- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 024e29: Re-use job.finish abstraction in dataset manager s...
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 024e296ea8fa6dc7c3b3da3e74ac9e520e8daf73 https://github.com/galaxyproject/galaxy/commit/024e296ea8fa6dc7c3b3da3e74ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Re-use job.finish abstraction in dataset manager stop_creating_job. It is used in purge a bit above and it is the better abstraction. Commit: f153400e95ff3888fab1b6c0fb7be5686a882532 https://github.com/galaxyproject/galaxy/commit/f153400e95ff3888fab1b6c0fb7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Rework jobs API to not use deprecated TestsDatasets mixin. Commit: 009e2cbf5e9592fd8af782b2cde36d8d1687c003 https://github.com/galaxyproject/galaxy/commit/009e2cbf5e9592fd8af782b2cde3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Improve interaction between job state and purged datasets. There are two basic behavior changes here and bunch of testing to verify the new behaviors. 1) Previously purging a dataset would cause a creating job to be cancelled but all outputs would need to be "deleted" in order to cause the creating job to be cancelled. After this change the behavior is the same for both deletion and purging - the job will run until all outputs are deleted or purged. 2) Previously Galaxy jobs wouldn't attempt to cleanup purged datasets that were created by a running tool - this cleanup now occurs. These are tackled as a pair because I assume the difference in the behaviors between deletion and purging was a hack around tools populating datasets that had been purged while running. Cancelling the job wasn't a sure fix - but it would reduce the likelihood of such problems. I think the new approach is a bit more robust and explicit. Commit: 967d0b6c0aef6fe331c4e9c92bc1b902363e660a https://github.com/galaxyproject/galaxy/commit/967d0b6c0aef6fe331c4e9c92bc1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3619 from jmchilton/purge_jobs_rework Improve interaction between job state and purged datasets. Compare: https://github.com/galaxyproject/galaxy/compare/1c716eb9da35...967d0b6c0aef

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[galaxyproject/galaxy] ca36c0: Have tool-search listen to change as well as keyup
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca36c0dbfd438708e35e18d06c603f2cc2ce7047 https://github.com/galaxyproject/galaxy/commit/ca36c0dbfd438708e35e18d06c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Have tool-search listen to change as well as keyup Commit: 1c716eb9da355864bd0116ce2579be3f03482e7c https://github.com/galaxyproject/galaxy/commit/1c716eb9da355864bd0116ce2579… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Merge pull request #3808 from dannon/trigger-search-input Have tool-search listen to change as well as keyup Compare: https://github.com/galaxyproject/galaxy/compare/a6240c4b8c74...1c716eb9da35

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[galaxyproject/galaxy] 15aa0b: Fix problem with cleaning up jobs in local runner.
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2 https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix problem with cleaning up jobs in local runner. Fixes #3801 (broken in b78287f as part of #3291). Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235 https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3803 from jmchilton/1701_fixes_0 [17.01] Fix problem with cleaning up jobs in local runner. Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment. Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822. Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes [17.01] More CONVERTER fixes for restricting tools' Python environment. Commit: 812b04bb3abec97f1f465e9e9136904bd7e4164c https://github.com/galaxyproject/galaxy/commit/812b04bb3abec97f1f465e9e9136… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3826 from galaxyproject/release_17.01 [usegalaxy] Merge 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/f9b8e6a51a17...812b04bb3abe

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[galaxyproject/infrastructure-playbook] 2c6e2d: Update orval access list
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2c6e2d24d1da0b667f97bcaf1edfd24e2dda9954 https://github.com/galaxyproject/infrastructure-playbook/commit/2c6e2d24d1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update orval access list

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[galaxyproject/infrastructure-playbook] ccef6d: Depot login for DaveC
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ccef6dfcc0641a1fe5daf49be17675e2ec54c8d1 https://github.com/galaxyproject/infrastructure-playbook/commit/ccef6dfcc06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Depot login for DaveC

