- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f63426: Fixes for testing Dockerfile recipe.
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6342616eb0b6c740b734664cc50b896ad39f4b8 https://github.com/galaxyproject/galaxy/commit/f6342616eb0b6c740b734664cc50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-25 (Sun, 25 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Fixes for testing Dockerfile recipe. The current Dockerfile build is broken because Selenium is not compatible with the latest chromedriver it seems (and the version in galaxy/testing-base:18.01.4 isn't compatible with the latest stable Chrome - version 65). I can't get older versions of Chrome to install with the current apt source but this does at least pin the version of chromedriver. Longer term it would be good to have the version of chrome we target to be pinned also, I hate that this Dockerfile isn't reproducible. Commit: 5a86b8d706b7d3b8244b2359e2f7740367df1e89 https://github.com/galaxyproject/galaxy/commit/5a86b8d706b7d3b8244b2359e2f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #5693 from jmchilton/docker_test_update Fixes for testing Dockerfile recipe. Compare: https://github.com/galaxyproject/galaxy/compare/f14c6ffe49b3...5a86b8d706b7

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[galaxyproject/galaxy] 412ff1: Add config rebuild left out of migration of option...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 412ff1e16ae50af06751d3aae936973ef954fc61 https://github.com/galaxyproject/galaxy/commit/412ff1e16ae50af06751d3aae936… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Add config rebuild left out of migration of options from 18.01 (I think) Commit: f14c6ffe49b397b884f678812f311fc0bd451e53 https://github.com/galaxyproject/galaxy/commit/f14c6ffe49b397b884f678812f31… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Merge pull request #5788 from dannon/configrebuild Config-rebuild w/ options doc Compare: https://github.com/galaxyproject/galaxy/compare/39d5ec89f885...f14c6ffe49b3

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[galaxyproject/galaxy] c99c7b: Fix type of some options in config_schema.yml
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB. Includes test case that fails against 18.01. Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip [18.01] Fix model operation tools that produce standalone datasets. Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Commit: 39d5ec89f885ffce8e3c9621439c76d9d0745aa6 https://github.com/galaxyproject/galaxy/commit/39d5ec89f885ffce8e3c9621439c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/45dd9889654c...39d5ec89f885

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[galaxyproject/galaxy] fb24e8: Sentry bug reports working for anonymous users
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb24e8f2e2c817ff324a57947fdf315cca969707 https://github.com/galaxyproject/galaxy/commit/fb24e8f2e2c817ff324a57947fdf… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Sentry bug reports working for anonymous users Commit: 45dd9889654cf839740b165763f6a40019cde2e0 https://github.com/galaxyproject/galaxy/commit/45dd9889654cf839740b165763f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5721 from erasche/sentry-reporter Sentry bug reports working for anonymous users Compare: https://github.com/galaxyproject/galaxy/compare/13fff60142ed...45dd9889654c

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[galaxyproject/galaxy] c99c7b: Fix type of some options in config_schema.yml
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Compare: https://github.com/galaxyproject/galaxy/compare/3876f12e7d3c...fbb47f6e03d0

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[galaxyproject/galaxy] ff0f0b: Fix model operations that produce datasets for 78b...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB. Includes test case that fails against 18.01. Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip [18.01] Fix model operation tools that produce standalone datasets. Compare: https://github.com/galaxyproject/galaxy/compare/6fb738b01a48...3876f12e7d3c

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[galaxyproject/galaxy] 9fc2d7: Fix LDAP when role_search_attribute is not defined
by GitHub 26 Mar '18

