- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 5554c2f9b98b4192e106fdce52fa067945f431e8 https://github.com/galaxyproject/galaxy/commit/5554c2f9b98b4192e106fdce52fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: b82676b8eec35313896614aa0fb5fdeeddacf541 https://github.com/galaxyproject/galaxy/commit/b82676b8eec35313896614aa0fb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: b5d0030b3ed4bf08aa26c29b72c4f5757874669c https://github.com/galaxyproject/galaxy/commit/b5d0030b3ed4bf08aa26c29b72c4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 662440e730791318b5ff3a9346f1ee6243c56208 https://github.com/galaxyproject/galaxy/commit/662440e730791318b5ff3a9346f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 8fa785427cf8d41fd420092baaaf574825bb9d0b https://github.com/galaxyproject/galaxy/commit/8fa785427cf8d41fd420092baaaf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5344 from mvdbeek/history_import_fixes [17.09] History import fixes Commit: 0fdb63e5e327ef6b82c928004b5e3301967f9eb3 https://github.com/galaxyproject/galaxy/commit/0fdb63e5e327ef6b82c928004b5e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- remove charlimit for fetching urls fixes #5349 this would only allow a number of urls that fit 1024 chars together moreover it would truncate (and break) the last one Commit: 3bf9b3ab1d718d5ecd02f7539015c5328d6c72ef https://github.com/galaxyproject/galaxy/commit/3bf9b3ab1d718d5ecd02f7539015… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5353 from martenson/remove-charlimit-for-fetch [17.09] remove charlimit for fetching urls Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Commit: 177aa2e7f994afc9f2749603e6d1ad20c9ffea77 https://github.com/galaxyproject/galaxy/commit/177aa2e7f994afc9f2749603e6d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 7996a4c0c73eb53774b2d871f496e36b9a6ec54a https://github.com/galaxyproject/galaxy/commit/7996a4c0c73eb53774b2d871f496… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Rebuild client for stable 17.09 Commit: 0e0303743dcb305bd2c3ea66f80b3be9ebdcd351 https://github.com/galaxyproject/galaxy/commit/0e0303743dcb305bd2c3ea66f80b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge branch 'release_17.09' into dev Commit: 84ae5db0f195adcbbb1a1074d6cc6d0729f1598a https://github.com/galaxyproject/galaxy/commit/84ae5db0f195adcbbb1a1074d6cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client formatting Compare: https://github.com/galaxyproject/galaxy/compare/ebafd19575ba...84ae5db0f195

1 0

[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Commit: 177aa2e7f994afc9f2749603e6d1ad20c9ffea77 https://github.com/galaxyproject/galaxy/commit/177aa2e7f994afc9f2749603e6d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 7996a4c0c73eb53774b2d871f496e36b9a6ec54a https://github.com/galaxyproject/galaxy/commit/7996a4c0c73eb53774b2d871f496… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Rebuild client for stable 17.09 Compare: https://github.com/galaxyproject/galaxy/compare/3bf9b3ab1d71...7996a4c0c73e

1 0

[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Compare: https://github.com/galaxyproject/galaxy/compare/d1510c739492...4288e96b77fc