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[galaxyproject/galaxy] d8af12: Update __init__.py
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment. Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822. Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes [17.01] More CONVERTER fixes for restricting tools' Python environment. Compare: https://github.com/galaxyproject/galaxy/compare/65cbddee7c3b...70b22dffc288

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[galaxyproject/galaxy] 229c0a: Update __init__.py
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 229c0a2339b38f6481a489e5a8454018458297d2 https://github.com/galaxyproject/galaxy/commit/229c0a2339b38f6481a489e5a845… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py using the lagacy python environemnt is also required for "CONVERTER_bed_to_fli_0" when displaying a bed file in trackster Commit: 37fd039bd5bf0ca2beda8183e298cd1454b16544 https://github.com/galaxyproject/galaxy/commit/37fd039bd5bf0ca2beda8183e298… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: a6240c4b8c7477d2aca39ef97217139962fd5848 https://github.com/galaxyproject/galaxy/commit/a6240c4b8c7477d2aca39ef97217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3822 from hrhotz/patch-1 fix bedfile display in trackster Compare: https://github.com/galaxyproject/galaxy/compare/a47828bf892f...a6240c4b8c74

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[galaxyproject/galaxy] ad68b1: Make ToolConfWatcher watch ToolCache
by GitHub 25 Mar '17

25 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad68b154d4cbecdbc2e96e58d9d3c4153e014eeb https://github.com/galaxyproject/galaxy/commit/ad68b154d4cbecdbc2e96e58d9d3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_toolbox.py Log Message: ----------- Make ToolConfWatcher watch ToolCache If any item in the tool cache has changed (local tool update, repository update, tool deleted) the toolbox will be reloaded and any tool changes are applied. Should fix https://github.com/galaxyproject/galaxy/issues/3813. Commit: c91c988c852e5a30e1c7c69168b5df770933dcd5 https://github.com/galaxyproject/galaxy/commit/c91c988c852e5a30e1c7c69168b5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Fix ToolConfWatcher test: can only watch existing files Commit: 5be7ebe780b487175563eb4661955a07df1d30cd https://github.com/galaxyproject/galaxy/commit/5be7ebe780b487175563eb466195… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M test/unit/tools/test_toolbox.py Log Message: ----------- Only call tool_cache.cleanup if tool_cache exists Commit: 4d9cf642a80025e28ea0276f8c41fcd9d9a53903 https://github.com/galaxyproject/galaxy/commit/4d9cf642a80025e28ea0276f8c41… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix toolshed startup by setting tool_cache to `None` (the toolshed loads an empty toolbox) Commit: 0bf2493233fd0afbc07da6620740536938d8d059 https://github.com/galaxyproject/galaxy/commit/0bf2493233fd0afbc07da6620740… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Wrap tool_cache cleanup in try/except clause Commit: 197aa402d72895d370307ce9724c86b892cded96 https://github.com/galaxyproject/galaxy/commit/197aa402d72895d370307ce9724c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-25 (Sat, 25 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Improve ToolCache cleanup logic Pull `removed_tool_ids` out of try/except, so that we can return `removed_tool_ids` even if an exception occured. Fix a typo in the `_should_cleanup` docstring. Many thanks for the suggestions @nsoranzo. Commit: a47828bf892f8e1627bcb5f00ae63be56c9b6fcf https://github.com/galaxyproject/galaxy/commit/a47828bf892f8e1627bcb5f00ae6… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-25 (Sat, 25 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge pull request #3814 from mvdbeek/repository_updates Awesome, thanks @mvdbeek ! Compare: https://github.com/galaxyproject/galaxy/compare/18a26c5f376b...a47828bf892f

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[galaxyproject/infrastructure-playbook] b129f6: Disable pipelining by default (for cloud stuff), u...
by GitHub 24 Mar '17