26 Mar '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 9fc2d78a10c2956b3b4de21b73a08b8acedd925e https://github.com/galaxyproject/galaxy/commit/9fc2d78a10c2956b3b4de21b73a0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Fix LDAP when role_search_attribute is not defined Commit: b0d094481a81d4efed4ca3916da6e4540b43b7d6 https://github.com/galaxyproject/galaxy/commit/b0d094481a81d4efed4ca3916da6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- [17.09] Fix mulled docker caching. Broken with 93ffc4055b145811b86191dae8b865ea45b55fcb. Alternative to https://github.com/galaxyproject/galaxy/pull/5248 that does not use ``shell=True``. Rebased with cleanup from @nsoranzo. Commit: 8fe5b5c14eee8aea1b16ee932be10aaf6b13b452 https://github.com/galaxyproject/galaxy/commit/8fe5b5c14eee8aea1b16ee932be1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Capture more HDA state transitions in the history panel. Commit: c6257f77f10080664ac01d156caee9abab43d703 https://github.com/galaxyproject/galaxy/commit/c6257f77f10080664ac01d156cae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5749 from jmchilton/history_panel_state_changes [18.01] Capture more HDA state transitions in the history panel. Commit: 54d91e585035bac3a9c72615ab70617b3ceb7669 https://github.com/galaxyproject/galaxy/commit/54d91e585035bac3a9c72615ab70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: 8ef320963a37566104af2da16580b002f6a42181 https://github.com/galaxyproject/galaxy/commit/8ef320963a37566104af2da16580… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 4ed7178d9bf550047efda22ba5f653e13f5d87bb https://github.com/galaxyproject/galaxy/commit/4ed7178d9bf550047efda22ba5f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: 64648aefd7e7f3a4062f1030001575fdb000cfc1 https://github.com/galaxyproject/galaxy/commit/64648aefd7e7f3a4062f10300015… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Ignore tool xml datatype settings for dragged history items Commit: 70392ddb3b08bdc7c3739add061ea1b45f78da38 https://github.com/galaxyproject/galaxy/commit/70392ddb3b08bdc7c3739add061e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove debug statements, use drop data where needed Commit: af514327cb86032b31880ec478fa383be2c7ab76 https://github.com/galaxyproject/galaxy/commit/af514327cb86032b31880ec478fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Validate type using collection, from @jmchilton Commit: 36467c1e768be5e32c7e91387c6246171d12e92a https://github.com/galaxyproject/galaxy/commit/36467c1e768be5e32c7e91387c62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add source to data entry Commit: 30ed27f9ad916b7bd31ad7366381807763ca2db2 https://github.com/galaxyproject/galaxy/commit/30ed27f9ad916b7bd31ad7366381… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add additional check for history items Commit: 5eaa1301c648ff43651c745136ab71eb2cfde06d https://github.com/galaxyproject/galaxy/commit/5eaa1301c648ff43651c745136ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Rebuild client. Commit: 3da1960c52b2cf893662ec1f865d67050c5500da https://github.com/galaxyproject/galaxy/commit/3da1960c52b2cf893662ec1f865d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- [18.01] Fix copying tags for collections when copying histories. Fixes #5757. Commit: 5a578bfd325777e7e50479b34d1a308940138f82 https://github.com/galaxyproject/galaxy/commit/5a578bfd325777e7e50479b34d1a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- uWSGI: Log listening URLs at startup. Commit: c720af066b704e591f3ff8806a68eb0a33a7fd4d https://github.com/galaxyproject/galaxy/commit/c720af066b704e591f3ff8806a68… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Attempt to log startup as late as possible Commit: 5ad8842b99572388432899f5c96fd4c6307cd082 https://github.com/galaxyproject/galaxy/commit/5ad8842b99572388432899f5c96f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix lint errors Commit: c779145bff4183926c3989828e9834a93b9baa25 https://github.com/galaxyproject/galaxy/commit/c779145bff4183926c3989828e98… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log also the PID. Python3 fix And make _socket_opts() more readable. Commit: 7dbde33b22ab6c334eec11f88a1596d1cfdcd64d https://github.com/galaxyproject/galaxy/commit/7dbde33b22ab6c334eec11f88a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5766 from jmchilton/copy_tag_fix [18.01] Fix copying tags for collections when copying histories. Commit: e41c8f792743a74e927e37fb37b788aa617ec1cd https://github.com/galaxyproject/galaxy/commit/e41c8f792743a74e927e37fb37b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge pull request #5770 from natefoo/uwsgi-log-start [18.01] uWSGI: Log listening URLs at startup. Commit: cb41e623510d579050553db6578997cf0815f608 https://github.com/galaxyproject/galaxy/commit/cb41e623510d579050553db65789… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5732 from nsoranzo/release_18.01_fix_ldap [18.01] Fix LDAP when role_search_attribute is not defined Commit: 66e624f90b31200b950ad1543af8453d654b3939 https://github.com/galaxyproject/galaxy/commit/66e624f90b31200b950ad1543af8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5765 from jmchilton/backport_cool_stuff_1801 [18.01] Backport various fixes from dev. Commit: 244273ad554df1ab3bf337016a35b3fbe565c3fe https://github.com/galaxyproject/galaxy/commit/244273ad554df1ab3bf337016a35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- [18.01] Fix /api/whoami for master API key. Just yield a null JSON response instead of the internal server error that happens currently. Commit: 198268a0aa9d62b0c3ca45f58734cc8fb5085875 https://github.com/galaxyproject/galaxy/commit/198268a0aa9d62b0c3ca45f58734… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #5773 from jmchilton/fix_whoami_1801 [18.01] Fix /api/whoami for master API key. Commit: beb28d4aff2a9c38f06a357f9ee013566ad635c6 https://github.com/galaxyproject/galaxy/commit/beb28d4aff2a9c38f06a357f9ee0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5735 from jmchilton/fix_mulled_docker_caching [17.09] Fix mulled docker caching. Commit: 6fb738b01a48a495a68ded61371d10b4bd306d8e https://github.com/galaxyproject/galaxy/commit/6fb738b01a48a495a68ded61371d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 5d0d66e7289d92740a0fd60b272c4f18317ec318 https://github.com/galaxyproject/galaxy/commit/5d0d66e7289d92740a0fd60b272c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge branch 'release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/7c962975750c...5d0d66e7289d

