Branch: refs/heads/release_15.07
Home: https://github.com/galaxyproject/galaxy
Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b
https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
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/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.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/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/libs/jquery/jquery.dynatree.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-choice.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
A large assortment of escaping fixes to primarily grids and javascript
templating, and one bad-data-ingress fix (copy history name).
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 05ed245353331489ee443ac483b1569dab38f500
https://github.com/galaxyproject/galaxy/commit/05ed245353331489ee443ac483b1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_review_grids.py
Log Message:
-----------
Fix the bad merge :(
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610
https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M lib/galaxy/util/xml_macros.py
M test/unit/tools/test_tool_loader.py
Log Message:
-----------
Fix macro bug with empty CDATA being None instead of ''.
Fixes galaxyproject/planemo#362 thanks for the report @erasche.
Test using the following command:
```
nosetests test/unit/tools/test_tool_loader.py
```
Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8
https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M lib/galaxy/util/xml_macros.py
M test/unit/tools/test_tool_loader.py
Log Message:
-----------
Merge pull request #1122 from jmchilton/empty_cdata_macro
[15.10] Fix macro bug with empty CDATA being None instead of ''.
Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7
https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
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/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.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/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/libs/jquery/jquery.dynatree.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-choice.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name).
Commit: f61ec1c3c01b51fe3449a583e1966cc3dff099f2
https://github.com/galaxyproject/galaxy/commit/f61ec1c3c01b51fe3449a583e196…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
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/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.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/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M lib/galaxy/util/xml_macros.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/maps/galaxy-app-base.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/ui/ui-select-default.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/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/ui/ui-select-default.js
M test/unit/tools/test_tool_loader.py
Log Message:
-----------
Merge and rebuild client
Compare: https://github.com/galaxyproject/galaxy/compare/96b17bd8560f...f61ec1c3c01b
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7
https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
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/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.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/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/libs/jquery/jquery.dynatree.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-choice.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name).
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 704144c16936e6ddedee9d509ee4361f50f152f2
https://github.com/galaxyproject/galaxy/commit/704144c16936e6ddedee9d509ee4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M lib/galaxy/tools/evaluation.py
Log Message:
-----------
Don't let $input hang cheetah evaluation...
If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation.
Commit: 0ff8a21891f7780dd30f81047cb5f8112c924b4a
https://github.com/galaxyproject/galaxy/commit/0ff8a21891f7780dd30f81047cb5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M lib/galaxy/tools/evaluation.py
A test/functional/tools/cheetah_problem_unbound_var.xml
A test/functional/tools/cheetah_problem_unbound_var_input.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add example tools demonstrating cheetah problem (unbound variable).
Refine default override of input to raise an exception instead of just throwing in a dummy string.
Commit: 7dedb3ff18f06b123ac9d64ac1d9b42948ba903c
https://github.com/galaxyproject/galaxy/commit/7dedb3ff18f06b123ac9d64ac1d9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
A test/functional/tools/cheetah_problem_syntax_error.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add another cheetah syntax error example...
... ensure the test framework run the tool, detects that there is an error, and handles things appropriately.
Commit: 96b17bd8560f938ee9d3244b6cf5b198864c44ce
https://github.com/galaxyproject/galaxy/commit/96b17bd8560f938ee9d3244b6cf5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
Changed paths:
M lib/galaxy/tools/evaluation.py
A test/functional/tools/cheetah_problem_syntax_error.xml
A test/functional/tools/cheetah_problem_unbound_var.xml
A test/functional/tools/cheetah_problem_unbound_var_input.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1117 from jmchilton/input_hang
Don't let $input hang cheetah evaluation...
Compare: https://github.com/galaxyproject/galaxy/compare/81f842743d0c...96b17bd8560f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: af36ca6d9467932036d19a448ca4c74affffae9a
https://github.com/galaxyproject/galaxy/commit/af36ca6d9467932036d19a448ca4…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
Changed paths:
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/static/js/ipython.js
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
add BAM iobio visualisation as Interactive Environment
Commit: 5188b4179063b3cc57c5c983d48a5fb62387d2b3
https://github.com/galaxyproject/galaxy/commit/5188b4179063b3cc57c5c983d48a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
Changed paths:
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
make travis happy
Commit: 81f842743d0c42522f7f80b603eccbc78d697a3c
https://github.com/galaxyproject/galaxy/commit/81f842743d0c42522f7f80b603ec…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-11-19 (Thu, 19 Nov 2015)
Changed paths:
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/static/js/ipython.js
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M lib/galaxy/web/base/interactive_environments.py
Log Message:
-----------
Merge pull request #1131 from bgruening/IE_iobio
Add BAM iobio visualisation as Interactive Environment
Compare: https://github.com/galaxyproject/galaxy/compare/5191c2136a91...81f842743d0c