24 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b129f6c6c8eb83debd820e49099d92a50e68c0f7 https://github.com/galaxyproject/infrastructure-playbook/commit/b129f6c6c8e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M ansible.cfg Log Message: ----------- Disable pipelining by default (for cloud stuff), unless this can be made conditional it's just too much of a pain. Commit: 206a8a617f317520f03452730eaa3c7725f83e54 https://github.com/galaxyproject/infrastructure-playbook/commit/206a8a617f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: A jetstreamdockerenv/README.md A jetstreamdockerenv/group_vars/all.yml A jetstreamdockerenv/group_vars/baseinstances.yml A jetstreamdockerenv/group_vars/imageinstances.yml A jetstreamdockerenv/inc_clouds_yaml.yml A jetstreamdockerenv/inc_delete.yml A jetstreamdockerenv/inc_spawn.yml A jetstreamdockerenv/inventory A jetstreamdockerenv/secret_group_vars/instances.yml A jetstreamdockerenv/snapshot_docker_base.yml A jetstreamdockerenv/snapshot_docker_image.yml A jetstreamdockerenv/ssh_config.jetstream_iu A jetstreamdockerenv/ssh_config.jetstream_tacc Log Message: ----------- Environment for creating Jetstream server and volume images for GIE docker swarm workers Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/aedc4f2b0a…

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[galaxyproject/infrastructure-playbook] b3b3f3: Ansible 2.2 fixes
by GitHub 24 Mar '17

24 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b3b3f3fec36886c1e66da5a704374b002b4d604b https://github.com/galaxyproject/infrastructure-playbook/commit/b3b3f3fec36… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M taccenv/playbook.yml Log Message: ----------- Ansible 2.2 fixes Commit: aedc4f2b0aca771a20930be5b237fcef9ccb4b82 https://github.com/galaxyproject/infrastructure-playbook/commit/aedc4f2b0ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M common_roles M roles/docker/README.md M roles/docker/defaults/main.yml M roles/docker/tasks/main.yml A roles/docker/tasks/ssl-ca.yml A roles/docker/tasks/ssl-client.yml M roles/docker/tasks/ssl-server.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory Log Message: ----------- Docker client updates Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/2095cbdca3…

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[galaxyproject/galaxy] ed9541: add ethercalc interactive environment
by GitHub 24 Mar '17

24 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed95412b36a0f349951e088ad5707f5c62e5851f https://github.com/galaxyproject/galaxy/commit/ed95412b36a0f349951e088ad570… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- add ethercalc interactive environment Commit: d47f582d152d095044ddb6454e880b8dedc7cab6 https://github.com/galaxyproject/galaxy/commit/d47f582d152d095044ddb6454e88… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- remove commented section Commit: 18a26c5f376b9c7be07f0998e817ef6262fc22c2 https://github.com/galaxyproject/galaxy/commit/18a26c5f376b9c7be07f0998e817… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- Merge pull request #3699 from shiltemann/ethercalc Ethercalc Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/5e97c017b980...18a26c5f376b

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[galaxyproject/galaxy] 0ced04: Flush out upload tests for Selenium.
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ced044897bc40f28b758e53b1019c422ea0410a https://github.com/galaxyproject/galaxy/commit/0ced044897bc40f28b758e53b101… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_uploads.py Log Message: ----------- Flush out upload tests for Selenium. - Use newer abstraction in the simplest upload test - verify the default extension (auto -> sam) and dbkey (?) also. - Add a test case that explicitly sets the extension of an upload and verifies. - Add a test case that explicitly sets a genome and verifies. - Add a test case that tests setting ext for all uploads and verifies. - Add a test case that tests setting genome for all uploads and verifies. Commit: 5e97c017b980cb7d478b5d17837f7438727e7551 https://github.com/galaxyproject/galaxy/commit/5e97c017b980cb7d478b5d17837f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3811 from jmchilton/upload_tests Implement more upload testing in Selenium. Compare: https://github.com/galaxyproject/galaxy/compare/b82d7311c103...5e97c017b980

