[galaxyproject/galaxy] d4c318: Explicitly add popper (necessary due to peer depen...

GitHub

23 May 2018 23 May '18

1:45 p.m.

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d4c318bfa0ecd24c87aa0195ba2e6cdcfaac1400 https://github.com/galaxyproject/galaxy/commit/d4c318bfa0ecd24c87aa0195ba2e6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Explicitly add popper (necessary due to peer dependency) Commit: f75463e5cfae4c3a288501836e88d72c2f662142 https://github.com/galaxyproject/galaxy/commit/f75463e5cfae4c3a288501836e88d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Remove extract_genomic_dna tool from sample. It has serious issues and a better version from the IUC is available at https://toolshed.g2.bx.psu.edu/repository?repository_id=5e1b70f8c4a31a72&changeset_revision=e400dcbc60d0. Alternative to https://github.com/galaxyproject/galaxy/pull/5618 until the tool is migrated out of Galaxy in some fashion. Keeping it in the code but not in the sample for now means existing deployers who want to keep it get to without making any changes but it prevents new deployers from having to figure out it is broken and a better version is available. Commit: fbec6ddc3246996291e2baa947aa8b7eb3c82bdc https://github.com/galaxyproject/galaxy/commit/fbec6ddc3246996291e2baa947aa8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5320 from bernt-matthias/topic/allow_empty_mail allow registration with empty email Commit: b0d094481a81d4efed4ca3916da6e4540b43b7d6 https://github.com/galaxyproject/galaxy/commit/b0d094481a81d4efed4ca3916da6e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- [17.09] Fix mulled docker caching. Broken with 93ffc4055b145811b86191dae8b865ea45b55fcb. Alternative to https://github.com/galaxyproject/galaxy/pull/5248 that does not use ``shell=True``. Rebased with cleanup from @nsoranzo. Commit: 64deb6311712c0d28edef6ce689d0ce184ccb226 https://github.com/galaxyproject/galaxy/commit/64deb6311712c0d28edef6ce689d0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- Fix broken API test. I think the URLs changed so checksum computation is failing. Commit: 274c480b9ecc4fba0feabba712d8f201aac1c183 https://github.com/galaxyproject/galaxy/commit/274c480b9ecc4fba0feabba712d8f... Author: E Rasche <hxr@hx42.org> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Allow formatting statsd data for influxdb Commit: 9e2b277fc7d614f5227629ff487b021be361219e https://github.com/galaxyproject/galaxy/commit/9e2b277fc7d614f5227629ff487b0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #5658 from blankenberg/uwsg-buffer-size Add buffer-size to galaxy.yml.sample Commit: 6422955a22d9a81359279bacd2ceacc079aff6ed https://github.com/galaxyproject/galaxy/commit/6422955a22d9a81359279bacd2cea... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: A scripts/apply_tags.py Log Message: ----------- Merge pull request #5669 from bgruening/propagate_tags_script Add script for propagating hashtags in a Galaxy history Commit: 240d72bdd57fe46664d9e045ff0a688c6fc64e2a https://github.com/galaxyproject/galaxy/commit/240d72bdd57fe46664d9e045ff0a6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #5741 from jmchilton/extract_genome_dna_remove_from_sample Remove extract_genomic_dna tool from tool sample. Commit: 40e87162597df53b8210f5cb789721633018f370 https://github.com/galaxyproject/galaxy/commit/40e87162597df53b8210f5cb78972... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #5692 from jmchilton/selenium_fixes_35 Hack to fix bug in uploader where it sometimes posts with empty "file_type". Commit: d1489ca57ce80b7fc85f59cf2158cc041898c101 https://github.com/galaxyproject/galaxy/commit/d1489ca57ce80b7fc85f59cf2158c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5714 from jmchilton/defeated_by_selenium Restructure and mark as flakey problematic library collection Selenium test. Commit: 46419ca168d0a6a4f623abbb12b43cdcb7f0adfd https://github.com/galaxyproject/galaxy/commit/46419ca168d0a6a4f623abbb12b43... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Import tweaks, force bootstrap js -- this breaks the Galaxy, temporarily Commit: 834726321fb30fd2934d254af153ff9f1ab05bfe https://github.com/galaxyproject/galaxy/commit/834726321fb30fd2934d254af153f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js Log Message: ----------- libs/backbone -> backbone (this is used externally, and both resolve to the same) Commit: c0ec919d2869e3ea700a285b7eda4adab2f7497b https://github.com/galaxyproject/galaxy/commit/c0ec919d2869e3ea700a285b7eda4... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove unused function Last use removed in commit 87db3952d38df4bc417dea2030a8ff5cdc93395f . Commit: 597b437b71c2a4f55e255bc5c6fd1a59339bb77d https://github.com/galaxyproject/galaxy/commit/597b437b71c2a4f55e255bc5c6fd1... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Simplify unicodify().encode() to smart_str() Belated follow-up to https://github.com/galaxyproject/galaxy/pull/1905 Commit: 03f5f5310ed75c912b93baa4da6cc0d858512164 https://github.com/galaxyproject/galaxy/commit/03f5f5310ed75c912b93baa4da6cc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/nginx.md M doc/source/admin/scaling.md M test/api/test_workflows.py Log Message: ----------- Fix typos Commit: 2921af9bda5fff72f5764cef37e7476b53f136d5 https://github.com/galaxyproject/galaxy/commit/2921af9bda5fff72f5764cef37e74... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Allow bool type in UWSGI_OPTIONS dict Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6ff... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: c74868a1e670a28b934807c5a2c161e431dc0f88 https://github.com/galaxyproject/galaxy/commit/c74868a1e670a28b934807c5a2c16... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Tool versions should follow PEP 440 to ensure a correct tool lineage. Commit: 8fe5b5c14eee8aea1b16ee932be10aaf6b13b452 https://github.com/galaxyproject/galaxy/commit/8fe5b5c14eee8aea1b16ee932be10... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Capture more HDA state transitions in the history panel. Commit: 460c40b63c7cb62003fbae5b877d371ff99a79e9 https://github.com/galaxyproject/galaxy/commit/460c40b63c7cb62003fbae5b877d3... Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py Log Message: ----------- Reset Unrelated Files to Their State in upstream/dev Commit: c621b8091228d3816d9f3e3bb194affbc9a85382 https://github.com/galaxyproject/galaxy/commit/c621b8091228d3816d9f3e3bb194a... Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/package.json M config/datatypes_conf.xml.sample M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run_tests.sh A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into configurable_priorities Commit: c20608b78e28e1354b1caab804192f05d7b5ff65 https://github.com/galaxyproject/galaxy/commit/c20608b78e28e1354b1caab804192... Author: Matthew Spelchak <mrs11teen@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: A lib/galaxy/workflow/resources/__init__.py Log Message: ----------- Reset One More File to Their State in upstream/dev Commit: 13882fe7cb00951673e6e81ce2fbcbeaf8054820 https://github.com/galaxyproject/galaxy/commit/13882fe7cb00951673e6e81ce2fbc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/ui/peek-column-selector.js Log Message: ----------- Peek column selector jquery handling, minor cleanup Commit: 81a418fe98ee2f26b35bae81060398431b9a096e https://github.com/galaxyproject/galaxy/commit/81a418fe98ee2f26b35bae8106039... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit integer validation Commit: 0823d0e554fbef8e7667f1efea8c78864d3318d7 https://github.com/galaxyproject/galaxy/commit/0823d0e554fbef8e7667f1efea8c7... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- Merge pull request #5740 from jmchilton/bagit_example_broken Fix broken bagit API test. Commit: b5236cd9065a707d0dd2d589426dbdbcb5f9a9f0 https://github.com/galaxyproject/galaxy/commit/b5236cd9065a707d0dd2d589426db... Author: E Rasche <hxr@hx42.org> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- should not hvae been on self Commit: 66643bd58cbac529a8b67a171a9b619f88d3449b https://github.com/galaxyproject/galaxy/commit/66643bd58cbac529a8b67a171a9b6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Try babel/importloader for parceljs. More structure overhaul Commit: fa5fae50c5a10ba2ae0db5d4ee2c92fd4dcc3188 https://github.com/galaxyproject/galaxy/commit/fa5fae50c5a10ba2ae0db5d4ee2c9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json Log Message: ----------- Fix license specifier to valid spdx form Commit: 4fb391b127b38872e81f9791a11a03702caf984e https://github.com/galaxyproject/galaxy/commit/4fb391b127b38872e81f9791a11a0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/.babelrc Log Message: ----------- Babelrc fixes Commit: 890e6327e8ddf85702fc1c1c2990779813396885 https://github.com/galaxyproject/galaxy/commit/890e6327e8ddf85702fc1c1c29907... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/nginx.md M doc/source/admin/scaling.md M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/remote_files.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5747 from nsoranzo/typos_refactors Typo fixes and small refactors Commit: 0369a4028d1732e727ae9e90adf4668a3b3b3ddd https://github.com/galaxyproject/galaxy/commit/0369a4028d1732e727ae9e90adf46... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #5746 from nsoranzo/pep440 Tool versions should follow PEP 440 Commit: e92ceea1f7471bc9f00fdbb6e8e982ebae4387ef https://github.com/galaxyproject/galaxy/commit/e92ceea1f7471bc9f00fdbb6e8e98... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Fix scatterplot. Commit: 9a11327b5eece638c3ba6f189853ae29449a9be0 https://github.com/galaxyproject/galaxy/commit/9a11327b5eece638c3ba6f189853a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Add final scatterplot build. Commit: 77d68846a15d776b507995cedaab55cd9ead3614 https://github.com/galaxyproject/galaxy/commit/77d68846a15d776b507995cedaab5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Strip stray debug... Commit: 187c540cd4aac7e1059fdaa6aaf56c87913f1d09 https://github.com/galaxyproject/galaxy/commit/187c540cd4aac7e1059fdaa6aaf56... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case Commit: 659721ac94e909ab31481059ffe1ea092a70047e https://github.com/galaxyproject/galaxy/commit/659721ac94e909ab31481059ffe1e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: a345b2e2658ebdd5eb92790dd3048a625e9f5cbb https://github.com/galaxyproject/galaxy/commit/a345b2e2658ebdd5eb92790dd3048... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Merge pull request #5645 from phac-nml/configurable_priorities Update Dynamic Tool Destinations With Configurable Priorities and Better Validation Commit: f6ae449ce8535c760d6d9a7b1a34d4e11f37ffb3 https://github.com/galaxyproject/galaxy/commit/f6ae449ce8535c760d6d9a7b1a34d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json Log Message: ----------- 0BSD is probably more correct here. Commit: 9ad1ba07f8d41ac9be62726a10e9a549c39a58fb https://github.com/galaxyproject/galaxy/commit/9ad1ba07f8d41ac9be62726a10e9a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Gulpfile standardization anticipating merges. Commit: 4a490970d923043007d8ddd8905dd9d87d9bafb6 https://github.com/galaxyproject/galaxy/commit/4a490970d923043007d8ddd8905dd... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: d3d8fc29f17f635e675ac047370d59ac7a9fd23e https://github.com/galaxyproject/galaxy/commit/d3d8fc29f17f635e675ac047370d5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/base/populators.py M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Another attempt to skip flakey Selenium tests. - Flakey was throwing nose's SkipTest but the Selenium framework was catching unittest's, fix that to use unittest version in both places. - There problematic test is still throwing exceptions in the tearDown which is still causing build failures, skip the whole test. Commit: 37b7828cb7bd2e7c326120f7b1d141291db80b69 https://github.com/galaxyproject/galaxy/commit/37b7828cb7bd2e7c326120f7b1d14... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #5752 from dannon/scatterplot_fixes Scatterplot Fixes Commit: ea0ebd849f3c62806dff9499ebd16f777ebd07ce https://github.com/galaxyproject/galaxy/commit/ea0ebd849f3c62806dff9499ebd16... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py M static/style/blue/base.css Log Message: ----------- Replace static redirect and username with proper variables. Commit: f634c40ad480775f56029290ce618fa411bde1ec https://github.com/galaxyproject/galaxy/commit/f634c40ad480775f56029290ce618... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/ui.less M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_metrics_conf.xml.sample A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/create_history_template.py M lib/galaxy/util/inflection.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M 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/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/1.csv A test-data/example-bag.zip A test-data/qname_sorted.bam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/multi_output_recurse.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase # Conflicts: # static/style/blue/base.css Commit: f130fa8222a61412a132a5e5c7d74849a765a92d https://github.com/galaxyproject/galaxy/commit/f130fa8222a61412a132a5e5c7d74... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/base/populators.py M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5754 from jmchilton/selenium_fixes_40 Another attempt to skip flakey Selenium tests. Commit: cfbac405d21a53bf305904a2509e43343f7ec145 https://github.com/galaxyproject/galaxy/commit/cfbac405d21a53bf305904a2509e4... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 6e36af5c0ec47a3ae14edd99f1044c8fb8b26d9a https://github.com/galaxyproject/galaxy/commit/6e36af5c0ec47a3ae14edd99f1044... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix linking option for library dataset uploads Broken in commit a45cbfeb8d7d7cc3df5e2561b422023986e805d0 . Found by BioBlend tests: https://travis-ci.org/galaxyproject/bioblend/jobs/356761960 Commit: 2ecf3ff239b2f4095807cbeecf099beca990264e https://github.com/galaxyproject/galaxy/commit/2ecf3ff239b2f4095807cbeecf099... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json Log Message: ----------- Lock a local parcel build to scatterplot (instead of my global, which was same version -- no need for a viz rebuild here) Commit: d28ae4e152eabef7be9307af0d277f7b07edde86 https://github.com/galaxyproject/galaxy/commit/d28ae4e152eabef7be9307af0d277... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json Log Message: ----------- Merge pull request #5759 from dannon/parcel_minor_followup For scatterplot, lock a local parcel build Commit: 7c3c36e7626769c653b9b3b8f6208c861c60a24d https://github.com/galaxyproject/galaxy/commit/7c3c36e7626769c653b9b3b8f6208... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A config/plugins/visualizations/scatterplot/static/logo.png Log Message: ----------- Add logo for scatterplot Commit: 0e150b4051b9ff567e5c5a26fb213d36d42ebdf9 https://github.com/galaxyproject/galaxy/commit/0e150b4051b9ff567e5c5a26fb213... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Rename tab to Visualize Commit: e0572e104fb4589c58415bb3d5f99ffe996b2f9c https://github.com/galaxyproject/galaxy/commit/e0572e104fb4589c58415bb3d5f99... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run_tests.sh A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 04fee6070bfa94a3788c89dc0cc1414469db20e6 https://github.com/galaxyproject/galaxy/commit/04fee6070bfa94a3788c89dc0cc14... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into select_to_text Commit: c6257f77f10080664ac01d156caee9abab43d703 https://github.com/galaxyproject/galaxy/commit/c6257f77f10080664ac01d156caee... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5749 from jmchilton/history_panel_state_changes [18.01] Capture more HDA state transitions in the history panel. Commit: 2e2ad26addfae8c91395821f75e44749c1aa04b2 https://github.com/galaxyproject/galaxy/commit/2e2ad26addfae8c91395821f75e44... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A client/deploy.js M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Incremental work testing staging of libs. May dump this, it's awfully slow via gulp and I can do it faster with regular js. Commit: d7d888eaed14a6610cf0f70ce1635c8b01c7af91 https://github.com/galaxyproject/galaxy/commit/d7d888eaed14a6610cf0f70ce1635... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: a339477e62f46d807862b18bb88ee963222aa703 https://github.com/galaxyproject/galaxy/commit/a339477e62f46d807862b18bb88ee... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/galaxy.yml.sample Log Message: ----------- Minor typo Commit: a2398a28ea90a55922bad7bbdc5aa50b02f4411f https://github.com/galaxyproject/galaxy/commit/a2398a28ea90a55922bad7bbdc5aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Annotate statsd_influxdb in new config schema, rebuild. Commit: bf59e0da0454f72b41af3feaacb7a0e471db6333 https://github.com/galaxyproject/galaxy/commit/bf59e0da0454f72b41af3feaacb7a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix (again) the typo I previously fixed and then I rebuilt over. D'oh. Commit: 7fe49481d7cc37541cc9ec010a871694b5987cfb https://github.com/galaxyproject/galaxy/commit/7fe49481d7cc37541cc9ec010a871... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Try mapping with glob syntax Commit: 31c1c6e5285ad5ce54271ceff1861b87996591b5 https://github.com/galaxyproject/galaxy/commit/31c1c6e5285ad5ce54271ceff1861... Author: Pablo Moreno <pablo.a.moreno@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Makes k8s namespace configurable, from the runner's perspective. Commit: c5e19d4a532be11d695a12d3b3dca42d877057a8 https://github.com/galaxyproject/galaxy/commit/c5e19d4a532be11d695a12d3b3dca... Author: Pablo Moreno <pablo.a.moreno@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of existing k8s jobs on restart, and avoids clashes with jobs of previous instances, establishing an optional trust mechanism. Commit: ade62bc3b15b25e76d7114c5ee9051cd5f575700 https://github.com/galaxyproject/galaxy/commit/ade62bc3b15b25e76d7114c5ee905... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Revise select display matching Commit: 913cd1e6d2e784272ad1b4ebcaab6cb64d464d32 https://github.com/galaxyproject/galaxy/commit/913cd1e6d2e784272ad1b4ebcaab6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M .gitignore M client/gulpfile.js Log Message: ----------- Fix up regex, .gitignore static/plugins Commit: 55c052d4da53c80611d02e8a815de18b0d8c339d https://github.com/galaxyproject/galaxy/commit/55c052d4da53c80611d02e8a815de... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5758 from nsoranzo/link_to_files Fix linking option for library dataset uploads Commit: 46b51944c68f65f8da5151ace54d2bcaeed353cd https://github.com/galaxyproject/galaxy/commit/46b51944c68f65f8da5151ace54d2... Author: Pablo Moreno <pablo.a.moreno@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- PEP style fixes k8s runner. Commit: c8fc45a44967d700f5b9c9589cf9549b6d800720 https://github.com/galaxyproject/galaxy/commit/c8fc45a44967d700f5b9c9589cf95... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5750 from guerler/fix_columnassigner Add additional validation to numeric input element Commit: 8290da24eaf0994c018b055ba9bbc73876540f7c https://github.com/galaxyproject/galaxy/commit/8290da24eaf0994c018b055ba9bbc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: 241ade62cd740bf62d2348859493ed7326799597 https://github.com/galaxyproject/galaxy/commit/241ade62cd740bf62d2348859493e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Align validation order for consistency Commit: 0b580ad13042b58c50c3291441f5e5a80d7579ba https://github.com/galaxyproject/galaxy/commit/0b580ad13042b58c50c3291441f5e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #5760 from phnmnl/galaxy-prs/k8s-namespace Makes Kubernetes namespace configurable, from the runner's perspective. Commit: 79f027743c234035a164522806c4a03b9876f0d9 https://github.com/galaxyproject/galaxy/commit/79f027743c234035a164522806c4a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5755 from jmchilton/workflow_speed_up More backend speed ups for user's workflow index query. Commit: 54d91e585035bac3a9c72615ab70617b3ceb7669 https://github.com/galaxyproject/galaxy/commit/54d91e585035bac3a9c72615ab706... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to numeric input element Commit: 8ef320963a37566104af2da16580b002f6a42181 https://github.com/galaxyproject/galaxy/commit/8ef320963a37566104af2da16580b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 4ed7178d9bf550047efda22ba5f653e13f5d87bb https://github.com/galaxyproject/galaxy/commit/4ed7178d9bf550047efda22ba5f65... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- More backend speed ups for user's workflow index query. Commit: 64648aefd7e7f3a4062f1030001575fdb000cfc1 https://github.com/galaxyproject/galaxy/commit/64648aefd7e7f3a4062f103000157... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Ignore tool xml datatype settings for dragged history items Commit: 70392ddb3b08bdc7c3739add061ea1b45f78da38 https://github.com/galaxyproject/galaxy/commit/70392ddb3b08bdc7c3739add061ea... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove debug statements, use drop data where needed Commit: af514327cb86032b31880ec478fa383be2c7ab76 https://github.com/galaxyproject/galaxy/commit/af514327cb86032b31880ec478fa3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Validate type using collection, from @jmchilton Commit: 36467c1e768be5e32c7e91387c6246171d12e92a https://github.com/galaxyproject/galaxy/commit/36467c1e768be5e32c7e91387c624... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add source to data entry Commit: 30ed27f9ad916b7bd31ad7366381807763ca2db2 https://github.com/galaxyproject/galaxy/commit/30ed27f9ad916b7bd31ad73663818... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add additional check for history items Commit: 5eaa1301c648ff43651c745136ab71eb2cfde06d https://github.com/galaxyproject/galaxy/commit/5eaa1301c648ff43651c745136ab7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Rebuild client. Commit: 45a541f5c76c4d328c756b27ff58c9d17c072eeb https://github.com/galaxyproject/galaxy/commit/45a541f5c76c4d328c756b27ff58c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #5715 from erasche/object-store-annoyance Downgrade the warning to an info Commit: 3da1960c52b2cf893662ec1f865d67050c5500da https://github.com/galaxyproject/galaxy/commit/3da1960c52b2cf893662ec1f865d6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- [18.01] Fix copying tags for collections when copying histories. Fixes #5757. Commit: a4e9fe6834c507137988a1739a3b6a261598ce37 https://github.com/galaxyproject/galaxy/commit/a4e9fe6834c507137988a1739a3b6... Author: Delphine Lariviere <lariviere.delphine@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh M .ci/jenkins/api/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md A client/.babelrc M client/GruntFile.js M 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test/base/testcase.py R test/base/tool_shed_util.py R test/base/twilltestcase.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A 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test/functional/tools/composite_output_tests.xml A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/config_vars.xml M test/functional/tools/create_2.xml A test/functional/tools/data_source.py A test/functional/tools/empty_datasets.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml A test/functional/tools/fail_writing_work_dir_file.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/identifier_in_actions.xml A test/functional/tools/identifier_source.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/job_properties.xml M test/functional/tools/metadata.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_multi_versionless.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/output_filter_with_input.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml A test/functional/tools/vcf_bgzip.xml A test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/tour_generator A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R 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test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1 from galaxyproject/dev Update from Galaxyproject repo Commit: ed86fe745f53b151dce03cf571f306d293e59ab9 https://github.com/galaxyproject/galaxy/commit/ed86fe745f53b151dce03cf571f30... Author: Delphine-L <lariviere.delphine@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py Log Message: ----------- add genbank.gz andgbk.gz datatypes Commit: 5a578bfd325777e7e50479b34d1a308940138f82 https://github.com/galaxyproject/galaxy/commit/5a578bfd325777e7e50479b34d1a3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- uWSGI: Log listening URLs at startup. Commit: c720af066b704e591f3ff8806a68eb0a33a7fd4d https://github.com/galaxyproject/galaxy/commit/c720af066b704e591f3ff8806a68e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Attempt to log startup as late as possible Commit: 5ad8842b99572388432899f5c96fd4c6307cd082 https://github.com/galaxyproject/galaxy/commit/5ad8842b99572388432899f5c96fd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix lint errors Commit: 8223c36b34dd221bf95ea591b75bb75ecef6d286 https://github.com/galaxyproject/galaxy/commit/8223c36b34dd221bf95ea591b75bb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Stage plugin static as a part of the client build Commit: c779145bff4183926c3989828e9834a93b9baa25 https://github.com/galaxyproject/galaxy/commit/c779145bff4183926c3989828e983... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log also the PID. Python3 fix And make _socket_opts() more readable. Commit: b147abe9e58d21ee29722cedbdd12c354a6b095b https://github.com/galaxyproject/galaxy/commit/b147abe9e58d21ee29722cedbdd12... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Minor es6'ing in vizview Commit: 3fbc41af2abb744352c8ebbcf7150ed3ac49b027 https://github.com/galaxyproject/galaxy/commit/3fbc41af2abb744352c8ebbcf7150... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Source viz logos out of /static Commit: 38080f721b7c6948f80544752644bcc9a5fad362 https://github.com/galaxyproject/galaxy/commit/38080f721b7c6948f80544752644b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Fix docstring 'visualization' typo. Commit: 8ace2457203399893236e07539a5e84f6fa8933a https://github.com/galaxyproject/galaxy/commit/8ace2457203399893236e07539a5e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Ignore seemingly harmless error when tearing down Selenium tests. Causes otherwise passing tests to fail for not particular reason. Cannot find a Selenium issue for this but it has been reported on in their IRC - seems like just a very rare, transient issue. xref https://jenkins.galaxyproject.org/job/docker-selenium/1830/testReport/junit/... Commit: cacef65139f061d8cc0767379344250da51e4ddd https://github.com/galaxyproject/galaxy/commit/cacef65139f061d8cc07673793442... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5742 from erasche/statsd-influxdb Allow formatting statsd data for influxdb Commit: 7dbde33b22ab6c334eec11f88a1596d1cfdcd64d https://github.com/galaxyproject/galaxy/commit/7dbde33b22ab6c334eec11f88a159... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5766 from jmchilton/copy_tag_fix [18.01] Fix copying tags for collections when copying histories. Commit: e41c8f792743a74e927e37fb37b788aa617ec1cd https://github.com/galaxyproject/galaxy/commit/e41c8f792743a74e927e37fb37b78... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge pull request #5770 from natefoo/uwsgi-log-start [18.01] uWSGI: Log listening URLs at startup. Commit: cb41e623510d579050553db6578997cf0815f608 https://github.com/galaxyproject/galaxy/commit/cb41e623510d579050553db657899... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5732 from nsoranzo/release_18.01_fix_ldap [18.01] Fix LDAP when role_search_attribute is not defined Commit: e84dd5db6b1eb924f4f6897103774152fc0e2cef https://github.com/galaxyproject/galaxy/commit/e84dd5db6b1eb924f4f6897103774... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Rudimentary check for old psycopg2==2.4.3, which we clean up before installing psycopg2-binary. Commit: 30c2ea0c3e61db387e7c31ecb7fd18216c0e083e https://github.com/galaxyproject/galaxy/commit/30c2ea0c3e61db387e7c31ecb7fd1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Make psycopg2 grep a little more robust Commit: d44b47741ba6e2fd670a150f7d35fb3e8cdb56a9 https://github.com/galaxyproject/galaxy/commit/d44b47741ba6e2fd670a150f7d35f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Specify format to squelch deprecation warning about columns/legacy Commit: 66e624f90b31200b950ad1543af8453d654b3939 https://github.com/galaxyproject/galaxy/commit/66e624f90b31200b950ad1543af84... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #5765 from jmchilton/backport_cool_stuff_1801 [18.01] Backport various fixes from dev. Commit: bca5b299b3394bd2071e2aee1068ef12dce396bd https://github.com/galaxyproject/galaxy/commit/bca5b299b3394bd2071e2aee1068e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5771 from jmchilton/selenium_fixes_41 Ignore seemingly harmless error when tearing down Selenium tests. Commit: 88e6e94a81271a85e280143c5ef12532b83615cc https://github.com/galaxyproject/galaxy/commit/88e6e94a81271a85e280143c5ef12... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/model/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 1e7c86323258676938a060077fca8ad8a41d43e4 https://github.com/galaxyproject/galaxy/commit/1e7c86323258676938a060077fca8... Author: Delphine-L <lariviere.delphine@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- addition of blank lines (test failures) Commit: 244273ad554df1ab3bf337016a35b3fbe565c3fe https://github.com/galaxyproject/galaxy/commit/244273ad554df1ab3bf337016a35b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- [18.01] Fix /api/whoami for master API key. Just yield a null JSON response instead of the internal server error that happens currently. Commit: 198268a0aa9d62b0c3ca45f58734cc8fb5085875 https://github.com/galaxyproject/galaxy/commit/198268a0aa9d62b0c3ca45f58734c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #5773 from jmchilton/fix_whoami_1801 [18.01] Fix /api/whoami for master API key. Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: e0b9e93b4b76e4e9d553e61f2faa71d6bf559981 https://github.com/galaxyproject/galaxy/commit/e0b9e93b4b76e4e9d553e61f2faa7... Author: Delphine-L <lariviere.delphine@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py Log Message: ----------- removed gbk.gz extension Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee034... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Small improvements to scripts/grt/export.py for testing. - Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell. Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b28... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py Log Message: ----------- Unification of Galaxy configuration parsing for scripts/* Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated. Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f36... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh Log Message: ----------- Remove unused and unuseful scripts. Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a678... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh Log Message: ----------- Drop data library whoosh/lucene scripts. We don't set that config option in Galaxy anymore so these are broken anyway. Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe1656735... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time. Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c393589... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Cleanup script integration tests. Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc56... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo. Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dcb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Fix missing ENV information in config parameter args. Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc. Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py Log Message: ----------- More grt fixes - spotted by @nsoranzo. Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f22180089... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Redact help for --config-section option for @nsoranzo. Kept the string in the file for in-code documentation but hiding it from users. Commit: beb28d4aff2a9c38f06a357f9ee013566ad635c6 https://github.com/galaxyproject/galaxy/commit/beb28d4aff2a9c38f06a357f9ee01... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5735 from jmchilton/fix_mulled_docker_caching [17.09] Fix mulled docker caching. Commit: 8f0a2d2360ea904707fa3f61f6e3541e8e159571 https://github.com/galaxyproject/galaxy/commit/8f0a2d2360ea904707fa3f61f6e35... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5706 from jmchilton/selenium_fixes_36 Fix setup code in library test landing page to rerun on test retry. Commit: 1993ef5c69fed7d07e4f830e5630dcb4ba4cb39d https://github.com/galaxyproject/galaxy/commit/1993ef5c69fed7d07e4f830e5630d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-25 (Sun, 25 Mar 2018) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #5686 from blankenberg/gff GFF updates to handle ##FASTA directive Commit: f6342616eb0b6c740b734664cc50b896ad39f4b8 https://github.com/galaxyproject/galaxy/commit/f6342616eb0b6c740b734664cc50b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-25 (Sun, 25 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Fixes for testing Dockerfile recipe. The current Dockerfile build is broken because Selenium is not compatible with the latest chromedriver it seems (and the version in galaxy/testing-base:18.01.4 isn't compatible with the latest stable Chrome - version 65). I can't get older versions of Chrome to install with the current apt source but this does at least pin the version of chromedriver. Longer term it would be good to have the version of chrome we target to be pinned also, I hate that this Dockerfile isn't reproducible. Commit: 6fb738b01a48a495a68ded61371d10b4bd306d8e https://github.com/galaxyproject/galaxy/commit/6fb738b01a48a495a68ded61371d1... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: ca2ed15fda1032aef308aa87fa770356e1f3e5c2 https://github.com/galaxyproject/galaxy/commit/ca2ed15fda1032aef308aa87fa770... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 2b3557ffce38a97080c9921846e06131aa43e2e9 https://github.com/galaxyproject/galaxy/commit/2b3557ffce38a97080c9921846e06... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case verifying we check column values before tool execution. Commit: 4764b46bba4f126a6bf72f3a0aee9e210426cb7c https://github.com/galaxyproject/galaxy/commit/4764b46bba4f126a6bf72f3a0aee9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R client/deploy.js Log Message: ----------- Not going to pursue this deploy method, yet -- probably will want to do this later with prod/dev scripts to have more control over the build (over a big chain of package scripts) Commit: e206af4f6de57a9d668808538892e54554611b5c https://github.com/galaxyproject/galaxy/commit/e206af4f6de57a9d668808538892e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Remove gulp-ignore, unnecessary Commit: 43543c36d93621a312d0e3351cb3db2c1904fec1 https://github.com/galaxyproject/galaxy/commit/43543c36d93621a312d0e3351cb3d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M tox.ini Log Message: ----------- Rev and re-lock Galaxy dependencies Drop pinned-hashed-requirements.txt files, they are not generated by pipenv any more since v11.1.2 . Commit: 13fff60142eda391e6b833ed02fec3bd4cb1072e https://github.com/galaxyproject/galaxy/commit/13fff60142eda391e6b833ed02fec... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M tox.ini Log Message: ----------- Merge pull request #5776 from nsoranzo/dep_update Rev and re-lock Galaxy dependencies Commit: 6875307b2ac84cdb98ebb54a14a3c1ab3a3e6adb https://github.com/galaxyproject/galaxy/commit/6875307b2ac84cdb98ebb54a14a3c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Drop static framework mapping for plugins; we're going to stage into the existing static paths instead since this method doesn't work in uwsgi Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Before and after queries here: https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user. Commit: 4969394a3cce550ea82d7ca7fa69e95c172f56d8 https://github.com/galaxyproject/galaxy/commit/4969394a3cce550ea82d7ca7fa69e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Static serving of staged logos Commit: 91e97b60968d6813bd7a28d0d60e778b288ac385 https://github.com/galaxyproject/galaxy/commit/91e97b60968d6813bd7a28d0d60e7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Refactor code for clarity Commit: cf2e6dc6d2951f316e9641a05d69a3f919feb05e https://github.com/galaxyproject/galaxy/commit/cf2e6dc6d2951f316e9641a05d69a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Fix scatterplot as example of mako entrypoint -- this needs to be generalized Commit: c12feecb76f96fd5fe058d9cf90331e7eb956c5b https://github.com/galaxyproject/galaxy/commit/c12feecb76f96fd5fe058d9cf9033... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Minor linting in ui-thumbnails Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB. Includes test case that fails against 18.01. Commit: 840e436ea1f181ebe0c8478145e2cd0e97dc1778 https://github.com/galaxyproject/galaxy/commit/840e436ea1f181ebe0c8478145e2c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add strict workflow building mode check to drill downs Commit: 52741200b24933d3c4af1f5a7fa5124d29d5daf6 https://github.com/galaxyproject/galaxy/commit/52741200b24933d3c4af1f5a7fa51... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use pipenv also for the default dependencies Commit: fb92257bc755ae12a5dad810c152967bfc68d8a1 https://github.com/galaxyproject/galaxy/commit/fb92257bc755ae12a5dad810c1529... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Exclude 2 problematic h5py versions A warning was appearing in the stderr of upload jobs due to https://github.com/h5py/h5py/issues/995 . Commit: f8aa29e2805b932a03a577fd329f881a3d047c98 https://github.com/galaxyproject/galaxy/commit/f8aa29e2805b932a03a577fd329f8... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin WebOb to latest compatible release Commit: e625b649dc0e823d0c92f8c997254215bcf9dcab https://github.com/galaxyproject/galaxy/commit/e625b649dc0e823d0c92f8c997254... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin Mercurial to latest compatible release Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip [18.01] Fix model operation tools that produce standalone datasets. Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515ba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Commit: 45dd9889654cf839740b165763f6a40019cde2e0 https://github.com/galaxyproject/galaxy/commit/45dd9889654cf839740b165763f6a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5721 from erasche/sentry-reporter Sentry bug reports working for anonymous users Commit: 39d5ec89f885ffce8e3c9621439c76d9d0745aa6 https://github.com/galaxyproject/galaxy/commit/39d5ec89f885ffce8e3c9621439c7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 412ff1e16ae50af06751d3aae936973ef954fc61 https://github.com/galaxyproject/galaxy/commit/412ff1e16ae50af06751d3aae9369... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Add config rebuild left out of migration of options from 18.01 (I think) Commit: 528201e56ac651087fba38d20803ecce320050aa https://github.com/galaxyproject/galaxy/commit/528201e56ac651087fba38d20803e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Add delayed column attribute to grid helper Commit: b4a30bcd824f5bbb6e68717b508dd522ab640f26 https://github.com/galaxyproject/galaxy/commit/b4a30bcd824f5bbb6e68717b508dd... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Revise uwsgi defaults and display. In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195. Commit: f14c6ffe49b397b884f678812f311fc0bd451e53 https://github.com/galaxyproject/galaxy/commit/f14c6ffe49b397b884f678812f311... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Merge pull request #5788 from dannon/configrebuild Config-rebuild w/ options doc Commit: db1b8bc64b35265faa04268ad382c86067a214bc https://github.com/galaxyproject/galaxy/commit/db1b8bc64b35265faa04268ad382c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use delayed flag for history grid Commit: 5a86b8d706b7d3b8244b2359e2f7740367df1e89 https://github.com/galaxyproject/galaxy/commit/5a86b8d706b7d3b8244b2359e2f77... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #5693 from jmchilton/docker_test_update Fixes for testing Dockerfile recipe. Commit: 61adffbd614cbbe409f207415073604f8e13a0ba https://github.com/galaxyproject/galaxy/commit/61adffbd614cbbe409f2074150736... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5786 from nsoranzo/default_pipfile Use pipenv also for the default dependencies Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py Log Message: ----------- Touch up script unification PR based on @natefoo comments. Commit: bf5d472e28505438c5f345ad29989b80fe3aae80 https://github.com/galaxyproject/galaxy/commit/bf5d472e28505438c5f345ad29989... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5702 from guerler/select_to_text Relax validation condition for dynamic parameters Commit: 8b5c0b223ef9092420b9912b153b0d257fe5a1a5 https://github.com/galaxyproject/galaxy/commit/8b5c0b223ef9092420b9912b153b0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Allow target top rendering for visualizations Commit: 0cdd9b9ecd235a34ba6018542156f9780bf22f77 https://github.com/galaxyproject/galaxy/commit/0cdd9b9ecd235a34ba6018542156f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Client formatting Commit: 2b2fd9289857b258f7e63f64668d776c49a54ec8 https://github.com/galaxyproject/galaxy/commit/2b2fd9289857b258f7e63f64668d7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use visualizations route to link to plugins Commit: 38c2a895009c03204026ca7d74af70f92dd29f4e https://github.com/galaxyproject/galaxy/commit/38c2a895009c03204026ca7d74af7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'visualization_header' of github.com:guerler/galaxy into visualization_header Commit: c5beedef6b9f4498e4df0adfb39ddc519715f997 https://github.com/galaxyproject/galaxy/commit/c5beedef6b9f4498e4df0adfb39dd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/charts.less M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge branch 'visualization_header' into dev Commit: 70915dfc9f2b54bd88ebce92812f4edf578e18d4 https://github.com/galaxyproject/galaxy/commit/70915dfc9f2b54bd88ebce92812f4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M 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config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M doc/source/admin/galaxy_options.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.py R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/galaxy-main M static/style/blue/base.css M test/api/test_tools.py M test/base/populators.py M test/docker/base/Dockerfile M test/selenium_tests/framework.py M test/selenium_tests/test_library_to_collections.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into viz-staging Commit: a97b3a469c83f8f6780fd0b84f70ea31e08b6f91 https://github.com/galaxyproject/galaxy/commit/a97b3a469c83f8f6780fd0b84f70e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M tox.ini Log Message: ----------- fex sniffing of compressed genbank files also add doctest for both compressed and uncompressed versions Commit: 2558d278010999b96aaf279c4eaf539614844de7 https://github.com/galaxyproject/galaxy/commit/2558d278010999b96aaf279c4eaf5... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M tox.ini Log Message: ----------- Merge pull request #5772 from Delphine-L/addGbkgz Add genbank.gz datatype Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d8638... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801 [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Commit: 449e25200b2099ddbd253ee7f528ee69e997c2aa https://github.com/galaxyproject/galaxy/commit/449e25200b2099ddbd253ee7f528e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b11... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: fa69c7507ba623a378aac517b11087d843f07067 https://github.com/galaxyproject/galaxy/commit/fa69c7507ba623a378aac517b1108... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #5743 from jmchilton/uwsg-buffer-size Revise uwsgi defaults and display. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acdee... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 0a1ccdba1275948e71cd4e2da86a182c2cb7a7eb https://github.com/galaxyproject/galaxy/commit/0a1ccdba1275948e71cd4e2da86a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Lock pysam to 0.14.1 in Pipfile. Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3faec... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: 4ae3222e10d6367c2d43b60e138fe9298903b2f3 https://github.com/galaxyproject/galaxy/commit/4ae3222e10d6367c2d43b60e138fe... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix history link to visualizations view Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de41... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe80... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: 16291826d2b1852a0823c259d2ce4dcf086b936a https://github.com/galaxyproject/galaxy/commit/16291826d2b1852a0823c259d2ce4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #5799 from guerler/fix_viz_list Fix history link to visualizations view Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff0760... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: 70128b5d69c0c7aef8c6cdfdbd2f84cbeac4f8f5 https://github.com/galaxyproject/galaxy/commit/70128b5d69c0c7aef8c6cdfdbd2f8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5789 from guerler/add_delay_handler Add delay attribute to grid handler Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe510... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Commit: 0ff93b0e537c4717111a833aeb6d33e63b41d2f6 https://github.com/galaxyproject/galaxy/commit/0ff93b0e537c4717111a833aeb6d3... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 8742614e5243c61ee15823c0cf8aa512e9bb026f https://github.com/galaxyproject/galaxy/commit/8742614e5243c61ee15823c0cf8aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Quieter grepping. Commit: 60ca4d4cc94966598c102ea5a473270ea15e9b22 https://github.com/galaxyproject/galaxy/commit/60ca4d4cc94966598c102ea5a4732... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Instead of using -q, send to /dev/null, since the early pipe exit blows up pip Commit: efb830241df74e743a7fa7b90c819bd713c8589b https://github.com/galaxyproject/galaxy/commit/efb830241df74e743a7fa7b90c819... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Fix popper.js/popper discrepancy. Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d82... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: c310f9738ecfb8b98c905557919e7402fc81d2d8 https://github.com/galaxyproject/galaxy/commit/c310f9738ecfb8b98c905557919e7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Fix manual tooltip destroy blowing up with bootstrap4 -- destroy is now dispose, at least for tips. Commit: a85b8a83cbfeb6aaba1b3e6d86f3ae737f369ed3 https://github.com/galaxyproject/galaxy/commit/a85b8a83cbfeb6aaba1b3e6d86f3a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Merge pull request #5798 from dannon/lock_pysam Lock pysam to 0.14.1 in Pipfile. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e492... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: ea1bfb0056edbb69ab149d8664098127494e7b60 https://github.com/galaxyproject/galaxy/commit/ea1bfb0056edbb69ab149d8664098... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Framework for constrained memory, I/O sniffing. - Every unbound readline is a huge potential memory problem, this shrinks the number of such readlines down quite a bit. - There should be no reason to re-read the same file as much as we do, this keeps a fixed amount of the beginning of the file in memory and tries to use it as much as possible. - Lazy loads the size of the file and reuses that to reduce disc contention in that way also. With new sniffing tests for various types. Many datatypes will not just inspect the first GALAXY_SNIFF_PREFIX_BYTES of the file. This value defaults to 1 Mb but can be increased to increase the amount of memory and time used by the sniffers (getting more correctness also). Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d006... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Commit: 63f674c26d371569a3aaf8887a53f97e8707f951 https://github.com/galaxyproject/galaxy/commit/63f674c26d371569a3aaf8887a53f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes for workflow import view, apply consistent routes Commit: 962811b586e7e2cbf4213fbeff914aac0c66a755 https://github.com/galaxyproject/galaxy/commit/962811b586e7e2cbf4213fbeff914... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: A client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Add vue component for workflow import form Commit: 20ce0e42d9ef5a26539de08e1749eb1617e2960a https://github.com/galaxyproject/galaxy/commit/20ce0e42d9ef5a26539de08e1749e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove legacy view Commit: e55f8c5f56fceae6d3ec2e53a019c43407b4dba3 https://github.com/galaxyproject/galaxy/commit/e55f8c5f56fceae6d3ec2e53a019c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add import workflow from file option to api endpoint Commit: 732a1848535a7b9fba0b32e277a2405ecbdac0b6 https://github.com/galaxyproject/galaxy/commit/732a1848535a7b9fba0b32e277a24... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: R client/galaxy/scripts/libs/bootstrap.js M client/webpack.config.js Log Message: ----------- Remove old (conflicting) bootstrap Commit: f086080c65e98ed60794fae6e4f7e552d5c9c42c https://github.com/galaxyproject/galaxy/commit/f086080c65e98ed60794fae6e4f7e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused controller endpoint, and disabled legacy option Commit: 6f72ed2527a67347313f7fef2d6e1b94d12fe30e https://github.com/galaxyproject/galaxy/commit/6f72ed2527a67347313f7fef2d6e1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue 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/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/style/scss/ui/icon-btn.scss M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Convert rest of btn-default to btn-secondary Commit: 68af8c9e780417a4e34de1ca349b1e5ace7c8e58 https://github.com/galaxyproject/galaxy/commit/68af8c9e780417a4e34de1ca349b1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary check Commit: 5173d6f222c684d132c05684aae3b6e0c47b6e0c https://github.com/galaxyproject/galaxy/commit/5173d6f222c684d132c05684aae3b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore broken installed_repository_file option Commit: b6ee0a53ec5c116e2aacb4f9e8f47868ba76bb51 https://github.com/galaxyproject/galaxy/commit/b6ee0a53ec5c116e2aacb4f9e8f47... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary spacing and unused variable Commit: 8a51d02ce641184bdb9da51eb6017004cfdfd777 https://github.com/galaxyproject/galaxy/commit/8a51d02ce641184bdb9da51eb6017... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix library usage, and parameter naming Fix file reading caller Avoid using bare except Fix file parameter name Add missing library Commit: e5a564ef17990ba4b7c6db6381ef8fb98cd5bab9 https://github.com/galaxyproject/galaxy/commit/e5a564ef17990ba4b7c6db6381ef8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add additional checks for installed repository handler, open files using with-block Commit: 6a57ba8d28fb2f7c95850411118adb9e17c23c72 https://github.com/galaxyproject/galaxy/commit/6a57ba8d28fb2f7c95850411118ad... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Use archive_source and not url Commit: 51e32b6beaabe35fbd8a1cbaf38200d46ce33e3f https://github.com/galaxyproject/galaxy/commit/51e32b6beaabe35fbd8a1cbaf3820... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix error message Commit: 4c483a884a0948f86ca47e4b32494fc40e6764b8 https://github.com/galaxyproject/galaxy/commit/4c483a884a0948f86ca47e4b32494... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Show warning if import was successful but has errors Commit: 12096d2a9fa4a7d177b419e0a7c7bbff9d1af982 https://github.com/galaxyproject/galaxy/commit/12096d2a9fa4a7d177b419e0a7c7b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix spacing in import block Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b4176... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix metadata setting for CRAM files Should fix https://github.com/galaxyproject/galaxy/issues/5801. Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f92... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: 887f0e3a3aa4eefe9a02951a970a2b4080906655 https://github.com/galaxyproject/galaxy/commit/887f0e3a3aa4eefe9a02951a970a2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Fix login form using flex-column (we should revisit general flex handling in forms, though) Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b94... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 31000b5c9f3cdc71f17f69ec210c22a6e1589255 https://github.com/galaxyproject/galaxy/commit/31000b5c9f3cdc71f17f69ec210c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Working towards more standard styling of masthead/navbar Commit: 9d5b0973c0bcdbe286062c25699c599ff545ac0a https://github.com/galaxyproject/galaxy/commit/9d5b0973c0bcdbe286062c25699c5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Leave brand/quota as absolutely positioned for now (yech...), center-justify tabs Commit: cd670a48605489437d28859302afa76cca58c261 https://github.com/galaxyproject/galaxy/commit/cd670a48605489437d28859302afa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js Log Message: ----------- rename generic-nav-view to communication-server-view so it's at least remotely descriptive Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata [18.01] Fix metadata setting for CRAM files Commit: 08c2c5b5ac7a8768a15a886cabed0fdc4963f37c https://github.com/galaxyproject/galaxy/commit/08c2c5b5ac7a8768a15a886cabed0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5698 from dannon/psycopg2_bump Bump psycopg2 to 2.7.4; Commit: 9e71e1d2f0e7c6586b3f5946edb033466a495258 https://github.com/galaxyproject/galaxy/commit/9e71e1d2f0e7c6586b3f5946edb03... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow anonymous users to view their jobs via the API. Commit: 083bdcbdd84da29b1e2692058bbebd6426e8b2ae https://github.com/galaxyproject/galaxy/commit/083bdcbdd84da29b1e2692058bbeb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Rule-based Collection Builder Vue-based component for defining collections by applying rules to a list of files or more general spreadsheet style information (e.g. sample sheets or tabular data from data sources containing URL or FTP file paths for files along with metadata). The widget is fairly complex but very broadly is broken into two panes - one to preview how rules are applied to build up tabular data defining collections (each row corresponding to a file with columns for metadata and such) and one that displays defined rules and allows for editing of these rules and creation of new ones. The goal behind defining rules this way instead of allowing the user to interact with the spreadsheet display directly is to enable scaling up collection creation. If a user wishes to upload hundreds of datasets - interacting with a widget directly for each input doesn't scale well and would be error prone. If a user wishes to upload hundreds of thousands of datasets - even loading this information in the GUI may not scale (though I've been impressed with the performance so far of this approach) and so we can potentially just display a preview of some of the rows and process the final set of rules on the backend. Since we can handle an arbitrary number of columns this way, we can define multiple list identifiers per file and so we can easily construct nested lists. Hence this allows creation of not just potentially larger collections but arbitrarily complex lists as well. Paired identifiers via indicator columns are also implemented. In order to operate over lists of datasets directly - the multi-select history widget now has a new option "Build Collection from Rules" along side the other collection builders. This mode uses the well established dataset collection API to build collections from HDAs. In order to operate on lists of FTP files or URLs - the upload widget has a new tab "Rule-based" tab that allows users to paste in tabular data or select a history dataset and then send this tabular data to the new builder widget. This will be extended to include FTP directories for instance over time. This mode uses the new data fetch API to build collections and handle uploads of arbitrary collections of files. The preview of the tabular data generated via rules is done via [Handsontable](https://handsontable.com/) - a JavaScript spreadsheet widget with a VueJS [wrapper component](https://github.com/handsontable/vue-handsontable-official). This turns out to be a fairly nice application for reactive components - as rules are added or modified the spreadsheet just naturally updates. In my hands the widget scales very nicely - I've uploaded files with tens of thousands of rows and rules modifying the data and changing the spreadsheet do not seem to cause siignificant delays in the web browser. Commit: ebf08c16493b8fd3e770bf3c33c1f3eea55dd374 https://github.com/galaxyproject/galaxy/commit/ebf08c16493b8fd3e770bf3c33c1f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Fix production build of vue-handsontable Commit: cfa1208a79dcd0bdda5c7632366c2bd2b6deea0d https://github.com/galaxyproject/galaxy/commit/cfa1208a79dcd0bdda5c7632366c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/yarn.lock Log Message: ----------- Yarn lock w/ new deps. Commit: b32e78f338fcbd586f77c64f0fa18aee6ce23d1b https://github.com/galaxyproject/galaxy/commit/b32e78f338fcbd586f77c64f0fa18... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix upload view initialization. Commit: 1c04bbe9f6a95c1c8050bc5a8cd69bd8030cf350 https://github.com/galaxyproject/galaxy/commit/1c04bbe9f6a95c1c8050bc5a8cd69... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/.babelrc M client/package.json M client/yarn.lock Log Message: ----------- Add babel plugin for vue template preprocessing. This allows precompilation without a vue runtime for nested local components in vue SFCs, and other situations. Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts [18.01] Fix scripts/ for YAML/ENV configuration processing Commit: f21965472ca94a71466c4ca39e93bff30add229e https://github.com/galaxyproject/galaxy/commit/f21965472ca94a71466c4ca39e93b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/common_startup.sh M scripts/get_uwsgi_args.py M tox.ini Log Message: ----------- Merge branch 'dev' into viz-staging-finalize Commit: 320cf473662af7e9a11b40aca160eccce8ec8842 https://github.com/galaxyproject/galaxy/commit/320cf473662af7e9a11b40aca160e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Encrypt random password of a user who is logged-in using OIDC. Commit: 0047bffd05d55c75daae3158c1dde3bada794aaa https://github.com/galaxyproject/galaxy/commit/0047bffd05d55c75daae3158c1dde... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Minor formatting for clarity in scss rules. Commit: 6b998e66fdc4d4d482b05e230406764a2461d8e9 https://github.com/galaxyproject/galaxy/commit/6b998e66fdc4d4d482b05e2304067... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M config/oidc_backends_config.xml.sample M config/oidc_config.xml.sample Log Message: ----------- Add a missing blank line at the end of OIDC config samples. Commit: 60e936cf426bfc729693cb76d310e1c641c602a8 https://github.com/galaxyproject/galaxy/commit/60e936cf426bfc729693cb76d310e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M config/oidc_config.xml.sample Log Message: ----------- Add a comment to OIDC config explaining the unit of settings. Commit: 4e8e6a8f01219ef17409a5efe925ca07358939f3 https://github.com/galaxyproject/galaxy/commit/4e8e6a8f01219ef17409a5efe925c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- add link to ftp help to upload modal Commit: 7d73220c539f5803e5663c5d65218316a03bc375 https://github.com/galaxyproject/galaxy/commit/7d73220c539f5803e5663c5d65218... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js Log Message: ----------- add link that explains quota management to quota indicator Commit: f0dde506d043b3d4070ddc0fa2b48dac23e4d645 https://github.com/galaxyproject/galaxy/commit/f0dde506d043b3d4070ddc0fa2b48... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove unused static url, fix routes in plugins Commit: e99c8ec65c652f51253155abe73a9b0ce77c2496 https://github.com/galaxyproject/galaxy/commit/e99c8ec65c652f51253155abe73a9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Remove static path mixin Commit: 9efcfd462dcb3e9dd78d088ff15e753cbc2f9dde https://github.com/galaxyproject/galaxy/commit/9efcfd462dcb3e9dd78d088ff15e7... Author: Jennifer Hillman-Jackson <jennaj@users.noreply.github.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M README.rst Log Message: ----------- Update README.rst Updated Roadmap link Commit: aae2f1d85c0b3b81ebdd943685945b4204d6dba8 https://github.com/galaxyproject/galaxy/commit/aae2f1d85c0b3b81ebdd943685945... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M lib/galaxy/managers/configuration.py Log Message: ----------- add note to FTP upload modal when oidc is enabled Commit: 03287ed195d65ce305e6414ed3659e43c9ac8444 https://github.com/galaxyproject/galaxy/commit/03287ed195d65ce305e6414ed3659... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Bugfix in upload_common -- ensure hda is added to a session prior to state setting. Commit: ac74b7ffb2215b3f73997a760a15b26f39e64d3b https://github.com/galaxyproject/galaxy/commit/ac74b7ffb2215b3f73997a760a15b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M README.rst Log Message: ----------- Merge pull request #5815 from jennaj/jennaj-readme-edit Update README.rst Commit: d288b3baa83018cb9a6a96677ca8fd287d746816 https://github.com/galaxyproject/galaxy/commit/d288b3baa83018cb9a6a96677ca8f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Adjust test cases Commit: fe78b5bd89a90b49de5cd95e7ee660296c95dc16 https://github.com/galaxyproject/galaxy/commit/fe78b5bd89a90b49de5cd95e7ee66... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Some updates to FTP-upload messages w.r.t OIDC-based log-ins. Commit: f2e5a69629df4dca65e35cf7a431a33874ef51c5 https://github.com/galaxyproject/galaxy/commit/f2e5a69629df4dca65e35cf7a431a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml Log Message: ----------- Fix unipept and venn viewers Commit: f3580ee70e154f2e8a97ba1e88cb6603b83220f2 https://github.com/galaxyproject/galaxy/commit/f3580ee70e154f2e8a97ba1e88cb6... Author: James Taylor <james@jamestaylor.org> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Masthead: small fix to make masthead a bit more useable Commit: afb744234449f85b4f60bb94fb20f9c959001883 https://github.com/galaxyproject/galaxy/commit/afb744234449f85b4f60bb94fb20f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Merge pull request #27 from jxtx/dannon-bs4 Masthead: small fix to make masthead a bit more useable Commit: e552bc4cbb592eb2fcb4658e287026a742aab286 https://github.com/galaxyproject/galaxy/commit/e552bc4cbb592eb2fcb4658e28702... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/.babelrc A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/api/jobs.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5365 from jmchilton/rule_based_uploader Rule-based Uploader / Builder Commit: a8072a1d8bf2bf5e232649df61fc6f954164fca3 https://github.com/galaxyproject/galaxy/commit/a8072a1d8bf2bf5e232649df61fc6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Merge pull request #5816 from dannon/upload_common_bugfix Bugfix in upload_common -- ensure hda is added to a session Commit: ed95d9f40b83b44959030d70b7b5157ee0714b08 https://github.com/galaxyproject/galaxy/commit/ed95d9f40b83b44959030d70b7b51... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check tool version when importing subworkflows from dictionary Commit: d9a755082281669c64b0c8ae02655fdd3039fa0d https://github.com/galaxyproject/galaxy/commit/d9a755082281669c64b0c8ae02655... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Always match exact tool version Commit: 6fbf0e38cc8eb936cbdc0aa5eb22549793151b0f https://github.com/galaxyproject/galaxy/commit/6fbf0e38cc8eb936cbdc0aa5eb225... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Allow upgrade when workflow is loaded into editor Commit: cd3a637325d2921ca45f7f370f1bf2087cb99f09 https://github.com/galaxyproject/galaxy/commit/cd3a637325d2921ca45f7f370f1bf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Allow tool version upgrade for the run form Commit: 160b618759b5bf288cf11b7cdf99372fe2961a36 https://github.com/galaxyproject/galaxy/commit/160b618759b5bf288cf11b7cdf993... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant default for tool version flag Commit: e362ea5a1623e4bbade583c6439456b2ebf475bf https://github.com/galaxyproject/galaxy/commit/e362ea5a1623e4bbade583c643945... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Return proper error message if module cannot be produced Commit: c320e777a91e2ca3688d5a92ce28f5b744d87ccf https://github.com/galaxyproject/galaxy/commit/c320e777a91e2ca3688d5a92ce28f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Add additional check for section handler Commit: bd7a71c7fa89f4f798387cb65524faeff7fd2c5f https://github.com/galaxyproject/galaxy/commit/bd7a71c7fa89f4f798387cb65524f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Apply consistent group value handling Commit: 028d07323d93f900cdca45a67533cb5a2ddc4795 https://github.com/galaxyproject/galaxy/commit/028d07323d93f900cdca45a67533c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Adjust test case Commit: 241c273e012ec69ddba09e3d8b1b55405942ec67 https://github.com/galaxyproject/galaxy/commit/241c273e012ec69ddba09e3d8b1b5... Author: James Taylor <james@jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: A client/galaxy/docs/bootstrap.md M client/package.json A client/styleguide.config.js M client/yarn.lock Log Message: ----------- Style: Adding vue-stylguidest. In `client`, run `yarn styleguide` to serve the styleguide on localhost. Currently this only include bootstrap buttons and no actual vue components, but it is useful for editing the styles. I will flesh this out with more of the bootstrap components we actually use and some Galaxy styles. Commit: eb0f924ce90a7fe4ad7c1006c7d9e749832ebf48 https://github.com/galaxyproject/galaxy/commit/eb0f924ce90a7fe4ad7c1006c7d9e... Author: James Taylor <james@jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/theme/blue.scss M static/style/blue/base.css Log Message: ----------- Style: restoring Galaxy colors as primary theme colors. Commit: 5a4d26e1c995f2750d29059aab29515a97398b45 https://github.com/galaxyproject/galaxy/commit/5a4d26e1c995f2750d29059aab295... Author: James Taylor <james@jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/styleguide.config.js Log Message: ----------- Style: adding more bootstrap and some key Galaxy styles to styleguide Commit: cd99baa7ef2c8ef7266089d1467b0ea77056c08f https://github.com/galaxyproject/galaxy/commit/cd99baa7ef2c8ef7266089d1467b0... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-01 (Sun, 01 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Styles: Improving colors and clearning up config. Hardcoded the old derived colors to use as a base, and then deriving from those. We may want to update even the base colors (blue, green, etc) using thise. Alert backgrounds are now very close. Since these are the history background colors they are the most important to match to maintain the look. Removed lots of configuration variables that are not used anymore for bootstrap 4. Commit: a303d0d520c36080a6ad448ca4baaeb3e2eb194c https://github.com/galaxyproject/galaxy/commit/a303d0d520c36080a6ad448ca4baa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M client/package.json A client/styleguide.config.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'jxtx/dannon-bs4' into bs4 Commit: d51d25fca2f7d6d03872090bd157471682fffea8 https://github.com/galaxyproject/galaxy/commit/d51d25fca2f7d6d03872090bd1574... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Update and re-lock vue-loader/vue-template-compiler to fix incompatible versions in build. Commit: 45559e29facd187fed1a550f82b52d90e069dda2 https://github.com/galaxyproject/galaxy/commit/45559e29facd187fed1a550f82b52... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/circster.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/embed_item.scss M client/galaxy/style/scss/flex.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/job.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/reports.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/toastr.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/dataset-choice.scss M client/galaxy/style/scss/ui/icon-btn.scss M client/galaxy/style/scss/ui/pagination.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M client/galaxy/style/scss/ui/peek-column-selector.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/yarn.lock M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css Log Message: ----------- Upgrade prettier (now handles .scss well), apply to style sources. Commit: 035a063e99835f26b165ddfa6b3ac32d601ae944 https://github.com/galaxyproject/galaxy/commit/035a063e99835f26b165ddfa6b3ac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M static/style/blue/base.css A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: bbabf30ba82e3b58675206ac1ae81488f932daf2 https://github.com/galaxyproject/galaxy/commit/bbabf30ba82e3b58675206ac1ae81... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade vue to 2.5.16, lock alongside vue-template-compiler Commit: 8d7e3be889be59177647008a51da1172227951e0 https://github.com/galaxyproject/galaxy/commit/8d7e3be889be59177647008a51da1... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Style: Fix buttons. Made primary button background light for consistency with old Galaxy. Galaxy buttons should be upgraded to use the contrast functions to select text based on background (someday). Fixed caret mixin (needed to be one level higher). All permutations of action/menu button look correct now. Tweaked spacing on alerts. Commit: ff64b6f06c03810bcfe727d4fdac2993cc501148 https://github.com/galaxyproject/galaxy/commit/ff64b6f06c03810bcfe727d4fdac2... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/circster.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/embed_item.scss M client/galaxy/style/scss/flex.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/job.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/reports.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/toastr.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/dataset-choice.scss M client/galaxy/style/scss/ui/icon-btn.scss M client/galaxy/style/scss/ui/pagination.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M client/galaxy/style/scss/ui/peek-column-selector.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge branch 'bs4' of git://github.com/dannon/galaxy into dannon-bs4 Commit: bfb2650d6915f2c9a1ec560c862e69c1ba146ebb https://github.com/galaxyproject/galaxy/commit/bfb2650d6915f2c9a1ec560c862e6... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Style: restore lighter button color lost in merge Commit: c80682e96cb98b50fb007f3e988b21d176861514 https://github.com/galaxyproject/galaxy/commit/c80682e96cb98b50fb007f3e988b2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #29 from jxtx/dannon-bs4 Dannon bs4 Commit: 8f70087927c8e7c5cd3f0242a968de7efc348704 https://github.com/galaxyproject/galaxy/commit/8f70087927c8e7c5cd3f0242a968d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Style build, including button styling fixes. Commit: 4e64c32c0629be6a3cca1f8ea640ccfcfa7f1a3c https://github.com/galaxyproject/galaxy/commit/4e64c32c0629be6a3cca1f8ea640c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/styleguide.config.js Log Message: ----------- Prettierify styleguide driver. Commit: 8c6109dd4475bee81a805e389b74dafdb1f19b96 https://github.com/galaxyproject/galaxy/commit/8c6109dd4475bee81a805e389b74d... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Styles: fixes for popmenus. Commit: beb47d46c4318f43bb68d5879c16e6dc20976ed8 https://github.com/galaxyproject/galaxy/commit/beb47d46c4318f43bb68d5879c16e... Author: James Taylor <james@jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Log Message: ----------- Merge branch 'bs4' of git://github.com/dannon/galaxy into dannon-bs4 Commit: 05081b11a55ac9eb0453573220b39606f46afc7d https://github.com/galaxyproject/galaxy/commit/05081b11a55ac9eb0453573220b39... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'jxtx/dannon-bs4' into bs4 Commit: e7ecab77349ee430d4d95978c7a71c0ae54b1d77 https://github.com/galaxyproject/galaxy/commit/e7ecab77349ee430d4d95978c7a71... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- If psycopg2-binary is installed (as might be if switching between branches), uninstalling psycopg2 will leave psycopg2-binary installed but in a broken state. If we're removing psycopg2, we need to remove psycopg2-binary at the same time, leaving psycopg2-binary to be correctly installed afterwards. Commit: 3f34055e8ae3dccdaf8d235662b3e82591959bbd https://github.com/galaxyproject/galaxy/commit/3f34055e8ae3dccdaf8d235662b3e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to fix selenium tests Fix lint Commit: 368691624bc408bdad2383f04e6fb5c266e2ff4a https://github.com/galaxyproject/galaxy/commit/368691624bc408bdad2383f04e6fb... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'exact_version_handling' into workflow_import Commit: 19c652cdb4ad6e444fa95be10d815fc5617e4e39 https://github.com/galaxyproject/galaxy/commit/19c652cdb4ad6e444fa95be10d815... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Exclude the JS GIE proxy's node modules from linting. Commit: 30337f40d4bc46089e0d3f79cedca2301d14123f https://github.com/galaxyproject/galaxy/commit/30337f40d4bc46089e0d3f79cedca... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #5826 from natefoo/flake8-exclude-proxy Exclude the JS GIE proxy's node modules from linting Commit: 62338abbd61f7ca6b854ce0954c8cdebf2442c65 https://github.com/galaxyproject/galaxy/commit/62338abbd61f7ca6b854ce0954c8c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5825 from dannon/psycopg2-binary-handling-touchup psycopg2-binary handling tweak Commit: f507d95df8f14288890a9557b1ede92a1f820894 https://github.com/galaxyproject/galaxy/commit/f507d95df8f14288890a9557b1ede... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Fix empty tool tips. Fixes upload button in bs4 branch. Commit: bd2fcd604dda66f812d84e5ad4d97336d660d7ce https://github.com/galaxyproject/galaxy/commit/bd2fcd604dda66f812d84e5ad4d97... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Cleanup in ui-buttons I did while fixing tooltip bug, rebased over @jmchilton's commit doing the same fix. Commit: 22b10a9ea47c7ed2b7d8127e798a4418fd4983d9 https://github.com/galaxyproject/galaxy/commit/22b10a9ea47c7ed2b7d8127e798a4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Re-sync client formatting. Commit: fef37a1f3f7dd5a8aa4336fe5b1a6f0dfecb961e https://github.com/galaxyproject/galaxy/commit/fef37a1f3f7dd5a8aa4336fe5b1a6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- Upload modal width fix. Commit: 891212949a4e5d570c8b57efb2bc88286dbbab61 https://github.com/galaxyproject/galaxy/commit/891212949a4e5d570c8b57efb2bc8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Fixes to tab styling. They stay in a line again now, some problems with active indicator I think still though. Commit: 7ba7b0f94237545b07de8747cea87cbb196bc1eb https://github.com/galaxyproject/galaxy/commit/7ba7b0f94237545b07de8747cea87... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Tabs - fix active indicator. Commit: f1ab83aac61b0841902fb50559578d45e070c4fa https://github.com/galaxyproject/galaxy/commit/f1ab83aac61b0841902fb50559578... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Selenium fixes for BS4 style changes. Commit: c9881fdc5ca751e70248e199b487e98734c39e07 https://github.com/galaxyproject/galaxy/commit/c9881fdc5ca751e70248e199b487e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 933abad8a76e6cdd659816e6ffe8acb5c8283595 https://github.com/galaxyproject/galaxy/commit/933abad8a76e6cdd659816e6ffe8a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Small button fixes - fixes workflow list & history options. As well as a few more Selenium tests. Commit: d091850e894a4f702ca19fe5788fd96a57fbbaee https://github.com/galaxyproject/galaxy/commit/d091850e894a4f702ca19fe5788fd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add tabs to styleguide. Commit: 310866d2c9da0cfcbd631ef8788eb069938e4f64 https://github.com/galaxyproject/galaxy/commit/310866d2c9da0cfcbd631ef8788eb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Fix more tooltips in ui-frames, ui-options. Commit: 31cfef98f88ceb0d4aa68a18d76d55b89d07795e https://github.com/galaxyproject/galaxy/commit/31cfef98f88ceb0d4aa68a18d76d5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Cleanup in ui-frames, ui-tabs while looking at tooltip handling. Commit: 18fbb0d99761c4449a93ebdec09268d1ff92bdc9 https://github.com/galaxyproject/galaxy/commit/18fbb0d99761c4449a93ebdec0926... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add radio button to styleguide (exactly as generated in a test of ui-options -- looks like we need to close those inputs?) Commit: fa4ab8248351d9434bc3d12e6af2afea21e5993e https://github.com/galaxyproject/galaxy/commit/fa4ab8248351d9434bc3d12e6af2a... Author: Olivier Sallou <olivier.sallou@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- If no dataset is found for dataset_id raise an exception Commit: 20526e4229e2c6f7341636495895c4abb2647976 https://github.com/galaxyproject/galaxy/commit/20526e4229e2c6f7341636495895c... Author: Olivier Sallou <olivier.sallou@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- change exception raised Commit: 3a3c796fcf154e94d910f24e6e40b59afa999265 https://github.com/galaxyproject/galaxy/commit/3a3c796fcf154e94d910f24e6e40b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix failing tests Commit: 9094a86f6314229aedec74a3925f7778b38b9f09 https://github.com/galaxyproject/galaxy/commit/9094a86f6314229aedec74a3925f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/bower.json R client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tours.js M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Upgrade bootstrap-tour and use from npm Commit: 679edd1661718256d46f260bc4ad170d0602120f https://github.com/galaxyproject/galaxy/commit/679edd1661718256d46f260bc4ad1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Go off-yarn to github's master branch for bs4-compatible bootstrap-tour. Commit: 40637a64050d4779025f60234d3af59dfa08f211 https://github.com/galaxyproject/galaxy/commit/40637a64050d4779025f60234d3af... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Take auto height for labels of radio buttons Commit: fafcd6e39a2d6e584373b6863e216bfb3def7370 https://github.com/galaxyproject/galaxy/commit/fafcd6e39a2d6e584373b6863e216... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui/paired-collection-creator.scss M static/style/blue/base.css Log Message: ----------- Fix paired collection creator for BS4 branch. This is ugly to say the least, but the upstream flex styles (like .flex-row) are marking their directions as important so we need to mark these as important for the embedded flex stuff to work I think. Commit: 2eccc293f548bafed6ca1f019f331ed27fc5e413 https://github.com/galaxyproject/galaxy/commit/2eccc293f548bafed6ca1f019f331... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Merge pull request #30 from anuprulez/dev Take auto height for labels of radio buttons Commit: 7e627c1ccc652a0b048f0ad09542cc3639fe2f46 https://github.com/galaxyproject/galaxy/commit/7e627c1ccc652a0b048f0ad09542c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M test/selenium_tests/test_registration.py Log Message: ----------- Fix registration.test_landing selenium test for BS4 branch. Commit: aeeaefed00d8cc3c86d1f1be3d9e3e04fb341621 https://github.com/galaxyproject/galaxy/commit/aeeaefed00d8cc3c86d1f1be3d9e3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Fix import order in tours.js Commit: d8c4315d79032aff1e689fd0a7ed3fed86fb944d https://github.com/galaxyproject/galaxy/commit/d8c4315d79032aff1e689fd0a7ed3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Build radio fixes Commit: ada2989aced9e35e2ee9f50066ef2e2a815c8002 https://github.com/galaxyproject/galaxy/commit/ada2989aced9e35e2ee9f50066ef2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add nametags display to galaxy style examples Commit: c3d4e849ca91535a57a55b8ae1e4ea544b40d283 https://github.com/galaxyproject/galaxy/commit/c3d4e849ca91535a57a55b8ae1e4e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix nametag display (instead of keeping over the old label classes, just upgrade everything to badge) Commit: b936102f9f6aba685beb46a68c326438de1d7c19 https://github.com/galaxyproject/galaxy/commit/b936102f9f6aba685beb46a68c326... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Convert toolpanel 'labels' into 'badges' Commit: ed1764969596ad7defd49c7532680946fd58b46f https://github.com/galaxyproject/galaxy/commit/ed1764969596ad7defd49c7532680... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Fix modal in workflow editor for BS4 branch changes. Commit: 3dc4cf11c07599651973ce21a1b95b1befc33543 https://github.com/galaxyproject/galaxy/commit/3dc4cf11c07599651973ce21a1b95... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Swap hashtags to badge-primary (they were info before, but primary more closely fits the color). Also drop example from galaxy styleguide, since they're just normal old badges, covered in the bootstrap examples of the styleguide Commit: eeea5b6b296a2c0084267cdfdc6549d3ad79fd55 https://github.com/galaxyproject/galaxy/commit/eeea5b6b296a2c0084267cdfdc654... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix alignment of terminals in workflow editor. Commit: 7ce621f0355cf7214efe7e256f0e9261ac73cb7c https://github.com/galaxyproject/galaxy/commit/7ce621f0355cf7214efe7e256f0e9... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix radio input horizontal alignment issue Commit: b553d72c09e621b930f03ec157568e1afc9d3669 https://github.com/galaxyproject/galaxy/commit/b553d72c09e621b930f03ec157568... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Merge pull request #31 from anuprulez/dev Fix radio input horizontal alignment issue Commit: d7b4d5e9fd7e6c4c5196b46f9050d1af8a2e6947 https://github.com/galaxyproject/galaxy/commit/d7b4d5e9fd7e6c4c5196b46f9050d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- BS4 - place rule builder buttons on one row again. Buttons got a bit bigger causing a row break in my two browsers at least, adding this extra 10 pixes seems to be enough. Commit: 7f7fc3ac08b1714a49aeede2a9c9bb0f391f95b0 https://github.com/galaxyproject/galaxy/commit/7f7fc3ac08b1714a49aeede2a9c9b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset info section usage. Figured out why the nested selectors won't work -- addressing the other inheritance issues worked around with in subsequent commits Commit: baf3f9e65769fa0cdb823de381ae4196cde33bf9 https://github.com/galaxyproject/galaxy/commit/baf3f9e65769fa0cdb823de381ae4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix a button hover @extend as well as the vertical-spacing and info-section inheritance Commit: b92e1a63ca05d8c31e15d68f9446b181f83a2ad3 https://github.com/galaxyproject/galaxy/commit/b92e1a63ca05d8c31e15d68f9446b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/collection.scss Log Message: ----------- Drop !optional from collection fa-lg; this exists now that fontawesome is integrated Commit: 9c71fb98da859d9ef7f048efb776085d2e024a69 https://github.com/galaxyproject/galaxy/commit/9c71fb98da859d9ef7f048efb7760... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix tag editor spacing. Commit: d41c5a7731e89ea50e4a964914b33923563c45a3 https://github.com/galaxyproject/galaxy/commit/d41c5a7731e89ea50e4a964914b33... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix final !optional tagged styles, this resolves the hda display issues. Commit: 6a0eeea368fc824c3d0b9d773f387dedbbea3193 https://github.com/galaxyproject/galaxy/commit/6a0eeea368fc824c3d0b9d773f387... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Resync client-format Commit: 360e33bf6ba0eb0ab6d4c4cbdb25cbfc88d48688 https://github.com/galaxyproject/galaxy/commit/360e33bf6ba0eb0ab6d4c4cbdb25c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Bootstrap adjustments for masthead Commit: 0043f2f3a0044e359522f2fe6e485469b008f330 https://github.com/galaxyproject/galaxy/commit/0043f2f3a0044e359522f2fe6e485... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: R templates/admin/view_data_tables_registry.mako Log Message: ----------- Remove unused template file. Commit: 4e4dbc88233d5309dfd5cc9b0923cc0e0d178ac7 https://github.com/galaxyproject/galaxy/commit/4e4dbc88233d5309dfd5cc9b0923c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Expand selenium test coverage. Initial admin app tests including screenshots of display applications, data tables, data types, and job management. Commit: fab65eabbbab59bd3871ec1c954740e063cae3c8 https://github.com/galaxyproject/galaxy/commit/fab65eabbbab59bd3871ec1c95474... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Simple tool forms in style guides. One to demonstrate simple mako forms are broken, another to demonstrate the more complex stuff generated by mvc.form seems to work fine. Is there any way to actually use the JS to generate these automatically? The tool form generates too complex of HTML for this approach to seem maintainable. Commit: fbd5541e4edd57870da924a2de11c2675b1d7bc4 https://github.com/galaxyproject/galaxy/commit/fbd5541e4edd57870da924a2de11c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Merge pull request #5836 from jmchilton/selenium_admin_init Initial Selenium Test Coverage for Admin App Commit: d1568ca50d708b2a2ef912d5ecf3bf5ba2327265 https://github.com/galaxyproject/galaxy/commit/d1568ca50d708b2a2ef912d5ecf3b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge branch 'bs4_masthead' into bs4 Commit: 4e1580c2ce679e77c8520f7e6c4965d5dcc41e58 https://github.com/galaxyproject/galaxy/commit/4e1580c2ce679e77c8520f7e6c496... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Minor formatting in merged menu Commit: 6a345d1ef07a288e67704db51e59947888bf3051 https://github.com/galaxyproject/galaxy/commit/6a345d1ef07a288e67704db51e599... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Selenium test fixes for 360e33bf6ba0eb0ab6d4c4cbdb25cbfc88d48688. Commit: 6a317958f7982dbc056d4613c4c38a6d68c85278 https://github.com/galaxyproject/galaxy/commit/6a317958f7982dbc056d4613c4c38... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss Log Message: ----------- Update the hashtags styling Commit: c2e7a9f8122f97257f14b2301d88c3d105e366af https://github.com/galaxyproject/galaxy/commit/c2e7a9f8122f97257f14b2301d88c... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix td, th alignment in the dataset upload modal Commit: c40443136e558966bdf3b3dc2d8f0752af23aefc https://github.com/galaxyproject/galaxy/commit/c40443136e558966bdf3b3dc2d8f0... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix upload button background color and fontsize and add its backdrop Commit: 506de02ec462d217220a531a8e40c0e02dbedcd7 https://github.com/galaxyproject/galaxy/commit/506de02ec462d217220a531a8e40c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: a6024d617fc35832a01eb0595d0ac4f3111790b9 https://github.com/galaxyproject/galaxy/commit/a6024d617fc35832a01eb0595d0ac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- The old floor/ceil handling of hN vars doesn't work w/ rem, rounds basically everything to 1em -- this fixes many header sizes back to old functionality. Commit: 1da06ba2b34a59ab6ea2dd4f1bd765142b423d63 https://github.com/galaxyproject/galaxy/commit/1da06ba2b34a59ab6ea2dd4f1bd76... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5839 from jmchilton/integration_test_fixes Skip new script tests in dev branch, they are breaking integration suite. Commit: 5d9c5e86e77492934f96220a65b6c37b8df0220b https://github.com/galaxyproject/galaxy/commit/5d9c5e86e77492934f96220a65b6c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Fix tourpage formatting Commit: 2b975b2d6a5cc4bce11001d6b4900a64479fe580 https://github.com/galaxyproject/galaxy/commit/2b975b2d6a5cc4bce11001d6b4900... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- add classes necessary for pagination in bs4 Commit: 77a4ed7625138bce9a53ea4cfe09e22c47748903 https://github.com/galaxyproject/galaxy/commit/77a4ed7625138bce9a53ea4cfe09e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix link targeting for 'back to shareable' list Commit: 9a37920acf261668bd6bad9ba27889df22e99ce3 https://github.com/galaxyproject/galaxy/commit/9a37920acf261668bd6bad9ba2788... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Fix navbar-brand-link being clickable to home Commit: 76d059297b23044c6f3c42121c6ced4c89d5dad0 https://github.com/galaxyproject/galaxy/commit/76d059297b23044c6f3c42121c6ce... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix brand link text decoration Commit: 8e876963612ba9a043b0ce7d168b767d390bd0ca https://github.com/galaxyproject/galaxy/commit/8e876963612ba9a043b0ce7d168b7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix more pagination styles in libraries, add example to guide Commit: 103025a471dd98a13d7e0b4c2847947257e557f2 https://github.com/galaxyproject/galaxy/commit/103025a471dd98a13d7e0b4c28479... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M static/style/blue/base.css Log Message: ----------- Lots of var cleanup, incremental commit to avoid merge conflicts Commit: 2a7ea1cb370a25590a66b6870561c1358093da85 https://github.com/galaxyproject/galaxy/commit/2a7ea1cb370a25590a66b6870561c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix scratchpad icon Commit: 712fb6b084fe66c84db7251adb2f8b1ad2ff57bc https://github.com/galaxyproject/galaxy/commit/712fb6b084fe66c84db7251adb2f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #34 from guerler/scratchicon Fix scratchpad icon Commit: 1aa5f673d22d24b90fbd8e14ada269f387b99870 https://github.com/galaxyproject/galaxy/commit/1aa5f673d22d24b90fbd8e14ada26... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/user/login.mako Log Message: ----------- Force block display for form-rows for now, instead of using flex Commit: d59508c9029876a79eb27f6bf327c3b38d37a8fd https://github.com/galaxyproject/galaxy/commit/d59508c9029876a79eb27f6bf327c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- replace toolbar control with flexbox Commit: 9239883fb46b7dd40b788c7bd954f131294a83a2 https://github.com/galaxyproject/galaxy/commit/9239883fb46b7dd40b788c7bd954f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Remove custom icon from dropdown menu Commit: 3924569d19367c1d7e856a701dfe68fe27f603ad https://github.com/galaxyproject/galaxy/commit/3924569d19367c1d7e856a701dfe6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #35 from guerler/fixdropdowns Remove custom icon from dropdown menu Commit: 3181fbb442b6a048255439c6dce1222f2a4dc919 https://github.com/galaxyproject/galaxy/commit/3181fbb442b6a048255439c6dce12... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- convert folder toolbar into flexfox, clean up styles Commit: 6b90e8f6c73637bb1c64177d68180111e5dae9f2 https://github.com/galaxyproject/galaxy/commit/6b90e8f6c73637bb1c64177d68180... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M static/style/blue/base.css M templates/user/login.mako Log Message: ----------- Merge branch 'bs4' of github.com:dannon/galaxy into bs4 Commit: f05a1393a19e15f942376db22dd51334d6232676 https://github.com/galaxyproject/galaxy/commit/f05a1393a19e15f942376db22dd51... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- replace the now-removed btn-xs with btn-sm project-wide Commit: 8261a2398a7981e77be056bae0e3c15f3a097a85 https://github.com/galaxyproject/galaxy/commit/8261a2398a7981e77be056bae0e3c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M create_db.sh M doc/source/admin/framework_dependencies.rst M extract_dataset_parts.sh M manage_db.sh M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Make the startup scripts play just as nicely with Conda as they do with virtualenv. Commit: c93bc84628f0c6f71fadc68d9024cd7d7012e893 https://github.com/galaxyproject/galaxy/commit/c93bc84628f0c6f71fadc68d9024c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M static/welcome.html.sample M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- replace the rest of btn-xs project-wide Commit: bdc902a9dfa3805ef368becee9b80a860944602c https://github.com/galaxyproject/galaxy/commit/bdc902a9dfa3805ef368becee9b80... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M static/welcome.html.sample Log Message: ----------- rename the btn-default in accordance to bs4 Commit: a88e19064a38415d867f4c118dd6938d8e368632 https://github.com/galaxyproject/galaxy/commit/a88e19064a38415d867f4c118dd69... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M config/galaxy.yml.sample M scripts/get_uwsgi_args.py Log Message: ----------- Don't set uWSGI's virtualenv option when running from Conda Commit: 643a1aa2ea8d265002471dd9555b85684b56f9a2 https://github.com/galaxyproject/galaxy/commit/643a1aa2ea8d265002471dd9555b8... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- fix all uses of breadcrumbs, bs4 requires item annotation Commit: 3a85f8189271326c9c30f60cbc0405e157ab16d2 https://github.com/galaxyproject/galaxy/commit/3a85f8189271326c9c30f60cbc040... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Cleanup while looking into grid zooming in chrome Commit: b3eff87a1ba0ec0f07c69045f2b279cab8476a7b https://github.com/galaxyproject/galaxy/commit/b3eff87a1ba0ec0f07c69045f2b27... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Clean up and useability enhancements Commit: 8045724984c161b055ed8aec65bc1acd58d80699 https://github.com/galaxyproject/galaxy/commit/8045724984c161b055ed8aec65bc1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improve error messages for tour Selenium test failures. Looks like the failing scratchbook tour is being caused by the upload settings buttons being broken, a known issue. Commit: 52ccc66a2e684eca639af9969db6297a2b9e4973 https://github.com/galaxyproject/galaxy/commit/52ccc66a2e684eca639af9969db62... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix nametag tests for switch to badges in BS4 branch. Commit: 9674735c4aa6d772121a2a69da2161648d42a22c https://github.com/galaxyproject/galaxy/commit/9674735c4aa6d772121a2a69da216... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Fix failing paired colleciton builder test by increasing test window size. This isn't an ideal fix - someone probably should go in and compress that widget to fit in the original 900 px. Commit: 6aa5b70b0a16d2e486c22f31570ac659af9b4774 https://github.com/galaxyproject/galaxy/commit/6aa5b70b0a16d2e486c22f31570ac... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow tagging test case for BS4 branch. Commit: c27434bcf380fb2267dcf12c4c35b80742838ec8 https://github.com/galaxyproject/galaxy/commit/c27434bcf380fb2267dcf12c4c35b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow rename test case for BS4 branch. Commit: c5262e8971679bd431cb0238391f0ec7d5ba087e https://github.com/galaxyproject/galaxy/commit/c5262e8971679bd431cb0238391f0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Look for both `base` and `root` conda envs Commit: 8df00ffedb718a2fd44b1e913a120df3aecf1485 https://github.com/galaxyproject/galaxy/commit/8df00ffedb718a2fd44b1e913a120... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix radiobuttons, fix tabs in styleguide Commit: 4cfddc12b91abfbf3fcbb63e83303397d9b51403 https://github.com/galaxyproject/galaxy/commit/4cfddc12b91abfbf3fcbb63e83303... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Hide default dropdown icon, restore custom icon Commit: b4a5b2a45ced7bb2515eeee8406fe390e9ce9c6c https://github.com/galaxyproject/galaxy/commit/b4a5b2a45ced7bb2515eeee8406fe... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css M static/welcome.html.sample M templates/user/login.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py Log Message: ----------- Merge branch 'bs4' into fixradio Commit: beb8e521ad0649485d9e498263419f107362401c https://github.com/galaxyproject/galaxy/commit/beb8e521ad0649485d9e498263419... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Restore custom dropdown icon, required for workflow editor Commit: 438158dd9193bf3b44194701a08173d9da330b21 https://github.com/galaxyproject/galaxy/commit/438158dd9193bf3b44194701a0817... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #36 from guerler/fixradio Fix radiobuttons, fix tabs in styleguide Commit: 3904139c3940f7eb91ec41f5750ec8a9d9f73b40 https://github.com/galaxyproject/galaxy/commit/3904139c3940f7eb91ec41f5750ec... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Cleanup in grid-view Commit: a46df8ce6bbc0a7f62d798b1699ea3584b1326ce https://github.com/galaxyproject/galaxy/commit/a46df8ce6bbc0a7f62d798b1699ea... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix js and css issues with popover Commit: 10780c1d694e08191a7fc5ed2c8d38a501789e24 https://github.com/galaxyproject/galaxy/commit/10780c1d694e08191a7fc5ed2c8d3... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Add arrows for the popovers Commit: 8e5f6b25cf0c51a8f09fd2e211922effdb1d9e00 https://github.com/galaxyproject/galaxy/commit/8e5f6b25cf0c51a8f09fd2e211922... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Client build and lint Commit: 54db0df20ba977b239cf4ec5db12e31ab74b5d06 https://github.com/galaxyproject/galaxy/commit/54db0df20ba977b239cf4ec5db12e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix chrome zoom bug with grid headers per 'https://github.com/galaxyproject/galaxy/issues/5848#issuecomment-378708567' Commit: 75d03ddf19f697ae048e9bbd6775388888351031 https://github.com/galaxyproject/galaxy/commit/75d03ddf19f697ae048e9bbd67753... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix for popup top Commit: 6fcd63beaa059628bf131becbeb444ef916d6b35 https://github.com/galaxyproject/galaxy/commit/6fcd63beaa059628bf131becbeb44... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Add popover static Commit: 7f302be2ac7500879287cc4f0d8a1b2fddabde65 https://github.com/galaxyproject/galaxy/commit/7f302be2ac7500879287cc4f0d8a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss Log Message: ----------- Removal/org of some unused bootstrap/fontawesome vars. Commit: a1e15083ccaa6090d2ad11ad2b3dee7b65ada559 https://github.com/galaxyproject/galaxy/commit/a1e15083ccaa6090d2ad11ad2b3de... