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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 22 Mar '17

22 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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lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M scripts/api/README M scripts/bootstrap_history.py A scripts/secret_decoder_ring.py M scripts/slideshow/slideshow_template.html A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map M static/maps/ui/autocom_tagging.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M 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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[galaxyproject/galaxy] e3255f: made collection ops help sections slightly more re...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/ec88dda1e9c9...c84b3ba0b8f9

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

21 Mar '17

Branch: refs/heads/release_17.01 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/e3e24facc721...ec88dda1e9c9

1 0

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

21 Mar '17

Branch: refs/heads/release_16.10 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/1b9a2868a178...490e565611b5

1 0

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

21 Mar '17

Branch: refs/heads/release_16.07 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/915b653b91af...80ecc79a4cb8

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[galaxyproject/galaxy] 61677d: made collection ops help sections slightly more re...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61677d2026f155868ad57a1289609c1aad1044e6 https://github.com/galaxyproject/galaxy/commit/61677d2026f155868ad57a128960… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-20 (Mon, 20 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: a8d0c46ee97b37df20ac2022af4309890ca0c6e0 https://github.com/galaxyproject/galaxy/commit/a8d0c46ee97b37df20ac2022af43… 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: eadbb16462f2bd6f6f8f8cf71d992f0c5389c80f https://github.com/galaxyproject/galaxy/commit/eadbb16462f2bd6f6f8f8cf71d99… Author: John Chilton <jmchilton(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 #3784 from nekrut/collection_ops_help_fixes made collection ops help sections slightly more readable Compare: https://github.com/galaxyproject/galaxy/compare/a5b0e760503d...eadbb16462f2

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[galaxyproject/infrastructure-playbook] 92e004: Decrease squid memory usage on stratum 1s
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 92e004b615d7297191f06b5a3c729d8ec6533207 https://github.com/galaxyproject/infrastructure-playbook/commit/92e004b615d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/group_vars/cvmfsstratum1servers.yml Log Message: ----------- Decrease squid memory usage on stratum 1s Commit: 9ad75c96e7be125768960f0bdd62fb30f569512f https://github.com/galaxyproject/infrastructure-playbook/commit/9ad75c96e7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml A galaxyenv/host_vars/jetstream-iu0.galaxyproject.org.yml A galaxyenv/host_vars/jetstream-tacc0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml A galaxyenv/secret_group_vars/dockersslservers.yml A jetstream_common/files/etc/dhclient.conf A jetstream_common/files/etc/ifcfg-eth1 M jetstreamiuenv/group_vars/controllers.yml A jetstreamtaccenv/files M jetstreamtaccenv/group_vars/controllers.yml A roles/cvmfs/meta/main.yml A roles/docker/README.md A roles/docker/defaults/main.yml A roles/docker/handlers/main.yml A roles/docker/tasks/install_debian.yml A roles/docker/tasks/install_redhat.yml A roles/docker/tasks/main.yml A roles/docker/tasks/ssl-ca-passphrase.yml A roles/docker/tasks/ssl-gen-ca.yml A roles/docker/tasks/ssl-gen-client-cert.yml A roles/docker/tasks/ssl-gen-server-cert.yml A roles/docker/tasks/ssl-server.yml A roles/docker_swarm/meta/main.yml A roles/docker_swarm/tasks/main.yml A roles/docker_swarm/tasks/swarm-init.yml Log Message: ----------- Add roles for docker and docker swarm, create a swarm on Jetstream and PSU Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c1e9057120…

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[galaxyproject/galaxy] 18cb50: Abstraction for re-use between collection creators...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18cb50ecea80b3feeac02a2ef07c4cbd816c39d4 https://github.com/galaxyproject/galaxy/commit/18cb50ecea80b3feeac02a2ef07c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: 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 A static/maps/mvc/collection/base-creator.js.map 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Abstraction for re-use between collection creators. The new mixin reduces the duplication between the list and list of paired collection creators. I'd like to add functionality related to hiding the original datasets (especially useful for direct upload of collections but previously requested also) but I'd like to reduce the duplication related to doing that first. This is a start in that direction. Commit: a5b0e760503dc09ac99d47bbcde1524c7f3e37a4 https://github.com/galaxyproject/galaxy/commit/a5b0e760503dc09ac99d47bbcde1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: 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 A static/maps/mvc/collection/base-creator.js.map 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.js 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 #3781 from jmchilton/collection-builders Abstraction for re-use between collection creators. Compare: https://github.com/galaxyproject/galaxy/compare/5428d39adb6b...a5b0e760503d