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[galaxyproject/galaxy] 79b26d: Fix collection operations not having a history.
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79b26d2273d46250b55f04eb6c1e0a0c03bf65bf https://github.com/galaxyproject/galaxy/commit/79b26d2273d46250b55f04eb6c1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Fix collection operations not having a history. Fixes #3437. Commit: b82d7311c1034afa32a5ce3caa8aaa44b63d4bb9 https://github.com/galaxyproject/galaxy/commit/b82d7311c1034afa32a5ce3caa8a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Merge pull request #3786 from jmchilton/zip_edit Fix collection operations not having a history. Compare: https://github.com/galaxyproject/galaxy/compare/fbd8507e3a34...b82d7311c103

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[galaxyproject/galaxy] 3036df: Avoid potential inconsistencies between differentl...
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3036df35f0f5089cfbfc69ecdc46dcf057a3d6bf https://github.com/galaxyproject/galaxy/commit/3036df35f0f5089cfbfc69ecdc46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid potential inconsistencies between differently stored labels Commit: fbd8507e3a34e8f46545c1bf4869f179e03dde4e https://github.com/galaxyproject/galaxy/commit/fbd8507e3a34e8f46545c1bf4869… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3793 from guerler/store_label_in_step Avoid potential inconsistencies between differently stored labels Compare: https://github.com/galaxyproject/galaxy/compare/9e61aff69314...fbd8507e3a34

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[galaxyproject/galaxy] a3b16b: Small improvements to Qunit tests.
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3b16bf69a4d6f09b9693ffbc6a54ed0910918e9 https://github.com/galaxyproject/galaxy/commit/a3b16bf69a4d6f09b9693ffbc6a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M run_tests.sh M test/qunit/package.json Log Message: ----------- Small improvements to Qunit tests. - Drop explicit requirement on phantomjs since we are moving away from explicit phantomjs testing (it is still pulled in by QUnit which is fine). - If ``npm install .`` has previously been executed from the ``test/qunit``, don't require globally available grunt to run the tests via ``run_tests.sh -q``. Commit: 9e61aff69314606bff4ad16d502295cfdcb0ed07 https://github.com/galaxyproject/galaxy/commit/9e61aff69314606bff4ad16d5022… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M run_tests.sh M test/qunit/package.json Log Message: ----------- Merge pull request #3810 from jmchilton/qunit_touchup Small improvements for driving Qunit tests. Compare: https://github.com/galaxyproject/galaxy/compare/3a52d07a900f...9e61aff69314

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[galaxyproject/infrastructure-playbook] 2095cb: fix lib rewrites
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2095cbdca3a73902cc817dcd7a3688a22a1351d1 https://github.com/galaxyproject/infrastructure-playbook/commit/2095cbdca3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- fix lib rewrites slash in the end of target was preventing it from work

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[galaxyproject/galaxy] 7fdb40: Trim down one translation, thanks @mvdbeek
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7fdb4064c6194534cb654f1afd5d9b5e9dd98ef3 https://github.com/galaxyproject/galaxy/commit/7fdb4064c6194534cb654f1afd5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Trim down one translation, thanks @mvdbeek Commit: 3a52d07a900f4d4fa9933bbccce1efe76708988d https://github.com/galaxyproject/galaxy/commit/3a52d07a900f4d4fa9933bbccce1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #3809 from dannon/minor_wording_tweak One minor translation followup tweak to French Localization Compare: https://github.com/galaxyproject/galaxy/compare/9e807dab3f7b...3a52d07a900f

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[galaxyproject/infrastructure-playbook] 3c809f: add redirects for data libraries hub pages
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3c809f2172630aab71c255873e54240dbf2cf9bb https://github.com/galaxyproject/infrastructure-playbook/commit/3c809f21726… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- add redirects for data libraries hub pages

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[galaxyproject/galaxy] 977b1a: Remove duplicate keys from nls locales.
by GitHub 23 Mar '17