1 0

[galaxyproject/galaxy] 5071b6: Add option to auto create user_library_import_dir ...
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5071b698718caae30115f463a184aa76f2017250 https://github.com/galaxyproject/galaxy/commit/5071b698718caae30115f463a184… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add option to auto create user_library_import_dir directories upon user login. Commit: 74e551d34cfb5bb50ca061f682de97084ade5a2e https://github.com/galaxyproject/galaxy/commit/74e551d34cfb5bb50ca061f682de… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- one less variable.. Commit: ae3afae8f002fccb1b236271da4204b1115eef23 https://github.com/galaxyproject/galaxy/commit/ae3afae8f002fccb1b236271da42… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- sort import order alphabetically Commit: 8553ea2c6e9fedb88579f1a7e9e8727fc2a977a7 https://github.com/galaxyproject/galaxy/commit/8553ea2c6e9fedb88579f1a7e9e8… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- move logic to webapps.py Commit: 729b0bf63b2990849809f32da45ef078d206069b https://github.com/galaxyproject/galaxy/commit/729b0bf63b2990849809f32da45e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- fix toolshed test with missing config attribute Commit: 4947ab0738a076ef7cc60856271a1585c259fa36 https://github.com/galaxyproject/galaxy/commit/4947ab0738a076ef7cc60856271a… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- use safemakedirs instead of private _ensure_directory Commit: ea7dbd1906bc612804448fd94af05e7812c60e38 https://github.com/galaxyproject/galaxy/commit/ea7dbd1906bc612804448fd94af0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.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/histories.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M templates/webapps/galaxy/history/display_structured.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/run_test_wrapper.sh 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 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/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_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_dockerized_jobs.py A test/integration/test_job_environments.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M tools/data_source/microbial_import_code.py Log Message: ----------- Merge remote-tracking branch 'origin/dev' into feature/auto_create_userfolder Commit: ebafd19575ba4898da9ed237683a76f8d3be7000 https://github.com/galaxyproject/galaxy/commit/ebafd19575ba4898da9ed237683a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-22 (Mon, 22 Jan 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/webapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5138 from scholtalbers/feature/auto_create_userfolder Add option to auto create user_library_import_dir directories upon user login Compare: https://github.com/galaxyproject/galaxy/compare/e14dde16fb9a...ebafd19575ba

1 0

[galaxyproject/galaxy] 208dcb: Stop walking up to parent HDA
by GitHub 21 Jan '18

21 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 208dcb9196466af1db363d4b307391d5ad36e042 https://github.com/galaxyproject/galaxy/commit/208dcb9196466af1db363d4b3073… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Stop walking up to parent HDA Commit: ca51898bc4038fc93fa53a5a2fa9367ab8db6b8b https://github.com/galaxyproject/galaxy/commit/ca51898bc4038fc93fa53a5a2fa9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Fix cleanup datasets script Commit: 654ed86b376f0b7492f2f4370a4e6a903a15d37f https://github.com/galaxyproject/galaxy/commit/654ed86b376f0b7492f2f4370a4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Setup a dummy registry to allow some more operations, e.g. accessing metadata Commit: 89d45416fbb75d10ad43940308bd2e0dc4d2ede2 https://github.com/galaxyproject/galaxy/commit/89d45416fbb75d10ad43940308bd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Import Registry directly Commit: e14dde16fb9ab4175f9a8f252eb4e7249dbb6d4f https://github.com/galaxyproject/galaxy/commit/e14dde16fb9ab4175f9a8f252eb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/db_shell.py Log Message: ----------- Merge pull request #5346 from mvdbeek/fix_hda_parent_access Fix dataset purging, dataset cleanup script and db_shell script Compare: https://github.com/galaxyproject/galaxy/compare/5be96485b5a7...e14dde16fb9a

1 0

[galaxyproject/galaxy] 991f79: Use print() function in common_startup.sh
by GitHub 21 Jan '18

21 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 991f79e630ddad44530fa3799cfcac34422cd95a https://github.com/galaxyproject/galaxy/commit/991f79e630ddad44530fa3799cfc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Use print() function in common_startup.sh Commit: 5be96485b5a79550eb0824e46a8fac9dca99e06a https://github.com/galaxyproject/galaxy/commit/5be96485b5a79550eb0824e46a8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5357 from mvdbeek/print_statement_fix Use print() function in common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/42b87dd5f922...5be96485b5a7

1 0

[galaxyproject/galaxy] aa3983: fix #5129: auto create ldap role(&group) and assig...
by GitHub 20 Jan '18