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[galaxyproject/galaxy] 1578ff: Add tool_list webhook plugin to create the tool li...
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1578ffe1ca5bf28a34f91a892eed286ab69a14ba https://github.com/galaxyproject/galaxy/commit/1578ffe1ca5bf28a34f91a892eed… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Add tool_list webhook plugin to create the tool list yaml file for this instance. Commit: 90ae42c3f1d0efc4f8b461e43a158eb5b7b95d4f https://github.com/galaxyproject/galaxy/commit/90ae42c3f1d0efc4f8b461e43a15… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Reduced API calls to speed it up. Commit: 6ece9acfde69fadd4e8b105c9c14ce572ddbfbcd https://github.com/galaxyproject/galaxy/commit/6ece9acfde69fadd4e8b105c9c14… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix linting. Commit: d7cf8a4b33991c3117f725a1d418706b758703b5 https://github.com/galaxyproject/galaxy/commit/d7cf8a4b33991c3117f725a1d418… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix Python 2.7 linting. Commit: bc203d022f92fd596514d935c0e569163e2cf4d1 https://github.com/galaxyproject/galaxy/commit/bc203d022f92fd596514d935c0e5… Author: Clemens BlanK <blankclemens(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Speed up list creation. Commit: 5428d39adb6bf37c61b8c17efb1b3157e0b242d2 https://github.com/galaxyproject/galaxy/commit/5428d39adb6bf37c61b8c17efb1b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Merge pull request #3753 from blankclemens/webhook_tool_list Webhook plugin: tool_list Compare: https://github.com/galaxyproject/galaxy/compare/3921aa573c0f...5428d39adb6b

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[galaxyproject/galaxy] 060271: deduplicate obsolete API readme
by GitHub 21 Mar '17

21 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0602712a35015bba52f3bc756b0ce0fa1c20728e https://github.com/galaxyproject/galaxy/commit/0602712a35015bba52f3bc756b0c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- deduplicate obsolete API readme Commit: 3921aa573c0fa7b900316cdad4d06e23c02b19b2 https://github.com/galaxyproject/galaxy/commit/3921aa573c0fa7b900316cdad4d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- Merge pull request #3777 from martenson/dedup-readme deduplicate obsolete API readme Compare: https://github.com/galaxyproject/galaxy/compare/5440889bf6a7...3921aa573c0f

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[galaxyproject/usegalaxy-playbook] 4324d0: update Main
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4324d0b90e7772248afb9204807c3d9f81d6dfe4 https://github.com/galaxyproject/usegalaxy-playbook/commit/4324d0b90e777224… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- update Main

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[galaxyproject/usegalaxy-playbook] ff5c6f: fix target for 101 rewrite
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ff5c6fe5bb2b146736696597fa7927b901be7528 https://github.com/galaxyproject/usegalaxy-playbook/commit/ff5c6fe5bb2b1467… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- fix target for 101 rewrite the canonical source is in the hub

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[galaxyproject/infrastructure-playbook] c1e905: Remove extra Jetstream instances
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c1e90571202d3d1ca9a3d0242ecc27595ad2e168 https://github.com/galaxyproject/infrastructure-playbook/commit/c1e90571202… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M jetstreamiuenv/inventory M jetstreamtaccenv/inventory Log Message: ----------- Remove extra Jetstream instances

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/release_16.04 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 Compare: https://github.com/galaxyproject/galaxy/compare/4cf70aea7977...2528a89bd087

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[galaxyproject/galaxy] 131aeb: Abstract uWSGI handling into new galaxy.web.stack ...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 131aeb66b4884200c6c9433aef9a80aabf98d132 https://github.com/galaxyproject/galaxy/commit/131aeb66b4884200c6c9433aef9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Abstract uWSGI handling into new galaxy.web.stack package. Commit: d18b4d13cbc25c85005e4b19a02abedbed7aba46 https://github.com/galaxyproject/galaxy/commit/d18b4d13cbc25c85005e4b19a02a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py Log Message: ----------- Add an exception for unsupported middleware wrapping for better failure handling. Commit: 5440889bf6a7c5f278860760cd8c4ba18708c263 https://github.com/galaxyproject/galaxy/commit/5440889bf6a7c5f278860760cd8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #3759 from natefoo/abstract-app-stack Abstract uWSGI handling into new galaxy.web.stack package Compare: https://github.com/galaxyproject/galaxy/compare/cd36aa0878ae...5440889bf6a7

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[galaxyproject/infrastructure-playbook] 1426a8: Update athena access list
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1426a8538568204c47adc82a92ddef6953b77eb4 https://github.com/galaxyproject/infrastructure-playbook/commit/1426a853856… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml Log Message: ----------- Update athena access list