23 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 977b1acc48e878fb90a7b52e973ae497052b8583 https://github.com/galaxyproject/galaxy/commit/977b1acc48e878fb90a7b52e973a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js Log Message: ----------- Remove duplicate keys from nls locales. Commit: d0eaeff9c4b47b922ae5c764fbe3722603ac1148 https://github.com/galaxyproject/galaxy/commit/d0eaeff9c4b47b922ae5c764fbe3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/locale.js M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/locale.js Log Message: ----------- Add FR localization template. Needs translation next. Commit: 02327e7085559bd776bfda8743dc99edd2c3f14f https://github.com/galaxyproject/galaxy/commit/02327e7085559bd776bfda8743dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: A client/galaxy/scripts/nls/fr/locale.js A static/maps/nls/fr/locale.js.map A static/scripts/nls/fr/locale.js Log Message: ----------- Add FR localization template (the actual files). Needs translation next. Commit: e7b1d45a3990ce6db9fcdaa92dac6a18cb605345 https://github.com/galaxyproject/galaxy/commit/e7b1d45a3990ce6db9fcdaa92dac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Add some basic (likely awful) FR translations just to check the machinery here. Commit: d7e4e8e162bbeb071e83d08bd22f17b8bc59602f https://github.com/galaxyproject/galaxy/commit/d7e4e8e162bbeb071e83d08bd22f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Readability formatting for existing locales to set a standard moving forward. Commit: d4462cb3213e81c2d25b7575ca3865c7720437fd https://github.com/galaxyproject/galaxy/commit/d4462cb3213e81c2d25b7575ca38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Localization support for menu. Commit: 4f82467117d12fe6bab70fb96e769d3c89d9c212 https://github.com/galaxyproject/galaxy/commit/4f82467117d12fe6bab70fb96e76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- FR locale masthead support. Commit: 2ebf46effae518fc9d0dc1c574d2d5a30407b3ce https://github.com/galaxyproject/galaxy/commit/2ebf46effae518fc9d0dc1c574d2… Author: Bérénice Batut <berenice.batut(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Correct some translation errors Commit: f7cb5b70fc6ba0142b88a467f8a06889a0c7911a https://github.com/galaxyproject/galaxy/commit/f7cb5b70fc6ba0142b88a467f8a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #10 from dannon/bebatut-patch-1 Correct some translation errors Commit: 542a84afd5552b94bfdaff4ca8a6c0c368f1489a https://github.com/galaxyproject/galaxy/commit/542a84afd5552b94bfdaff4ca8a6… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- first pass Commit: c4f906cb729e08412924186726dfaba12bf2f2d8 https://github.com/galaxyproject/galaxy/commit/c4f906cb729e08412924186726df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #11 from lecorguille/i18n first pass Commit: 90de3671f132848a9eaae9048bf091f1969d0caf https://github.com/galaxyproject/galaxy/commit/90de3671f132848a9eaae9048bf0… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- pass 2 Commit: face53037d476bbc59e4674f861e903c23d52109 https://github.com/galaxyproject/galaxy/commit/face53037d476bbc59e4674f861e… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- pass 2 from Gildas Commit: 6b38ccada116ce2445a9bfc6fb513b54feacb65b https://github.com/galaxyproject/galaxy/commit/6b38ccada116ce2445a9bfc6fb51… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Uncomment and format FR localization. Commit: 9704b73500db07fde28c778a9977c6aa22aa237a https://github.com/galaxyproject/galaxy/commit/9704b73500db07fde28c778a9977… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Build client. Commit: 78074243d734c81891795d3ad25dffbe70130a29 https://github.com/galaxyproject/galaxy/commit/78074243d734c81891795d3ad25d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Forgot localization for 'Login' Commit: eaf631efbfe7dc7b0624ded57adb4410dab93f30 https://github.com/galaxyproject/galaxy/commit/eaf631efbfe7dc7b0624ded57adb… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- second pass Commit: 6d803463318a721bab91d4458fc8b1da540cc091 https://github.com/galaxyproject/galaxy/commit/6d803463318a721bab91d4458fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #14 from lecorguille/i18npass2 second pass Commit: 0221bdf9c71b5567af8928a121d62970850fa8c2 https://github.com/galaxyproject/galaxy/commit/0221bdf9c71b5567af8928a121d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- One