20 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa3983bf9152a78bf2b577a1a4f3e51ecc387c64 https://github.com/galaxyproject/galaxy/commit/aa3983bf9152a78bf2b577a1a4f3… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py Log Message: ----------- fix #5129: auto create ldap role(&group) and assign to newly auto-registered user Commit: 86231f39f0b38b6d61f46c09009ad79c0b56ae11 https://github.com/galaxyproject/galaxy/commit/86231f39f0b38b6d61f46c09009a… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - remove unused Exception variable Commit: 87da3da0c80cf4519554bd2599f22f1e2ab2f496 https://github.com/galaxyproject/galaxy/commit/87da3da0c80cf4519554bd2599f2… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - remove unnecessary log statement Commit: b934da49b21e70b422435b87155e8bacc8003e58 https://github.com/galaxyproject/galaxy/commit/b934da49b21e70b422435b87155e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - add some options to only create the role, group or both. and whether or not to assign to role only to the group Commit: 79aaa3492d30dc4a612988274e0c727318c95cdd https://github.com/galaxyproject/galaxy/commit/79aaa3492d30dc4a612988274e0c… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Also catch empty string - e.g. upon create user from the admin page Commit: a6435eade58071798ba76ac8c22b01927e768ed5 https://github.com/galaxyproject/galaxy/commit/a6435eade58071798ba76ac8c22b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/register.mako Log Message: ----------- On top of 5129, this allows to pre-populate an ldap user from the admin interface. An option is added to show/hide the pre-populate form in the admin register user form. Commit: 1128e8a4ee094d7b471730f7513b182fb135b647 https://github.com/galaxyproject/galaxy/commit/1128e8a4ee094d7b471730f7513b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/util.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- some fixes to ensure groups and roles are created on pre-populating users Commit: aa4ab1cc0565b56c25da421fe89f5df9406f4cbd https://github.com/galaxyproject/galaxy/commit/aa4ab1cc0565b56c25da421fe89f… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- fix linting errors Commit: 8be4addaa995b6a4cf2c9bad1d2d4b88a4b0ce78 https://github.com/galaxyproject/galaxy/commit/8be4addaa995b6a4cf2c9bad1d2d… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/auth_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py M templates/user/register.mako Log Message: ----------- update ldap role creation based on comments on PR #5136 and PR #5136 Commit: dea3b73dd2ecc7117c622379ac4067f2b9a378c1 https://github.com/galaxyproject/galaxy/commit/dea3b73dd2ecc7117c622379ac40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.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-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-model.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/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-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-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.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/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/gulpfile.js M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M config/user_preferences_extra_conf.yml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md A doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst A doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst A doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/api/quickstart.rst M doc/source/conf.py M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py A 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/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/jobs.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/repositories.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/biostar.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.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/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py A scripts/maintenance.sh M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/vue.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/bam_native_from_sam.bam M test-data/neostore.zip A test-data/new_element_sort_order.txt M test-data/sam_with_header.sam M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.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/data/test_workflow_1.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.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 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/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml 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_dockerized_jobs.py A test/integration/test_job_environments.py M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into feature/populate_ldap_user Commit: 42b87dd5f922c1d65739fd9f22ea2601220a1c65 https://github.com/galaxyproject/galaxy/commit/42b87dd5f922c1d65739fd9f22ea… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-20 (Sat, 20 Jan 2018) Changed paths: M config/auth_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py M templates/user/register.mako Log Message: ----------- Merge pull request #5238 from scholtalbers/feature/populate_ldap_user add an admin form to pre-populate an ldap user Compare: https://github.com/galaxyproject/galaxy/compare/718eb6cbf4db...42b87dd5f922

1 0

[galaxyproject/galaxy] 0fdb63: remove charlimit for fetching urls
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0fdb63e5e327ef6b82c928004b5e3301967f9eb3 https://github.com/galaxyproject/galaxy/commit/0fdb63e5e327ef6b82c928004b5e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- remove charlimit for fetching urls fixes #5349 this would only allow a number of urls that fit 1024 chars together moreover it would truncate (and break) the last one Commit: 3bf9b3ab1d718d5ecd02f7539015c5328d6c72ef https://github.com/galaxyproject/galaxy/commit/3bf9b3ab1d718d5ecd02f7539015… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5353 from martenson/remove-charlimit-for-fetch [17.09] remove charlimit for fetching urls Compare: https://github.com/galaxyproject/galaxy/compare/8fa785427cf8...3bf9b3ab1d71