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[galaxyproject/infrastructure-playbook] c42389: add hub redirects for API pages
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c42389db42d441f7ba3828e8fcf39dfaff0fef88 https://github.com/galaxyproject/infrastructure-playbook/commit/c42389db42d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- add hub redirects for API pages

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[galaxyproject/galaxy] 376212: Fix for uploading rdata datasets when explicitly d...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy 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: 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: 3b4cf0d578d871f8bf3e005e0b5d7c65c78d1b2d https://github.com/galaxyproject/galaxy/commit/3b4cf0d578d871f8bf3e005e0b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> 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 #3778 from galaxyproject/release_17.01 [usegalaxy] merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/f76e0921d7d2...3b4cf0d578d8

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[galaxyproject/usegalaxy-playbook] d37d80: Add Dockerfiles for galaxy-update and galaxy-insta...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d37d808bf7a6f3b8e5688fd0581289deb0aca4ab https://github.com/galaxyproject/usegalaxy-playbook/commit/d37d808bf7a6f3b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A common/docker/galaxy-installer/Dockerfile.main A common/docker/galaxy-installer/Dockerfile.test A common/docker/galaxy-installer/run_main.sh A common/docker/galaxy-installer/run_test.sh A common/docker/galaxy-update/Dockerfile A common/docker/galaxy-update/condarc Log Message: ----------- Add Dockerfiles for galaxy-update and galaxy-installer. Note galaxy.ini not included.

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[galaxyproject/galaxy] 77b298: Fix run_tests.sh --dockerize for Mac OS X usage.
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77b29880c8e9eddaf282e8738542aa57a189f6d2 https://github.com/galaxyproject/galaxy/commit/77b29880c8e9eddaf282e8738542… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh --dockerize for Mac OS X usage. Without this I get the error message below and the tests do not execute. ``` ./run_tests.sh: line 279: UID: readonly variable ``` This was likely broken with b75ee68d9f6305646a55d816fb1173210e36eab9. Commit: d1eab2685f652f0b6f8c8119c51acf080c54556e https://github.com/galaxyproject/galaxy/commit/d1eab2685f652f0b6f8c8119c51a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Provide a fallback for GALAXY_TEST_UID if manually running Docker tests. Commit: d6654838f361a1e3064619cb059f9137579dc376 https://github.com/galaxyproject/galaxy/commit/d6654838f361a1e3064619cb059f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix pip install cache inside Galaxy testing container. It is causing Jenkins to fail throughout on https://github.com/galaxyproject/galaxy/pull/3179. Commit: b1f12d41f66c2b07929c037363fc6d94b890b283 https://github.com/galaxyproject/galaxy/commit/b1f12d41f66c2b07929c037363fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Simplify run_test_wrapper.sh per @natefoo comments. https://github.com/galaxyproject/galaxy/pull/3755/files#r106182107 Commit: cd36aa0878aed1a604a256098241068df169e4a3 https://github.com/galaxyproject/galaxy/commit/cd36aa0878aed1a604a256098241… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3755 from jmchilton/docker_test_fixes Assorted Fixes for Dockerized Test Setup Compare: https://github.com/galaxyproject/galaxy/compare/8e77fe93b8e0...cd36aa0878ae

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[galaxyproject/galaxy] 376212: Fix for uploading rdata datasets when explicitly d...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/6ab5cc1caf8c...e3e24facc721

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[galaxyproject/galaxy] 718df4: Prune empty tag handler
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 718df44921db25eedf21f5fefb2b4a6ac7bc7792 https://github.com/galaxyproject/galaxy/commit/718df44921db25eedf21f5fefb2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: R lib/galaxy/tags/tag_handler.py Log Message: ----------- Prune empty tag handler Commit: 1b5d95a5800aeed632888a42473a7ce24b9623c5 https://github.com/galaxyproject/galaxy/commit/1b5d95a5800aeed632888a42473a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: R lib/galaxy/tags/__init__.py Log Message: ----------- Remove unused (and empty) tags module. Commit: 72b3b8596253500cbbf54bfe7a5415b08f46b14d https://github.com/galaxyproject/galaxy/commit/72b3b8596253500cbbf54bfe7a54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Fix bug(?) that prevented associating multiple values to a tag. Commit: 8e77fe93b8e0b1eae57d454adc13a86a376bae35 https://github.com/galaxyproject/galaxy/commit/8e77fe93b8e0b1eae57d454adc13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3760 from dannon/nametag_fixes Tagging tweaks Compare: https://github.com/galaxyproject/galaxy/compare/031ce2307367...8e77fe93b8e0

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