- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c634a9: Fix unit test that uses fake trans.user_is_admin f...
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c634a9d3e6b8c5db2469931ce2e5d88f977938f9 https://github.com/galaxyproject/galaxy/commit/c634a9d3e6b8c5db2469931ce2e5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Fix unit test that uses fake trans.user_is_admin for the change to a property made in aad1e3fd0ac3c44bba81d7c278beb06b2016117b. Commit: 9375ae9ff4eff58a0eec6ab3ce3ee247711c9a45 https://github.com/galaxyproject/galaxy/commit/9375ae9ff4eff58a0eec6ab3ce3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge pull request #6842 from natefoo/user-is-admin-property Fix unit test that uses fake trans.user_is_admin Compare: https://github.com/galaxyproject/galaxy/compare/f317be200eb1...9375ae9ff4ef **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 5d4755: Installed replace_column_by_key_value_file and add...
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5d47553625cb2dbde761fd60fb53f2a088173456 https://github.com/galaxyproject/usegalaxy-playbook/commit/5d47553625cb2dbd… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed replace_column_by_key_value_file and add_input_name_as_column. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6b3f67: Replace deprecated assertEquals() method
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b3f6727709350b144e81513b9c22d8c648e203b https://github.com/galaxyproject/galaxy/commit/6b3f6727709350b144e81513b9c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows_from_yaml.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Replace deprecated assertEquals() method Fix warnings during py34-unit tests like: ``` /home/travis/build/galaxyproject/galaxy/test/unit/workflows/test_extract_summary.py:46: DeprecationWarning: Please use assertEqual instead. self.assertEquals(job_dict[hda.job], [('out1', derived_hda_2)]) ``` See e.g. https://travis-ci.org/galaxyproject/galaxy/jobs/438829277 Commit: 2e6f96bcf661d54886d0d27e703650746380c681 https://github.com/galaxyproject/galaxy/commit/2e6f96bcf661d54886d0d27e7036… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove unneeded parentheses Commit: f317be200eb1c38c7938e9cc8b5e80f3c9e5dbaa https://github.com/galaxyproject/galaxy/commit/f317be200eb1c38c7938e9cc8b5e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows_from_yaml.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6841 from nsoranzo/assertEqual Replace deprecated assertEquals() method Compare: https://github.com/galaxyproject/galaxy/compare/c44b7cf8e8df...f317be200eb1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b99fed: Update to latest galaxy-lib
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b99fedefa81b3ca59c27eb64ea9a7e9865cd9db8 https://github.com/galaxyproject/galaxy/commit/b99fedefa81b3ca59c27eb64ea9a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update to latest galaxy-lib Includes: - change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 ) - channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 ) Commit: c83c5cb78475c96d8e49510619c76f737cca5c8e https://github.com/galaxyproject/galaxy/commit/c83c5cb78475c96d8e49510619c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Change conda channel priority: conda-forge > bioconda xref. https://github.com/bioconda/bioconda-utils/issues/330 Commit: 9b6833b5a04cea06d245086b7b74a24a524b0064 https://github.com/galaxyproject/galaxy/commit/9b6833b5a04cea06d245086b7b74… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- make config-rebuild Commit: a43a60656a49ad0b53574dce61738764cf466287 https://github.com/galaxyproject/galaxy/commit/a43a60656a49ad0b53574dce6173… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6830 from nsoranzo/release_18.09_channel_priority_update [18.09] Update conda channel priority: conda-forge > bioconda Compare: https://github.com/galaxyproject/galaxy/compare/5205ed7eebe4...a43a60656a49 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] aad1e3: Convert user_is_admin and user_can_do_run_as to pr...
by GitHub 09 Oct '18

09 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aad1e3fd0ac3c44bba81d7c278beb06b2016117b https://github.com/galaxyproject/galaxy/commit/aad1e3fd0ac3c44bba81d7c278be… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako Log Message: ----------- Convert user_is_admin and user_can_do_run_as to properties Commit: c44b7cf8e8df53612ca17d8aa2013b5e35695511 https://github.com/galaxyproject/galaxy/commit/c44b7cf8e8df53612ca17d8aa201… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/examples.py.sample M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako Log Message: ----------- Merge pull request #6835 from natefoo/user-is-admin-property Convert user_is_admin and user_can_do_run_as to properties Compare: https://github.com/galaxyproject/galaxy/compare/1f389ae3e773...c44b7cf8e8df **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 381d6a: Add two recently merged PRs.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] adcd73: Fix broken gxformat2 imports.
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: adcd7333325dc34b7edcb5540730b350ff3f4e33 https://github.com/galaxyproject/galaxy/commit/adcd7333325dc34b7edcb5540730… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Fix broken gxformat2 imports. Commit: 1f389ae3e77352920566f09c4f1be1a1e40ff862 https://github.com/galaxyproject/galaxy/commit/1f389ae3e77352920566f09c4f1b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M test/manual/workflows_scaling.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6834 from jmchilton/fix_gxformat2_imports Fix broken gxformat2 imports. Compare: https://github.com/galaxyproject/galaxy/compare/8ed5d8c9414f...1f389ae3e773 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 1d6596: Automatically return roundup nodes to service upon...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1d659600da46427c171cc9d02495e227484b124d https://github.com/galaxyproject/infrastructure-playbook/commit/1d659600da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Automatically return roundup nodes to service upon reboot **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] a5b5bf: Add some additional body filter spam rules
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a5b5bfcb0227884187392f752e3c8a29612cc399 https://github.com/galaxyproject/infrastructure-playbook/commit/a5b5bfcb022… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M roles/postfix/templates/local.cf.j2 Log Message: ----------- Add some additional body filter spam rules **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9044e6: Upgrade concurrently; this fixes a 'null' return f...
by GitHub 08 Oct '18

08 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9044e614f03b4d0daa3e67e32be15d7d3f1268f1 https://github.com/galaxyproject/galaxy/commit/9044e614f03b4d0daa3e67e32be1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. Commit: 5205ed7eebe4b9a2a25d0f19abd5fd732f42e302 https://github.com/galaxyproject/galaxy/commit/5205ed7eebe4b9a2a25d0f19abd5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6828 from dannon/null_exit_bug_fix [18.09] Upgrade concurrently for 'null' return fix Compare: https://github.com/galaxyproject/galaxy/compare/58ea67eb457c...5205ed7eebe4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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