1 0

[galaxyproject/galaxy] 7d1504: Fix bam conversion test tool
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d15049c48d030a6d7a21e039bfb91baf2094036 https://github.com/galaxyproject/galaxy/commit/7d15049c48d030a6d7a21e039bfb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Fix bam conversion test tool Starting with 16344a6 we attempt to set metadata also for files that have no content. BAM files need to contain at least a header. To avoid failing tests we only create the appropriate output based on the input. Commit: 718eb6cbf4db0719df226bb70436415e211e75d4 https://github.com/galaxyproject/galaxy/commit/718eb6cbf4db0719df226bb70436… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Merge pull request #5351 from mvdbeek/sam_to_bam_native_fix Fix bam conversion test tool Compare: https://github.com/galaxyproject/galaxy/compare/080148a16190...718eb6cbf4db

1 0

[galaxyproject/usegalaxy-playbook] 7706bc: Collect some env variable metrics on Test jobs
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7706bce050b0902342d8d4305713a4121484a3a8 https://github.com/galaxyproject/usegalaxy-playbook/commit/7706bce050b09023… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/config/job_metrics_conf.xml Log Message: ----------- Collect some env variable metrics on Test jobs Commit: ec2642fabe9333bdf4320503a7f4932516fff650 https://github.com/galaxyproject/usegalaxy-playbook/commit/ec2642fabe9333bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable config changes Commit: 506f8477b28018e3bbe6e4b3f3127fc86c028a6c https://github.com/galaxyproject/usegalaxy-playbook/commit/506f8477b28018e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: a5ffd805369897f169d57f81428d79a036c019e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/a5ffd805369897f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Main mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/aa74d76efb82...…

1 0

[galaxyproject/galaxy] 8d8bf5: Dockerized job integration testing.
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d8bf5eaffeda0f229bf56cb45e4adbb05b12d57 https://github.com/galaxyproject/galaxy/commit/8d8bf5eaffeda0f229bf56cb45e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/test_dockerized_jobs.py Log Message: ----------- Dockerized job integration testing. Add simple test cases for both mulled containers and explicit Docker image resolution. Commit: cd04ff30665ae6f15a6af35152af54d630458e60 https://github.com/galaxyproject/galaxy/commit/cd04ff30665ae6f15a6af35152af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Set group id in addition to user id when running docker containers by default. Noticed cwltool does this and it is a good idea. It wasn't the bug I was tracking but it is a solid improvement. Commit: 4bf47d08770c14010bf925c73ccba2262dfe78ee https://github.com/galaxyproject/galaxy/commit/4bf47d08770c14010bf925c73ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/base/integration_util.py 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/samples_tool_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 M test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Improved home and temp directory handling. Home Directory Handling ----------------------- - For profile < 18.01 tools: - If use_shared_home="false" is set on the command block - the tool will be given a clean $HOME directory. - If ``shared_home_dir`` is set in Galaxy's config or the job destination configuration, Galaxy will set $HOME in the tool's job environment to point at this directory. - For profile >= 18.01 tools, jobs will be given a clean home directory by default unless ``use_shared_home="true"`` is set. If that is set, the profile < 18.01 behavior is used. In addition to these changes for Galaxy tools, the tool framework itself has been updated to allow other potential behaviors including the CWL defaults. Integration tests for each of these cases has been added. Upgrading to 18.01 - we recommend dropping overriding ``HOME`` in any Galaxy environment configuration (e.g. env directives in job_conf.xml). If any such configuration is found, we recommend instead setting "shared_home_dir" for destinations to the that cluster destination's shared HOME directory. If all destinations share a single HOME directory, this can be set in galaxy.ini instead of job_conf.xml. Temp Directory Handling ----------------------- There were serious disagreements with how to proceed here. I felt we should aggressively isolate tool TMP directories and provide deployers options to tweak these through structured arguments. Nicola felt we should defer to the environment variables already being set job_conf.xml - but tweak their meanings by default. Nate fell somewhere in between. I think all sides have merit and could make sense depending on what you want to improve (easing cognative load, reducing out-of-box errors, easing advanced deployer configs, structured reasonsing of paths by Galaxy, etc...). I've navigated a path here that doesn't particularly reduce out of the box errors as I wanted by setting up a per-job temp directory by default but does make it possible and shouldn't break any existing configurations and doesn't make it anything more difficult to manage these things via environment variables. The new approach doesn't change any thing by default for Galaxy tools (regardless of tool profile version). The only way to achieve new behaviors is for the deployer to set a job_conf parameter called "tmp_dir". If this is set, it can be set to "True" (to default to a new, clean directory below the job directory) or to a shell expression to allow setting this dynamically at runtime to paths or paths beneath directories as needed on a per-destination basis. If a temp directory is set this way all three variables TMP, TMPDIR, and TEMP are set. Docker Environment Handling --------------------------- - Mirror the CWL behavior of mounting an external /tmp by default. - For newer tools, pass through the HOME, TMP, TMPDIR, and TEMP environment variables into the Docker container in addition to GALAXY_SLOTS. - Fix the pass through of environment variables into Docker containers. Commit: db0633eb8965306f4a7a8cca36e882cffc73ad55 https://github.com/galaxyproject/galaxy/commit/db0633eb8965306f4a7a8cca36e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M test/integration/test_dockerized_jobs.py M test/integration/test_job_environments.py M test/unit/tools/test_evaluation.py Log Message: ----------- Follow up on comments for #5193. Commit: 080148a16190988a18df6709ba1bd9f650ea10de https://github.com/galaxyproject/galaxy/commit/080148a16190988a18df6709ba1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/base/driver_util.py M test/base/integration_util.py 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 A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_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_dockerized_jobs.py A test/integration/test_job_environments.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #5193 from jmchilton/structured_job_environment_1 Improved home and temp directory handling. Compare: https://github.com/galaxyproject/galaxy/compare/1cac9ad54fea...080148a16190