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[galaxyproject/usegalaxy-playbook] 638603: install vcffilter
by GitHub 26 Mar '18

26 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 638603b2064f188a03761933cddf000e2bae819f https://github.com/galaxyproject/usegalaxy-playbook/commit/638603b2064f188a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- install vcffilter

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[galaxyproject/galaxy] 43543c: Rev and re-lock Galaxy dependencies
by GitHub 26 Mar '18

26 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43543c36d93621a312d0e3351cb3db2c1904fec1 https://github.com/galaxyproject/galaxy/commit/43543c36d93621a312d0e3351cb3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M tox.ini Log Message: ----------- Rev and re-lock Galaxy dependencies Drop pinned-hashed-requirements.txt files, they are not generated by pipenv any more since v11.1.2 . Commit: 13fff60142eda391e6b833ed02fec3bd4cb1072e https://github.com/galaxyproject/galaxy/commit/13fff60142eda391e6b833ed02fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M tox.ini Log Message: ----------- Merge pull request #5776 from nsoranzo/dep_update Rev and re-lock Galaxy dependencies Compare: https://github.com/galaxyproject/galaxy/compare/ca2ed15fda10...13fff60142ed

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[galaxyproject/galaxy] b0d094: [17.09] Fix mulled docker caching.
by GitHub 26 Mar '18

26 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b0d094481a81d4efed4ca3916da6e4540b43b7d6 https://github.com/galaxyproject/galaxy/commit/b0d094481a81d4efed4ca3916da6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- [17.09] Fix mulled docker caching. Broken with 93ffc4055b145811b86191dae8b865ea45b55fcb. Alternative to https://github.com/galaxyproject/galaxy/pull/5248 that does not use ``shell=True``. Rebased with cleanup from @nsoranzo. Commit: 244273ad554df1ab3bf337016a35b3fbe565c3fe https://github.com/galaxyproject/galaxy/commit/244273ad554df1ab3bf337016a35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- [18.01] Fix /api/whoami for master API key. Just yield a null JSON response instead of the internal server error that happens currently. Commit: 198268a0aa9d62b0c3ca45f58734cc8fb5085875 https://github.com/galaxyproject/galaxy/commit/198268a0aa9d62b0c3ca45f58734… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #5773 from jmchilton/fix_whoami_1801 [18.01] Fix /api/whoami for master API key. Commit: beb28d4aff2a9c38f06a357f9ee013566ad635c6 https://github.com/galaxyproject/galaxy/commit/beb28d4aff2a9c38f06a357f9ee0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5735 from jmchilton/fix_mulled_docker_caching [17.09] Fix mulled docker caching. Commit: 6fb738b01a48a495a68ded61371d10b4bd306d8e https://github.com/galaxyproject/galaxy/commit/6fb738b01a48a495a68ded61371d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: ca2ed15fda1032aef308aa87fa770356e1f3e5c2 https://github.com/galaxyproject/galaxy/commit/ca2ed15fda1032aef308aa87fa77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1993ef5c69fe...ca2ed15fda10

