September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 19bc49: Binary sniffing; along with the registry forcing c...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 19bc49d207a92288dc402900cfa0125b8da45111 https://github.com/galaxyproject/galaxy/commit/19bc49d207a92288dc402900cfa0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 Commit: aff8c708a925205332c4190e3ada5712dc04519e https://github.com/galaxyproject/galaxy/commit/aff8c708a925205332c4190e3ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #774 from dannon/stable_sniffers [15.07] Binary sniffing; along with the registry forcing case insensitivity t… Compare: https://github.com/galaxyproject/galaxy/compare/6044a5158c2a...aff8c708a925

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[galaxyproject/galaxy] ef23ab: WIP: Improved state tracking of HDCA in history pa...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef23abc6df1dfc1b5ca10d380c2e7a840862c76a https://github.com/galaxyproject/galaxy/commit/ef23abc6df1dfc1b5ca10d380c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/model/__init__.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hdca-li.js M test/api/test_dataset_collections.py Log Message: ----------- WIP: Improved state tracking of HDCA in history panel. For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color. Commit: 98f6dcc4dea061db7c04fbe8e2cd86898d10343b https://github.com/galaxyproject/galaxy/commit/98f6dcc4dea061db7c04fbe8e2cd… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render HDCAs when their models change Commit: d4534bb814bb5716152dad8dfc9bfc53c3983ebb https://github.com/galaxyproject/galaxy/commit/d4534bb814bb5716152dad8dfc9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #11 from carlfeberhard/jmchilton Render HDCAs when their models change Commit: a90a4fcebaee0a1c975bf0c90598bd72a7e7f833 https://github.com/galaxyproject/galaxy/commit/a90a4fcebaee0a1c975bf0c90598… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/model/__init__.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hdca-li.js M test/api/test_dataset_collections.py Log Message: ----------- Merge pull request #755 from jmchilton/hdca_structure_state_tracking Improved state tracking of HDCA in history panel. Compare: https://github.com/galaxyproject/galaxy/compare/595d7d5fd8f0...a90a4fcebaee

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[galaxyproject/galaxy] b9913d: Swap tool form to use Galaxy.modal
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b9913d29316de4058197739b2ae4cfed5c5ae2f3 https://github.com/galaxyproject/galaxy/commit/b9913d29316de4058197739b2ae4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Swap tool form to use Galaxy.modal Commit: 83bd9dd541079f0571b90044e1a64d8318377039 https://github.com/galaxyproject/galaxy/commit/83bd9dd541079f0571b90044e1a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- repack without --develop Commit: acfd8673b6817cc9d4b94947bb13293d1e384968 https://github.com/galaxyproject/galaxy/commit/acfd8673b6817cc9d4b94947bb13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M test/functional/tools/multi_output_configured.xml Log Message: ----------- Merge from dev." Commit: 3d697937c7f9d3aff0178f013692d795c3b73eb6 https://github.com/galaxyproject/galaxy/commit/3d697937c7f9d3aff0178f013692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Rerun improvement -- instead of allowing someone to try to rerun the upload tool and showing an error message, just don't provide the option for it in the first place. Commit: fe642fe7fa66a53b4fbb1f89e200c10ead7854a6 https://github.com/galaxyproject/galaxy/commit/fe642fe7fa66a53b4fbb1f89e200… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Tweak tool execution to automatically pull detail ids for new hdas on execution success model update so rerun can be immediate. Commit: 6804ce681be29baca1c1d50737b427b95b0a66ee https://github.com/galaxyproject/galaxy/commit/6804ce681be29baca1c1d50737b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/root/index.mako M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Merge dev, resolve conflicts from console re-enablement. Commit: 53f7ac02d23939c8b17ad93ead787527dc1c805b https://github.com/galaxyproject/galaxy/commit/53f7ac02d23939c8b17ad93ead78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Don't use a local reference to modal -- the intent here was to allow component-isolated modals as in other places, but we can do (or not) that at a later time. Commit: dc0dd6ec4b7a5f47595d43133e5f9d3d999a7e15 https://github.com/galaxyproject/galaxy/commit/dc0dd6ec4b7a5f47595d43133e5f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Simplify logic. Commit: 15a516b57799e61eaca90a3b7d9dc188a012b808 https://github.com/galaxyproject/galaxy/commit/15a516b57799e61eaca90a3b7d9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Remove 'disabled' cruft, since we opted to simply not show the button rather than disable it. Commit: 595d7d5fd8f0efc51b93e35018839831f6eac7f7 https://github.com/galaxyproject/galaxy/commit/595d7d5fd8f0efc51b93e3501883… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Merge pull request #781 from dannon/rerun_tweaks Rerun/toolform tweaks Compare: https://github.com/galaxyproject/galaxy/compare/e4c1e8b23226...595d7d5fd8f0