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Glyphicons are gone, fontawesome is the way now. Commit: 9c911ce68911be9ca25486ea960d59a017946529 https://github.com/galaxyproject/galaxy/commit/9c911ce68911be9ca25486ea960d5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Continued bootstrap variables work. Commit: e8e62aa21e33cce202fc064e5cfa2d4d32dc2011 https://github.com/galaxyproject/galaxy/commit/e8e62aa21e33cce202fc064e5cfa2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss Log Message: ----------- Finish removing unused bootstrap vars. The ones that are no longer bootstrap vars, but we are using, I have relocated to galaxy variables (since they aren't bootstrap customizations) Commit: 717695a68cb2d64191c4afeed01b7a3e9935d55d https://github.com/galaxyproject/galaxy/commit/717695a68cb2d64191c4afeed01b7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix incorrect tooltip init; improve bs4 styling Commit: deda753de9f6943251cf06bd02b37dae78bac59e https://github.com/galaxyproject/galaxy/commit/deda753de9f6943251cf06bd02b37... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing. Commit: 58028e1f6dbf0275f08846dc653e94d607079c86 https://github.com/galaxyproject/galaxy/commit/58028e1f6dbf0275f08846dc653e9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #5859 from natefoo/gie-slashfix Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing Commit: e06393a0827c14c4df692bed0b42814f3dba1323 https://github.com/galaxyproject/galaxy/commit/e06393a0827c14c4df692bed0b428... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- rename from table-condensed to table-sm as bs4 did Commit: f0cc88024fdd9e028eda0a06a74747a30840fb1b https://github.com/galaxyproject/galaxy/commit/f0cc88024fdd9e028eda0a06a7474... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/trackster.scss M static/style/blue/trackster.css Log Message: ----------- Track down tag/label translation goof, fixing top trackster label track. Commit: 164701b943ce543627d96242458940031ba50577 https://github.com/galaxyproject/galaxy/commit/164701b943ce543627d9624245894... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/trackster.scss M static/style/blue/trackster.css Log Message: ----------- Fix icon-hover-mixin for trackster. This fixes the little track configuration icons. Commit: 02e92e21155ce19383041477d20c33ea44779f48 https://github.com/galaxyproject/galaxy/commit/02e92e21155ce19383041477d20c3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Fix conditional parameter handling for textselect field Commit: 52af42989b6937be3e80e8a8818906ae5d244ed9 https://github.com/galaxyproject/galaxy/commit/52af42989b6937be3e80e8a881890... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Fix scratchbook tour handles. This should fix one remaining selenium test for BS4. Commit: f1cd7813371516937f4e42e2ab790b49f5e92669 https://github.com/galaxyproject/galaxy/commit/f1cd7813371516937f4e42e2ab790... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Fix workflow management selenium test (I hope) Commit: 54122c15ed351808cde805362d0e47605f88e545 https://github.com/galaxyproject/galaxy/commit/54122c15ed351808cde805362d0e4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add wait unwait features to select field handler Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) 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/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Commit: a23f0d505761ba713da9484af18e7c10fc6dbed2 https://github.com/galaxyproject/galaxy/commit/a23f0d505761ba713da9484af18e7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 075abee7666599a9b8dcf74d38ee5d337c7a85eb https://github.com/galaxyproject/galaxy/commit/075abee7666599a9b8dcf74d38ee5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M .gitignore M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/gulpfile.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #5810 from guerler/viz-staging-finalize Plugin directory staging Commit: 3d7c8a233c1838200431dd057990ff373235c696 https://github.com/galaxyproject/galaxy/commit/3d7c8a233c1838200431dd057990f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M test/selenium_tests/test_library_landing.py Log Message: ----------- Fix one failing library selenium test. Commit: f990661ba8f5754ddf9e7eae0f09e095eb9c0256 https://github.com/galaxyproject/galaxy/commit/f990661ba8f5754ddf9e7eae0f09e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Cleanup and build Commit: bf4f43d96a4cf3bdf090d82822a688677600e3f2 https://github.com/galaxyproject/galaxy/commit/bf4f43d96a4cf3bdf090d82822a68... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Rough implentation of the DockerAPIInterface. Commit: 2e9c25da28535c268467e9dc5dc982b067ed14bc https://github.com/galaxyproject/galaxy/commit/2e9c25da28535c268467e9dc5dc98... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Create a general method for handling galaxy.containers param -> docker-py param mapping. Plus some cleanup. Commit: b7531593697175ad9c8f110e9943c9086c779ae4 https://github.com/galaxyproject/galaxy/commit/b7531593697175ad9c8f110e9943c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Corrections to Docker spec handling Commit: ac9fce9a3c5e6995bafa5fbac602c2b2a4ccb003 https://github.com/galaxyproject/galaxy/commit/ac9fce9a3c5e6995bafa5fbac602c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- WIP Docker Swarm API interface Commit: 0bba56d106dbeedfac2c67226a749bf6354df4e2 https://github.com/galaxyproject/galaxy/commit/0bba56d106dbeedfac2c67226a749... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker API TLS support Commit: 26d265e0107143a62e7799ecf51ea85ac698696c https://github.com/galaxyproject/galaxy/commit/26d265e0107143a62e7799ecf51ea... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker service fixes Commit: c8ab4fae4db13b106dcd1dbc4f109cc66c305d8a https://github.com/galaxyproject/galaxy/commit/c8ab4fae4db13b106dcd1dbc4f109... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Enable setting defaults for docker API data structures. Commit: 360e43095a5036c8cedd452a5809160780f361a8 https://github.com/galaxyproject/galaxy/commit/360e43095a5036c8cedd452a58091... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker swarm interface for the API Commit: 0e357ca73729f67f27a31b83a7df6c5c74c43c99 https://github.com/galaxyproject/galaxy/commit/0e357ca73729f67f27a31b83a7df6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Lint fixes Commit: 2794a650f5cd885f684d79e5124e349ccdf09879 https://github.com/galaxyproject/galaxy/commit/2794a650f5cd885f684d79e5124e3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Fixes for swarm manager. Commit: 806703a5e2ac679bcac496bb9acd36a9b248ce48 https://github.com/galaxyproject/galaxy/commit/806703a5e2ac679bcac496bb9acd3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Move DockerVolume to containers lib model and fix bugs. Commit: 9cd589508d260a8e04191701aa86e98548e97def https://github.com/galaxyproject/galaxy/commit/9cd589508d260a8e04191701aa86e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/util/__init__.py Log Message: ----------- More detailed swarm manager state logging Commit: 605a156d618b352c0755af0b3e6e9e0922c126f8 https://github.com/galaxyproject/galaxy/commit/605a156d618b352c0755af0b3e6e9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Attempt to handle "phantom" docker tasks Commit: 0d90235b1c5e6742bc65f270c5ac0e19b48ee1d0 https://github.com/galaxyproject/galaxy/commit/0d90235b1c5e6742bc65f270c5ac0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix lint/unit test errors Commit: 9de17e248feb2fa39e3a026727df75a5f42b7c59 https://github.com/galaxyproject/galaxy/commit/9de17e248feb2fa39e3a026727df7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add some error handling to the Docker API interface Commit: 507fed9e3c2e2ea6a7fc9938400c7642701bc3ad https://github.com/galaxyproject/galaxy/commit/507fed9e3c2e2ea6a7fc9938400c7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix lint error Commit: 10e0314e8fe8d378fdeb97bfa0b3466e95e35f07 https://github.com/galaxyproject/galaxy/commit/10e0314e8fe8d378fdeb97bfa0b34... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/util/json.py Log Message: ----------- Move json format function to galaxy.util.json Commit: 8369d88295554639926ad5ddac445a20e449a0e4 https://github.com/galaxyproject/galaxy/commit/8369d88295554639926ad5ddac445... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional docker dependency for containers interface Commit: 5537ce1fa748422a27aea062165095cfba07c754 https://github.com/galaxyproject/galaxy/commit/5537ce1fa748422a27aea06216509... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Handle the case where a node claims a task exists but the tasks/services API disagrees Commit: 559fb9df9ba0379b975aaa2b5df7ac963c18f037 https://github.com/galaxyproject/galaxy/commit/559fb9df9ba0379b975aaa2b5df7a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Allow docker client callers to pass in a test function that the client wrapper will call on certain types of expected failures. If the function returns a truthy value, it is returned instead. This is useful for state-altering changes where the request may have succeeded but the response failed. Commit: 9db3d23eaca5ce7270a9480038acd52f52951298 https://github.com/galaxyproject/galaxy/commit/9db3d23eaca5ce7270a9480038acd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py Log Message: ----------- Use consistent whitespace in containers lib classes Commit: 8b3fe214763341ffa0a1b614a464de5b9b8561b7 https://github.com/galaxyproject/galaxy/commit/8b3fe214763341ffa0a1b614a464d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Refactor rules def toward reuse outside RuleCollectionBuilder.vue. Commit: 47795ea707fcb3575aa823ea143691b53e795c8d https://github.com/galaxyproject/galaxy/commit/47795ea707fcb3575aa823ea14369... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Cleanup rule UI code, refactor toward use w/existing collections. Commit: 595c7621419d457587c486d2c05b60ccf35fbb5d https://github.com/galaxyproject/galaxy/commit/595c7621419d457587c486d2c05b6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Add reset and close buttons for upload widget when selecting rules. Commit: 109e97d82ad9d578966ed98a051f0dce6aeb1682 https://github.com/galaxyproject/galaxy/commit/109e97d82ad9d578966ed98a051f0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Rules editor - add X to column definitions inside edit mode. Previously these were only available in preview mode. Commit: d12635375aac0008d987ab71aedfc5a24b115663 https://github.com/galaxyproject/galaxy/commit/d12635375aac0008d987ab71aedfc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Improve styling, wording of rule editor buttons. - Replace "Okay" with "Apply" on button labels. - Create CSS style for buttons in rule editor part of the component. - More consistency - right-align all the buttons, more consistent spacing. - Make primary action that button blue to make the buttons look a little bland. Commit: 2254dba7342040c86d28b2c97153d253fe175791 https://github.com/galaxyproject/galaxy/commit/2254dba7342040c86d28b2c97153d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Bug fix for conditional rule button rendering... Commit: c34b23b428898f0da5657d96fd048969829d0a91 https://github.com/galaxyproject/galaxy/commit/c34b23b428898f0da5657d96fd048... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Rule builder - more correct, better abstracted logic for display name input. Commit: b184f197475e72038d3b80e4828d1298723f1f68 https://github.com/galaxyproject/galaxy/commit/b184f197475e72038d3b80e4828d1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Explicitly specify options parsed to text select wrapper Commit: 4f84b9cacc31c0946d421a01f9729792850c4ae2 https://github.com/galaxyproject/galaxy/commit/4f84b9cacc31c0946d421a01f9729... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Assign change handler from select model Commit: 5ffaf9fae546957ec0ebdd634ee0baaea6bbca3c https://github.com/galaxyproject/galaxy/commit/5ffaf9fae546957ec0ebdd634ee0b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- use `random.sample` to generate random password for a user. Commit: 259daf1749cd202da233e568e7621cae2b5c3ffe https://github.com/galaxyproject/galaxy/commit/259daf1749cd202da233e568e7621... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M 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config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py M static/style/blue/base.css R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_tools.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_uploads.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase # Conflicts: # lib/galaxy/dependencies/pinned-requirements.txt # lib/galaxy/dependencies/requirements.txt Commit: 86e13a51c552abda08b2e2fd4022bb9d3648e5b5 https://github.com/galaxyproject/galaxy/commit/86e13a51c552abda08b2e2fd4022b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add OIDC requirements to pipfiles/default/pinned-requirements.txt Commit: c42d642233d962fc513c1039771acb00718d7348 https://github.com/galaxyproject/galaxy/commit/c42d642233d962fc513c1039771ac... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Containers: - Improve documentation of docker API param mapping - Improve sample containers config file - Fix constraints - A couple other minor bug/logging fixes Commit: b205956b3882a4b1dbc0529742ba8f5aafddafe5 https://github.com/galaxyproject/galaxy/commit/b205956b3882a4b1dbc0529742ba8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker: Don't retry 4xx errors indefinitely. Possibly need to do this for more APIErrors. Commit: b3f589cc9349be2e583f2f085c1d2f696d087d80 https://github.com/galaxyproject/galaxy/commit/b3f589cc9349be2e583f2f085c1d2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-07 (Sat, 07 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/package.json M client/yarn.lock M test-data/rules/uniprot.json M test/selenium_tests/test_uploads.py Log Message: ----------- For rule builder, use Python-like regular expressions in-browser. Leverages the [pyre-to-regexp](https://github.com/jmchilton/pyre-to-regexp) that I recently published for this purpose. Commit: c520bb400c2a75270c87896b155d24fc574ef7d5 https://github.com/galaxyproject/galaxy/commit/c520bb400c2a75270c87896b155d2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-07 (Sat, 07 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Type fix for JS rule builder code. Commit: f85c575975e4ff5d10014f682d4c27d456f31049 https://github.com/galaxyproject/galaxy/commit/f85c575975e4ff5d10014f682d4c2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix radiobutton toggling Commit: 33f5f4db5d2b241fb16710439c71e11e5e4de502 https://github.com/galaxyproject/galaxy/commit/33f5f4db5d2b241fb16710439c71e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #37 from guerler/toggle_radio Fix radio button toggling Commit: ae8b8d9fdfd3bcaaa91d40acefa2bfba4b970715 https://github.com/galaxyproject/galaxy/commit/ae8b8d9fdfd3bcaaa91d40acefa2b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M client/README.md M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/gulpfile.js M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/test_scripts.py A test/selenium_tests/test_admin_app.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: c99d121674dc2ab51509d0dc548b841aeb590900 https://github.com/galaxyproject/galaxy/commit/c99d121674dc2ab51509d0dc548b8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Post-merge cleanup and build. Commit: d9efb4ff4c2c15f6ebd2d133760ff08fb80a623f https://github.com/galaxyproject/galaxy/commit/d9efb4ff4c2c15f6ebd2d133760ff... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Merge pull request #5864 from guerler/fix_expansion Fix conditional parameter handling Commit: 9e2ada9a008addbfbcf1d764d80d216dca6978a0 https://github.com/galaxyproject/galaxy/commit/9e2ada9a008addbfbcf1d764d80d2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Infinite loop retry is probably bad. This should help with surviving transient errors. Commit: ca7b3fd59355df39304d37972f46940e88f1a975 https://github.com/galaxyproject/galaxy/commit/ca7b3fd59355df39304d37972f469... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix tests due to missing name in mock module Commit: 8ba207de7199c66090f9526e451b8095751790d8 https://github.com/galaxyproject/galaxy/commit/8ba207de7199c66090f9526e451b8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore error handling variation Commit: 1263161e8292f5c494f0236dbf41bc338afb9e64 https://github.com/galaxyproject/galaxy/commit/1263161e8292f5c494f0236dbf41b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Remove changes to pinned-requirements.txt Commit: 7f1e07b19f5a59a801d7f9df0084e9bce18b8ebf https://github.com/galaxyproject/galaxy/commit/7f1e07b19f5a59a801d7f9df0084e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add PSA requirement to pipfile and run `make update-dependencies`. Commit: cd7e0b1eeef4b07ff21e3dce244b3e5611b352d6 https://github.com/galaxyproject/galaxy/commit/cd7e0b1eeef4b07ff21e3dce244b3... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase Commit: f1b5849f33463670bf37ba9dab1d296a8efa8851 https://github.com/galaxyproject/galaxy/commit/f1b5849f33463670bf37ba9dab1d2... Author: Steven Weaver <sweaver@temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M 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into dev Commit: ff15eeddbc8083ecd56a0dbaa03ca8cda7226111 https://github.com/galaxyproject/galaxy/commit/ff15eeddbc8083ecd56a0dbaa03ca... Author: Steven Weaver <sweaver@temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- updating hivtrace plugin to use new static paths Commit: fefd686b298cd573b49b6fc15d4531ffd3d852d2 https://github.com/galaxyproject/galaxy/commit/fefd686b298cd573b49b6fc15d453... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Increase yarn's network timeout Commit: 2fa340842cca7b46da121743153f5d31afe16eea https://github.com/galaxyproject/galaxy/commit/2fa340842cca7b46da121743153f5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove api flag check from workflow manager Commit: 1ed2b8f34e00295f1228650fec879df7535b828c https://github.com/galaxyproject/galaxy/commit/1ed2b8f34e00295f1228650fec879... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- replaced pinned-requirements file with s symlink. Commit: 8d5c1d08d8e3eb8a459343b2b4f4e4376407ea5d https://github.com/galaxyproject/galaxy/commit/8d5c1d08d8e3eb8a459343b2b4f4e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add source to workflow name Commit: 75c2c4f2494be66a459aece8e1707a6024e36e61 https://github.com/galaxyproject/galaxy/commit/75c2c4f2494be66a459aece8e1707... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix import from myexperiment service Commit: 2cb4d52d4dbb1b3a74a5bcf01205cfa6cb3181f1 https://github.com/galaxyproject/galaxy/commit/2cb4d52d4dbb1b3a74a5bcf01205c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix default parameters for 3rd party workflow import controller Commit: eec4533d6957f29b055352d5e5d2b0a5b500c420 https://github.com/galaxyproject/galaxy/commit/eec4533d6957f29b055352d5e5d2b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Remove view specific utility function from shared utils Commit: 00d48f0814f1893a2da31738f24fb0161e54c1a7 https://github.com/galaxyproject/galaxy/commit/00d48f0814f1893a2da31738f24fb... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add the missing pyjwkest requirement to pipfile. Commit: cea328effab5b56e9fca19b1a20f3289165a595a https://github.com/galaxyproject/galaxy/commit/cea328effab5b56e9fca19b1a20f3... Author: Steven Weaver <sweaver@temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/hivtrace/config/hivtrace.xml Log Message: ----------- adding hivtrace datatype and updating visualization to use it Commit: ed72b94e1e3a11be8ba5c4f8bd63b93877b32cd9 https://github.com/galaxyproject/galaxy/commit/ed72b94e1e3a11be8ba5c4f8bd63b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5870 from dannon/yarn-network-timeout Increase yarn's network timeout Commit: d01be5d51d266c2afae729ad41bfaecc566e74cf https://github.com/galaxyproject/galaxy/commit/d01be5d51d266c2afae729ad41bfa... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Create `set_random_password` function in galaxy user. Commit: 5baccd5e305d3c7d3c31dbcea39e0029afe8e855 https://github.com/galaxyproject/galaxy/commit/5baccd5e305d3c7d3c31dbcea39e0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Fix masthead highlighting Commit: bda1567fd7921bb343ac29324fd0b948ddf25243 https://github.com/galaxyproject/galaxy/commit/bda1567fd7921bb343ac29324fd0b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Remove unused model index Commit: cd1585a38e34d3246f8f6688ab480bde41c77f42 https://github.com/galaxyproject/galaxy/commit/cd1585a38e34d3246f8f6688ab480... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix background color of active tab Commit: 72b3f5635140596a86dbf2897181c6e9b14f4d9b https://github.com/galaxyproject/galaxy/commit/72b3f5635140596a86dbf2897181c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix dropdown operations buttons in grids Commit: 3ccb57152efdc734ea34a88d554fa4c2d7aa30d5 https://github.com/galaxyproject/galaxy/commit/3ccb57152efdc734ea34a88d554fa... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix pagination style for grids Commit: de5ac42fa9672d6bcf1b7e0c958c13adff2dafa8 https://github.com/galaxyproject/galaxy/commit/de5ac42fa9672d6bcf1b7e0c958c1... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- more tolerant sanitizing Commit: 4a6eb37b47261f6f3f77573ac9610a8a5ddc4e0d https://github.com/galaxyproject/galaxy/commit/4a6eb37b47261f6f3f77573ac9610... Author: E Rasche <hxr@hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add config option Commit: abfb69252a733d967dddcf7f3b6ea69f61645ff8 https://github.com/galaxyproject/galaxy/commit/abfb69252a733d967dddcf7f3b6ea... Author: E Rasche <hxr@hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Some progress on this Commit: 16f9e58af5cceb9eb7f969a581bbf66316a99986 https://github.com/galaxyproject/galaxy/commit/16f9e58af5cceb9eb7f969a581bbf... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- quotes Commit: 75b923b677825a78076f4533113580ad3386b357 https://github.com/galaxyproject/galaxy/commit/75b923b677825a78076f453311358... Author: E Rasche <hxr@hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- do not log usernames Commit: d23bb5689ed97c9e8c3c0bb12c1926594bf7ad3c https://github.com/galaxyproject/galaxy/commit/d23bb5689ed97c9e8c3c0bb12c192... Author: E Rasche <hxr@hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Redact docker logs Commit: 21b700ba27fbcada8c0529a032af0eea45a8f7f3 https://github.com/galaxyproject/galaxy/commit/21b700ba27fbcada8c0529a032af0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #39 from guerler/fix_dropdown_grids Fix dropdown operations buttons and pagination links in grids Commit: bb9963dddce6e1287785ae4452f3883229ed7a6c https://github.com/galaxyproject/galaxy/commit/bb9963dddce6e1287785ae4452f38... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- fix quote escaping Commit: 05740cfb48e2b74101e961a89c8530f8352b8778 https://github.com/galaxyproject/galaxy/commit/05740cfb48e2b74101e961a89c853... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M Makefile M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 187fde6be5ce10a18cd494bc043b93a37b8eeaec https://github.com/galaxyproject/galaxy/commit/187fde6be5ce10a18cd494bc043b9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- datalibs: change the default tooltip trigger to back to only hover Commit: deb398f62ef36990ab919d5e1c3473c717276785 https://github.com/galaxyproject/galaxy/commit/deb398f62ef36990ab919d5e1c347... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-libraryrow-view.js Log Message: ----------- move tooltip that renders on top of button to the left which would trigger showing/hiding endlessly Commit: 91a25d0a08b969c9d6b7161fae6f34eff1c66f59 https://github.com/galaxyproject/galaxy/commit/91a25d0a08b969c9d6b7161fae6f3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py Log Message: ----------- Support manager failover for Docker Swarm mode Commit: a3a472cdbaff61f65ce1e2fd0909ce1d6b59d4c5 https://github.com/galaxyproject/galaxy/commit/a3a472cdbaff61f65ce1e2fd0909c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Bump to bootstrap 4.1 (second try -- sorry for the rebase) Commit: 5127fd29570171f55d41e7458a5e2d7cec9a9837 https://github.com/galaxyproject/galaxy/commit/5127fd29570171f55d41e7458a5e2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Swarm manager: log services that do not have tasks on any node. Commit: d5a345f8e9498e0d0ae346d25cf029cf572586bc https://github.com/galaxyproject/galaxy/commit/d5a345f8e9498e0d0ae346d25cf02... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Attempt to fix jenkins selenium building git/cache bug. Commit: 405ed92b3dac12f9ad004194cb8b6a34c13e7b54 https://github.com/galaxyproject/galaxy/commit/405ed92b3dac12f9ad004194cb8b6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- fix empty history message being rendered on the bottom bs4 messes with out flex settings in some way Commit: 938bb010897e593a81beab28ae85d449640edddd https://github.com/galaxyproject/galaxy/commit/938bb010897e593a81beab28ae85d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Strip failed attempt to fix yarn cache/git issue for jenkins Commit: 4eb40607dee22381861933747c07e44ca824c691 https://github.com/galaxyproject/galaxy/commit/4eb40607dee22381861933747c07e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- re-add our default border to all buttons we want to bootstrapize more, but this will ensure that the transition period will be less broken Commit: 05c99b9ff7e172a36f0ff265179144ee04f2defe https://github.com/galaxyproject/galaxy/commit/05c99b9ff7e172a36f0ff26517914... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- fix popover for multihistory filtering Commit: fd3f8c9b635ed6e51b21068bd14c929487980573 https://github.com/galaxyproject/galaxy/commit/fd3f8c9b635ed6e51b21068bd14c9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- fix multihistory button margins also make 'Done' stand out more Commit: 484f5f6ec1bc44077fac4291d4868bb871a2392a https://github.com/galaxyproject/galaxy/commit/484f5f6ec1bc44077fac4291d4868... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/galaxy.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/controllers/authnz.py M templates/user/login.mako Log Message: ----------- Merge pull request #4474 from VJalili/oauth2-after-rebase User authentication using OpenID Connect protocol Commit: 6bb404e7a6ff7485bb528f16692d13f916490a3b https://github.com/galaxyproject/galaxy/commit/6bb404e7a6ff7485bb528f16692d1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Merge pull request #27 from VJalili/openid-ftp Some updates to FTP-upload messages w.r.t OIDC-based log-ins. Commit: 674a48cee3f1508843c2ac0580df3d5092e869b5 https://github.com/galaxyproject/galaxy/commit/674a48cee3f1508843c2ac0580df3... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #38 from guerler/fix_masthead_highlighting Fix masthead highlighting Commit: 9a36dc3a98751c6d4b498790cef7b29486c28e24 https://github.com/galaxyproject/galaxy/commit/9a36dc3a98751c6d4b498790cef7b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- More (minor) post-merge cleanup Commit: 9148865ee3bfb68ee3702f4ff12b869ef5ecd367 https://github.com/galaxyproject/galaxy/commit/9148865ee3bfb68ee3702f4ff12b8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- Constrain gray border to btn-secondary (the gray one); it looked strange around other classes, though we can certainly add color-appropriate borders to those if we need. Commit: e4ab6d2464aa8142bdc99291111c295211868d89 https://github.com/galaxyproject/galaxy/commit/e4ab6d2464aa8142bdc99291111c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix masthead color Commit: 7d00ee25d151cb4aebc19eb82f72e4fa224c8a58 https://github.com/galaxyproject/galaxy/commit/7d00ee25d151cb4aebc19eb82f72e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Explicitly state button style in grid templates. Commit: b2c8eb9e575480aa90256c9192ef92f0bb28c60a https://github.com/galaxyproject/galaxy/commit/b2c8eb9e575480aa90256c9192ef9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix popovers in masthead Commit: 20c061c6c57c3cc6a6113d9a8cdcd7d330c2af67 https://github.com/galaxyproject/galaxy/commit/20c061c6c57c3cc6a6113d9a8cdcd... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Allow modal scrolling Commit: 70788984d40b72090590dec979a475e95328d085 https://github.com/galaxyproject/galaxy/commit/70788984d40b72090590dec979a47... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js Log Message: ----------- Upload default-view refactoring while looking for popover issues Commit: 37cd8cf8cad56bcc085dc2cb545e0afd4fcddcdb https://github.com/galaxyproject/galaxy/commit/37cd8cf8cad56bcc085dc2cb545e0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js Log Message: ----------- Fix visibility of custom popover handler Commit: 4618bb25cfc869bd632817a8e753399c508bc1fa https://github.com/galaxyproject/galaxy/commit/4618bb25cfc869bd632817a8e7533... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Move style fixes into custom popover Remove debug test Commit: e4665061ef9b9bb9413e7c69396b97c9ff61ebba https://github.com/galaxyproject/galaxy/commit/e4665061ef9b9bb9413e7c69396b9... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #40 from guerler/popup Popover fixes Commit: 4d117c83d3a71cf60f174d54b40201dcbe1cf065 https://github.com/galaxyproject/galaxy/commit/4d117c83d3a71cf60f174d54b4020... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js Log Message: ----------- Popover refactoring. Commit: ab385d42a33c4d8396b6c791e313521d859a3c48 https://github.com/galaxyproject/galaxy/commit/ab385d42a33c4d8396b6c791e3135... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge, cleanup, rebuild after popup fixes. Commit: 79f664aa4e482d81ae3392f6cc0a9c927a144518 https://github.com/galaxyproject/galaxy/commit/79f664aa4e482d81ae3392f6cc0a9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- More, better workflow editor Selenium tests. - More stuff tested: - Setting input name and annotation, saving, reloading. - Simple tests for collection inputs in addition to data inputs. - A simple workflow renders its connections. - More screenshots. - Expanded use of navigation.yml for abstraction description of elements. - More abstractions for probing the workflow in the editor - should serve as a basis for additional tests. - Decorate editor DOM to allow finding elements in reproducible ways (enables testing, but should help with tours as well). - Make editor tests more robust by: - Doing more appropriate waiting, instead of adding sleeps for jQuery interactions. - Not assuming each test occurs with a fresh user (and hence workflow list). Commit: 01d33124e54586d08313d1009ebc383604802951 https://github.com/galaxyproject/galaxy/commit/01d33124e54586d08313d1009ebc3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Use button group in workflows list Commit: c8806c9a3dd6bf0458556b1eb36ab40574a37252 https://github.com/galaxyproject/galaxy/commit/c8806c9a3dd6bf0458556b1eb36ab... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix split button usage in workflows list; now looks like other grids. This is getting rewritten, but I wanted to change it since this looks like a bug to the end-user. Commit: 2eca6a252bfde71c921b24b302a8d1655caac514 https://github.com/galaxyproject/galaxy/commit/2eca6a252bfde71c921b24b302a8d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Use `extras` to specify additional social_auth_core dependencies - Fix oscillating environment markers due to slight differences in how packages specify their requirements - Update requirements files with `make update-dependencies` Commit: c03b699f66ba0a96e8455cf2ac43f928385d3835 https://github.com/galaxyproject/galaxy/commit/c03b699f66ba0a96e8455cf2ac43f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- reword Commit: 11204b17650045d73244d68db3133698b3e96b35 https://github.com/galaxyproject/galaxy/commit/11204b17650045d73244d68db3133... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #5877 from nsoranzo/dependencies_update Use `extras` to specify additional social_auth_core dependencies Commit: 6ee1c44df765c060a8396e14c17639b4bd8d20d9 https://github.com/galaxyproject/galaxy/commit/6ee1c44df765c060a8396e14c1763... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M lib/galaxy/managers/configuration.py Log Message: ----------- Merge pull request #5814 from martenson/openid-ftp add note to FTP modal when oidc is enabled Commit: acff3b2e9555c042cfcaa2e6c798b0ecd74d0449 https://github.com/galaxyproject/galaxy/commit/acff3b2e9555c042cfcaa2e6c798b... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #5876 from jmchilton/editor_tests More, better workflow editor Selenium tests. Commit: fa1231e9ec162df80442432c36ed1cb8b8ab2d42 https://github.com/galaxyproject/galaxy/commit/fa1231e9ec162df80442432c36ed1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Minor build fixes. Fix qunit issue and linting issue introduced with #5876. Commit: 1583db76ebebbcecf67dbf334dc1b24f5748b382 https://github.com/galaxyproject/galaxy/commit/1583db76ebebbcecf67dbf334dc1b... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #5878 from jmchilton/fixbuild Minor build fixes. Commit: 82d71a2aee1077e6394c056fe0de4517a944ed06 https://github.com/galaxyproject/galaxy/commit/82d71a2aee1077e6394c056fe0de4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- datalibs remove toolbar paginator, big buttons need more space Commit: d13fc00a7446ff8c444cc89c0d7b8668d2147e09 https://github.com/galaxyproject/galaxy/commit/d13fc00a7446ff8c444cc89c0d7b8... Author: Oleksandr Moskalenko <om@rc.ufl.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Move the statement below _galaxy_setup_environment to ensure that custom PATH to a non-system SLURM install will be applied if set in environment_setup_file Commit: 40e923ceb88c28bac7a951e66af28302369b56eb https://github.com/galaxyproject/galaxy/commit/40e923ceb88c28bac7a951e66af28... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix alignment of folder rows Commit: 2cec29c043f6a57e7abc74149b928d990ef2364e https://github.com/galaxyproject/galaxy/commit/2cec29c043f6a57e7abc74149b928... Author: Oleksandr Moskalenko <om@rc.ufl.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update cluster config docs for virtualenv issue for drmaa real user jobs. Commit: bc7da96bb63c14bef2a1b7081171c4d791223f8c https://github.com/galaxyproject/galaxy/commit/bc7da96bb63c14bef2a1b7081171c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh A lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/controllers/authnz.py M templates/user/login.mako M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: f56d8b6bd2ec48ff17cace8d94274fa8bec00679 https://github.com/galaxyproject/galaxy/commit/f56d8b6bd2ec48ff17cace8d94274... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow dropdown navigation Commit: 4babdd1d6d3a8614fd5299acf84801162a613ead https://github.com/galaxyproject/galaxy/commit/4babdd1d6d3a8614fd5299acf8480... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow index name navigation Commit: faba3e88c1efcfe13c998b31ca799217d6c8dbf9 https://github.com/galaxyproject/galaxy/commit/faba3e88c1efcfe13c998b31ca799... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js Log Message: ----------- remove unused id attr Commit: 08e80cf42bb4f21070ccb627980c0b140e55c75c https://github.com/galaxyproject/galaxy/commit/08e80cf42bb4f21070ccb627980c0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js Log Message: ----------- datalibs: fix styling of menu in dataset detail Commit: 7daa7143511d688f7538aa822a7a1e54b1c87214 https://github.com/galaxyproject/galaxy/commit/7daa7143511d688f7538aa822a7a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Fix final workflow management test for new list structure. Commit: 267e2cc182085d3c73ecb1632635969d33aead28 https://github.com/galaxyproject/galaxy/commit/267e2cc182085d3c73ecb16326359... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- reduce size of the span so the tooltip is more reliable Commit: 57ad6d76d7354a3d2558ddfe65475d788a5a3152 https://github.com/galaxyproject/galaxy/commit/57ad6d76d7354a3d2558ddfe65475... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Avoid mutable default arguments in navigates_galaxy Commit: d0a4024a84c8fa28ab3ad1839ba9dc4596b83932 https://github.com/galaxyproject/galaxy/commit/d0a4024a84c8fa28ab3ad1839ba9d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix saved history testing menu options to work with new dropdowns. Commit: 2624e63c26ce01dcab2ea48ea2f3ce1c09011b1b https://github.com/galaxyproject/galaxy/commit/2624e63c26ce01dcab2ea48ea2f3c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Drop [Done] button from multiview, rebuild and format client. Commit: 1bc1720ea8a0c55628201a91f8496f6df588e90f https://github.com/galaxyproject/galaxy/commit/1bc1720ea8a0c55628201a91f8496... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5881 from moskalenko/doc Update cluster docs for virtualenv issue in drmaa real user jobs Commit: e651b34156a3af022bac250464d92ca6394c3d85 https://github.com/galaxyproject/galaxy/commit/e651b34156a3af022bac250464d92... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py A scripts/docker_swarm_manager.py Log Message: ----------- Remove swarm manager from lib Commit: 2cc650078d3a9fc92355ba2dd326287fabe009a6 https://github.com/galaxyproject/galaxy/commit/2cc650078d3a9fc92355ba2dd3262... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M test/api/test_workflows.py A test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- More, better workflow editor Selenium tests - part 2. - More stuff tested: - Connecting and disconnecting simple terminals as well as mapping terminals (ribbons). - Rendering simple workflows, workflow with output collections, workflow with mapping, and workflow with a subworkflow. - Collapsing side panels in the workflow editor. - Small tweaks to editor DOM. - More screenshots. Commit: a280211ca65ca88b3a7cd92d0d3c1d15b874d462 https://github.com/galaxyproject/galaxy/commit/a280211ca65ca88b3a7cd92d0d3c1... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/galaxy into singlecellobject Commit: d31c05a67d40daa12fc3a2dbcdea35d1971d0e3d https://github.com/galaxyproject/galaxy/commit/d31c05a67d40daa12fc3a2dbcdea3... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- removed sniffers, removed pinned, removed classes Commit: 695ed3ac68d9f690f649b7e57c1bdf4625cc20fe https://github.com/galaxyproject/galaxy/commit/695ed3ac68d9f690f649b7e57c1bd... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: R lib/galaxy/datatypes/test/test.rds R lib/galaxy/datatypes/test/test.sce R lib/galaxy/datatypes/test/test_error.rds Log Message: ----------- removed test data Commit: 22f095edfb14c3f7f0da997501576dd31418021e https://github.com/galaxyproject/galaxy/commit/22f095edfb14c3f7f0da997501576... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Multi-panel refactoring while looking into fixes. Commit: 3a0d459c76fe741efe5299c85492cefc854e8a43 https://github.com/galaxyproject/galaxy/commit/3a0d459c76fe741efe5299c85492c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix flex direction for multihistory w/ column expansion off the page to the right. Commit: 6e16b776df306d4f04c4bcf3ec523f53986a4bc8 https://github.com/galaxyproject/galaxy/commit/6e16b776df306d4f04c4bcf3ec523... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M test/api/test_workflows.py A test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #5882 from jmchilton/editor_tests_2 More, better workflow editor Selenium tests - part 2. Commit: f7f8bfcc0c16230aa658486c30f247b830f7fdbd https://github.com/galaxyproject/galaxy/commit/f7f8bfcc0c16230aa658486c30f24... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M doc/source/admin/cluster.md M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M test/api/test_workflows.py A test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 1861d11e42f66bcd5970a15e3be821dcc434e7c0 https://github.com/galaxyproject/galaxy/commit/1861d11e42f66bcd5970a15e3be82... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/gulpfile.js Log Message: ----------- Re-stage bootstrap-tours/etc which are depended on by external plugins -- we can fix this when that isn't the case. Fix default task duplication in gulpfile (minor). Commit: 54a2bea27c4bd734518eb8fd7b2d15959c927b7a https://github.com/galaxyproject/galaxy/commit/54a2bea27c4bd734518eb8fd7b2d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix tool describing tour test selectors. Commit: 5599b41c07586b8638864ceaf1a467ef8ba798b1 https://github.com/galaxyproject/galaxy/commit/5599b41c07586b8638864ceaf1a46... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue 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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M static/style/blue/base.css Log Message: ----------- Swap pull-* for float-* across the board. Commit: eb67d422ef644cb43c3d66d02c86fd1d5ee41e0a https://github.com/galaxyproject/galaxy/commit/eb67d422ef644cb43c3d66d02c86f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/package.json M client/yarn.lock M test-data/rules/uniprot.json M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5823 from jmchilton/rule_tweaks Various Improvements for the Rule Builder Widget Commit: b0d867efa352fb4c82535efadf0666757c530eec https://github.com/galaxyproject/galaxy/commit/b0d867efa352fb4c82535efadf066... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #5821 from guerler/exact_version_handling Avoid silent tool upgrades during workflow imports Commit: 8750c1a10555f48ee4f148c2d59d19e519b6b54b https://github.com/galaxyproject/galaxy/commit/8750c1a10555f48ee4f148c2d59d1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- switch to badrequest exceptions Commit: 0ab89c9c7c46115c542da7f25559695e6e0dec98 https://github.com/galaxyproject/galaxy/commit/0ab89c9c7c46115c542da7f255596... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: A test/base/data/rules_dsl_spec.yml Log Message: ----------- Implement specification for rules DSL, useful for testing both Python and JS. Commit: 1b90d89814ea7a140d830cf0b499eb35e2a9fea9 https://github.com/galaxyproject/galaxy/commit/1b90d89814ea7a140d830cf0b499e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json Log Message: ----------- Mocha based client unit testing of rule tests. Commit: 3302b46775cdc76976a4bdc36353e014c6d5edbd https://github.com/galaxyproject/galaxy/commit/3302b46775cdc76976a4bdc36353e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- remove deprecated feature, deprecate method, link to preferred implementation Commit: d3038f859a03ad4b29eb6143ea9d88f915cfaac2 https://github.com/galaxyproject/galaxy/commit/d3038f859a03ad4b29eb6143ea9d8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Load containers interface on app load if enable_beta_containers_interface is set. Commit: 860aaf8241759f915501dba221a49b80a18a4e3e https://github.com/galaxyproject/galaxy/commit/860aaf8241759f915501dba221a49... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix docker interface failover by making the docker.APIClient wrapper use class vars, since we only ever want callers to use one APIClient. Commit: 564f7ecafe61d0c890cb9cde58640ce221935067 https://github.com/galaxyproject/galaxy/commit/564f7ecafe61d0c890cb9cde58640... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M scripts/docker_swarm_manager.py Log Message: ----------- Make the swarm manager recover on uncaught exceptions. It should do a better job of catching them in the application, but this is good enough for the moment. Commit: b24a1b723dd0d378b5f5c181f74f3340409839d8 https://github.com/galaxyproject/galaxy/commit/b24a1b723dd0d378b5f5c181f74f3... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small fix for workflow editor Selenium testing. Commit: 54721122e7439eeea2d2c6840ed668f827eed577 https://github.com/galaxyproject/galaxy/commit/54721122e7439eeea2d2c6840ed66... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Small fixes, enhancements for workflow run Selenium tests. Commit: 8f529d177ada3ef179a982d05dd4f04ba82e8abe https://github.com/galaxyproject/galaxy/commit/8f529d177ada3ef179a982d05dd4f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Improve a few workflow run API test cases. Use the more abstract test_data specification that will translate to GUI testing. Commit: aafd9de76ba61e2e3b2467188bb53e93c8b6fb2b https://github.com/galaxyproject/galaxy/commit/aafd9de76ba61e2e3b2467188bb53... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Add more complicated workflow run test case. Re-use test_data specification used by many of the API workflow tests and a workflow used by another test. Add abstractions and DOM element for mapping labeled test data to tool form inputs. Commit: 25e4d0448476e77cf58a4a975b6468c2e56e625b https://github.com/galaxyproject/galaxy/commit/25e4d0448476e77cf58a4a975b646... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- remove unused import Commit: e91163a9fcc96c772c8891ba554d0a7d9f7857c7 https://github.com/galaxyproject/galaxy/commit/e91163a9fcc96c772c8891ba554d0... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #5829 from osallou/fix_no_dataset_found Fix no dataset found Commit: 5f9a64c233736f81233b285d391d130dddc3ef8a https://github.com/galaxyproject/galaxy/commit/5f9a64c233736f81233b285d391d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Refactor multipanel controls to not use float-*, use normal in-panel positioning. Commit: feb3e9ddf039e56f972149e7338138fb662745b4 https://github.com/galaxyproject/galaxy/commit/feb3e9ddf039e56f972149e733813... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix lint error Commit: 225f6af3c07b44a672ac0571f57cf7c5766a3056 https://github.com/galaxyproject/galaxy/commit/225f6af3c07b44a672ac0571f57cf... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5880 from moskalenko/dev Move the memory statement below _galaxy_setup_environment Commit: fbd9d81409df888cd99c4d3f05875721b4505baf https://github.com/galaxyproject/galaxy/commit/fbd9d81409df888cd99c4d3f05875... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused variable Commit: ffe9c3bd294c55b4c4576dcc5187a3593d1bf9a1 https://github.com/galaxyproject/galaxy/commit/ffe9c3bd294c55b4c4576dcc5187a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused source identifier Commit: 30e3658b8b0e2f6b975dc6ccccb0cc8cc040247c https://github.com/galaxyproject/galaxy/commit/30e3658b8b0e2f6b975dc6ccccb0c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #5793 from jmchilton/bounded_memory_datatypes Sniffing framework with constrained memory and I/O. Commit: d5cb6f636b19128ce64934fbae91a82e21d4c668 https://github.com/galaxyproject/galaxy/commit/d5cb6f636b19128ce64934fbae91a... Author: Mehmet Tekman <m.tekman@ucl.ac.uk> Date: 2018-04-14 (Sat, 14 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- renamed type Commit: 4f41e9d2742da555959b7494d2efe802630305aa https://github.com/galaxyproject/galaxy/commit/4f41e9d2742da555959b7494d2efe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Improve foreground clipping of inactive histories Commit: dc563eae75cc4394aafdeef5ae9cd04213326225 https://github.com/galaxyproject/galaxy/commit/dc563eae75cc4394aafdeef5ae9cd... Author: Pablo Moreno <pablo.a.moreno@gmail.com> Date: 2018-04-15 (Sun, 15 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds timeout behaviour for k8s existing job deletion Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e309500... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: a1d76681f6c816ac55ea7fac859822f6d4e908ea https://github.com/galaxyproject/galaxy/commit/a1d76681f6c816ac55ea7fac85982... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json A test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #5888 from jmchilton/mocha_tests Mocha/Chai test framework + Rules DSL specification w/tests. Commit: 4ea51e9fc491bf64b24bade16dc45495f77f28b8 https://github.com/galaxyproject/galaxy/commit/4ea51e9fc491bf64b24bade16dc45... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M Makefile M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/karma.config.js M client/package.json M client/yarn.lock M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test-data/rules/uniprot.json A test/base/data/rules_dsl_spec.yml M test/selenium_tests/test_uploads.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 793b47025119ba708ec6d0a841c4c1ae3179b784 https://github.com/galaxyproject/galaxy/commit/793b47025119ba708ec6d0a841c4c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Fix botched merge (I think). Commit: df7a3ddb02189237d4085d409b51b216c11c932d https://github.com/galaxyproject/galaxy/commit/df7a3ddb02189237d4085d409b51b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix qunit test app imports for bootstrap4 Commit: e97018ae238f23f07cb3ff36d0bbdf2df30f9d7a https://github.com/galaxyproject/galaxy/commit/e97018ae238f23f07cb3ff36d0bbd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix more tooltip/title usage. Resolves one broken qunit test. Commit: 99f0db584553ba51d34e87593aac5e28a1bb7653 https://github.com/galaxyproject/galaxy/commit/99f0db584553ba51d34e87593aac5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/style/scss/dataset.scss Log Message: ----------- Cleanup while tracking down qunit test fails. Commit: 6ea22bfe18b60374f9ed6ed49c34f5a6ff4b707f https://github.com/galaxyproject/galaxy/commit/6ea22bfe18b60374f9ed6ed49c34f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: 19e05677fa5e9a3a5a8947a551369204a00d535c https://github.com/galaxyproject/galaxy/commit/19e05677fa5e9a3a5a8947a551369... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Commit: 2bb388db201fc261afcfe9bb9337ad383f9e2734 https://github.com/galaxyproject/galaxy/commit/2bb388db201fc261afcfe9bb9337a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: f9f571476bf3cb69fd6db4e48aebccddab3fa077 https://github.com/galaxyproject/galaxy/commit/f9f571476bf3cb69fd6db4e48aebc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js Log Message: ----------- update default color for qunit test Commit: a9598060c5dd84a5721acee648cbaf57143b4147 https://github.com/galaxyproject/galaxy/commit/a9598060c5dd84a5721acee648cba... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- radically increase the contrast of bs dropdown items the default hover was barely visible, also the 'active' state is now bright so you can clearle notice what you clicked Commit: 48df5f4d0eb13ee2a865959ff755208f05f57e31 https://github.com/galaxyproject/galaxy/commit/48df5f4d0eb13ee2a865959ff7552... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix more datalib dropdown items to be properly bs4 Commit: f6b52bafe3866f469da8090ce06bbad659e0a731 https://github.com/galaxyproject/galaxy/commit/f6b52bafe3866f469da8090ce06bb... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5892 from nsoranzo/test_most_scripts Exclude only test_grt_export integration test Commit: 1ff16ddfc401ffcf6edf3b9d14585293ced728a4 https://github.com/galaxyproject/galaxy/commit/1ff16ddfc401ffcf6edf3b9d14585... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: 8901f075b10841dc4bfa18721e87dcc8eb52716f https://github.com/galaxyproject/galaxy/commit/8901f075b10841dc4bfa18721e87d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Incremental work fixing a bunch of masthead tests, adding new ones. Commit: 244efc6593486e495882825191068b9d560fa793 https://github.com/galaxyproject/galaxy/commit/244efc6593486e495882825191068... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Fix some scratchbook js while working on qunit tests. Commit: 127167d1f320dd880eee500a249afccfa5561834 https://github.com/galaxyproject/galaxy/commit/127167d1f320dd880eee500a249af... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Finish masthead QUnit tests Commit: 6dcb3120cad949020aed8dea8a5aad3fb133e91e https://github.com/galaxyproject/galaxy/commit/6dcb3120cad949020aed8dea8a5aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Fix final qunit tests Commit: c4e1242312702aea4734a5a96a2bcd15b017c2ec https://github.com/galaxyproject/galaxy/commit/c4e1242312702aea4734a5a96a2bc... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5893 from martenson/backport-skip [18.01] Skip new script tests in dev branch, breaking integration suite Commit: c8baad98859b84fc2cd53d62d6b9dbfbe0cbb270 https://github.com/galaxyproject/galaxy/commit/c8baad98859b84fc2cd53d62d6b9d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix formatting of test-app.js Commit: ebf288f63e7221ca70360fe2c96b389f8fdb3dc5 https://github.com/galaxyproject/galaxy/commit/ebf288f63e7221ca70360fe2c96b3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Commit: 43cd9335f1bd1111dd339b7d09085cb86de2d9d7 https://github.com/galaxyproject/galaxy/commit/43cd9335f1bd1111dd339b7d09085... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix for Selenium workflow editor test not fully updating annotation. Sometimes the last character of the annotation is missing - gotta wait for the last update of form listener I suppose. Commit: 2ad87ac71b521704a810689c2776a987ad9779b1 https://github.com/galaxyproject/galaxy/commit/2ad87ac71b521704a810689c2776a... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #5896 from jmchilton/selenium_fixes_42 Fix for Selenium workflow editor test not fully updating annotation. Commit: 8ed3854f07e93f28774f76ed83f505471153ddb7 https://github.com/galaxyproject/galaxy/commit/8ed3854f07e93f28774f76ed83f50... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Merge pull request #5869 from veg/dev HIV-TRACE visualization plug-in Commit: fc546cb1abd2060eea159cc1198e09b55fbaaf41 https://github.com/galaxyproject/galaxy/commit/fc546cb1abd2060eea159cc1198e0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- allow admins to set any role for library datasets permissions this bug led to a funny problem where admins couldn't add themselves Commit: 51c05d7a28926a1257fb0b9b82d16f0a5b9d7ab2 https://github.com/galaxyproject/galaxy/commit/51c05d7a28926a1257fb0b9b82d16... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- modify checks that will never be true Commit: 7f9fcf99e403194558f5eb7a3f5545ee25a91c65 https://github.com/galaxyproject/galaxy/commit/7f9fcf99e403194558f5eb7a3f554... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- refactor the lib dataset update permissions process to mirror the library's Commit: 013a0cbc5570341f9a47be7ac39feecb9ec86e33 https://github.com/galaxyproject/galaxy/commit/013a0cbc5570341f9a47be7ac39fe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- This fixes display of the tour index names -- previously unnoticed since the id was displaying fine as the fallback. Commit: 5d82c1a09f9afb727df3f7ea29a72f54138a6a77 https://github.com/galaxyproject/galaxy/commit/5d82c1a09f9afb727df3f7ea29a72... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M .gitignore M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js M 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static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample M templates/base/base_panels.mako M templates/sharing_base.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #5807 from dannon/bs4 Bootstrap 4 !!!! Commit: ae6fbd6f75b460cd0e41f644a03bb9f4cff468ff https://github.com/galaxyproject/galaxy/commit/ae6fbd6f75b460cd0e41f644a03bb... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Use random password generation function of user class. Commit: 10090476267c1a2cec8103c4d3844057e682c730 https://github.com/galaxyproject/galaxy/commit/10090476267c1a2cec8103c4d3844... Author: Vahid <VJalili@users.noreply.github.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Add OIDC and OAuth2.0 config to authentication docs Commit: 767a456544335b302a9c9b42fba30df34c61c296 https://github.com/galaxyproject/galaxy/commit/767a456544335b302a9c9b42fba30... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Fix proxy, add logo and example file to repo for hivtrace Delete example file Commit: cfa48d4aa6c1602a7bdef578ccbc31653a75ee26 https://github.com/galaxyproject/galaxy/commit/cfa48d4aa6c1602a7bdef578ccbc3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused client route Commit: 19ed0e224235a5b10ce34d012d06075f07ea4a0c https://github.com/galaxyproject/galaxy/commit/19ed0e224235a5b10ce34d012d060... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Merge pull request #5907 from guerler/remove_unused_route Remove unused client route Commit: 5522c78d9d1ebcb490285528a8587ff7157a6d6d https://github.com/galaxyproject/galaxy/commit/5522c78d9d1ebcb490285528a8587... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Add `index` to OIDC controller to list authnzs associated with a user. Commit: 3922065d8a294b609a2b2f9c2a89cbb0f192b9b4 https://github.com/galaxyproject/galaxy/commit/3922065d8a294b609a2b2f9c2a89c... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Merge pull request #5902 from guerler/add_logo_hivtrace Add proxy, logo and example file for hivtrace Commit: 68dad22d1e15a30d8ee49f2f8002cdd7d7dfc723 https://github.com/galaxyproject/galaxy/commit/68dad22d1e15a30d8ee49f2f8002c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add router to authnz index. Commit: 60b5a9a52ab853bf9ff3adf09bbcc6ae0c4d7992 https://github.com/galaxyproject/galaxy/commit/60b5a9a52ab853bf9ff3adf09bbcc... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #5886 from jmchilton/selenium_workflow_run More, better workflow run Selenium tests. Commit: b71a163a8ce84403cec829e12265573e44d4f668 https://github.com/galaxyproject/galaxy/commit/b71a163a8ce84403cec829e122655... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Merge pull request #5906 from VJalili/patch-6 Add OIDC and OAuth2.0 config to authentication docs Commit: 881dc3601823da61c3a883f17907132f07afd0bd https://github.com/galaxyproject/galaxy/commit/881dc3601823da61c3a883f179071... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #5908 from VJalili/oidc_index OIDC controller index Commit: 20f47b2aa64946da3890a6c51ae6a94f8e6c37fa https://github.com/galaxyproject/galaxy/commit/20f47b2aa64946da3890a6c51ae6a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Hack to fix Git in node container. Fixes https://github.com/galaxyproject/galaxy/issues/5912 maybe - who knows. Commit: 6a541af4dcdfe537b5ee216b022f36ba0c78d920 https://github.com/galaxyproject/galaxy/commit/6a541af4dcdfe537b5ee216b022f3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- This forces the panel control sizing correctly, instead of being smushed up in the flex column (issue was on Chrome, worked fine in Firefox) Commit: 921fde4b8cdce2ab32846ba473846f1388b0592a https://github.com/galaxyproject/galaxy/commit/921fde4b8cdce2ab32846ba473846... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/app.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/util/__init__.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py A scripts/docker_swarm_manager.py Log Message: ----------- Merge pull request #5861 from natefoo/containers-docker-lib Implement the API version of the Docker containers interface Commit: 679083c935c10013dc4a24f9f2a8ead77651c567 https://github.com/galaxyproject/galaxy/commit/679083c935c10013dc4a24f9f2a8e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5899 from martenson/fix-admin-datalib-perms Fix admin datalib dataset perms Commit: fe4bff1fb9d84c057b40f04a9285ca5ca4dfb5fc https://github.com/galaxyproject/galaxy/commit/fe4bff1fb9d84c057b40f04a9285c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #5804 from guerler/workflow_import Use vue and api to handle workflow imports Commit: 8baea1f7c7551920bc2318b34247a29462a4e035 https://github.com/galaxyproject/galaxy/commit/8baea1f7c7551920bc2318b34247a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M 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scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py A scripts/docker_swarm_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A 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templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into singlecellobject Commit: 1c433d7d041d50d6e4c5bd886a606ff3af588d9f https://github.com/galaxyproject/galaxy/commit/1c433d7d041d50d6e4c5bd886a606... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5716 from mtekman/singlecellobject Add datatype(s): RDS object and SingleCellExperiment class Commit: df292fbf0e8c3246ec518a58385ea5a1233f0d45 https://github.com/galaxyproject/galaxy/commit/df292fbf0e8c3246ec518a58385ea... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Fix trackster links Commit: 65d4aff437d03f5c1dae9f9fe4646426a1fe9e35 https://github.com/galaxyproject/galaxy/commit/65d4aff437d03f5c1dae9f9fe4646... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #5811 from martenson/quota-meter add link that explains quota management to quota indicator Commit: 2829a1f1646b2ba85faf986b56799daccafb1060 https://github.com/galaxyproject/galaxy/commit/2829a1f1646b2ba85faf986b56799... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/galaxy.yml.sample M create_db.sh M doc/source/admin/framework_dependencies.rst M extract_dataset_parts.sh M lib/galaxy/dependencies/conda-file.sh M manage_db.sh M run_tests.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #5854 from natefoo/run-scripts-conda Improve startup interoperability with Conda Commit: 04ad5cf47dd8af5763af2b30465beeaf07692d49 https://github.com/galaxyproject/galaxy/commit/04ad5cf47dd8af5763af2b30465be... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #5887 from martenson/remove-intid remove deprecated feature, deprecate method, link to preferred impl. Commit: 3c99c546070c33498dce6ed4d7c592eb059ef748 https://github.com/galaxyproject/galaxy/commit/3c99c546070c33498dce6ed4d7c59... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Merge pull request #5900 from dannon/fix_tour_index_names This fixes display of the tour index names -- previously unnoticed since Commit: e922a95297a82e66cc3d360afaf68c303ca87267 https://github.com/galaxyproject/galaxy/commit/e922a95297a82e66cc3d360afaf68... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #5904 from VJalili/rndpassword Use random password generation function of user class ... Commit: 89ac586fff3e768f6f8c1f4bce30ab4958e35ab3 https://github.com/galaxyproject/galaxy/commit/89ac586fff3e768f6f8c1f4bce30a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M tools/filters/sorter.py Log Message: ----------- flake8 fixes Commit: a22d7c3d9aaabb9c6db535c2201df18090e34e6d https://github.com/galaxyproject/galaxy/commit/a22d7c3d9aaabb9c6db535c2201df... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #5913 from jmchilton/node_container_fix Hack to fix Git in node container. Commit: f6066d34fa403cf10cabdcaa58e420d6b7cc83b6 https://github.com/galaxyproject/galaxy/commit/f6066d34fa403cf10cabdcaa58e42... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder style fixes - bs4 branch fallout. Commit: 5bd45837dd3f044e72e8abbe90ea701be4627e80 https://github.com/galaxyproject/galaxy/commit/5bd45837dd3f044e72e8abbe90ea7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Set a minimum width for column selectors. Commit: 63620ba4007e81799606e91ef0549f32905fe791 https://github.com/galaxyproject/galaxy/commit/63620ba4007e81799606e91ef0549... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve styling, validation of Build button in rule upload table. Commit: 20c8260108e3829425cd2b7dfb75ca8ddc1d1356 https://github.com/galaxyproject/galaxy/commit/20c8260108e3829425cd2b7dfb75c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Redo footer inputs for rule builder. Gives more space for name and genome - dynamically resizes to space given with some reasonable minimum and maximum widths for widgets. Commit: f2d6a2d6b43ae32ce1302c7b2e0d5e0c9296ef94 https://github.com/galaxyproject/galaxy/commit/f2d6a2d6b43ae32ce1302c7b2e0d5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix click handler for BS4 changes. Commit: b59ea1633f4ec9724acf133ad8095bf9e8e6c99f https://github.com/galaxyproject/galaxy/commit/b59ea1633f4ec9724acf133ad8095... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Proper bootstrap 4 dropdown menus in the RuleBuilder. Commit: 6c020a6dbcde225ebecde45ce72a816c1d1e8f7c https://github.com/galaxyproject/galaxy/commit/6c020a6dbcde225ebecde45ce72a8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix uploads of link-only datasets to data library `ext` was never being set in the case of link only datasets, where I think the right thing is to fall back on `dataset.file_type`. Fixes https://github.com/galaxyproject/galaxy/issues/5915. Commit: 2e18ed2c9794405706a713ac08fc1dd769391bdf https://github.com/galaxyproject/galaxy/commit/2e18ed2c9794405706a713ac08fc1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Set ext explicitly to dataset.file_type since it is being used again later. Thanks @nsoranzo! Commit: 3182dfa70e4220621fe5eb85a05b2f5430a31d3d https://github.com/galaxyproject/galaxy/commit/3182dfa70e4220621fe5eb85a05b2... Author: E Rasche <hxr@hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- correct signal num Commit: 313a0ff2973c8f528b88013d17761df449fd174b https://github.com/galaxyproject/galaxy/commit/313a0ff2973c8f528b88013d17761... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- check that source before trying to move Commit: 43c418053c65f0ea7ecf840da3a38e080a4ebe85 https://github.com/galaxyproject/galaxy/commit/43c418053c65f0ea7ecf840da3a38... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5917 from mvdbeek/fix_link_only_add_datasets Fix uploads of link-only datasets to data library Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: 0b191abaf18271b9a51f21a13808e2b74c6cf0b1 https://github.com/galaxyproject/galaxy/commit/0b191abaf18271b9a51f21a13808e... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- pass the condition by a json file instead of arg Commit: fb291eb530858c79c83be10502d4b78b585d77cb https://github.com/galaxyproject/galaxy/commit/fb291eb530858c79c83be10502d4b... Author: E Rasche <hxr@hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- check memory later Commit: c85f07cf5fa2452122487cb66c3955fc88c6ea45 https://github.com/galaxyproject/galaxy/commit/c85f07cf5fa2452122487cb66c395... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5921 from erasche/fix-docs [18.01] correct signal num in docs Commit: 6178863d3cb617b283d5c15e27ad65a699abb649 https://github.com/galaxyproject/galaxy/commit/6178863d3cb617b283d5c15e27ad6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge pull request #5914 from dannon/fix-multipanel-height Multiview history panel-control fix. Commit: fe0a4853b96ddc163ebfb09f961885b88c5577dd https://github.com/galaxyproject/galaxy/commit/fe0a4853b96ddc163ebfb09f96188... Author: E Rasche <hxr@hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- forgot to document github bug reporter Commit: 393f055a2307f090f71dc2c7750b8487cfafcd96 https://github.com/galaxyproject/galaxy/commit/393f055a2307f090f71dc2c7750b8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Merge pull request #5928 from erasche/document-gh-reporter [18.01] forgot to document github bug reporter Commit: 50f9ca82ba158736e7ed735e3d949a65127a5111 https://github.com/galaxyproject/galaxy/commit/50f9ca82ba158736e7ed735e3d949... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Don't attempt to determine ports at GIE container launch time if they fail to be determined on the first attempt. They'll be determined by the readiness check instead. Commit: 145903eae313a238830aab279a1070a007facee5 https://github.com/galaxyproject/galaxy/commit/145903eae313a238830aab279a107... 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test/functional/tools/bibtex.xml A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/code_file.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_dynamic_nested_from_json.xml A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/collection_split_on_column.xml M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/config_vars.xml M test/functional/tools/create_2.xml A test/functional/tools/data_source.py A test/functional/tools/empty_datasets.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml A test/functional/tools/fail_writing_work_dir_file.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/identifier_in_actions.xml A test/functional/tools/identifier_source.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/job_properties.xml M test/functional/tools/metadata.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/output_filter_with_input.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml A test/functional/tools/vcf_bgzip.xml A test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/tour_generator A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css A test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/galaxy_selenium/sizzle.py A test/galaxy_selenium/smart_components.py A test/integration/dockerized_job_conf.xml A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_config_options_users.py A test/integration/test_data_manager_table_reload.py A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/integration/test_job_resubmission.py A test/integration/test_local_job_cancellation.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_mules_as_job_handlers.py M test/integration/test_resolvers.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py A test/integration/test_upload_configuration_options.py M test/integration/test_workflow_handler_configuration.py A test/integration/test_workflow_scheduling_options.py A test/integration/tool_sheds_conf.xml A test/integration/uses_shed.py M test/manual/launch_and_run.sh M test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into sort_header Commit: d11f76b0315f6f29d6232e3a440d50fd1481bb55 https://github.com/galaxyproject/galaxy/commit/d11f76b0315f6f29d6232e3a440d5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/filters/sorter.py Log Message: ----------- More flake8 fixes for sorter.py. Commit: 21c10e960b21c35776812cca53427425f4ff5667 https://github.com/galaxyproject/galaxy/commit/21c10e960b21c35776812cca53427... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M tools/filters/sorter.py M tools/filters/sorter.xml Log Message: ----------- Merge pull request #4235 from lecorguille/sort_header Sort header Commit: fce2dd3ae801cd13a542388746b84f9cca2a4c48 https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b84... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Eliminate compressed datatype boiler plate. Just annotate auto_compressed_types="gz|bz2|gz,bz2" in datatypes_conf.xml and get for free: - The compressed datatype with correct extension, no need to have a class definition. - Converters from the compressed datatype to the uncompressed datatype. - A sniffer in the correct order. Additionally, the hacky way we were controlling whether types would be sniffed or not has been improved. This can now be set in the datatypes_conf.xml file or read from a global Galaxy configuration option for options that haven't been explicitly set on a per-datatype basis in the configuration (sniff_compressed_dynamic_datatypes_default). This should simplify all future datatypes moving in this direction and introduces the possibility of also just loading them in dynamically as needed based on what the tools in the tool panel annotate for inputs and outputs. See a tool with an input of type "genbank.gz" should be enough to trigger this someday I hope. Commit: 379714e5beace2ca7b31eab064f22862902b1831 https://github.com/galaxyproject/galaxy/commit/379714e5beace2ca7b31eab064f22... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- remove sniffers that no longer exist from sample config Commit: b9fe69fb8b46ffc2c9842d672c547413439f12d8 https://github.com/galaxyproject/galaxy/commit/b9fe69fb8b46ffc2c9842d672c547... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5794 from jmchilton/dynamic_compressed_types Infrastructure for dynamic compressed datatypes Commit: 2dfb4875bba0059a4b44bd77e7fadb7adf6af7d7 https://github.com/galaxyproject/galaxy/commit/2dfb4875bba0059a4b44bd77e7fad... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix bug with remove workflow outputs from a node. Fixes https://github.com/galaxyproject/galaxy/issues/5931. Commit: 5e13f48889348079632f852f6f1608012ea0160d https://github.com/galaxyproject/galaxy/commit/5e13f48889348079632f852f6f160... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Update to latest galaxy-lib. - Add linting for PEP440 compliance. https://github.com/galaxyproject/galaxy-lib/pull/106 - Improved abstraction usage in tool test data handling. https://github.com/galaxyproject/galaxy-lib/pull/105 - Make requests an optional dependency when loading galaxy.containers (still required at runtime). Commit: e6d752c85930bde846eb57e26de8a8716bf92b08 https://github.com/galaxyproject/galaxy/commit/e6d752c85930bde846eb57e26de8a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix for running in containers when job_tmp is set in job_conf.xml. Commit: 2fe7579d12c352b878bd9a9f3751ce7db1fb2bba https://github.com/galaxyproject/galaxy/commit/2fe7579d12c352b878bd9a9f3751c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix for running jobs in containers. Broken with 5861. Commit: dc4902353f3254aa962f8efe1ea4e2af5f7499ab https://github.com/galaxyproject/galaxy/commit/dc4902353f3254aa962f8efe1ea4e... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.xml Log Message: ----------- add test case for fixed bug Commit: dadb4fcda723ab14421b07cb4b1747aa3e8b325d https://github.com/galaxyproject/galaxy/commit/dadb4fcda723ab14421b07cb4b174... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- change back version Commit: aecbdac334a18ff1f82494fc6c0b58de90ad610c https://github.com/galaxyproject/galaxy/commit/aecbdac334a18ff1f82494fc6c0b5... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/__init__.py Log Message: ----------- move the dir existance check out of move_merge Commit: 09fcf13aafb5dd6aa1f3b31446af91c7ca2ea3a6 https://github.com/galaxyproject/galaxy/commit/09fcf13aafb5dd6aa1f3b31446af9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #5872 from abretaud/filter_sanitize Filter tool: fix too strict sanitizing Commit: 33a28b8b8b6d36e7ab972c9f3241ce92bd4fbc2b https://github.com/galaxyproject/galaxy/commit/33a28b8b8b6d36e7ab972c9f3241c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #5761 from phnmnl/galaxy-prs/k8s-improves-job-handling-existing-jobs Kubernetes: Improves handling of existing jobs on Galaxy restart. Commit: c2467f27ae547b05513f011868c0d4a2d456c606 https://github.com/galaxyproject/galaxy/commit/c2467f27ae547b05513f011868c0d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5922 from abretaud/movemerge Fix error with data managers when trying to move_merge inexistant extra_files dir Commit: 13661adcad91e99a9fc029fab7324194a63db605 https://github.com/galaxyproject/galaxy/commit/13661adcad91e99a9fc029fab7324... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5909 from jmchilton/rule_builder_styling Rule builder styling fixes. Commit: a5c75d2f954f697497747412fd2a998fa61019b0 https://github.com/galaxyproject/galaxy/commit/a5c75d2f954f697497747412fd2a9... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Correct access for FTP files in composite datatype Commit: 89ff880bcde0916c6ea3ae70fabb0e4366b3fdd0 https://github.com/galaxyproject/galaxy/commit/89ff880bcde0916c6ea3ae70fabb0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Improve dropdown click and highlighting behavior Commit: f6c00e79217501b7622c151bac119726f8004a64 https://github.com/galaxyproject/galaxy/commit/f6c00e79217501b7622c151bac119... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- improve ux of various builder elements Commit: f0e0b5c9fc88119ee5f2d380d38b0aa3e89079e1 https://github.com/galaxyproject/galaxy/commit/f0e0b5c9fc88119ee5f2d380d38b0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix rule source edit cancel button. Commit: c4ad1f55e49c374eac8724d7ffbb787e5ac37c15 https://github.com/galaxyproject/galaxy/commit/c4ad1f55e49c374eac8724d7ffbb7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Disable reorient button. Commit: 1df00bfb51afbbf5969429aae274a88315e40d51 https://github.com/galaxyproject/galaxy/commit/1df00bfb51afbbf5969429aae274a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/package.json M client/webpack.config.js Log Message: ----------- Add bootstrap vue as a dependency. Commit: 847695a16248986b8f2d798f420f887f127b6d6a https://github.com/galaxyproject/galaxy/commit/847695a16248986b8f2d798f420f8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Use bootstrap-vue to add many new tooltips to rule builder. Commit: 798d7d86795fd9dbee51f3551a051245111129ab https://github.com/galaxyproject/galaxy/commit/798d7d86795fd9dbee51f3551a051... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- bootstrap-vue popover describing regex. Commit: 5e78c00824b6ba2e97cd46b671133de9cec43ad1 https://github.com/galaxyproject/galaxy/commit/5e78c00824b6ba2e97cd46b671133... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- various UX and style improvements Commit: 34689c7629d7c1a2c00afb5d43ca22a62e76b4c9 https://github.com/galaxyproject/galaxy/commit/34689c7629d7c1a2c00afb5d43ca2... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge branch 'ux-stylechanges' of github.com:jmchilton/galaxy into ux-stylechanges Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e443... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: 909075c67839830207bda14c455139eecaf979b8 https://github.com/galaxyproject/galaxy/commit/909075c67839830207bda14c45513... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - tweak tooltip placement so it doesn't overlap menu. Fixes test cases. Commit: d94cd0a9c20b497e17b7bfe3a5d059513d367e16 https://github.com/galaxyproject/galaxy/commit/d94cd0a9c20b497e17b7bfe3a5d05... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder Another tweak to fix test cases. Commit: d51812b832dbd1268e6ac76a1c22af05880d4525 https://github.com/galaxyproject/galaxy/commit/d51812b832dbd1268e6ac76a1c22a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/package.json M client/webpack.config.js Log Message: ----------- Merge pull request #5940 from jmchilton/ux-stylechanges More Rule Builder Style Changes Commit: e40c61b9a740974f3784b2cef90d1f973dabed52 https://github.com/galaxyproject/galaxy/commit/e40c61b9a740974f3784b2cef90d1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Merge pull request #5916 from guerler/fix_trackster_link Fix trackster links Commit: 0881547bfcc0be8fbe101885543303c152103265 https://github.com/galaxyproject/galaxy/commit/0881547bfcc0be8fbe10188554330... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'guerler/fix_drop_selection' into dev Commit: 5c3e6648519d6591bcf3e71b6d2b4e1ba2fe1170 https://github.com/galaxyproject/galaxy/commit/5c3e6648519d6591bcf3e71b6d2b4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/yarn.lock Log Message: ----------- Client format after merges. Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e6... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: feb3e5688dd6d97402a201e77e0179ac6dc30670 https://github.com/galaxyproject/galaxy/commit/feb3e5688dd6d97402a201e77e017... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5935 from jmchilton/workflow_outputs_fix Fix bug with removing workflow outputs from a node. Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270db... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Commit: 284795b94f2fa7f2a9ad4dc82990195815de1e9c https://github.com/galaxyproject/galaxy/commit/284795b94f2fa7f2a9ad4dc829901... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 3ab2afb5e5bd82b3aa89500b9c2f80913a054316 https://github.com/galaxyproject/galaxy/commit/3ab2afb5e5bd82b3aa89500b9c2f8... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- backport move_merge fix from #5922 Commit: 5acb2dff792fbb799215537335425b820bd16d4d https://github.com/galaxyproject/galaxy/commit/5acb2dff792fbb799215537335425... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5937 from jmchilton/docker_fix_tmp Fix for running in containers when job_tmp is set in job_conf.xml. Commit: 9e3cc281564a2f3cb91ae5c10b3ad501230228ae https://github.com/galaxyproject/galaxy/commit/9e3cc281564a2f3cb91ae5c10b3ad... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #5938 from jmchilton/docker_fix_containers_lib Fix for running jobs in containers. Commit: a77ea2751e2659797421ab49d03d5dc9d11f67eb https://github.com/galaxyproject/galaxy/commit/a77ea2751e2659797421ab49d03d5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Fix history list shared error Commit: 8de398c7e440d979f036a15cfa46f0570a617893 https://github.com/galaxyproject/galaxy/commit/8de398c7e440d979f036a15cfa46f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Refactoring while bugfixing in history-list Commit: ab92eb6691903e35b75c16bee8f77e0b40db8085 https://github.com/galaxyproject/galaxy/commit/ab92eb6691903e35b75c16bee8f77... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Allow using the rule based collection builders right from libraries. Commit: 7fd12ec7b83ee303aedb9d77b31d479000b7b5f3 https://github.com/galaxyproject/galaxy/commit/7fd12ec7b83ee303aedb9d77b31d4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/package.json M client/webpack.config.js Log Message: ----------- Rev handsontable client dep - fixes global style contamination of that component. Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085af... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5da... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a457... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 63a3cfad30656b7fa8516e9c386f144f0f3b1fe3 https://github.com/galaxyproject/galaxy/commit/63a3cfad30656b7fa8516e9c386f1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Commit: d4a890f2fc46c4dd82a77e3a5772546d88a6b95d https://github.com/galaxyproject/galaxy/commit/d4a890f2fc46c4dd82a77e3a57725... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix links in rule builder to not interfere with the library router. Commit: 1209f35a1a6b5647a58b5c5f5c93d73388db8d64 https://github.com/galaxyproject/galaxy/commit/1209f35a1a6b5647a58b5c5f5c93d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Pleasant error handling if duplicate identifiers encountered. - Print a pretty error for this scenerio. - Improve the error state of the widget to add a cancel and "okay" button - the cancel button dimisses the widget and the okay button gives the reseracher a chance to return to the rules and try again. Commit: 0f88e4e9ebe4b4724f4c6ecc3c7ecd5d0fce7cc6 https://github.com/galaxyproject/galaxy/commit/0f88e4e9ebe4b4724f4c6ecc3c7ec... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Merge pull request #5962 from dannon/fix_shared_history_list_bug Fix shared history list bug Commit: f042f51b366e4c6c82643f30b0fd7bc5fde7950a https://github.com/galaxyproject/galaxy/commit/f042f51b366e4c6c82643f30b0fd7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Style improvements for error messages in RuleBuilder. Commit: 8d052bad353959bf2465bac5322b5a939f3f5b68 https://github.com/galaxyproject/galaxy/commit/8d052bad353959bf2465bac5322b5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- bootstrap4 regression fix - extra large rule builder modal. Make the rule builder expand to larger screens more aggressively again, the BS4 branch capped the width at like 900px - make this much larger. Fixes https://github.com/galaxyproject/galaxy/projects/10#card-8949949. Commit: 581e949dff5ae99195960af48ba7aad0edbec3c4 https://github.com/galaxyproject/galaxy/commit/581e949dff5ae99195960af48ba7a... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #5965 from jmchilton/modal_width_fix bootstrap4 regression fix - extra large rule builder modal. Commit: 393f436ce5946440df2e0b6de04ebc6558a57b3f https://github.com/galaxyproject/galaxy/commit/393f436ce5946440df2e0b6de04eb... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/package.json M client/webpack.config.js Log Message: ----------- Merge pull request #5929 from jmchilton/library_2_rules Allow using the rule based collection builders right from libraries. Commit: 0a3682804f9acf39cff12826eea04905a211e45d https://github.com/galaxyproject/galaxy/commit/0a3682804f9acf39cff12826eea04... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Revert "Fix links in rule builder to not interfere with the library router." This reverts commit d4a890f2fc46c4dd82a77e3a5772546d88a6b95d. Commit: d9904bf595c3815c4827bb0852004d036600936e https://github.com/galaxyproject/galaxy/commit/d9904bf595c3815c4827bb0852004... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix for split columns rule definition. Commit: 8af243c176fd9c261277327750aaa71806add4ef https://github.com/galaxyproject/galaxy/commit/8af243c176fd9c261277327750aaa... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py Log Message: ----------- Allow rule based operations on existing collections. Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions. For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules". This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions. This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running. Commit: c225c5dbd651b048b3354e97a8821d8148b559fe https://github.com/galaxyproject/galaxy/commit/c225c5dbd651b048b3354e97a8821... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Add simple help for apply rules tool. Commit: d2b8ad9105e5c06c8ab3685672c1a6dc64b31406 https://github.com/galaxyproject/galaxy/commit/d2b8ad9105e5c06c8ab3685672c1a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- RuleBuilder tool param fix for to_dict. An exception in generating a "text representation" of a None value was preventing the rest of to_dict from running properly for that parameter value. This restores the rule preview table in the tool form. Commit: a6d052a6819d2bc277744b3e2633785c31c844fb https://github.com/galaxyproject/galaxy/commit/a6d052a6819d2bc277744b3e26337... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix modal title for apply_rules branch changes. Commit: 383eb0d2736269d24d595ed5b8aa730908812be3 https://github.com/galaxyproject/galaxy/commit/383eb0d2736269d24d595ed5b8aa7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Add apply rules tool to standard tool xml sample Commit: f4eda4fd173b64d782a39da97d7a2b224a7637c3 https://github.com/galaxyproject/galaxy/commit/f4eda4fd173b64d782a39da97d7a2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Fix up help language in apply_rules tool. Commit: 88bf6bbdaa2d15355192eb3c9087151f7712209d https://github.com/galaxyproject/galaxy/commit/88bf6bbdaa2d15355192eb3c90871... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5943 from erasche/fix-ftp-composite-upload [18.01] Correct access for FTP files in composite datatype Commit: 4f4cb148b748aa5ca3b1f27d978565728f7df7d8 https://github.com/galaxyproject/galaxy/commit/4f4cb148b748aa5ca3b1f27d97856... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- better fix for href containing hashes removing href messes with styles and also with bs4 (e.g. active highlighting of dropdowns was broken) Commit: f3455f5276d1abd44ac4e68b9a9e62059640a19f https://github.com/galaxyproject/galaxy/commit/f3455f5276d1abd44ac4e68b9a9e6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #5968 from martenson/ux-builder rule builder - better fix for inactive links Commit: 2fcfec1bd3b8b31e39c2ae67816c723d96ebf177 https://github.com/galaxyproject/galaxy/commit/2fcfec1bd3b8b31e39c2ae67816c7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Data Libary -> Rule Builder fixes. - Missed allowing collection name in library mode - I told Martin this possible because I thought it was and the library collection type text states it is possible but I didn't fix the switch in rule-definitions.js and notice the problems in createCollection associated with that. - Fix to drop file type and genome selector when coming from libraries because this targets existing datasets - think this might have slipped back in a bad merge. - Fix modal title when coming from data library folders. - Improve text instructions when coming from a library. Fixes #5967. Commit: cf2f6d7dcf2dba76dc02f1fe6ab0abd360584ef4 https://github.com/galaxyproject/galaxy/commit/cf2f6d7dcf2dba76dc02f1fe6ab0a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix selenium tests failing because APPLY_RULES appears twice in panel. Commit: 7712f69b69d90def8fba5c961b11ecf2169f72df https://github.com/galaxyproject/galaxy/commit/7712f69b69d90def8fba5c961b11e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/wig_to_bigwig.xml Log Message: ----------- Rev tool versions for tools with updated ucsc tool requirements. Commit: 3aa01b060477fe3fe0f59c73ca3ee75605e08182 https://github.com/galaxyproject/galaxy/commit/3aa01b060477fe3fe0f59c73ca3ee... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- initial pass fixing toolshed nav structure -- need to follow up on dependencies Commit: 1d5d83feac999797a127aee7d3b64a0811d1ed49 https://github.com/galaxyproject/galaxy/commit/1d5d83feac999797a127aee7d3b64... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #5969 from jmchilton/rule_fixes_1 Data Library -> Rule Builder fixes. Commit: dbd86642d514badcc0fedf3f822f19d7b4dd9d15 https://github.com/galaxyproject/galaxy/commit/dbd86642d514badcc0fedf3f822f1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge other recent rule PRs into apply_rules branch. Commit: 34016542d9e6987bd615f6e0051d2c6cd1d4dd95 https://github.com/galaxyproject/galaxy/commit/34016542d9e6987bd615f6e0051d2... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge pull request #5544 from natefoo/split-ucsc-requirements Update all tools/converters using UCSC binaries to depend only on the binary they are using Commit: 20e9934bc5922f8d20dd31540a4dce9086495832 https://github.com/galaxyproject/galaxy/commit/20e9934bc5922f8d20dd31540a4dc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5958 from abretaud/movemerge1801 [18.01] Backport to 18.01 the move_merge fix from #5922 Commit: 3dbcc7c83c75b32a6447d110a67f945b54e30542 https://github.com/galaxyproject/galaxy/commit/3dbcc7c83c75b32a6447d110a67f9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Pin the version of node we use in CI, etc.... Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well). Commit: 1985911a7d10a6cf9b8d0aa5500468edfb955823 https://github.com/galaxyproject/galaxy/commit/1985911a7d10a6cf9b8d0aa550046... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge pull request #5936 from jmchilton/galaxy-lib-20180419 Update to latest galaxy-lib. Commit: 8f8dc08a4cbe1490ab12d05909926c928563c743 https://github.com/galaxyproject/galaxy/commit/8f8dc08a4cbe1490ab12d05909926... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5972 from jmchilton/pin_node Pin the version of node we use in CI, etc.... Commit: 2515267ca5a058d2029c589357f518b1cfb372b8 https://github.com/galaxyproject/galaxy/commit/2515267ca5a058d2029c589357f51... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/wig_to_bigwig.xml Log Message: ----------- Add `version` attribute to tool requirements instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` . Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 . See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for an explanation why that's preferrable for future-proof reproducibility. Also, small fixes to `tools/evolution/codingSnps.xml` . Commit: e7158658d026b7559adb173cea1ac0a26852bca8 https://github.com/galaxyproject/galaxy/commit/e7158658d026b7559adb173cea1ac... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #5819 from jmchilton/apply_rules Allow rule based operations on existing collections. Commit: 4d66d8025107bbeba5cf15ac5f177d600d7bf2d1 https://github.com/galaxyproject/galaxy/commit/4d66d8025107bbeba5cf15ac5f177... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/yarn.lock M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Fixes to toolshed/menu for BS4 Commit: 1624b6ce7d382c5ad1a883a5ca7f86106460e96c https://github.com/galaxyproject/galaxy/commit/1624b6ce7d382c5ad1a883a5ca7f8... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge pull request #5973 from nsoranzo/followup_on_5544 Add `version` attribute to some tool requirements Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: c1e5fb82901600bd109fba133bc0f7c62313b3ea https://github.com/galaxyproject/galaxy/commit/c1e5fb82901600bd109fba133bc0f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Commit: 8d4666578d4dc2c0374ef105659d69931efa1f4e https://github.com/galaxyproject/galaxy/commit/8d4666578d4dc2c0374ef105659d6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.rc1 Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b0... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: c41c84eec6e8cfc6291dd85ce58ba4b34b394bb1 https://github.com/galaxyproject/galaxy/commit/c41c84eec6e8cfc6291dd85ce58ba... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: dbb08fe7620610812189049481740215c12f9eb6 https://github.com/galaxyproject/galaxy/commit/dbb08fe7620610812189049481740... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5980 from martenson/version-18.05 [18.05] Update version to 18.05.rc1 Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f570... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: 84af648f017dad95871bb43b65e8d860391066c8 https://github.com/galaxyproject/galaxy/commit/84af648f017dad95871bb43b65e8d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Cgroup metric plugin: attempt to deal with multiline params, and store numeric values in the numeric table. Also fix a display bug. Commit: a7a4e12e79a91a2a17fa86d65077233f8cfcb35c https://github.com/galaxyproject/galaxy/commit/a7a4e12e79a91a2a17fa86d650772... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix collection element count getting lost during collection copies. Commit: 3c7bffb8352fb419d9ca2ff2c5d1bbdf26d8a7b6 https://github.com/galaxyproject/galaxy/commit/3c7bffb8352fb419d9ca2ff2c5d1b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix ftp imports in rule builder. Commit: 8470815163336d54078b713452ae9dcd58dfe53f https://github.com/galaxyproject/galaxy/commit/8470815163336d54078b713452ae9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix add row number rule. Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df95... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Commit: a3e69636662cfeae0ebc1b66fcc03b0b7fe13be8 https://github.com/galaxyproject/galaxy/commit/a3e69636662cfeae0ebc1b66fcc03... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 7ce49394c3a73fc64e23603ffcab8f39ff3159a0 https://github.com/galaxyproject/galaxy/commit/7ce49394c3a73fc64e23603ffcab8... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: a29770ca554b5aaf8ea6533ee413fed77042a0ea https://github.com/galaxyproject/galaxy/commit/a29770ca554b5aaf8ea6533ee413f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Pin the version of node we use in CI, etc.... Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well). Commit: c7b426089aa7ec0e0ba874e03ed9dad60a9d1909 https://github.com/galaxyproject/galaxy/commit/c7b426089aa7ec0e0ba874e03ed9d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #6000 from jmchilton/fix_build_maybe [18.01] Backport #5972 Commit: 0ca1401bd8387717edb31a69e11d3adc09258757 https://github.com/galaxyproject/galaxy/commit/0ca1401bd8387717edb31a69e11d3... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- ToolBuildOptimize - Eliminate check_security on dataset matcher. It was only used for collections and we need to drop it as prohibitively expensive to calculate. No need to filter collections ahead of time that way anyhow - it is the tool action's job to block the execution of datasets without permission so hopefully we aren't deriving any security value from this filter. Commit: c3303939c05ae8af9a2b11a12d5f433ee0d8072e https://github.com/galaxyproject/galaxy/commit/c3303939c05ae8af9a2b11a12d5f4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- ToolBuildOptimize - Optimize state checking in dataset matcher. Pre-calculate valid states, skip now unneeded helper method. Commit: 7ca2ef587cd26682e3b4b28c7cdb8907cfeae862 https://github.com/galaxyproject/galaxy/commit/7ca2ef587cd26682e3b4b28c7cdb8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- DatasetMatcherClean - Skip second, unneeded call to filter(). xref 8f813712f50ca21183d2efe59ee0e2a665520f95 to some degree. Commit: 412f03d8446cb362bbfe27d5832bcf37aef2d4d6 https://github.com/galaxyproject/galaxy/commit/412f03d8446cb362bbfe27d5832bc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- DatasetMatcherClean - Eliminate DatasetMatcher.value - it is never set. Also eliminate any logic related to it having a value. This had a purpose originally, but is no longer set. Cleaning this up makes subsequent commits a bit cleaner also. Commit: ca80232db3a93a02dcd42f2698b54e7a8d2aeef1 https://github.com/galaxyproject/galaxy/commit/ca80232db3a93a02dcd42f2698b54... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- DatasetMatcherClean - Remove unused method. It calls things that I'm changing in subsequent commits so I thought I'd just axe it now to clear things up. Commit: efe5d8b973ffdd22963ec75db7820ff1731db916 https://github.com/galaxyproject/galaxy/commit/efe5d8b973ffdd22963ec75db7820... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- DatasetMatcherClean - Implement DatasetMatcherFactory to reason for whole tool. In subsequent commit I'll use this central store of all the inputs for a tool to determine if summary data about collections can be used instead of processing individual datasets one at a time. Even this commit though uses the abstraction to optimize datatype checking and cache commons checks when possible - should lead to a lot fewer objects being created when processing a large history. Commit: 2eea566c10eaf2b7dad21cdff82e0a14a1893fde https://github.com/galaxyproject/galaxy/commit/2eea566c10eaf2b7dad21cdff82e0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- ToolBuildOptimize - Add SummaryDatasetCollectionMatcher. Use summary data pulled from the database for collections when possible instead of loading potentially hundreds of thousands of individual datasets. Commit: 740c4c93445d5833038e74ccb39413752eeeeb8c https://github.com/galaxyproject/galaxy/commit/740c4c93445d5833038e74ccb3941... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- ToolBuildOptimize - do not fetch hidden datasets for inclusion. Only fetch visible datasets into big, cached list of history datasets under consideration. Hidden datasets don't seem to be used by the fetcher or initial value stuff so it seems fine to exclude them. The advantage should be clear for histories with a large number of datasets hidden below a signficantly smaller number collections. Commit: afe938fe04f1b70d77a357afd03df8252a375770 https://github.com/galaxyproject/galaxy/commit/afe938fe04f1b70d77a357afd03df... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- ToolBuildOptimize - fetch fewer collections, prefetch more of HDCA. Low hanging fruit is to exclude hidden collections, that probably won't buy much for typical uses. This eliminates one extra tag query per dataset collection that appears in the rendered result, this probably buys us a bit more than the hidden collection thing but is still probably a good choice (unless there collections with a large number of tags :(...). This also eliminates the extra fetch of the first, outer-est collection associated the history dataset collection - not its elements just the collection. This saves a number of queries roughly equal to the number of HDCAs in the history and unlike the tag thing there is no downside really here - there will always be one collection. Before and after profiling of a tool form build: https://gist.github.com/jmchilton/d68565662f7f4b7ee2640f09fbb92962 Commit: cbaff1dca2e34cd869227844a04a761332a7eb27 https://github.com/galaxyproject/galaxy/commit/cbaff1dca2e34cd869227844a04a7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Correct uWSGI UNIX domain socket syntax. Commit: e3331817283bdffa4a6fbf65627f44a1faf61239 https://github.com/galaxyproject/galaxy/commit/e3331817283bdffa4a6fbf65627f4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #5991 from jmchilton/rule_fixes_2 [18.05] Small Rule Builder Fixes Commit: 9da13d2d3d3a444e9cd45880496c883b30b475b0 https://github.com/galaxyproject/galaxy/commit/9da13d2d3d3a444e9cd45880496c8... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5990 from jmchilton/collection_count_fix [18.01] Fix collection element count getting lost during collection copies. Commit: 26ab5388ba31de646d365fbc8528a86b7dc7949a https://github.com/galaxyproject/galaxy/commit/26ab5388ba31de646d365fbc8528a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #5930 from natefoo/gie-late-ports [18.01] Only try to determine GIE container ports once at launch, then hand off to readiness check Commit: bd63c04c2e1988e838a033830f60e1ad6c2d9bf7 https://github.com/galaxyproject/galaxy/commit/bd63c04c2e1988e838a033830f60e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into release_18.05 Commit: 352ba5f634ff5469039afa4cb6ec5b6fecabe6c6 https://github.com/galaxyproject/galaxy/commit/352ba5f634ff5469039afa4cb6ec5... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- show tooltip only on hover for upload button Commit: 5265e93be9fc2cf8c65400d8c1853169377868a9 https://github.com/galaxyproject/galaxy/commit/5265e93be9fc2cf8c65400d8c1853... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js Log Message: ----------- move some tooltips to the top so they don't interfere with other actions when shown Commit: 20e9e0a018967e413380728275b843615ba0c6f4 https://github.com/galaxyproject/galaxy/commit/20e9e0a018967e413380728275b84... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Format 'logged in as' correctly for the toolshed Commit: 103cb51ec368438642504c3f98b76c363db478bb https://github.com/galaxyproject/galaxy/commit/103cb51ec368438642504c3f98b76... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #6003 from natefoo/uwsgi-socket-docs [18.01] Correct uWSGI UNIX domain socket syntax in docs Commit: bf0543743ff832375e1b7128bdaa4fc5b0714038 https://github.com/galaxyproject/galaxy/commit/bf0543743ff832375e1b7128bdaa4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- Merge remote-tracking branch 'martenson/tooltip-ux' into release_18.05 Commit: 3a45c1617a0f2b24c6cea344a30aab51c36947ce https://github.com/galaxyproject/galaxy/commit/3a45c1617a0f2b24c6cea344a30aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/yarn.lock Log Message: ----------- Client build/format on merge to 18.05 Commit: 4a7bc238a6ed80d3e2791bd567e5f2c0e8edb3a8 https://github.com/galaxyproject/galaxy/commit/4a7bc238a6ed80d3e2791bd567e5f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #5979 from dannon/fix_toolshed_nav Fix toolshed nav for BS4 Commit: 916078beb0b5936644e666dc91b6c99e8f6aab35 https://github.com/galaxyproject/galaxy/commit/916078beb0b5936644e666dc91b6c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 0c9fd0e6de6d884dc5324288d74bdf049bc57e3d https://github.com/galaxyproject/galaxy/commit/0c9fd0e6de6d884dc5324288d74bd... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.05_new_viz.png A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Release notes for 18.05. Commit: fc4bcc0a7e9fc7b01c4a4a069118077d01c236c5 https://github.com/galaxyproject/galaxy/commit/fc4bcc0a7e9fc7b01c4a4a0691180... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Handle Slurm 17.11's OUT_OF_MEMORY job state. Commit: 717e1104c1e32f79b84de6ffbc481b105087f17f https://github.com/galaxyproject/galaxy/commit/717e1104c1e32f79b84de6ffbc481... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- enable testing for more BAM types Commit: abf23cdc0bb22542577e5ddefac38242c9ddf8ee https://github.com/galaxyproject/galaxy/commit/abf23cdc0bb22542577e5ddefac38... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #6010 from bgruening/test_bam_subtypes [18.01] enable testing for more BAM types Commit: 276858e38e8126332c0952b581c09a2034b6a8d8 https://github.com/galaxyproject/galaxy/commit/276858e38e8126332c0952b581c09... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst Log Message: ----------- Fixes to the 18.05 release thanks to @nsoranzo's review. Commit: f3e49fb1e16ea063bd64de9f59914bf1ba2ada5c https://github.com/galaxyproject/galaxy/commit/f3e49fb1e16ea063bd64de9f59914... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- One more typo Commit: fbc7d49de1b71e7a1a0e544a9c18c5651dad9dd8 https://github.com/galaxyproject/galaxy/commit/fbc7d49de1b71e7a1a0e544a9c18c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Fix for data collection parameters in tool state optimization branch. Commit: 3ee40bfe53088b57da6b3a44efd5ac835ec6f1e7 https://github.com/galaxyproject/galaxy/commit/3ee40bfe53088b57da6b3a44efd5a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #5989 from natefoo/cgroup-metric-fixes [18.05] Fixes for the Cgroup metric plugin Commit: fdfe79f67edd3af8967f916badffcd13aadb78d6 https://github.com/galaxyproject/galaxy/commit/fdfe79f67edd3af8967f916badffc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix library to list of pairs collection builder. Commit: aad435e2655c252934b9f98a8c6962f9038c56ac https://github.com/galaxyproject/galaxy/commit/aad435e2655c252934b9f98a8c696... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- rename the style for the renamed class Commit: f50fe5d455594996ba4eb900e0adbf1face67de3 https://github.com/galaxyproject/galaxy/commit/f50fe5d455594996ba4eb900e0adb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Rebuild client. Commit: b477329842e7209b2fa2b9389e48b0606b7d8824 https://github.com/galaxyproject/galaxy/commit/b477329842e7209b2fa2b9389e48b... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6015 from jmchilton/fix_library_paired [18.01] Fix library to list of pairs collection builder. Commit: 790ec387d7e3bebec66dd19aaa38e16e2d2266c4 https://github.com/galaxyproject/galaxy/commit/790ec387d7e3bebec66dd19aaa38e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Commit: aebc0da8914f5a2dc3fdc7c68805b174d058f56e https://github.com/galaxyproject/galaxy/commit/aebc0da8914f5a2dc3fdc7c68805b... Author: Dannon <dannon.baker@gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6020 from natefoo/lastz-1.3 [18.01] lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Commit: 6872325d80c26ca352ee3d68b4727cf59299d239 https://github.com/galaxyproject/galaxy/commit/6872325d80c26ca352ee3d68b4727... Author: E Rasche <hxr@hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Remove user IDs from job names Commit: 7f0df84ff70a8062a8f12c23e60d21ab80ff77ac https://github.com/galaxyproject/galaxy/commit/7f0df84ff70a8062a8f12c23e60d2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6019 from martenson/fix-paginationstyle [18.05] Fix grid pagination style Commit: fad0392166b6ff24cae0767e9fa6f9c25e28c10f https://github.com/galaxyproject/galaxy/commit/fad0392166b6ff24cae0767e9fa6f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Disable broken tests. Commit: 4043e1020c765759ade1a762ec98751b1d263e95 https://github.com/galaxyproject/galaxy/commit/4043e1020c765759ade1a762ec987... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #6024 from jmchilton/release_18.05_broken_tests [18.05] Disable broken tests workflow annotation tests. Commit: 20c3d09d85bb29d7a1ff299abc7c93dbc6c6b772 https://github.com/galaxyproject/galaxy/commit/20c3d09d85bb29d7a1ff299abc7c9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh to respect args after --. Bug fix because we are clearly parsing it above and then ignoring the arguments afterward anyway. This will allow me to divide up the Selenium tests without any changes using Jenkins' configuration matrix plugin I think. Commit: ebc8c7ef50779f89001597331df862611aad45da https://github.com/galaxyproject/galaxy/commit/ebc8c7ef50779f89001597331df86... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M templates/webapps/tool_shed/user/manage_email_alerts.mako Log Message: ----------- ads missing method import Commit: 40d0d997d38ea6832c83a78c880db0af5c23a90a https://github.com/galaxyproject/galaxy/commit/40d0d997d38ea6832c83a78c880db... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- revert the erroneous rewrite to call security TS security does not have this method introduced in https://github.com/galaxyproject/galaxy/pull/5238 Commit: 8842e8d4512782db9c941098d091d1d8827eb868 https://github.com/galaxyproject/galaxy/commit/8842e8d4512782db9c941098d091d... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6025 from jmchilton/release_18.05_broken_tests [18.05] Fix run_tests.sh to respect args after --. Commit: 23762f48a3385ffbf08112eb95739672a4656db7 https://github.com/galaxyproject/galaxy/commit/23762f48a3385ffbf08112eb95739... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Docker fixes - release 18.05 edition. - Rev to new container with 18.05 dependencies pre-installed. - Enable caching of Yarn stuffs to enable - Redo fix for git not working in node container - was mounting /etc/passwd but that wasn't compat. with Mac OS X, setting these environment variables are. - Rearrange startup script a bit to make it load faster (wait for Selenium right before the tests not before waiting for DB). - Fix random error in logs related to Selenium trying to read something in /root by passing -H to set the Selenium user's home directory. Commit: 92a4a138621eeb761bebf2d3c29781450ce2c4b6 https://github.com/galaxyproject/galaxy/commit/92a4a138621eeb761bebf2d3c2978... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/tool_shed/util/admin_util.py M templates/webapps/tool_shed/user/manage_email_alerts.mako Log Message: ----------- Merge pull request #6026 from martenson/ts-fixes [18.05] fix missing import and removed method in TS Commit: b35340c77f262309d225cf2a9e526ac7e67194cc https://github.com/galaxyproject/galaxy/commit/b35340c77f262309d225cf2a9e526... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge pull request #5997 from jmchilton/1801_tool_state_opt [18.01] Fix tool state performance for large collections. Commit: 808686cd6050fbc93b5b41185dd713993d8651d0 https://github.com/galaxyproject/galaxy/commit/808686cd6050fbc93b5b41185dd71... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 3e4e28543d06081e9e8b77b11ae458b663678fec https://github.com/galaxyproject/galaxy/commit/3e4e28543d06081e9e8b77b11ae45... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Call superclass __init__ in DockerService Commit: 6984d5f4a2c2c20f61cbac19aa6244826c47c8d8 https://github.com/galaxyproject/galaxy/commit/6984d5f4a2c2c20f61cbac19aa624... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Don't raise an exception if a Docker service doesn't have an environment and its env property is accessed Commit: 0e13690b729d1f9776dc0bbe20c53d2af0aa7e6d https://github.com/galaxyproject/galaxy/commit/0e13690b729d1f9776dc0bbe20c53... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/containers/__init__.py Log Message: ----------- Don't attempt to iterate None in container's map_ports method. Commit: e62fd46644a21bc65d7001b9a0aa064997417348 https://github.com/galaxyproject/galaxy/commit/e62fd46644a21bc65d7001b9a0aa0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py Log Message: ----------- Merge pull request #6037 from natefoo/containers-bugfix [18.05] Fix a few more bugs with the containers interface Commit: b67ecd42097558a6fac347a163b3acf9d6fe121f https://github.com/galaxyproject/galaxy/commit/b67ecd42097558a6fac347a163b3a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix merge from 18.01. Commit: b84de1e82b36ae94be33ca4bf6e85e4c3ed748d2 https://github.com/galaxyproject/galaxy/commit/b84de1e82b36ae94be33ca4bf6e85... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Remove on-focus tooltips from rule builder. Commit: cacbcdf6755a1e930439d93021b08d27ff12318d https://github.com/galaxyproject/galaxy/commit/cacbcdf6755a1e930439d93021b08... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6039 from jmchilton/fix_1801_merge [18.05] Fix merge from 18.01. Commit: db8d7e65fedab9795cf41ef6b498358180c727dc https://github.com/galaxyproject/galaxy/commit/db8d7e65fedab9795cf41ef6b4983... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix #6038. Commit: cb38b2495d9e42ee3e0e8acc13fc60214334c75f https://github.com/galaxyproject/galaxy/commit/cb38b2495d9e42ee3e0e8acc13fc6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6040 from jmchilton/remove_focus_tooltip [18.05] Two more rule builder fixes. Commit: b8e5893b0d4efee3d2b256bf08b95906a2fd370e https://github.com/galaxyproject/galaxy/commit/b8e5893b0d4efee3d2b256bf08b95... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix for building doubly nested collections. The late addition of validation code added for identifier uniqueness checking broke this I think. Commit: 618de018b9507a58945c318a4ac49447ff30023b https://github.com/galaxyproject/galaxy/commit/618de018b9507a58945c318a4ac49... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #6029 from jmchilton/release_18.05_broken_tests [18.05] Docker fixes - release 18.05 edition. Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: e11da5fba90d3ce4823481334888a602e229b588 https://github.com/galaxyproject/galaxy/commit/e11da5fba90d3ce4823481334888a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Fix jqplot: boxplot, histogram Fix heatmap clustering Fix nvd3 tool based types Remove global d3 object from heatmap and jqplot Commit: a8fe9a73942fd09a5e65ee51d7407952b362f6d4 https://github.com/galaxyproject/galaxy/commit/a8fe9a73942fd09a5e65ee51d7407... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- The link for specific individual history view has changed, but wasn't updated here in the error report. Commit: 6a2c678dcedf426319b77a24f686807ceff0b603 https://github.com/galaxyproject/galaxy/commit/6a2c678dcedf426319b77a24f6868... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Bump bootstrap from 4.1.0 to 4.1.1 -- has a few bugfixes and hides the chatty and irrelevant (for us) deprecation warning on client build. Commit: ba6c3e6c625c8f2f024408541ad2196efdd5b1e4 https://github.com/galaxyproject/galaxy/commit/ba6c3e6c625c8f2f024408541ad21... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Merge pull request #6047 from guerler/fix_charts [18.05] Fix and repack chart tool-based visualizations Commit: 666fec9f7b005676b1dd14e4a01a9a3df3861968 https://github.com/galaxyproject/galaxy/commit/666fec9f7b005676b1dd14e4a01a9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Merge pull request #6052 from dannon/bs4_411 [18.05] Bump bootstrap from 4.1.0 to 4.1.1 Commit: 3829b0727d4ef05bdc1680f38babac7ac152350d https://github.com/galaxyproject/galaxy/commit/3829b0727d4ef05bdc1680f38baba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M templates/display_common.mako Log Message: ----------- Fix one more use of histories/view Commit: 8b733df8953431f16b2bd12e4cdd49090115e082 https://github.com/galaxyproject/galaxy/commit/8b733df8953431f16b2bd12e4cdd4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/tools/errors.py M templates/display_common.mako Log Message: ----------- Merge pull request #6051 from dannon/fix_tool_error_report [18.05] Fix tool error report history view link Commit: 3292445872d9333753728828528947dc802a30be https://github.com/galaxyproject/galaxy/commit/3292445872d933375372882852894... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6045 from jmchilton/remove_focus_tooltip [18.05] Fix for building doubly nested collections. Commit: eb29adc2efd8bad0f15dc6a51b2a3cd33216b8f9 https://github.com/galaxyproject/galaxy/commit/eb29adc2efd8bad0f15dc6a51b2a3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Downgrade python-genomespaceclient to 0.2 Commit: f371d3f7094086ae183b3abc9cb3dc38ff361886 https://github.com/galaxyproject/galaxy/commit/f371d3f7094086ae183b3abc9cb3d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix paired identifier casting issue. Commit: 3b5d8ae99c5d6d8f040d6554320bb50e41fa58a4 https://github.com/galaxyproject/galaxy/commit/3b5d8ae99c5d6d8f040d6554320bb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix x in column definition screen to eliminate correct def. Commit: 5bd2cbd80b35cc5ddddce808f17c13ce1381bc36 https://github.com/galaxyproject/galaxy/commit/5bd2cbd80b35cc5ddddce808f17c1... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Alter `extra_data` column on an oidc-related table from TXT to JSON. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850d... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Commit: 1b41cbba59bb09bdac305ff9de8d64dc4f873ee9 https://github.com/galaxyproject/galaxy/commit/1b41cbba59bb09bdac305ff9de8d6... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Merge pull request #6057 from VJalili/alter_extra_data [18.05] Alter the type of extra_data column of OIDC table. Commit: 96dcf54c438809c988eb063cf079bc7dbf4a5fe0 https://github.com/galaxyproject/galaxy/commit/96dcf54c438809c988eb063cf079b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix quota styling for new anchor/link. Commit: 6bb5fa02fc20fdfbb69085a5a0bfe57dfc7ef93a https://github.com/galaxyproject/galaxy/commit/6bb5fa02fc20fdfbb69085a5a0bfe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Use standard styling for quotameter; this fixes danger/warning/success indicators and visibility. Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aae... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: 89c12d6da2c797dbe2803768ad27657ac9a8e999 https://github.com/galaxyproject/galaxy/commit/89c12d6da2c797dbe2803768ad276... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- More standard quota-meter-text color Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6f... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Commit: 011e76a72647a48a3415a36bd19c17e2688175df https://github.com/galaxyproject/galaxy/commit/011e76a72647a48a3415a36bd19c1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6056 from jmchilton/rule_Builder_fixes_2 [18.05] Yet more rule builder fixes. Commit: b7c8fbe7c20c8c02cef182d7843a21d15346c1f1 https://github.com/galaxyproject/galaxy/commit/b7c8fbe7c20c8c02cef182d7843a2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Tinker with brand-succcess, address the brightness concern (which makes many locations look better, at least to me) Commit: 19d06cb971c23444065df718260ac307293c8926 https://github.com/galaxyproject/galaxy/commit/19d06cb971c23444065df718260ac... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: d729c31ffd6e7198e5970eaeda2bcf3a65c20ba6 https://github.com/galaxyproject/galaxy/commit/d729c31ffd6e7198e5970eaeda2bc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 23b0169a17f3a4b1b705ee0dc0afe613e1cc29cd https://github.com/galaxyproject/galaxy/commit/23b0169a17f3a4b1b705ee0dc0afe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix non-capped usage display as well. Commit: 2a9e44e7a217f0ec3d48dd10811b23bd8da86c44 https://github.com/galaxyproject/galaxy/commit/2a9e44e7a217f0ec3d48dd10811b2... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #6065 from jmchilton/rule_fixes_4 [18.05] Rules - bug fix for apply_rules tool on nested collections. Commit: 7c44139dc82e6cf1486b23593c811e0f653af932 https://github.com/galaxyproject/galaxy/commit/7c44139dc82e6cf1486b23593c811... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6062 from dannon/fix_quotameter_styling Fix quotameter styling Commit: ca48d49ea87b0716d27e8968c677b252c83b5ae9 https://github.com/galaxyproject/galaxy/commit/ca48d49ea87b0716d27e8968c677b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Style fix for published grid pages Commit: 8aaee18cae21f645170e14a32db0fc0f172cfd01 https://github.com/galaxyproject/galaxy/commit/8aaee18cae21f645170e14a32db0f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Merge pull request #6067 from guerler/bootstrap_shared_grid Style fix for published grid pages Commit: 400bcf1b04adf6afb8e83efc6379e527c93fa810 https://github.com/galaxyproject/galaxy/commit/400bcf1b04adf6afb8e83efc6379e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-06 (Sun, 06 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #6064 from jmchilton/rule_fixes_3 [18.05] Rules - test case & bug fixes for adding cols from regex groups. Commit: 8255d1ccc819c88c7d5ee197bbb5ed9d49759fc4 https://github.com/galaxyproject/galaxy/commit/8255d1ccc819c88c7d5ee197bbb5e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #5613 from erasche/fix-fraking-grt [18.01] File sizes not being annotated in GRT Commit: 830561a7bcd18a2aa80b8c0d5e1dc359ea9744ed https://github.com/galaxyproject/galaxy/commit/830561a7bcd18a2aa80b8c0d5e1dc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Fix nested collection element downloads in UI. Fixes #6035. Commit: 765a834497ebfc555ac0de98cbbae9ad395f1c49 https://github.com/galaxyproject/galaxy/commit/765a834497ebfc555ac0de98cbbae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Memory statement and cd both before instrument_pre_commands Commit: 0cfac515b546334e810caecf5cd02de8298de30a https://github.com/galaxyproject/galaxy/commit/0cfac515b546334e810caecf5cd02... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 0031eb59beb0c04e602353824e61d0aa735f573b https://github.com/galaxyproject/galaxy/commit/0031eb59beb0c04e602353824e61d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: 7d4109bac1588cd67cc06b093b1fc18b509a69c9 https://github.com/galaxyproject/galaxy/commit/7d4109bac1588cd67cc06b093b1fc... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge pull request #6073 from jmchilton/fix6035 [18.05] Fix nested collection element downloads in UI. Commit: 483e879ca6fee1e58b6f9c99bf07291064ad5065 https://github.com/galaxyproject/galaxy/commit/483e879ca6fee1e58b6f9c99bf072... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix dropdown zindex handling for history panels Commit: 7cc01380afd017c5cac2af2b2d735b2265774a68 https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d735... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Update bs4 style dropdowns, minor cleanup Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 7b558ddc5965f6223c862680341e81b345c73d82 https://github.com/galaxyproject/galaxy/commit/7b558ddc5965f6223c862680341e8... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6079 from dannon/dropdown-zindex-fix [18.05] Dropdown zindex fix Commit: e55cf0114f6f230a1b7935a73336546efd9b57b2 https://github.com/galaxyproject/galaxy/commit/e55cf0114f6f230a1b7935a733365... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- reword text feedback on viz job submission Commit: de5ed28120fdd35495c837148c48526aec7a45d8 https://github.com/galaxyproject/galaxy/commit/de5ed28120fdd35495c837148c485... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Merge pull request #6090 from martenson/text-adjustment reword text feedback on viz job submission Commit: 098f638d26355abe54c83bd43b8daf1078e1ccd3 https://github.com/galaxyproject/galaxy/commit/098f638d26355abe54c83bd43b8da... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5925 from erasche/cd-before-metrics [18.01] jobscript - check memory later Commit: c4a909a66e86f2a60fa4c2b637e817a82143e2b5 https://github.com/galaxyproject/galaxy/commit/c4a909a66e86f2a60fa4c2b637e81... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Simplify config_form logic for editor's to_dict Commit: 1083fa4ddb611300892516d1947dfd975e60978e https://github.com/galaxyproject/galaxy/commit/1083fa4ddb611300892516d1947df... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- [18.05] Fix sniff validation for dynamic compressed types. This was broken in a bad PR merge/rebase process since the validation mode didn't exist when the initial dynamic compressed types PR was opened. Commit: fba70530abf4470e98fc6f1d56d770f33092530b https://github.com/galaxyproject/galaxy/commit/fba70530abf4470e98fc6f1d56d77... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #6091 from jmchilton/sniff_prefix_fixes [18.05] Fix sniff validation for dynamic compressed types. Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a58... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e6... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Commit: a7e7ac723ff7379cf201be9b99acae95ebb8851d https://github.com/galaxyproject/galaxy/commit/a7e7ac723ff7379cf201be9b99aca... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Escape tool names in the onclick event handlers for the workflow editor's toolbox. Commit: 1f608a67de540e657d418ed2abf050c605f5fba1 https://github.com/galaxyproject/galaxy/commit/1f608a67de540e657d418ed2abf05... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6099 from dannon/workflow_editor_escape [18.05] Escape tool names in the onclick event handlers for the workflow edit… Commit: eae69c26f89aa6b809a3186131f59b32d590bb9e https://github.com/galaxyproject/galaxy/commit/eae69c26f89aa6b809a3186131f59... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M run_tests.sh Log Message: ----------- [18.05] Fix parsing last argument when running functional tests. Causes Planemo to double test tools. Commit: 07a34f8c5759fa9d609cd008524aaef473259762 https://github.com/galaxyproject/galaxy/commit/07a34f8c5759fa9d609cd008524aa... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Add file missing file required for converting bz2 compressed files. Should have been included with #5794. Commit: 993f5f52db08e1851ee9c7e6dd64f3c5e50ee957 https://github.com/galaxyproject/galaxy/commit/993f5f52db08e1851ee9c7e6dd64f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix DynamicOptions.get_options() when loc file is missing Fix https://github.com/galaxyproject/galaxy/issues/2987 Commit: 208d1de2e13b84f6a9551cd7ca08b859a16be57e https://github.com/galaxyproject/galaxy/commit/208d1de2e13b84f6a9551cd7ca08b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Set the level for SLOREQs to 'warning' Commit: 88202fbc575888285a0ea847fa94baef2595551e https://github.com/galaxyproject/galaxy/commit/88202fbc575888285a0ea847fa94b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow speficying columns by name for attribute_value_splitter filter Commit: 9ef3449f174ab6128af3bab8bcde75b4cecdcca8 https://github.com/galaxyproject/galaxy/commit/9ef3449f174ab6128af3bab8bcde7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #6102 from dannon/sentry_add_type_tag [18.05] Set the level for SLOREQs to 'warning' Commit: 63abfd657a38355357b476c044afa05d7d07b594 https://github.com/galaxyproject/galaxy/commit/63abfd657a38355357b476c044afa... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Merge pull request #6101 from jmchilton/more_conversion_fixes [18.05] Add file missing file required for converting bz2 compressed files. Commit: ea22750604bb2b14a437eddc6ab34dd9d4d9fba7 https://github.com/galaxyproject/galaxy/commit/ea22750604bb2b14a437eddc6ab34... Author: Ann Loraine <aloraine@uncc.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Change BioViz URL to http://bioviz.org/galaxy.html from http://bioviz.org/igb/galaxy.html Commit: ef7d90a3dec1c0e517a196999d892b34af6896d1 https://github.com/galaxyproject/galaxy/commit/ef7d90a3dec1c0e517a196999d892... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: fa4d7b49a786e36f85033e953da4c8604f089ec4 https://github.com/galaxyproject/galaxy/commit/fa4d7b49a786e36f85033e953da4c... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6075 from dannon/workflow_building_mode [18.05] Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: 9bc73824a5419072b65158a09c0f6c30a9c5b3f0 https://github.com/galaxyproject/galaxy/commit/9bc73824a5419072b65158a09c0f6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- [18.05] Fix matches_any() checks for dynamic compressed types. See huge conversation on #6093. Commit: ba1f369e2f1c124ffacd60b329364d79d63ed513 https://github.com/galaxyproject/galaxy/commit/ba1f369e2f1c124ffacd60b329364... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Encode dataset ids when loading trackster visualizations Commit: b7f26be45fd0fa13876cfdfdd37c460b9947474b https://github.com/galaxyproject/galaxy/commit/b7f26be45fd0fa13876cfdfdd37c4... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6095 from jmchilton/fix_double_test [18.05] Fix parsing last argument when running functional tests. Commit: ffe7981cc2f902fafa1dc3c8d3203ec3a2f8b4df https://github.com/galaxyproject/galaxy/commit/ffe7981cc2f902fafa1dc3c8d3203... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- broken access Commit: fbbbb472977094fb89be1cbde818cdee0e5961a9 https://github.com/galaxyproject/galaxy/commit/fbbbb472977094fb89be1cbde818c... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- override expose_user_{name,email} Commit: 8992620ee19e4b6dbd58dfa411eecfba306613bf https://github.com/galaxyproject/galaxy/commit/8992620ee19e4b6dbd58dfa411eec... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- hash email/username Commit: 92e4ef8d93375c5283d92bab0587339237be2436 https://github.com/galaxyproject/galaxy/commit/92e4ef8d93375c5283d92bab05873... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix job running Commit: da1a6085ac10681a2f983245c52f96563a742efc https://github.com/galaxyproject/galaxy/commit/da1a6085ac10681a2f983245c52f9... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Also wipe out roles Commit: b4bd972b71ca5a535f07942c1e16ac96962a3298 https://github.com/galaxyproject/galaxy/commit/b4bd972b71ca5a535f07942c1e16a... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- update documentation Commit: b6a22584aaed8df8ea3ffc1d1db96c65fe887878 https://github.com/galaxyproject/galaxy/commit/b6a22584aaed8df8ea3ffc1d1db96... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6112 from guerler/fix_hda_access [18.05] Encode dataset ids when loading trackster visualizations Commit: 82e5d7d50c00ee13640c24e832d3a733a463abff https://github.com/galaxyproject/galaxy/commit/82e5d7d50c00ee13640c24e832d3a... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- add custom logger Commit: 3cfe8040b6f239a53bf1e048104c7d9af7958149 https://github.com/galaxyproject/galaxy/commit/3cfe8040b6f239a53bf1e048104c7... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- allow tests to pass Commit: 148d56a9c9d12df6d3d8fbe48a713f75cca6a468 https://github.com/galaxyproject/galaxy/commit/148d56a9c9d12df6d3d8fbe48a713... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Many more matches_any tests, better categorization of them with comments. Some of these suggested by @nsoranzo. Commit: 590fb5c48bf340837eb5e70fb3f608382f9f8ebf https://github.com/galaxyproject/galaxy/commit/590fb5c48bf340837eb5e70fb3f60... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/localdb.py Log Message: ----------- remove print Commit: 8ca8ead4e592beb73ab92fa1324ee2060beb9188 https://github.com/galaxyproject/galaxy/commit/8ca8ead4e592beb73ab92fa1324ee... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge pull request #6111 from jmchilton/dynamic_compressed_types_fix_4 [18.05] Fix matches_any() checks for dynamic compressed types. Commit: f52028f40093af71632e530c79a83bd7148944ed https://github.com/galaxyproject/galaxy/commit/f52028f40093af71632e530c79a83... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Fixes at least 4 more bugs related to sniffing of compressed datatypes. - Incorrect parsing of default auto sniff flag value. - Not respecting flag value when adding to dict of compressed sniffers. - Not checking the right value when checking for compressed datatype instances to add to sniff order. - Not filtering out the sniffers from being automatically added during the default stage of sniffer handling where all types with sniff are added at the end. This last point is the most complicated. I added a hack with #6091 so that the compressed sniffers would only return True if in validation mode or explicitly enabled. I'm not convinced that approached worked and I'm definitely convinced it was a bad approach. The better, cleaner approach is to just always let the sniffer return its truth regardless of validation mode or not and instead only add it to the list of sniffers if it should be enabled. This is what I was assuming would happen but I found this method append_to_sniff_order that was adding sniffers back in that I didn't want added. Commit: 8a58711e391de36b62fc20dc4db5f8ccd55f786d https://github.com/galaxyproject/galaxy/commit/8a58711e391de36b62fc20dc4db5f... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/data.py M tools/data_source/upload.py Log Message: ----------- Remove validate_mode prop for sniffing, no longer needed with previous fixes. This does undo an attempt that Nate made to auto sniff fastq.gz files when they can't be converted anyway, but that was kind of broken in its own way.

...