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[galaxyproject/galaxy] b0d094: [17.09] Fix mulled docker caching.
by GitHub 26 Mar '18

26 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b0d094481a81d4efed4ca3916da6e4540b43b7d6 https://github.com/galaxyproject/galaxy/commit/b0d094481a81d4efed4ca3916da6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- [17.09] Fix mulled docker caching. Broken with 93ffc4055b145811b86191dae8b865ea45b55fcb. Alternative to https://github.com/galaxyproject/galaxy/pull/5248 that does not use ``shell=True``. Rebased with cleanup from @nsoranzo. Commit: beb28d4aff2a9c38f06a357f9ee013566ad635c6 https://github.com/galaxyproject/galaxy/commit/beb28d4aff2a9c38f06a357f9ee0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5735 from jmchilton/fix_mulled_docker_caching [17.09] Fix mulled docker caching. Commit: 6fb738b01a48a495a68ded61371d10b4bd306d8e https://github.com/galaxyproject/galaxy/commit/6fb738b01a48a495a68ded61371d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/198268a0aa9d...6fb738b01a48

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[galaxyproject/galaxy] 4e0604: GFF updates to handle ##FASTA directive
by GitHub 25 Mar '18

25 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e060473d872bfe21dbfa950ce42ab1574d03780 https://github.com/galaxyproject/galaxy/commit/4e060473d872bfe21dbfa950ce42… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- GFF updates to handle ##FASTA directive Commit: 1993ef5c69fed7d07e4f830e5630dcb4ba4cb39d https://github.com/galaxyproject/galaxy/commit/1993ef5c69fed7d07e4f830e5630… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-25 (Sun, 25 Mar 2018) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #5686 from blankenberg/gff GFF updates to handle ##FASTA directive Compare: https://github.com/galaxyproject/galaxy/compare/8f0a2d2360ea...1993ef5c69fe

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[galaxyproject/galaxy] d39b4b: Fix setup code in library test landing page to rer...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d39b4beef292ffddad4e8c062e921eb0e80d75a1 https://github.com/galaxyproject/galaxy/commit/d39b4beef292ffddad4e8c062e92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Fix setup code in library test landing page to rerun on test retry. Commit: 8f0a2d2360ea904707fa3f61f6e3541e8e159571 https://github.com/galaxyproject/galaxy/commit/8f0a2d2360ea904707fa3f61f6e3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5706 from jmchilton/selenium_fixes_36 Fix setup code in library test landing page to rerun on test retry. Compare: https://github.com/galaxyproject/galaxy/compare/88e6e94a8127...8f0a2d2360ea

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[galaxyproject/galaxy] b0d094: [17.09] Fix mulled docker caching.
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: b0d094481a81d4efed4ca3916da6e4540b43b7d6 https://github.com/galaxyproject/galaxy/commit/b0d094481a81d4efed4ca3916da6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- [17.09] Fix mulled docker caching. Broken with 93ffc4055b145811b86191dae8b865ea45b55fcb. Alternative to https://github.com/galaxyproject/galaxy/pull/5248 that does not use ``shell=True``. Rebased with cleanup from @nsoranzo. Commit: beb28d4aff2a9c38f06a357f9ee013566ad635c6 https://github.com/galaxyproject/galaxy/commit/beb28d4aff2a9c38f06a357f9ee0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5735 from jmchilton/fix_mulled_docker_caching [17.09] Fix mulled docker caching. Compare: https://github.com/galaxyproject/galaxy/compare/5dcd9ed0255c...beb28d4aff2a