last rebuild w/ final changes. Commit: 11ee6ea6384e3fde47fb0eb10d466461ffc050ee https://github.com/galaxyproject/galaxy/commit/11ee6ea6384e3fde47fb0eb10d46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix 'logged in as' localization usage. Commit: fe35ed009e72a65b0e120d4d29c8614652560db1 https://github.com/galaxyproject/galaxy/commit/fe35ed009e72a65b0e120d4d29c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Fix localization of Preferences Commit: 576ad4f95aa50fa80aa1de993bcbf03da5d2da98 https://github.com/galaxyproject/galaxy/commit/576ad4f95aa50fa80aa1de993bcb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Add preferences to core translations, update search datasets Commit: af849e506257419f73dbac58d7618bc00104b60c https://github.com/galaxyproject/galaxy/commit/af849e506257419f73dbac58d761… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- fix Yvan integration :P Commit: dc201094aa3cf07967f1c16ae6bef88718476e37 https://github.com/galaxyproject/galaxy/commit/dc201094aa3cf07967f1c16ae6be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Duplicated word in localization Commit: 8aaee3d33b378a8fd9d29b90f9003b0217c7ad43 https://github.com/galaxyproject/galaxy/commit/8aaee3d33b378a8fd9d29b90f900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #15 from lecorguille/i18npass3 Fix Yvan integration :P Commit: cc37049af8c08e50e6ca81ce83f93f35a0711c6e https://github.com/galaxyproject/galaxy/commit/cc37049af8c08e50e6ca81ce83f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge branch 'i18n' of github.com:dannon/galaxy into i18n Commit: ae049fe54068408866265ad2f040ee5b0aa8a763 https://github.com/galaxyproject/galaxy/commit/ae049fe54068408866265ad2f040… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge more fixes, rebuild. Commit: 269aac614b5d19ffbfc3ec1ad7e4330ba9c0b847 https://github.com/galaxyproject/galaxy/commit/269aac614b5d19ffbfc3ec1ad7e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Apply some suggested FR localization wording changes. Commit: 54af1979676c817b00044e645383e638b86fdcfa https://github.com/galaxyproject/galaxy/commit/54af1979676c817b00044e645383… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Add more translation points for localization. Commit: 8eb40ae7fb9d59586e40a7a85abdf5e222c903bd https://github.com/galaxyproject/galaxy/commit/8eb40ae7fb9d59586e40a7a85abd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Correct 'Get Data' usage, since we won't be translating that in the first pass Commit: 10ddd3d3bdb238f1ff0de26326fcaca07c81a316 https://github.com/galaxyproject/galaxy/commit/10ddd3d3bdb238f1ff0de26326fc… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- new points Commit: 390adffb988ff4f1c6b723e4f5776ed5186c26bb https://github.com/galaxyproject/galaxy/commit/390adffb988ff4f1c6b723e4f577… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #17 from lecorguille/i18n_history_options new points history options Commit: c58fa9a349ce4432f1febd5f530fc4afdd4893bd https://github.com/galaxyproject/galaxy/commit/c58fa9a349ce4432f1febd5f530f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M .ci/py3_sources.txt M README.rst A client/galaxy/scripts/mvc/collection/base-creator.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/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml R lib/galaxy/util/postfork.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run_tests.sh M scripts/api/README M scripts/secret_decoder_ring.py A static/maps/mvc/collection/base-creator.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/library/library-foldertoolbar-view.js.map M static/maps/nls/fr/locale.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.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/library/library-foldertoolbar-view.js M static/scripts/nls/fr/locale.js R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/api/test_libraries.py M test/docker/base/run_test_wrapper.sh M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Rebuild client and merge from upstream. Commit: 9e807dab3f7b98e77ca2358e1204a6220879764c https://github.com/galaxyproject/galaxy/commit/9e807dab3f7b98e77ca2358e1204… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/layout/menu.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #3762 from dannon/i18n i18n improvements and French localization Compare: https://github.com/galaxyproject/galaxy/compare/7457b7611513...9e807dab3f7b

