December 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 38d316: Fix history list selector
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38d3163b2c7d0e9c4e428f4884cbed971a2f5bae https://github.com/galaxyproject/galaxy/commit/38d3163b2c7d0e9c4e428f4884cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: 10720fa4f9e26b3feec1a90468f4ecc726a99c05 https://github.com/galaxyproject/galaxy/commit/10720fa4f9e26b3feec1a90468f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fixup and test core.history.yaml tour. Commit: c000e68baae47dc7624465dacc3c6aa0217ece0a https://github.com/galaxyproject/galaxy/commit/c000e68baae47dc7624465dacc3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3185 from dannon/tour_history_fixes History Introduction tour fixes for structural changes Compare: https://github.com/galaxyproject/galaxy/compare/7ae30948be60...c000e68baae4

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[galaxyproject/galaxy] 318e5a: Update UCSC_SERVERS list to include new SOE prefix...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 318e5a23ad0ef2d50debfe72a0366ec5fd8513c3 https://github.com/galaxyproject/galaxy/commit/318e5a23ad0ef2d50debfe72a036… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Update UCSC_SERVERS list to include new SOE prefix. Commit: 7ae30948be60e34bc7b54cbf74f23da45414bad1 https://github.com/galaxyproject/galaxy/commit/7ae30948be60e34bc7b54cbf74f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3345 from dannon/ucsc_redirect_fix Update UCSC_SERVERS list to include new(ish?) soe subdomain Compare: https://github.com/galaxyproject/galaxy/compare/306c64d1bc3c...7ae30948be60

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[galaxyproject/galaxy] 05cd16: Fix explicit Docker container resolution.
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 05cd16f11cb523345894816ab6cc8165ebe71559 https://github.com/galaxyproject/galaxy/commit/05cd16f11cb523345894816ab6cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. Commit: 17a752d1f2fbc19fdccbd9dd24ca1bdfd26aae5e https://github.com/galaxyproject/galaxy/commit/17a752d1f2fbc19fdccbd9dd24ca… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. Compare: https://github.com/galaxyproject/galaxy/compare/14549d0f1b20...17a752d1f2fb

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 4969c4a308fd5bfc8bc52739b024765147af49e8 https://github.com/galaxyproject/galaxy/commit/4969c4a308fd5bfc8bc52739b024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py Commit: 14549d0f1b202a720dfc2dbb1f6501fc2cd8fd49 https://github.com/galaxyproject/galaxy/commit/14549d0f1b202a720dfc2dbb1f65… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. Compare: https://github.com/galaxyproject/galaxy/compare/5eafa8bae312...14549d0f1b20

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[galaxyproject/galaxy] fe2a1d: Do not replace Galaxy's Python environment for sel...
by GitHub 21 Dec '16

21 Dec '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Compare: https://github.com/galaxyproject/galaxy/compare/22fda449f9d4...8b75305c49c3

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[galaxyproject/galaxy] 99000f: update rename dataset action to accept . in repeat...
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99000fbed3b6c13274a3ddf9eb58310cb40653f7 https://github.com/galaxyproject/galaxy/commit/99000fbed3b6c13274a3ddf9eb58… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'. e.g. for filter bam 0.0.1: #{input_bams_0.input_bam} and #{input_bams_0.input_bam|basename} work. And for filter bam 0.0.2: #{input_bams1} and #{input_bams2|basename} work. Commit: 306c64d1bc3cec871f38b522ad3f7bf8e0ca3a66 https://github.com/galaxyproject/galaxy/commit/306c64d1bc3cec871f38b522ad3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3197 from scholtalbers/workflows-rename-output-minor-update update rename dataset action to accept . in repeat input parameters Compare: https://github.com/galaxyproject/galaxy/compare/538447be76da...306c64d1bc3c