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[galaxyproject/usegalaxy-playbook] 390278: run star_fusion on bridges
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3902785a66bfe8da46e36224e6c1eb39922d2805 https://github.com/galaxyproject/usegalaxy-playbook/commit/3902785a66bfe8da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- run star_fusion on bridges should have similar mem reqs as rna_star

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[galaxyproject/usegalaxy-playbook] 34a4dd: update Main's tools
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 34a4dd4815981e23ec7f3a436048cf990c3146ce https://github.com/galaxyproject/usegalaxy-playbook/commit/34a4dd4815981e23… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main's tools * remove all of anton's vcflib tools (were hidden) * remove all versions of vcffilter * update bamtools * update Deseq2 * update bowtie2 * update samtool_filter2 * update xy_plot * update sra_tools * update fastq_paired_end * install star_fusion * update stringtie * update featurecounts * update bwa

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[galaxyproject/galaxy] 244273: [18.01] Fix /api/whoami for master API key.
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 244273ad554df1ab3bf337016a35b3fbe565c3fe https://github.com/galaxyproject/galaxy/commit/244273ad554df1ab3bf337016a35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- [18.01] Fix /api/whoami for master API key. Just yield a null JSON response instead of the internal server error that happens currently. Commit: 198268a0aa9d62b0c3ca45f58734cc8fb5085875 https://github.com/galaxyproject/galaxy/commit/198268a0aa9d62b0c3ca45f58734… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #5773 from jmchilton/fix_whoami_1801 [18.01] Fix /api/whoami for master API key. Compare: https://github.com/galaxyproject/galaxy/compare/66e624f90b31...198268a0aa9d

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[galaxyproject/galaxy] 9fc2d7: Fix LDAP when role_search_attribute is not defined
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9fc2d78a10c2956b3b4de21b73a08b8acedd925e https://github.com/galaxyproject/galaxy/commit/9fc2d78a10c2956b3b4de21b73a0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Fix LDAP when role_search_attribute is not defined Commit: 54d91e585035bac3a9c72615ab70617b3ceb7669 https://github.com/galaxyproject/galaxy/commit/54d91e585035bac3a9c72615ab70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: 8ef320963a37566104af2da16580b002f6a42181 https://github.com/galaxyproject/galaxy/commit/8ef320963a37566104af2da16580… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 4ed7178d9bf550047efda22ba5f653e13f5d87bb https://github.com/galaxyproject/galaxy/commit/4ed7178d9bf550047efda22ba5f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: 64648aefd7e7f3a4062f1030001575fdb000cfc1 https://github.com/galaxyproject/galaxy/commit/64648aefd7e7f3a4062f10300015… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Ignore tool xml datatype settings for dragged history items Commit: 70392ddb3b08bdc7c3739add061ea1b45f78da38 https://github.com/galaxyproject/galaxy/commit/70392ddb3b08bdc7c3739add061e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove debug statements, use drop data where needed Commit: af514327cb86032b31880ec478fa383be2c7ab76 https://github.com/galaxyproject/galaxy/commit/af514327cb86032b31880ec478fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Validate type using collection, from @jmchilton Commit: 36467c1e768be5e32c7e91387c6246171d12e92a https://github.com/galaxyproject/galaxy/commit/36467c1e768be5e32c7e91387c62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add source to data entry Commit: 30ed27f9ad916b7bd31ad7366381807763ca2db2 https://github.com/galaxyproject/galaxy/commit/30ed27f9ad916b7bd31ad7366381… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add additional check for history items Commit: 5eaa1301c648ff43651c745136ab71eb2cfde06d https://github.com/galaxyproject/galaxy/commit/5eaa1301c648ff43651c745136ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Rebuild client. Commit: 3da1960c52b2cf893662ec1f865d67050c5500da https://github.com/galaxyproject/galaxy/commit/3da1960c52b2cf893662ec1f865d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- [18.01] Fix copying tags for collections when copying histories. Fixes #5757. Commit: 5a578bfd325777e7e50479b34d1a308940138f82 https://github.com/galaxyproject/galaxy/commit/5a578bfd325777e7e50479b34d1a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- uWSGI: Log listening URLs at startup. Commit: c720af066b704e591f3ff8806a68eb0a33a7fd4d https://github.com/galaxyproject/galaxy/commit/c720af066b704e591f3ff8806a68… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Attempt to log startup as late as possible Commit: 5ad8842b99572388432899f5c96fd4c6307cd082 https://github.com/galaxyproject/galaxy/commit/5ad8842b99572388432899f5c96f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix lint errors Commit: c779145bff4183926c3989828e9834a93b9baa25 https://github.com/galaxyproject/galaxy/commit/c779145bff4183926c3989828e98… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log also the PID. Python3 fix And make _socket_opts() more readable. Commit: 7dbde33b22ab6c334eec11f88a1596d1cfdcd64d https://github.com/galaxyproject/galaxy/commit/7dbde33b22ab6c334eec11f88a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5766 from jmchilton/copy_tag_fix [18.01] Fix copying tags for collections when copying histories. Commit: e41c8f792743a74e927e37fb37b788aa617ec1cd https://github.com/galaxyproject/galaxy/commit/e41c8f792743a74e927e37fb37b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge pull request #5770 from natefoo/uwsgi-log-start [18.01] uWSGI: Log listening URLs at startup. Commit: cb41e623510d579050553db6578997cf0815f608 https://github.com/galaxyproject/galaxy/commit/cb41e623510d579050553db65789… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5732 from nsoranzo/release_18.01_fix_ldap [18.01] Fix LDAP when role_search_attribute is not defined Commit: 66e624f90b31200b950ad1543af8453d654b3939 https://github.com/galaxyproject/galaxy/commit/66e624f90b31200b950ad1543af8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5765 from jmchilton/backport_cool_stuff_1801 [18.01] Backport various fixes from dev. Commit: 88e6e94a81271a85e280143c5ef12532b83615cc https://github.com/galaxyproject/galaxy/commit/88e6e94a81271a85e280143c5ef1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/model/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bca5b299b339...88e6e94a8127