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[galaxyproject/galaxy] 81ad14: Backport keyup to change input
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81ad14a4e7c26dc5b3a5f9a026b72b2cbaad9266 https://github.com/galaxyproject/galaxy/commit/81ad14a4e7c26dc5b3a5f9a026b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Backport keyup to change input Commit: 6044a5158c2ac86aab45613e6193a9d782899a9e https://github.com/galaxyproject/galaxy/commit/6044a5158c2ac86aab45613e6193… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Merge pull request #780 from dannon/cherrypick_stuff_for_triple_approval [15.07] Backport keyup to change input Commit: a6715ebceccf036174ca5738e71a3e1052189411 https://github.com/galaxyproject/galaxy/commit/a6715ebceccf036174ca5738e71a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js M templates/user/login.mako Log Message: ----------- Merge branch 'release_15.07' Commit: e4c1e8b23226f901495ab4d3ab3689d5bc2344af https://github.com/galaxyproject/galaxy/commit/e4c1e8b23226f901495ab4d3ab36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A static/maps/mvc/upload/upload-row.js.map A static/scripts/mvc/upload/upload-row.js Log Message: ----------- Merge master->dev Compare: https://github.com/galaxyproject/galaxy/compare/183e5cd7c6fe...e4c1e8b23226

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[galaxyproject/galaxy] e95145: With Pulsar, ensure AMQP consumers receive publish...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: e951455be37a787a26678e66e607004a9b8ce954 https://github.com/galaxyproject/galaxy/commit/e951455be37a787a26678e66e607… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- With Pulsar, ensure AMQP consumers receive published messages. Commit: 5bae90156fa7998b575981ac452db21f34683085 https://github.com/galaxyproject/galaxy/commit/5bae90156fa7998b575981ac452d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/util.py Log Message: ----------- Fix a couple flake8 errors including a supposed PEP-8 violation that is actually a PEP-8-suggested acceptable option of how to handle the offending situation. =P Commit: 8778da43cb641a925c421b188aabe053be56e313 https://github.com/galaxyproject/galaxy/commit/8778da43cb641a925c421b188aab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/manager.py Log Message: ----------- Disable amqp_acknowledge by default, additional fixes from Pulsar's pickier flake8 checks. Commit: ff8e821013e59527bb2bdfacffef2a2db7e562d2 https://github.com/galaxyproject/galaxy/commit/ff8e821013e59527bb2bdfacffef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge pull request #704 from natefoo/amqp_ack [15.07] With Pulsar, ensure AMQP consumers receive published messages Commit: 448ff738f35ad3f8d627257f46c681a6a4907778 https://github.com/galaxyproject/galaxy/commit/448ff738f35ad3f8d627257f46c6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix incorrect indentation preventing changing of name/description of TS categories Commit: 16fb094f1a101064d6f2981166b060b1ba30aa0e https://github.com/galaxyproject/galaxy/commit/16fb094f1a101064d6f2981166b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #717 from martenson/fix-ts-edit-category [15.07] fix incorrect indentation preventing changing of name/description Commit: d41c137e2d6b4d9871bb25c5162745dda36e2f31 https://github.com/galaxyproject/galaxy/commit/d41c137e2d6b4d9871bb25c51627… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. (cherry picked from commit 451196e4d39800995d7b1ea1f69b177294c3c632) Commit: 358dc4071462347dacecd1f6ec125d650b261db0 https://github.com/galaxyproject/galaxy/commit/358dc4071462347dacecd1f6ec12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #718 from blankenberg/openid_15.07 [15.07] Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: 819c7dce408f35f69457cd92803c63cf3efca0c4 https://github.com/galaxyproject/galaxy/commit/819c7dce408f35f69457cd92803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: 88abd3451d1b8cb7161fde7559684d5378dc76fc https://github.com/galaxyproject/galaxy/commit/88abd3451d1b8cb7161fde755968… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #719 from natefoo/amqp_ack [15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: d3bd0fa57765bd2d03f255099c2b4f0501ac6466 https://github.com/galaxyproject/galaxy/commit/d3bd0fa57765bd2d03f255099c2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Do not change the state of jobs if a state update is received after they are set to a terminal state. Commit: 85552f73f712a9491af8d141a27369b21b615075 https://github.com/galaxyproject/galaxy/commit/85552f73f712a9491af8d141a273… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #737 from natefoo/job-terminal-update [15.07] Don't update the state of terminal jobs Commit: 81ad14a4e7c26dc5b3a5f9a026b72b2cbaad9266 https://github.com/galaxyproject/galaxy/commit/81ad14a4e7c26dc5b3a5f9a026b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Backport keyup to change input Commit: 6044a5158c2ac86aab45613e6193a9d782899a9e https://github.com/galaxyproject/galaxy/commit/6044a5158c2ac86aab45613e6193… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Merge pull request #780 from dannon/cherrypick_stuff_for_triple_approval [15.07] Backport keyup to change input Commit: a6715ebceccf036174ca5738e71a3e1052189411 https://github.com/galaxyproject/galaxy/commit/a6715ebceccf036174ca5738e71a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js M templates/user/login.mako Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/2284b2242c72...a6715ebceccf

