Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 9fc2d78a10c2956b3b4de21b73a08b8acedd925e https://github.com/galaxyproject/galaxy/commit/9fc2d78a10c2956b3b4de21b73a08... Author: Nicola Soranzo <nicola.soranzo@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/b0d094481a81d4efed4ca3916da6e... Author: John Chilton <jmchilton@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/8fe5b5c14eee8aea1b16ee932be10... Author: John Chilton <jmchilton@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/c6257f77f10080664ac01d156caee... Author: Dannon Baker <dannon.baker@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/54d91e585035bac3a9c72615ab706... Author: guerler <aysam.guerler@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/8ef320963a37566104af2da16580b... Author: John Chilton <jmchilton@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/4ed7178d9bf550047efda22ba5f65... Author: John Chilton <jmchilton@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/64648aefd7e7f3a4062f103000157... Author: guerler <aysam.guerler@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/70392ddb3b08bdc7c3739add061ea... Author: guerler <aysam.guerler@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/af514327cb86032b31880ec478fa3... Author: guerler <aysam.guerler@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/36467c1e768be5e32c7e91387c624... Author: guerler <aysam.guerler@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/30ed27f9ad916b7bd31ad73663818... Author: guerler <aysam.guerler@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/5eaa1301c648ff43651c745136ab7... Author: John Chilton <jmchilton@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/3da1960c52b2cf893662ec1f865d6... Author: John Chilton <jmchilton@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/5a578bfd325777e7e50479b34d1a3... Author: Nate Coraor <nate@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/c720af066b704e591f3ff8806a68e... Author: Nate Coraor <nate@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/5ad8842b99572388432899f5c96fd... Author: Nate Coraor <nate@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/c779145bff4183926c3989828e983... Author: Nicola Soranzo <nicola.soranzo@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/7dbde33b22ab6c334eec11f88a159... Author: Dannon Baker <dannon.baker@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/e41c8f792743a74e927e37fb37b78... Author: Dannon Baker <dannon.baker@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/cb41e623510d579050553db657899... Author: Dannon Baker <dannon.baker@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/66e624f90b31200b950ad1543af84... Author: Martin Cech <marten@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/244273ad554df1ab3bf337016a35b... Author: John Chilton <jmchilton@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/198268a0aa9d62b0c3ca45f58734c... Author: Dannon Baker <dannon.baker@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/beb28d4aff2a9c38f06a357f9ee01... Author: Martin Cech <marten@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/6fb738b01a48a495a68ded61371d1... Author: Nicola Soranzo <nicola.soranzo@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/5d0d66e7289d92740a0fd60b272c4... Author: Martin Cech <marten@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