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[galaxyproject/galaxy] 8ace24: Ignore seemingly harmless error when tearing down ...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ace2457203399893236e07539a5e84f6fa8933a https://github.com/galaxyproject/galaxy/commit/8ace2457203399893236e07539a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Ignore seemingly harmless error when tearing down Selenium tests. Causes otherwise passing tests to fail for not particular reason. Cannot find a Selenium issue for this but it has been reported on in their IRC - seems like just a very rare, transient issue. xref https://jenkins.galaxyproject.org/job/docker-selenium/1830/testReport/junit… Commit: bca5b299b3394bd2071e2aee1068ef12dce396bd https://github.com/galaxyproject/galaxy/commit/bca5b299b3394bd2071e2aee1068… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5771 from jmchilton/selenium_fixes_41 Ignore seemingly harmless error when tearing down Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/cacef65139f0...bca5b299b339

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[galaxyproject/galaxy] 54d91e: Add additional validation to numeric input element
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 54d91e585035bac3a9c72615ab70617b3ceb7669 https://github.com/galaxyproject/galaxy/commit/54d91e585035bac3a9c72615ab70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: 8ef320963a37566104af2da16580b002f6a42181 https://github.com/galaxyproject/galaxy/commit/8ef320963a37566104af2da16580… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 4ed7178d9bf550047efda22ba5f653e13f5d87bb https://github.com/galaxyproject/galaxy/commit/4ed7178d9bf550047efda22ba5f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: 64648aefd7e7f3a4062f1030001575fdb000cfc1 https://github.com/galaxyproject/galaxy/commit/64648aefd7e7f3a4062f10300015… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Ignore tool xml datatype settings for dragged history items Commit: 70392ddb3b08bdc7c3739add061ea1b45f78da38 https://github.com/galaxyproject/galaxy/commit/70392ddb3b08bdc7c3739add061e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove debug statements, use drop data where needed Commit: af514327cb86032b31880ec478fa383be2c7ab76 https://github.com/galaxyproject/galaxy/commit/af514327cb86032b31880ec478fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Validate type using collection, from @jmchilton Commit: 36467c1e768be5e32c7e91387c6246171d12e92a https://github.com/galaxyproject/galaxy/commit/36467c1e768be5e32c7e91387c62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add source to data entry Commit: 30ed27f9ad916b7bd31ad7366381807763ca2db2 https://github.com/galaxyproject/galaxy/commit/30ed27f9ad916b7bd31ad7366381… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add additional check for history items Commit: 5eaa1301c648ff43651c745136ab71eb2cfde06d https://github.com/galaxyproject/galaxy/commit/5eaa1301c648ff43651c745136ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Rebuild client. Commit: 66e624f90b31200b950ad1543af8453d654b3939 https://github.com/galaxyproject/galaxy/commit/66e624f90b31200b950ad1543af8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5765 from jmchilton/backport_cool_stuff_1801 [18.01] Backport various fixes from dev. Compare: https://github.com/galaxyproject/galaxy/compare/cb41e623510d...66e624f90b31