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[galaxyproject/galaxy] 96678f: More IPython to Jupyter changes
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96678f57ccef01f322a6c6525defaa73333e56d0 https://github.com/galaxyproject/galaxy/commit/96678f57ccef01f322a6c6525def… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- More IPython to Jupyter changes Follow-up on #3294. Commit: 538447be76da011508eb4a8784eefe2b9e45b270 https://github.com/galaxyproject/galaxy/commit/538447be76da011508eb4a8784ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #3333 from nsoranzo/followup_on_3294 More IPython to Jupyter changes Compare: https://github.com/galaxyproject/galaxy/compare/af90b42a68d1...538447be76da

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[galaxyproject/galaxy] c61be9: Prettier Job information page
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61be93b70fd65b4bccf5f8416b58086ae98a085 https://github.com/galaxyproject/galaxy/commit/c61be93b70fd65b4bccf5f8416b5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Prettier Job information page Commit: fe2ec33d0bb67b0cbf0ef9297b737592f4f938bb https://github.com/galaxyproject/galaxy/commit/fe2ec33d0bb67b0cbf0ef9297b73… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove empty header from non-admin view Commit: dd062b5ca8de36a43b133a58b09d374ce07d63bd https://github.com/galaxyproject/galaxy/commit/dd062b5ca8de36a43b133a58b09d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako Log Message: ----------- Remove replace, just don't add in first place Commit: 1c7055fe3b974d06c8e166e39ac1a53d2f078642 https://github.com/galaxyproject/galaxy/commit/1c7055fe3b974d06c8e166e39ac1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Split metric table into sections Commit: 4756cab4cbcca729e3db66f33a8d031b796eb8d2 https://github.com/galaxyproject/galaxy/commit/4756cab4cbcca729e3db66f33a8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove visual noise Commit: 64b0d0326097f96c7637bd6355ca790c4ef8d4be https://github.com/galaxyproject/galaxy/commit/64b0d0326097f96c7637bd6355ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- cleanup css a bit Commit: cc32dcae4be031a95c393fd4efee459d398ae9c7 https://github.com/galaxyproject/galaxy/commit/cc32dcae4be031a95c393fd4efee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Initial tool form and dataset detail selenium testing. - Test parameters and tables appear on dataset details page after running a tool. - Test a simple tool execution with an integer field. - Test re-run a tool. - Test a tool with a data drop down. - Improved select2 abstractions. Commit: 097cf7f0fbcce7bc82539e17c12f7355deeaa558 https://github.com/galaxyproject/galaxy/commit/097cf7f0fbcce7bc82539e17c12f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Job metrics: Sort metrics on displayed title not key used for database. Commit: ef1fd488241a18952df146d30852054ab27a4a63 https://github.com/galaxyproject/galaxy/commit/ef1fd488241a18952df146d30852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Fix bad merge in cc32dcae4be031a95c393fd4efee459d398ae9c7. Spotted by @erasche. Commit: a5af4d155f6e4ab549c50e51703de49ee3052d16 https://github.com/galaxyproject/galaxy/commit/a5af4d155f6e4ab549c50e51703d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix Python 3 linting error for #3340. Commit: af90b42a68d119118d3fd2845738ef4835799af1 https://github.com/galaxyproject/galaxy/commit/af90b42a68d119118d3fd2845738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3340 from erasche/nicer_info_page Prettier Job Information Page Compare: https://github.com/galaxyproject/galaxy/compare/e407b4b2c722...af90b42a68d1

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[galaxyproject/galaxy] 9bb570: Allow admins to see API keys under REMOTE_USER
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bb570f62f8e6f135f2776808a6a92e91ec8b7cb https://github.com/galaxyproject/galaxy/commit/9bb570f62f8e6f135f2776808a6a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Allow admins to see API keys under REMOTE_USER Commit: e407b4b2c7226fc00d5cf2c42126ab83409bca7a https://github.com/galaxyproject/galaxy/commit/e407b4b2c7226fc00d5cf2c42126… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3338 from erasche/admin_see_apikeys Allow admins to see API keys under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/e1b54f60f20e...e407b4b2c722

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[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Commit: e1b54f60f20e13353d9742fb15ec4cfd2c48fd2e https://github.com/galaxyproject/galaxy/commit/e1b54f60f20e13353d9742fb15ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-20 (Tue, 20 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/43075015dd7b...e1b54f60f20e

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