/test-common.js
R test/qunit/test-libs/qunit-1.14.0.css
R test/qunit/test-libs/qunit-1.14.0.js
A test/qunit/test-libs/qunit-1.23.1.css
A test/qunit/test-libs/qunit-1.23.1.js
A test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-1.9.1.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Update qunit and sinon
Commit: b7dc5cdf8f66f964e17ed41564b410df97bea9d0
https://github.com/galaxyproject/galaxy/commit/b7dc5cdf8f66f964e17ed41564b4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M test/qunit/tests/page_tests.js
Log Message:
-----------
Fix page test
Commit: 74a53c4ebd99fe928ef92e89dba5034945724e5e
https://github.com/galaxyproject/galaxy/commit/74a53c4ebd99fe928ef92e89dba5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M test/qunit/test-common.js
Log Message:
-----------
QUnit can't be shim/init'd since it's a proper AMD module including a define.
Commit: 6e5aea08c49603c415ac58f8edf6608f03ca54c3
https://github.com/galaxyproject/galaxy/commit/6e5aea08c49603c415ac58f8edf6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M test/qunit/tests/metrics-logger.js
Log Message:
-----------
Remove unnecessary MockStorage from Metrics test
Commit: 468f17418e9445a18d8b2c2c62fe1d884c331fa4
https://github.com/galaxyproject/galaxy/commit/468f17418e9445a18d8b2c2c62fe…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M test/qunit/tests/list-of-pairs-collection-creator.js
Log Message:
-----------
Fix collection test
Commit: 09e8f0ab9b838025b5c9b4e9936774018cf789da
https://github.com/galaxyproject/galaxy/commit/09e8f0ab9b838025b5c9b4e99367…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M client/galaxy/scripts/utils/metrics-logger.js
M static/maps/utils/metrics-logger.js.map
M static/scripts/utils/metrics-logger.js
M test/qunit/test-common.js
R test/qunit/test-libs/qunit-1.14.0.css
R test/qunit/test-libs/qunit-1.14.0.js
A test/qunit/test-libs/qunit-1.23.1.css
A test/qunit/test-libs/qunit-1.23.1.js
A test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-1.9.1.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Merge pull request #2338 from guerler/update_qunit_000
Update qunit and sinon
Compare: https://github.com/galaxyproject/galaxy/compare/fcc0d123ea4e...09e8f0ab9b83