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[galaxyproject/usegalaxy-playbook] 21d22b: Installed MiModD, rearranged tool panel.
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 21d22b469562cef4a1603d18e09467cd13ed7cba https://github.com/galaxyproject/usegalaxy-playbook/commit/21d22b469562cef4… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed MiModD, rearranged tool panel.

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[galaxyproject/galaxy] 9fc2d7: Fix LDAP when role_search_attribute is not defined
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 9fc2d78a10c2956b3b4de21b73a08b8acedd925e https://github.com/galaxyproject/galaxy/commit/9fc2d78a10c2956b3b4de21b73a0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Fix LDAP when role_search_attribute is not defined Commit: cb41e623510d579050553db6578997cf0815f608 https://github.com/galaxyproject/galaxy/commit/cb41e623510d579050553db65789… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5732 from nsoranzo/release_18.01_fix_ldap [18.01] Fix LDAP when role_search_attribute is not defined Compare: https://github.com/galaxyproject/galaxy/compare/e41c8f792743...cb41e623510d

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[galaxyproject/galaxy] 5a578b: uWSGI: Log listening URLs at startup.
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 5a578bfd325777e7e50479b34d1a308940138f82 https://github.com/galaxyproject/galaxy/commit/5a578bfd325777e7e50479b34d1a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- uWSGI: Log listening URLs at startup. Commit: c720af066b704e591f3ff8806a68eb0a33a7fd4d https://github.com/galaxyproject/galaxy/commit/c720af066b704e591f3ff8806a68… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Attempt to log startup as late as possible Commit: 5ad8842b99572388432899f5c96fd4c6307cd082 https://github.com/galaxyproject/galaxy/commit/5ad8842b99572388432899f5c96f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix lint errors Commit: c779145bff4183926c3989828e9834a93b9baa25 https://github.com/galaxyproject/galaxy/commit/c779145bff4183926c3989828e98… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log also the PID. Python3 fix And make _socket_opts() more readable. Commit: e41c8f792743a74e927e37fb37b788aa617ec1cd https://github.com/galaxyproject/galaxy/commit/e41c8f792743a74e927e37fb37b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge pull request #5770 from natefoo/uwsgi-log-start [18.01] uWSGI: Log listening URLs at startup. Compare: https://github.com/galaxyproject/galaxy/compare/7dbde33b22ab...e41c8f792743

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[galaxyproject/galaxy] 3da196: [18.01] Fix copying tags for collections when copy...
by GitHub 23 Mar '18

23 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 3da1960c52b2cf893662ec1f865d67050c5500da https://github.com/galaxyproject/galaxy/commit/3da1960c52b2cf893662ec1f865d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- [18.01] Fix copying tags for collections when copying histories. Fixes #5757. Commit: 7dbde33b22ab6c334eec11f88a1596d1cfdcd64d https://github.com/galaxyproject/galaxy/commit/7dbde33b22ab6c334eec11f88a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5766 from jmchilton/copy_tag_fix [18.01] Fix copying tags for collections when copying histories. Compare: https://github.com/galaxyproject/galaxy/compare/c6257f77f100...7dbde33b22ab

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[galaxyproject/usegalaxy-playbook] 4895cd: Remove banner
by GitHub 22 Mar '18

22 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4895cd662d3765ac8553cc6b2a9603d049f26740 https://github.com/galaxyproject/usegalaxy-playbook/commit/4895cd662d3765ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove banner

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