galaxy-commits March 2018

galaxy-commits@lists.galaxyproject.org

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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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