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[galaxyproject/infrastructure-playbook] a024f5: '%20' to '\ ' in rewrites
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a024f5eb254b5a048c2d73e9eea272a1fe594af2 https://github.com/galaxyproject/infrastructure-playbook/commit/a024f5eb254… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- '%20' to '\ ' in rewrites

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[galaxyproject/infrastructure-playbook] ddf163: Added redirect support for two old bit.urls.
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ddf16395cda9812205d155bce8dc619dcb2243eb https://github.com/galaxyproject/infrastructure-playbook/commit/ddf16395cda… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Added redirect support for two old bit.urls. These were created back when the moin wiki still had spaces in paths. Commit: 1bd59300eb7080891dd1eed13ddc67e212337c7c https://github.com/galaxyproject/infrastructure-playbook/commit/1bd59300eb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Merge pull request #14 from galaxyproject/old-bitly Added redirect support for two old bit.urls. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/9ad75c96e7…

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[galaxyproject/infrastructure-playbook] ddf163: Added redirect support for two old bit.urls.
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/old-bitly Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ddf16395cda9812205d155bce8dc619dcb2243eb https://github.com/galaxyproject/infrastructure-playbook/commit/ddf16395cda… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Added redirect support for two old bit.urls. These were created back when the moin wiki still had spaces in paths.

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[galaxyproject/galaxy] 15aa0b: Fix problem with cleaning up jobs in local runner.
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2 https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix problem with cleaning up jobs in local runner. Fixes #3801 (broken in b78287f as part of #3291). Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235 https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3803 from jmchilton/1701_fixes_0 [17.01] Fix problem with cleaning up jobs in local runner. Commit: 7457b7611513159551a604afe13927a1a50dc6da https://github.com/galaxyproject/galaxy/commit/7457b7611513159551a604afe139… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3807 from galaxyproject/release_17.01 Merge Release 17.01 in Dev Compare: https://github.com/galaxyproject/galaxy/compare/8a033b720b37...7457b7611513

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[galaxyproject/galaxy] 9d736d: Fix container resolution.
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d736dd42eba2e8bd116d575c7d1278e15183ba3 https://github.com/galaxyproject/galaxy/commit/9d736dd42eba2e8bd116d575c7d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py Log Message: ----------- Fix container resolution. Without these decorators swapped - resolving containers results in the following Exception: ``` TypeError: unbound method __str__() must be called with ContainerResolver instance as first argument (got nothing instead) ``` I think this recent merge commit 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 introduced this problem as it merged the two decorators together. Commit: 8a033b720b370a7e7e9049fa22a5c7a78f0d5a85 https://github.com/galaxyproject/galaxy/commit/8a033b720b370a7e7e9049fa22a5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py Log Message: ----------- Merge pull request #3805 from jmchilton/container_resolution_fix Fix container resolution. Compare: https://github.com/galaxyproject/galaxy/compare/f8950feb30ca...8a033b720b37

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[galaxyproject/galaxy] 15aa0b: Fix problem with cleaning up jobs in local runner.
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2 https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix problem with cleaning up jobs in local runner. Fixes #3801 (broken in b78287f as part of #3291). Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235 https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3803 from jmchilton/1701_fixes_0 [17.01] Fix problem with cleaning up jobs in local runner. Compare: https://github.com/galaxyproject/galaxy/compare/c84b3ba0b8f9...65cbddee7c3b

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