From Gitter:

jmchilton: natefoo "# Link mode can't decompress anyway, so enable sniffing for keep-compressed datatypes even when auto_decompress is enabled" Did you test this hack? I get the thought process but it seems like it results in uploaded fastq.gz files defaulting to fastqcssanger.gz? Maybe it didn't at some point though? Nate Coraor: ummmmmmmmmmmm maybe probably not John Chilton: I have four fixes for compressed datatypes that all fall apart because of this hack... can I just use the configured sniff order or do you want me to try to preserve this and write a test case Nate Coraor: nah go ahead and de-hack John Chilton: There is a good argument to be made for making the behavior more consistent anyway right? Cool thanks Commit: 2d103a09bce34ac64a5decdff316a92f9223c54c https://github.com/galaxyproject/galaxy/commit/2d103a09bce34ac64a5decdff316a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix sniff_compressed_dynamic_datatypes_default config option not propagating to upload tool. Resolving the default when unspecified in the XML before writing out datatype confs fixes this. This makes this option always explicit in the datatypes conf that is shared with the upload tool. Commit: efc97a440096372d01427942cb19ac82a0d23dd3 https://github.com/galaxyproject/galaxy/commit/efc97a440096372d01427942cb19a... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6054 from natefoo/genomespaceclient-downgrade [18.05] Downgrade python-genomespaceclient to 0.2 Commit: 5d048486ac56e500abad5c46032dc962097bd9d5 https://github.com/galaxyproject/galaxy/commit/5d048486ac56e500abad5c46032dc... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Rework into separate permissions per @jmchilton suggestion Commit: e25b086dc13e023b139e8844347051f8c1eb1ce3 https://github.com/galaxyproject/galaxy/commit/e25b086dc13e023b139e884434705... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #6103 from nsoranzo/release_17.09_fix_2987 [17.09] Fix DynamicOptions.get_options() when loc file is missing Commit: 4dedc900b56573a5bc0443daca096afa66da072b https://github.com/galaxyproject/galaxy/commit/4dedc900b56573a5bc0443daca096... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Showed up in esntry as referencing fname before assignment Commit: 890b446974b03daa098130392ee538a1320daa16 https://github.com/galaxyproject/galaxy/commit/890b446974b03daa098130392ee53... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #6119 from erasche/error-temp-lib-dl [18.01] Showed up in sentry as referencing fname before assignment Commit: e26691244fc28d15f7ddd8e8913508fba3786b1c https://github.com/galaxyproject/galaxy/commit/e26691244fc28d15f7ddd8e891350... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 67257da24b484f093c6cdba68d4e0d0c358ac571 https://github.com/galaxyproject/galaxy/commit/67257da24b484f093c6cdba68d4e0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fixes for compressed datatype fixes thanks to @nsoranzo. Commit: 3137d84ad7d7901dd4c65f56b7a8cefba5c467c7 https://github.com/galaxyproject/galaxy/commit/3137d84ad7d7901dd4c65f56b7a8c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: f1eaaea24e67d96c7c45913beac8622cfa0afdc8 https://github.com/galaxyproject/galaxy/commit/f1eaaea24e67d96c7c45913beac86... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 7b4b2a0f77f35cefc691782b51a9a12dec0da5be https://github.com/galaxyproject/galaxy/commit/7b4b2a0f77f35cefc691782b51a9a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix for lack of feedback on rule builder job failures. Present users with the job standard error and also check for binary sniffing problems and report them with a pretty message suggesting specifying a file type. Commit: 3a4cc360a4d5e68571f6498b3345b4741add5ab3 https://github.com/galaxyproject/galaxy/commit/3a4cc360a4d5e68571f6498b3345b... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- fix upload status colors to work with bs4 Commit: f06adba766a987aa8ac59ed99d537008e76a4913 https://github.com/galaxyproject/galaxy/commit/f06adba766a987aa8ac59ed99d537... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M test/unit/datatypes/test_datatypes_registry.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6115 from jmchilton/dynamic_compressed_types_fix_5 [18.05] More compressed datatype sniffing fixes. Commit: 80e0ffccb24be54edbfef9e6b2c2d00ae24f6141 https://github.com/galaxyproject/galaxy/commit/80e0ffccb24be54edbfef9e6b2c2d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- add mock config to fix unittests; fix lint Commit: 7681a4d33e035e9cc8b918211e2961b42c621cf1 https://github.com/galaxyproject/galaxy/commit/7681a4d33e035e9cc8b918211e296... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- replace forgotten older config option Commit: a4f99c8cc9514765a68e2c9296c813e7b9f23674 https://github.com/galaxyproject/galaxy/commit/a4f99c8cc9514765a68e2c9296c81... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6121 from jmchilton/rule_builder_error_better [18.05] Fix for lack of feedback on rule builder job failures. Commit: 4c92aca576c24b96fa0adeb7903283ed44b4012a https://github.com/galaxyproject/galaxy/commit/4c92aca576c24b96fa0adeb790328... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE volume usage Commit: c76e21c030958d7bafd95cc6d13257350bc9acf6 https://github.com/galaxyproject/galaxy/commit/c76e21c030958d7bafd95cc6d1325... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Consistency in container_path : host_path Commit: 35b96475a16b48242a674a6de45d5ef3959deae8 https://github.com/galaxyproject/galaxy/commit/35b96475a16b48242a674a6de45d5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Missing upload tests. Lots of upload and datatype behavior changes conflicting in 18.05 - these tests would have helped a lot. Commit: e2d516be2a0580277f5e8aeaa8d55558640abb92 https://github.com/galaxyproject/galaxy/commit/e2d516be2a0580277f5e8aeaa8d55... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6128 from dannon/fix_cli_gies [18.05] Fix GIE volume wrangling Commit: 616c1b971a01d7a7cf2967e1fea225c4466d13eb https://github.com/galaxyproject/galaxy/commit/616c1b971a01d7a7cf2967e1fea22... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-12 (Sat, 12 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Add a text label length limit for select2's used in the upload dialog Reduce limit to a 100 characters Match encapsulated values in title string Commit: 2a8a793013c0ec46024c64d63349172e04ee059f https://github.com/galaxyproject/galaxy/commit/2a8a793013c0ec46024c64d633491... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Mirror option across all schemas Commit: 3d39e0fad0418edecf0169beff778236bf7e4a84 https://github.com/galaxyproject/galaxy/commit/3d39e0fad0418edecf0169beff778... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- read policy options Commit: ee985e6bbcfe8c3cf3e2fdcdfb8257c999612a86 https://github.com/galaxyproject/galaxy/commit/ee985e6bbcfe8c3cf3e2fdcdfb825... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- Update documentation Commit: 5f99db40d247c6bdac7b33fca3aece80d443986d https://github.com/galaxyproject/galaxy/commit/5f99db40d247c6bdac7b33fca3aec... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6125 from jmchilton/upload_tests_3 [18.05] Fix missing upload tests. Commit: 19c5c7395e2deba983f3e7f80a9cdccaf9a2b8d6 https://github.com/galaxyproject/galaxy/commit/19c5c7395e2deba983f3e7f80a9cd... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #6124 from martenson/fix-upload-colorstate [18.05] fix upload status colors to work with bs4 Commit: 01248c24118e293921ab92550cec32007e19ab2f https://github.com/galaxyproject/galaxy/commit/01248c24118e293921ab92550cec3... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- document a bunch of undocumented options Commit: 6cc20f263491fb570bdbcc29911d278b4e48d2a1 https://github.com/galaxyproject/galaxy/commit/6cc20f263491fb570bdbcc29911d2... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst Log Message: ----------- start writing compliance documentation Commit: a8e75e0f602283e8fc506f332183011758b8de74 https://github.com/galaxyproject/galaxy/commit/a8e75e0f602283e8fc506f3321830... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Need to fail safely unfortunately if we cannot access app Commit: 15ceedfbc059494da18e077336f0264e65e5a7cb https://github.com/galaxyproject/galaxy/commit/15ceedfbc059494da18e077336f02... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Unbreak toolshed user deletion Commit: 157cc410e2b0a2a8ab1476d4ba4b3210afd2e535 https://github.com/galaxyproject/galaxy/commit/157cc410e2b0a2a8ab1476d4ba4b3... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/util/admin_util.py Log Message: ----------- duplicate deletion/redaction logic Commit: 3dbbc56e9689deabd62d71a3db926d697d681891 https://github.com/galaxyproject/galaxy/commit/3dbbc56e9689deabd62d71a3db926... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Redact addresses as well Commit: c122b3f57306399b2f9d993d61e22054ee0586a9 https://github.com/galaxyproject/galaxy/commit/c122b3f57306399b2f9d993d61e22... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- better docs Commit: ff007c4b72c504999fde2cf09f891cb2fdc543d3 https://github.com/galaxyproject/galaxy/commit/ff007c4b72c504999fde2cf09f891... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- rename main variable Commit: 2005c102e629d5dd5082c26facd2282fbfb1015b https://github.com/galaxyproject/galaxy/commit/2005c102e629d5dd5082c26facd22... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- force user_deletion on for GDPR users Commit: 2f351bf3a77e842b5790e5993e4565be998ca3ff https://github.com/galaxyproject/galaxy/commit/2f351bf3a77e842b5790e5993e456... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- rebuild configuratoin Commit: 41e6910df2b101551b4fc8ebc55ed3f1ff0b39b6 https://github.com/galaxyproject/galaxy/commit/41e6910df2b101551b4fc8ebc55ed... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- document more gdpr stuff :( Commit: b381adb5fe6d76950ebc56c0635649a33cfdc819 https://github.com/galaxyproject/galaxy/commit/b381adb5fe6d76950ebc56c063564... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- automatically add to logging config block Commit: 8be2da03b52e819d5e4e4ac76dea983f4f0c2448 https://github.com/galaxyproject/galaxy/commit/8be2da03b52e819d5e4e4ac76dea9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Improve dialog message while waiting for rule builder job. Commit: 788ed8aa43296537c6439d0fea7a5446ffe15da0 https://github.com/galaxyproject/galaxy/commit/788ed8aa43296537c6439d0fea7a5... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve data initialization of rule builder for long term support. A mistake was made in the rush to rule-builder-all-the-stuffs - libraries, hdas, and FTP all initialized a different set of columns from the data (which is probably fine) but with no indication this was happening in the underlying rules (which is definitely not fine). To understand why this was a mistake and see why in the long term this hurts reproducibility, take loading rules for HDAs from the history panel as an example. In the initial implementation it would pre-initialize two columns - one for "hid" and one for "name" - any rules that were generated from there would start with an implicit assumption of two columns. This is a problem because if someone saves some rules and we (Galaxy developers) decide later on that name tag should be in the initial list but HID doesn't make sense and make that change - we basically are breaking all existing rules to support a very logical change in behavior. Likewise, Galaxy produces a hash with last modified date and size for each FTP entry - this is data we have and could stick in the rule builder by default - but if we change that over time existing FTP rules will break. It would be much more sustainable to instead include the initial column generation information in the initial rules generated - so that each of these modalities start in reality with an empty table and the initial set of rules describe what metadata to pull initial columns from. This way if you save a set of rules it will include the initial column choices, and if they are pasted in at some later point where columns are picked differently - the rules will still work because you are replacing the initial column definitions. The initial rules implementation didn't have this concept of loading columns from metadata - but this was added to support loading existing identifiers as part of the "Apply Rules to Existing Collection" tool. This commit extends that idea to do the same thing (but with different columns) when loading data from HDAs, FTP, and data libraries. Commit: c5ab87ee5909e0871fb62fcb2e82cdaecf5f8166 https://github.com/galaxyproject/galaxy/commit/c5ab87ee5909e0871fb62fcb2e82c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Fix repeated additions of the separator, define vars. Commit: 9789aa7d637f8e0a1de558f01ef90a136f7e79a3 https://github.com/galaxyproject/galaxy/commit/9789aa7d637f8e0a1de558f01ef90... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #26 from dannon/max_select2_length Fix a minor bug, a little bit of cleanup. Commit: b0d730fa76cf8392a19cea5fe08a72aab2fccc2a https://github.com/galaxyproject/galaxy/commit/b0d730fa76cf8392a19cea5fe08a7... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #6130 from guerler/max_select2_length [18.05] Limit select2 text label length to 100 characters Commit: effd5f92f245f13faa53ceeb41734124d14a0eb8 https://github.com/galaxyproject/galaxy/commit/effd5f92f245f13faa53ceeb41734... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/functional/tools/job_properties.xml Log Message: ----------- Lint job_properties test tool Commit: 85e5d7fcd3261d3283ff3fa78d0c2b78fe429f4b https://github.com/galaxyproject/galaxy/commit/85e5d7fcd3261d3283ff3fa78d0c2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix required tools to run workflow API tests Commit: efb0f02d345cb9a5d415fa4dd9ac1bf8ca507f5d https://github.com/galaxyproject/galaxy/commit/efb0f02d345cb9a5d415fa4dd9ac1... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Hide replacement datasets when rerunning a failed dataset in a mapped-over collection Commit: e5ea32465a64fed1acfa63b7385272a6f9ccee15 https://github.com/galaxyproject/galaxy/commit/e5ea32465a64fed1acfa63b738527... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- More validation for rule builder. - Require a URL or FTP column for raw pasted data. - Require list identifiers if creating collections. - Require name in more scenerios that require a name. Commit: 5c036bc2647799c70b11b2a4e4ce0fae8d103cdc https://github.com/galaxyproject/galaxy/commit/5c036bc2647799c70b11b2a4e4ce0... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6133 from jmchilton/rule_fixes_7 [18.05] Improve dialog message while waiting for rule builder job. Commit: 1dc47498463f886bdf23fe4cf3db75a69018a480 https://github.com/galaxyproject/galaxy/commit/1dc47498463f886bdf23fe4cf3db7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- iteration of gdpr compliance docs Commit: cba219cc02ce54c0cac77d915a144f91e9b6377f https://github.com/galaxyproject/galaxy/commit/cba219cc02ce54c0cac77d915a144... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix import order Commit: b4de30b5fc6056bd8c9dfb7898332b1264c159e6 https://github.com/galaxyproject/galaxy/commit/b4de30b5fc6056bd8c9dfb7898332... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Small fixes for upload flags (auto_decompress, check_content, space_to_tab). Commit: 076e1ddaecd4f2744346c503b0108d8189f35bd1 https://github.com/galaxyproject/galaxy/commit/076e1ddaecd4f2744346c503b0108... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6136 from jmchilton/rule_fixes_9 [18.05] More validation for rule builder. Commit: 3d6443b58bfa0200cf775b569c542be326476493 https://github.com/galaxyproject/galaxy/commit/3d6443b58bfa0200cf775b569c542... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge pull request #6134 from jmchilton/rule_fixes_8 Improve data initialization of rule builder for long term support. Commit: a310b0a121e19c126b2c5bdaa093b2f2bb056c5a https://github.com/galaxyproject/galaxy/commit/a310b0a121e19c126b2c5bdaa093b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix minor typo in rule builder. Commit: 48de2ecf21d5b68596e308b2a37696eff54e37d0 https://github.com/galaxyproject/galaxy/commit/48de2ecf21d5b68596e308b2a3769... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- client-format Commit: cdbae706e603f57af4a795907ef2cdfc0b058482 https://github.com/galaxyproject/galaxy/commit/cdbae706e603f57af4a795907ef2c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Respect auto_decompress in fetch API, synchronize upload APIs. Commit: 242d5459e13c502527971dc2b21ed1ac4ab119cd https://github.com/galaxyproject/galaxy/commit/242d5459e13c502527971dc2b21ed... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- "Fix" RuleBuilder to auto decompress compressed files. Work arounds just aren't there yet. Commit: 4531d80dbcaf5671fdcb56627f3cc948cd710c4e https://github.com/galaxyproject/galaxy/commit/4531d80dbcaf5671fdcb56627f3cc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When re-running a failed dataset collection element, update JobToOutputDatasetCollectionAssociation to the new job Otherwise, if re-running fails once, then re-running it again successfully will let the other workflow jobs resume, but the collection element is not replaced and the collection remains red. Commit: bf51c8352648b4a56a4a162deee4c37ee8e551db https://github.com/galaxyproject/galaxy/commit/bf51c8352648b4a56a4a162deee4c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6140 from dannon/minor_typo [18.05] Minor typo in rule builder Commit: 5903edd4dab84e076da2a4f01129ca2c231646f5 https://github.com/galaxyproject/galaxy/commit/5903edd4dab84e076da2a4f01129c... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Merge pull request #6109 from aloraine/update_bioviz_link Update BioViz URL Commit: 11a31a1ae70be3ae41fb04b38852cab87ded1bd9 https://github.com/galaxyproject/galaxy/commit/11a31a1ae70be3ae41fb04b38852c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Update tool build API for implicit collection conversion. Commit: 7532de99c9c64fa92667f80f641984005fd85f01 https://github.com/galaxyproject/galaxy/commit/7532de99c9c64fa92667f80f64198... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge pull request #6137 from nsoranzo/release_18.01_fix_workflow_resume_with_mapped_over_input [18.01] Fixes for workflow resume with mapped over inputs Commit: 8f5fc79db6561a15e2eba5ead5471fcd61defb81 https://github.com/galaxyproject/galaxy/commit/8f5fc79db6561a15e2eba5ead5471... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6141 from jmchilton/rules_fix_10 [18.05] "Fix" rule builder to auto decompress uploaded files. Commit: ec83035c2a4c7037afd56c615a3f5351d1e7e539 https://github.com/galaxyproject/galaxy/commit/ec83035c2a4c7037afd56c615a3f5... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6007 from natefoo/slurm-oom [18.01] Handle Slurm 17.11's OUT_OF_MEMORY job state Commit: f8bfb821692e2bd88bd6dea7052062b6c0422fe3 https://github.com/galaxyproject/galaxy/commit/f8bfb821692e2bd88bd6dea705206... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- fix what :eagle: :eyes: spotted Commit: 3a9a46f772ba9c7d2ed96af3096e3f8a55fe3b01 https://github.com/galaxyproject/galaxy/commit/3a9a46f772ba9c7d2ed96af3096e3... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/tool_shed/util/admin_util.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6069 from erasche/gdpr [18.05] GDPR Compliance Mode Commit: 63d4ea900b0fe8f1c3e653ebff33d7d9c3c25d05 https://github.com/galaxyproject/galaxy/commit/63d4ea900b0fe8f1c3e653ebff33d... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst R doc/source/releases/18.05_new_viz.png Log Message: ----------- add most important PRs added Commit: 5d6249ec6fb45db681ad727c63612d20cb40a013 https://github.com/galaxyproject/galaxy/commit/5d6249ec6fb45db681ad727c63612... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add security and breaking changes to release notes Commit: 77e187ddd1d6571de72f4a67a4fc7eeb148ae14c https://github.com/galaxyproject/galaxy/commit/77e187ddd1d6571de72f4a67a4fc7... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- match styling with older RN Commit: d70aadd6d10337e0cc43df325f52a8ce2ec31376 https://github.com/galaxyproject/galaxy/commit/d70aadd6d10337e0cc43df325f52a... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add minor tinies Commit: c4f74c19f3d5b3f550fe384a94bd524d1e93acfc https://github.com/galaxyproject/galaxy/commit/c4f74c19f3d5b3f550fe384a94bd5... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add more breaking changes Commit: 04d1536edff9d9d467a8158ca536fdffecf097bb https://github.com/galaxyproject/galaxy/commit/04d1536edff9d9d467a8158ca536f... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05.rst Log Message: ----------- Fix typos Commit: 82dce758f1ad7b6d9d517531eea5497e9ac5ed3f https://github.com/galaxyproject/galaxy/commit/82dce758f1ad7b6d9d517531eea54... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- Small fixes Commit: b114b1d6bafc334dc63b08d6654b24bec7ab87d5 https://github.com/galaxyproject/galaxy/commit/b114b1d6bafc334dc63b08d6654b2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d2dc22d97f35ff1c4cc780ce03c3a6e41ded86cb https://github.com/galaxyproject/galaxy/commit/d2dc22d97f35ff1c4cc780ce03c3a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use RetryActionExecutor when executing commands via paramiko This should work around issues like ``` galaxy.jobs.runners ERROR 2018-05-16 10:15:55,522 [p:13768,w:0,m:1] [ShellRunner.work_thread-3] (34130) Unhandled exception calling queue_job Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 112, in run_next method(arg) File "lib/galaxy/jobs/runners/cli.py", line 94, in queue_job chmod_out = shell.execute("chmod +x %s" % tool_script) File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 77, in execute self.connect() File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 69, in connect timeout=self.timeout) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 424, in connect passphrase, File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 714, in _auth raise saved_exception SSHException: not a valid OPENSSH private key file ``` that can intermittently occur with rapid submission of many small jobs. Commit: 206daec262d974bb8e50a091da91a102cb35c022 https://github.com/galaxyproject/galaxy/commit/206daec262d974bb8e50a091da91a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6006 from jmchilton/release_18.05_release_notes [18.05] Release notes for 18.05. Commit: fe37996de35ccf675f07dd5c7efbaa28b7d89da7 https://github.com/galaxyproject/galaxy/commit/fe37996de35ccf675f07dd5c7efba... Author: Martin Cech <cech.marten@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/releases/18.05_announce.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- rename the config option to enable_gdpr_beta to reflect the information that we do not guarantee compliance Commit: df6842a4054de142d6d5926354f81b52a6ec7530 https://github.com/galaxyproject/galaxy/commit/df6842a4054de142d6d5926354f81... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Remove the success green on dropdown click; the text already toggles to let you know you clicked, and this is much, much less jarring Commit: 4ed11c16b8c7a05eda2089ed528b7b1dca8d79e3 https://github.com/galaxyproject/galaxy/commit/4ed11c16b8c7a05eda2089ed528b7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Use defined -dark instead of a flat black Commit: 5c455c4472f88cae48beab85864f970c49ea2544 https://github.com/galaxyproject/galaxy/commit/5c455c4472f88cae48beab85864f9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6144 from jmchilton/allow_implicit_conversion [18.05] Fix tool build API for implicit collection conversion. Commit: bfa69401ec869f83b8f52b1a1301145c6f551b03 https://github.com/galaxyproject/galaxy/commit/bfa69401ec869f83b8f52b1a13011... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Gold for active text click. Readable. Contrasts. Still indicates a click. Commit: 7029cb936a9f016a7f714dcbdc88709231ee8d5a https://github.com/galaxyproject/galaxy/commit/7029cb936a9f016a7f714dcbdc887... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #6149 from mvdbeek/fix_stuck_jobs_when_paramiko_fails [18.05] Use RetryActionExecutor when executing commands via paramiko Commit: a6df95508d5c9ea3bcd3be67d31cf91cc4bc281a https://github.com/galaxyproject/galaxy/commit/a6df95508d5c9ea3bcd3be67d31cf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Commit: 680948b1a5351b3819f6b7c55720f2bd2e68cadc https://github.com/galaxyproject/galaxy/commit/680948b1a5351b3819f6b7c55720f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Previous changes overstepped; this should be enough to fix the prefix serving at least in the multiview, and I'm not seeing errors elsewhere (yet). We should look at other urlRoot usage though; it likely has issues. This reverts commit 62811d0a40aafe5db8c5121ff857788c59880b56. Commit: b488c1d12b7742e64d95fba434bdb15aef57dd2c https://github.com/galaxyproject/galaxy/commit/b488c1d12b7742e64d95fba434bdb... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6151 from dannon/urlroot_fixes [18.05] Backbone model url handling Commit: 10a2e68b82a3e175afe33f4686b9b015e7ac4ec4 https://github.com/galaxyproject/galaxy/commit/10a2e68b82a3e175afe33f4686b9b... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/releases/18.05_announce.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6152 from martenson/compliance-rename [18.05] rename the config option to enable_beta_gdpr Commit: 47950b1707b44b130355e3c2f98d3204be581fa1 https://github.com/galaxyproject/galaxy/commit/47950b1707b44b130355e3c2f98d3... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6155 from dannon/no-more-green [18.05] Dropdown active color tweaks Commit: 3208a685aab130477171c8638673aa77c99495bc https://github.com/galaxyproject/galaxy/commit/3208a685aab130477171c8638673a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Fix fetching collection state for static histories. See comment in code. Commit: 6cfe5880e13e0f704782afb72ebafd7fac3d45d4 https://github.com/galaxyproject/galaxy/commit/6cfe5880e13e0f704782afb72ebaf... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix structured_like unqualified references + test. Update tool XSD to encourage using fully qualified inputs. Reorganized the existing tests for consistency with other test tools I think. (Rebased with fixes, including XSD fixes from @nsoranzo.) Commit: 02fa00185aa704266cafa7a3fade90a800cada80 https://github.com/galaxyproject/galaxy/commit/02fa00185aa704266cafa7a3fade9... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/job-states-model.js Log Message: ----------- Merge pull request #6165 from jmchilton/fix_history_view [18.05] Fix fetching collection state for static histories. Commit: 3aace5d60e0068fec34cb2ce51abb749fe4469a1 https://github.com/galaxyproject/galaxy/commit/3aace5d60e0068fec34cb2ce51abb... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: 3221afd8d49f9ba00c10448ac33b25e93c9c3c82 https://github.com/galaxyproject/galaxy/commit/3221afd8d49f9ba00c10448ac33b2... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6162 from jmchilton/structured_like_conditional [18.01] Fix structured_like unqualified references + test. Commit: 6f9a93bad11c189be1b26b6e11d1733c39b2f58d https://github.com/galaxyproject/galaxy/commit/6f9a93bad11c189be1b26b6e11d17... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6169 from guerler/rerun_no_admin [18.05] Fix job reruns for imported histories Commit: 240ad36e20f34f1083b7d148340d4fadd72f8884 https://github.com/galaxyproject/galaxy/commit/240ad36e20f34f1083b7d148340d4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: 5d6bc5721a25a76fa9e671d2e6c6fab9300b6001 https://github.com/galaxyproject/galaxy/commit/5d6bc5721a25a76fa9e671d2e6c6f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: c8ecb0b38dd172a73e0bd5ee86ce80fe83a1007e https://github.com/galaxyproject/galaxy/commit/c8ecb0b38dd172a73e0bd5ee86ce8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: 6a30fe14f1ac018b424b38cba69827ddbfff186a https://github.com/galaxyproject/galaxy/commit/6a30fe14f1ac018b424b38cba6982... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: c6ce1342df0155fa848f551df41f01c016fcc98f https://github.com/galaxyproject/galaxy/commit/c6ce1342df0155fa848f551df41f0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. Commit: bd4f562005e26d56b5e4c9476748fb14f0fed242 https://github.com/galaxyproject/galaxy/commit/bd4f562005e26d56b5e4c9476748f... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6170 from mvdbeek/backport_6169 [18.01] Backport #6169 Fix dataset access validation when attempting job reruns Commit: 5489504e9794f31e26adc901f5612fcfb7d4a91d https://github.com/galaxyproject/galaxy/commit/5489504e9794f31e26adc901f5612... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: afc8d0abd81b56b0eb1797e9acca2e574976939b https://github.com/galaxyproject/galaxy/commit/afc8d0abd81b56b0eb1797e9acca2... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #6172 from nsoranzo/release_18.05_backport_virtualenv_config [18.05] Restore config comment Commit: 84c59917e6e0c4b90d4f29720d547de816302230 https://github.com/galaxyproject/galaxy/commit/84c59917e6e0c4b90d4f29720d547... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Allow non-ascii chars in passwords. Commit: c253436b4a7c646910bdc1f8ce9c2f01fe43f1ff https://github.com/galaxyproject/galaxy/commit/c253436b4a7c646910bdc1f8ce9c2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Append means take a collection type and extend it by the current type - so appending to list to paired -> list:paired for instance. ANY_COLLECTION_TYPE is a representation of incomplete information - it means this type description might be any kind of collection type (the way we use "input" to mean any kind of datatype in the editor). This is really a second order approximation of what a correct solution would be - a first order approximation would somehow represent the result of append being at least of "depth" specified (list:* or *:list instead of * for instance). A not approximation would be to do that but use ANY_COLLECTION_TYPE much less frequently by capturing type_source information and propagating it throughout the workflow properly. But these are harder things to do, this incorrect fix will allow many valid workflows to be editted that currently cannot be so I think it is good. "Fixes" #5205. Commit: f8fc8232a68dd1b0693ff9b007734cfa087cccdf https://github.com/galaxyproject/galaxy/commit/f8fc8232a68dd1b0693ff9b007734... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-19 (Sat, 19 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #6178 from jmchilton/fix_append_for_any_collection_Type [18.05] Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Commit: 872dbfb3c42ec36ffe3c452e164e0dcc2545c3cb https://github.com/galaxyproject/galaxy/commit/872dbfb3c42ec36ffe3c452e164e0... Author: Ubuntu <ubuntu@ip-172-31-23-81.ec2.internal> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- adding idat Commit: 258c4a4d8fddacba64a5cc7ac634910a4839b371 https://github.com/galaxyproject/galaxy/commit/258c4a4d8fddacba64a5cc7ac6349... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6179 from kpbioteam/idat [18.05] add idat datatype Commit: f56150468984cc96e37fe52cefd33499e5f422b4 https://github.com/galaxyproject/galaxy/commit/f56150468984cc96e37fe52cefd33... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev subprocess32 dependency - that older version is not compatible with manylinux. https://github.com/google/python-subprocess32/issues/12 Commit: f07ba172418bdea209481b56b60980d2c9906823 https://github.com/galaxyproject/galaxy/commit/f07ba172418bdea209481b56b6098... Author: Helena Rasche <hxr@hx42.org> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- extraneous self Commit: 92ebf285088c744cef588a05b941ca6adf7848ee https://github.com/galaxyproject/galaxy/commit/92ebf285088c744cef588a05b941c... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #6184 from erasche/gdpr [18.05] extraneous self causing bug reporter to fail Commit: fcde0d669f3e65bf92f05dc517fe550d017c86c4 https://github.com/galaxyproject/galaxy/commit/fcde0d669f3e65bf92f05dc517fe5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Avoid overlapping change handlers Commit: 805854aa6b16eb2b68b6ab5f94b92e84342c2f9e https://github.com/galaxyproject/galaxy/commit/805854aa6b16eb2b68b6ab5f94b92... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6183 from jmchilton/subprocess32_rev [18.05] Rev subprocess32 dependency - that older version is not compatible with manylinux. Commit: 49c824cf01d3b03d7041dc9a2ebe438471dd27e0 https://github.com/galaxyproject/galaxy/commit/49c824cf01d3b03d7041dc9a2ebe4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #6185 from guerler/fix_repeat_inputs [18.05] Fix repeated inputs Commit: a00bd8bf8eb22bfb38be9146c244fd22f60d3a8f https://github.com/galaxyproject/galaxy/commit/a00bd8bf8eb22bfb38be9146c244f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- escape pipe in details so we can have pipes inside markdown tables Commit: 4d38c25c9f746370d9070dfc3d00a488a3b9e27f https://github.com/galaxyproject/galaxy/commit/4d38c25c9f746370d9070dfc3d00a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Right align button menu popup Commit: 2fe24e470d9e555674685006475c9f5cbe00f0c3 https://github.com/galaxyproject/galaxy/commit/2fe24e470d9e555674685006475c9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #6188 from guerler/fix_popup_right [18.05] Right align button menu popup Commit: b931356ef3ea6a2b99add6ed180fa81c64b59632 https://github.com/galaxyproject/galaxy/commit/b931356ef3ea6a2b99add6ed180fa... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Fix sphinx. Commit: 440f17875f6b5ce36147ee1e830162e40c0c0d48 https://github.com/galaxyproject/galaxy/commit/440f17875f6b5ce36147ee1e83016... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge pull request #6191 from jmchilton/fix_sphinx [18.05] Lock dependency on Sphinx to <1.7. Commit: 01d2a5c2ae7e5a1f3b5fcfdd2b1eca766a69d5ec https://github.com/galaxyproject/galaxy/commit/01d2a5c2ae7e5a1f3b5fcfdd2b1ec... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix parsing of `scontrol show job` Fix the following traceback: ``` galaxy.jobs.runners.slurm ERROR 2018-05-22 13:01:07,050 (1024816/14094939) Failure in SLURM _complete_terminal_job(), job final state will be: failed Traceback (most recent call last): File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 86, in _complete_terminal_job slurm_state = _get_slurm_state() File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 81, in _get_slurm_state job_info_dict = dict([out_param.split('=', 1) for out_param in stdout.split()]) ValueError: dictionary update sequence element #52 has length 1; 2 is required ``` Commit: 939c3be132b9cd606cd5f1189293f15000a486d8 https://github.com/galaxyproject/galaxy/commit/939c3be132b9cd606cd5f1189293f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6194 from nsoranzo/fix__get_slurm_state [18.01] Fix parsing of `scontrol show job` Commit: 65c1cd761c48ba121a847d4d501eb8a97a911e70 https://github.com/galaxyproject/galaxy/commit/65c1cd761c48ba121a847d4d501eb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix data_source.py for upload changes in 18.05 release cycle. handle_uploaded_dataset_file was used by tools external to ``lib/`` include data_source.py and potentially tools in the tool shed. This restores the interface as a wrapper around a new method handle_uploaded_dataset_file_internal. Broken in https://github.com/galaxyproject/galaxy/commit/ef6f7f62ab679928045c816a3cb71... I believe. Commit: 9a840537cb5037e280a8db14125a46fbb422d305 https://github.com/galaxyproject/galaxy/commit/9a840537cb5037e280a8db14125a4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- pass the check for pipe presence in details the docs build fine and the table renders fine too Commit: 6f79f28f1793c135b1e0f332987fd62e9dea93b6 https://github.com/galaxyproject/galaxy/commit/6f79f28f1793c135b1e0f332987fd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- Merge pull request #6187 from martenson/fix-doc-markdown-table [18.01] escape pipe while parsing xsd details Commit: a5297af19017a009fe887a5c04dae281ab234cae https://github.com/galaxyproject/galaxy/commit/a5297af19017a009fe887a5c04dae... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: cfaf7186bda346445e0c1e0bd706eefe826b9323 https://github.com/galaxyproject/galaxy/commit/cfaf7186bda346445e0c1e0bd706e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Support building and publishing pre-release docs Commit: ebc6734ed787fd4b10858d622e3c7e49d33309ac https://github.com/galaxyproject/galaxy/commit/ebc6734ed787fd4b10858d622e3c7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge pull request #6199 from natefoo/docs-pre-release [18.05] Support building and publishing pre-release docs Commit: 44e57ba8b45d2ddd624333547ec1adeb62d70b9c https://github.com/galaxyproject/galaxy/commit/44e57ba8b45d2ddd624333547ec1a... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #6196 from jmchilton/fix_metadata [18.05] Fix data_source.py for upload changes in 18.05 release cycle. Commit: 72d07e07d5164519e31bfe5811ce9dbd980ecf1e https://github.com/galaxyproject/galaxy/commit/72d07e07d5164519e31bfe5811ce9... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- remove mention of 18.09, that is only for dev Commit: a8e0eda44db84f756004e266865d16d0fb13eb3e https://github.com/galaxyproject/galaxy/commit/a8e0eda44db84f756004e266865d1... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Merge pull request #6175 from dannon/password_fixes [18.05] Allow non-ascii chars in pbkdf2 passwords Commit: 55f7280d790fcaf9bc74d543f22541d86521cef0 https://github.com/galaxyproject/galaxy/commit/55f7280d790fcaf9bc74d543f2254... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py A test/unit/test_security_passwords.py Log Message: ----------- More password encoding handling fixes. Fix handling comparison of older hashes in Python 2 and fix the hanlding of both for Python 3. The previous iteration gave me some errors in Python 3, I brought in and adapted @mvdbeek's Python 3 fixes to fix these: ``` ====================================================================== ERROR: test_security_passwords.test_hash_and_check ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy-lib/.tox/py34/lib/python3.4/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/john/workspace/galaxy-lib/tests/test_security_passwords.py", line 12, in test_hash_and_check simple_pass_hash = passwords.hash_password(simple_pass) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 21, in hash_password return hash_password_PBKDF2(password) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 44, in hash_password_PBKDF2 hashed = pbkdf2_bin(smart_str(password), salt, COST_FACTOR, KEY_LENGTH, getattr(hashlib, HASH_FUNCTION)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 78, in pbkdf2_bin rv = u = _pseudorandom(salt + _pack_int(block)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 75, in _pseudorandom return [ord(_) for _ in h.digest()] File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 75, in <listcomp> return [ord(_) for _ in h.digest()] TypeError: ord() expected string of length 1, but int found ====================================================================== ERROR: test_security_passwords.test_hash_consistent ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy-lib/.tox/py34/lib/python3.4/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/john/workspace/galaxy-lib/tests/test_security_passwords.py", line 38, in test_hash_consistent assert passwords.check_password(simple_pass, simple_pass_hash) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 30, in check_password if check_password_PBKDF2(guess, hashed): File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 53, in check_password_PBKDF2 hashed_guess = pbkdf2_bin(smart_str(guess), salt, int(cost_factor), KEY_LENGTH, getattr(hashlib, hash_function)) File "/Users/john/workspace/galaxy-lib/galaxy/security/passwords.py", line 78, in pbkdf2_bin rv = u = _pseudorandom(salt + _pack_int(block)) TypeError: Can't convert 'bytes' object to str implicitly ``` Added tests that all now pass in Python 3 - including generating some passwords in Python 3 and verifying they pass when checked in Python 2 and vice versa. Commit: a301d240165f0c14acc7126b36084293bdb59e45 https://github.com/galaxyproject/galaxy/commit/a301d240165f0c14acc7126b36084... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix for loading container resolvers config file Commit: bd049665d1201a3c35d3bd1e3ff48891cd54fbcd https://github.com/galaxyproject/galaxy/commit/bd049665d1201a3c35d3bd1e3ff48... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6203 from martenson/remove-1809 [18.05] remove mention of 18.09, that is only for dev Commit: ab656c7e2d57cce71006c519e5c737617ac04084 https://github.com/galaxyproject/galaxy/commit/ab656c7e2d57cce71006c519e5c73... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #6205 from natefoo/container-resolvers-conf-fix [18.05] Container resolvers conf fix Commit: ec5924dd649ccd4936398c9df82000c1f1ce4a24 https://github.com/galaxyproject/galaxy/commit/ec5924dd649ccd4936398c9df8200... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py A test/unit/test_security_passwords.py Log Message: ----------- Merge pull request #6204 from jmchilton/password_fixes [18.05] More password encoding handling fixes. Commit: ce362e60abbafdffa65acaf68f9492cec7196a9d https://github.com/galaxyproject/galaxy/commit/ce362e60abbafdffa65acaf68f949... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05 Compare: https://github.com/galaxyproject/galaxy/compare/8833d1a8a49d...ce362e60abba **NOTE:** This service 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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