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[galaxyproject/galaxy] 81ad14: Backport keyup to change input
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 81ad14a4e7c26dc5b3a5f9a026b72b2cbaad9266 https://github.com/galaxyproject/galaxy/commit/81ad14a4e7c26dc5b3a5f9a026b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Backport keyup to change input Commit: 6044a5158c2ac86aab45613e6193a9d782899a9e https://github.com/galaxyproject/galaxy/commit/6044a5158c2ac86aab45613e6193… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-row.js M static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/upload/upload-row.js Log Message: ----------- Merge pull request #780 from dannon/cherrypick_stuff_for_triple_approval [15.07] Backport keyup to change input Compare: https://github.com/galaxyproject/galaxy/compare/85552f73f712...6044a5158c2a

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[galaxyproject/galaxy] 130b3f: Add docker command wrapper. For example, to change...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 130b3f2d75f7f6af4087078f4f653c3ee645774b https://github.com/galaxyproject/galaxy/commit/130b3f2d75f7f6af4087078f4f65… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add docker command wrapper. For example, to change the current group to docker, which is needed when user belongs to (too) many groups) Commit: 54c4861b0d0f405b3c12348d40ed29fab8ff03b1 https://github.com/galaxyproject/galaxy/commit/54c4861b0d0f405b3c12348d40ed… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- space issue fixed Commit: 3167b426265d89e500fe50cd145004cdb5d4bc5c https://github.com/galaxyproject/galaxy/commit/3167b426265d89e500fe50cd1450… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M lib/galaxy/jobs/__init__.py M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- fixed merge conflict - but is this correct? Commit: 183e5cd7c6fe20cb9682fa78260c6466c9851497 https://github.com/galaxyproject/galaxy/commit/183e5cd7c6fe20cb9682fa78260c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #777 from scholtalbers/docker-cmd-wrapper Add docker command wrapper. Compare: https://github.com/galaxyproject/galaxy/compare/6a450b9c3178...183e5cd7c6fe

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[galaxyproject/galaxy] 292642: Fix upload event binding to be input and change in...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 292642ed91de908bf4e1e3f8705147bc7fd2ca1b https://github.com/galaxyproject/galaxy/commit/292642ed91de908bf4e1e3f87051… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Fix upload event binding to be input and change instead of just relying on keyup. This fixes https://github.com/galaxyproject/galaxy/issues/762 Commit: 76a683e878246b54e14dc4f9fcf3d17916b17564 https://github.com/galaxyproject/galaxy/commit/76a683e878246b54e14dc4f9fcf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge branch 'dev' into upload_fix Commit: 2ee34167921a92a8c14c3f1694e43bce3efc27cf https://github.com/galaxyproject/galaxy/commit/2ee34167921a92a8c14c3f1694e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- One more location where keyup should be replaced Commit: 6a450b9c31788586ec6d781984a145c7ce570d8a https://github.com/galaxyproject/galaxy/commit/6a450b9c31788586ec6d781984a1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #778 from dannon/upload_fix Fix upload event binding to be input and change instead of just relyi… Compare: https://github.com/galaxyproject/galaxy/compare/e9ddc21661ff...6a450b9c3178

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[galaxyproject/galaxy] 02e612: In log of collecting job metrics, print id, if ava...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02e61226b5681186426809d3497fdb2f0d46e466 https://github.com/galaxyproject/galaxy/commit/02e61226b5681186426809d3497f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In log of collecting job metrics, print id, if available, in addition to the string representation of the has_metrics object. Commit: e9ddc21661ffe27ed87e04a6c852c9914a22bacc https://github.com/galaxyproject/galaxy/commit/e9ddc21661ffe27ed87e04a6c852… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #772 from blankenberg/job-metrics In log of collecting job metrics, print id of has_metrics object Compare: https://github.com/galaxyproject/galaxy/compare/8b404205c07b...e9ddc21661ff

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[galaxyproject/galaxy] b1841e: Client build: do not drop console when compressing...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1841e22d924b53a3a75306bf773b0b0ad4f02a6 https://github.com/galaxyproject/galaxy/commit/b1841e22d924b53a3a75306bf773… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Client build: do not drop console when compressing, when not compressing do not mangle variable names Commit: 8b404205c07bcc7971cdc3d38cb369a0fc7d4940 https://github.com/galaxyproject/galaxy/commit/8b404205c07bcc7971cdc3d38cb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Resolve client merge conflict, repack. Compare: https://github.com/galaxyproject/galaxy/compare/91da5f806805...8b404205c07b

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