March 2017 - galaxy-commits - lists.galaxyproject.org

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

22 Mar '17

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

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

22 Mar '17

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

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

22 Mar '17

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

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

22 Mar '17

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

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

22 Mar '17

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

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

22 Mar '17

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

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[galaxyproject/galaxy] 2eefe8: Fix usage of _.extend in joint collection builder ...
by GitHub 22 Mar '17

22 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eefe8571a00497c6faefff64cf86224bae05825 https://github.com/galaxyproject/galaxy/commit/2eefe8571a00497c6faefff64cf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Fix usage of _.extend in joint collection builder templates. Fixes bug introduced in #3781. #minor Commit: f8950feb30ca3caa94d48f487d9d7079839143a0 https://github.com/galaxyproject/galaxy/commit/f8950feb30ca3caa94d48f487d9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #3799 from jmchilton/fix_extend_usage Fix usage of _.extend in joint collection builder templates. Compare: https://github.com/galaxyproject/galaxy/compare/3ed60db5ce9b...f8950feb30ca

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[galaxyproject/galaxy] dda11d: [17.01] Fix container resolver log statements expo...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- [17.01] Fix container resolver log statements exposing pointers. These log statements: ``` 2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None] 2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None] 2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>] ``` Become: ``` 2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None] 2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None] 2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]] ``` Rebased with suggestion from @nsoranzo :eagle::eyes: Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3 https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #3679 from jmchilton/fix_logs [17.01] Fix container resolver log statements exposing pointers. Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH. Should fix #3499 (thanks for the explicit heads up @mvdbeek). Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes [17.01] Annotate converters that appear to need galaxy on PYTHONPATH. Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6 https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b7625… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools by merging select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako (thx @nsoranzo for this suggestion). Commit: e8922295bd5753e0be262f141b25a05622972ee6 https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Commit: 376212eff900d28450165ddf715f3d9a29870ca9 https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for uploading rdata datasets when explicitly declaring datatype. Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension. TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues. Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219 https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142ef… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3 https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca2056369… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix datetime import Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- add the activation functionality to API users controller it was invoked but not included resulting in errors Commit: 642956a899ea2b97348be698bd81dd11a85d113e https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove unused import Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898 https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- only request verificaion when needed thanks @nsoranzo Commit: 56c710adbc1f10579511c506503493241df4176c https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c5065034… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- reqork the activation logic when email is changed thanks to @nsoranzo for help Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031 https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge pull request #3686 from mvdbeek/datamanager_conda_install [17.01] Allow display of install_resolver_checkbox when installing data manag… Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c4398… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-18 (Sat, 18 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3771 from martenson/fix-users-api [17.01] Fixes for users API Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix [17.01] Fix for uploading rdata datasets when explicitly declaring datatype. Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19 https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3791 from galaxyproject/release_16.10 merge 16.10 into 17.01 Commit: c84b3ba0b8f9de983d43ea17c165856d23960911 https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes [17.01] Backport collection operation help fixes Commit: 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 https://github.com/galaxyproject/galaxy/commit/3ed60db5ce9bf2acb954c843c14f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: lib/galaxy/tools/deps/container_resolvers/__init__.py static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/279548574136...3ed60db5ce9b

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[galaxyproject/galaxy] e0f80d: Add possibility to load collections into library
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0f80db701b2c843c78074b9957452aa2eb3fe58 https://github.com/galaxyproject/galaxy/commit/e0f80db701b2c843c78074b99574… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_libraries.py Log Message: ----------- Add possibility to load collections into library and to conserve element_identifier. Commit: 8906f515e1df604c62a0faf6744b309b396431d5 https://github.com/galaxyproject/galaxy/commit/8906f515e1df604c62a0faf6744b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Add first working version of js needed for collection import Commit: 08449059f4e3c62fd281fcbeae67cdce149241c0 https://github.com/galaxyproject/galaxy/commit/08449059f4e3c62fd281fcbeae67… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M test/api/test_libraries.py Log Message: ----------- Test adding a single dataset to a folder and test creating library using from_hdca_id Commit: 8b9fd288bc4a05b177a56665229cbd9b58f4de3c https://github.com/galaxyproject/galaxy/commit/8b9fd288bc4a05b177a56665229c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M test/api/test_libraries.py Log Message: ----------- Test creating library datatsets fails when not owning HDA Commit: 26050f6deafe51fc38632dc4a02c284ec0ea993d https://github.com/galaxyproject/galaxy/commit/26050f6deafe51fc38632dc4a02c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Move functionality shared between folder and library api into UsesLibraryMixinItems Commit: e7a0c186a9494f3589364dfc5f76e25bcd97dbad https://github.com/galaxyproject/galaxy/commit/e7a0c186a9494f3589364dfc5f76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- Simplify exception handling Commit: 46af8ba4c3007f33f68c0b0d95f2dc166e69a14f https://github.com/galaxyproject/galaxy/commit/46af8ba4c3007f33f68c0b0d95f2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Simplify exceptions some more Commit: 6e7d290d0c462772cf51118f83e3f6c39a170ede https://github.com/galaxyproject/galaxy/commit/6e7d290d0c462772cf51118f83e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- Remove unused rval variable Commit: 828422fe5e6d419ec1af28e0c62b7a8759bae9b8 https://github.com/galaxyproject/galaxy/commit/828422fe5e6d419ec1af28e0c62b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Only show items in selector if item is visible and state is ok Commit: 75994c8816cdac0af80614db629553495dcb6bff https://github.com/galaxyproject/galaxy/commit/75994c8816cdac0af80614db6295… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Always set new ldda's to visible Commit: 7a6579878a09862e1cd5919ba7d94c527f3b0e56 https://github.com/galaxyproject/galaxy/commit/7a6579878a09862e1cd5919ba7d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix markup and add a stylistic space Commit: 234361253a168eaf4b4c86fe4a1963a511271c86 https://github.com/galaxyproject/galaxy/commit/234361253a168eaf4b4c86fe4a19… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M 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static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M static/style/blue/base.css M templates/admin/reload_tool.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/TESTING.md M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py M test/qunit/tests/form_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into add_hdca_to_library Commit: 3dcd174f2b2f0e78d58b3e9d7e19103bd299b128 https://github.com/galaxyproject/galaxy/commit/3dcd174f2b2f0e78d58b3e9d7e19… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack Commit: 279548574136817c226fad61c52168cfab199fb8 https://github.com/galaxyproject/galaxy/commit/279548574136817c226fad61c521… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M test/api/test_libraries.py Log Message: ----------- Merge pull request #3559 from mvdbeek/add_hdca_to_library Add possibility to load collection into library Compare: https://github.com/galaxyproject/galaxy/compare/eadbb16462f2...279548574136

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19 https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3791 from galaxyproject/release_16.10 merge 16.10 into 17.01 Commit: c84b3ba0b8f9de983d43ea17c165856d23960911 https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes [17.01] Backport collection operation help fixes Commit: f9b8e6a51a179a0c41e1657e1b9eb92e017a0a1a https://github.com/galaxyproject/galaxy/commit/f9b8e6a51a179a0c41e1657e1b9e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3792 from galaxyproject/release_17.01 [usegalaxy] merge 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/3b4cf0d578d8...f9b8e6a51a17

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