Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aa7968aa9d13ab5de9fcebd427e5eca356cc1de4
https://github.com/galaxyproject/galaxy/commit/aa7968aa9d13ab5de9fcebd427e5…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-31 (Mon, 31 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/job_info.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/system.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Changed class naming to reflect use
Commit: 0a1617024c7923c12531fa9e18da3494833a6f1f
https://github.com/galaxyproject/galaxy/commit/0a1617024c7923c12531fa9e18da…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2015-08-31 (Mon, 31 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/job_info.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/system.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Merge pull request #675 from Airistotal/dev
Changed class naming to reflect use
Compare: https://github.com/galaxyproject/galaxy/compare/f61f696724a0...0a1617024c79
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 469d8b463e4711770925f4152c95769b7c1d04dc
https://github.com/galaxyproject/galaxy/commit/469d8b463e4711770925f4152c95…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-28 (Fri, 28 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Fixed change in class overlap
Commit: ec8cba20398dcfe0fdd7a46ad93cf78fadc310ec
https://github.com/galaxyproject/galaxy/commit/ec8cba20398dcfe0fdd7a46ad93c…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-28 (Fri, 28 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M client/galaxy/style/less/reports.less
A doc/source/api/quickstart.rst
M doc/source/api_doc.rst
A doc/source/dev/faq.rst
A doc/source/dev/index.rst
M doc/source/index.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/shed_util_common.py
M test/base/asserts/__init__.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/qunit/README.txt
M test/qunit/package.json
M test/unit/managers/test_DatasetManager.py
M test/unit/tools/test_tool_loader.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Conflicts:
client/galaxy/style/less/reports.less
static/style/blue/base.css
static/style/blue/reports.css
Commit: f61f696724a0b264a8706d6bf682fa09c178bc5e
https://github.com/galaxyproject/galaxy/commit/f61f696724a0b264a8706d6bf682…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2015-08-31 (Mon, 31 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
Log Message:
-----------
Merge pull request #669 from Airistotal/dev
Fix centering bug in firefox
Compare: https://github.com/galaxyproject/galaxy/compare/d4af323d35e4...f61f696724a0
Branch: refs/heads/release_15.07
Home: https://github.com/galaxyproject/galaxy
Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b
https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-08-24 (Mon, 24 Aug 2015)
Changed paths:
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
Log Message:
-----------
When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture.
Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975
https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-08-28 (Fri, 28 Aug 2015)
Changed paths:
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
Log Message:
-----------
Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload
[release_15.07] Fix setting of toolshed repository attributes in special cases.
Compare: https://github.com/galaxyproject/galaxy/compare/4fcdf9fda1d2...525188d2a871
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f28ddf779cc18ae87eff2c1d28c65622e367dbfb
https://github.com/galaxyproject/galaxy/commit/f28ddf779cc18ae87eff2c1d28c6…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-28 (Fri, 28 Aug 2015)
Changed paths:
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
Use new path variable syntax available since Routes 1.9
The old syntax is now documented only in the "Backward compatibility" section
of Routes documentation. It is still supported, but may be removed in the
future.
Commit: eae62ca2cb122f5a0a674027fadc0a28d9dd179e
https://github.com/galaxyproject/galaxy/commit/eae62ca2cb122f5a0a674027fadc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-28 (Fri, 28 Aug 2015)
Changed paths:
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
Merge pull request #665 from nsoranzo/dev
Use new path variable syntax available since Routes 1.9
Compare: https://github.com/galaxyproject/galaxy/compare/bada494b85c9...eae62ca2cb12
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7ce4bde8781645b09bb7ce54b9b7114c41ff9c36
https://github.com/galaxyproject/galaxy/commit/7ce4bde8781645b09bb7ce54b9b7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/jobs/actions/post.py
Log Message:
-----------
Allow accessing repeat and conditional elements in PJA parameters.
Use . instead of the | that would be the actual association name. Cannot use | because it is treated as a special character in this code. Parameters with . in the names break Galaxy in subtle ways anyway and so treating them as a special character here should not be a problem.
Commit: bada494b85c93c5662275ab5652e29e7bfb9a0ac
https://github.com/galaxyproject/galaxy/commit/bada494b85c93c5662275ab5652e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/jobs/actions/post.py
Log Message:
-----------
Merge pull request #662 from jmchilton/repeat_rename
Allow accessing repeat and conditional elements in PJA parameters.
Compare: https://github.com/galaxyproject/galaxy/compare/396bcc782082...bada494b85c9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e99353bd1cb83fc55ac4678c43bbf4ce8bcbed55
https://github.com/galaxyproject/galaxy/commit/e99353bd1cb83fc55ac4678c43bb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
fix TS API endpoint to correctly consume full relpath of the image
Commit: 23a978709528d55ab02c4127e785df909adb47c4
https://github.com/galaxyproject/galaxy/commit/23a978709528d55ab02c4127e785…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
remove replaces for static prefix in image relpaths
this is not a problem when in Tool Shed and it prevents people form using these paths
ping @bgruening
Commit: 183ddbed3e9d01f24d66fd0d49454ecdb9e95aa6
https://github.com/galaxyproject/galaxy/commit/183ddbed3e9d01f24d66fd0d4945…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Eliminate ${static_path} from tool shed image links.
I did not find a reason to use it.
Commit: 396bcc782082e2965f67fc6ec87b02e79cf74859
https://github.com/galaxyproject/galaxy/commit/396bcc782082e2965f67fc6ec87b…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #660 from martenson/fix-tool-image-paths
Fix tool image paths.
Compare: https://github.com/galaxyproject/galaxy/compare/5d4d32a43221...396bcc782082