1 0

[galaxyproject/galaxy] dedb1d: Fix history import by file on multi-handler setups
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dedb1d3f4ca83539baea9c4ff5654c3b44614540 https://github.com/galaxyproject/galaxy/commit/dedb1d3f4ca83539baea9c4ff565… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 1cac9ad54fead782a28619ae60b46cdc73491c75 https://github.com/galaxyproject/galaxy/commit/1cac9ad54fead782a28619ae60b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M scripts/functional_tests.py A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/8f65cd46b0ec...1cac9ad54fea

1 0

[galaxyproject/galaxy] f5af95: add BamNative datatype
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5af9539b9d50e0c0e99ade18eea8af6f7beb0e4 https://github.com/galaxyproject/galaxy/commit/f5af9539b9d50e0c0e99ade18eea… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add BamNative datatype Commit: 017dad025db9a06c9c6d2430203f52fdec959f68 https://github.com/galaxyproject/galaxy/commit/017dad025db9a06c9c6d2430203f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test-data/bam_native_from_sam.bam Log Message: ----------- add new test file Commit: eea55a9258342e8de32162c9e62563de0f6438b8 https://github.com/galaxyproject/galaxy/commit/eea55a9258342e8de32162c9e625… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test/functional/tools/sam_to_bam_native.xml Log Message: ----------- add new test tool Commit: 2a093f25f6fdb6ebf4a8bba84050130c4929e6c3 https://github.com/galaxyproject/galaxy/commit/2a093f25f6fdb6ebf4a8bba84050… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add new bam_native datatype to the registry Commit: 4d7bc9a778afa171bd7498004733943543af5730 https://github.com/galaxyproject/galaxy/commit/4d7bc9a778afa171bd7498004733… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- bam to bigwig converter, converts also bam_native Commit: 2569851498f76d2fc416bd96ab4007c579bb0ffd https://github.com/galaxyproject/galaxy/commit/2569851498f76d2fc416bd96ab40… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M test-data/sam_with_header.sam Log Message: ----------- use unsorted sam file for tests Commit: 8b55e0a33a52fe45fc5fdaa171607c7f253021c9 https://github.com/galaxyproject/galaxy/commit/8b55e0a33a52fe45fc5fdaa17160… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- add two converters Commit: 640cfb1e7d8be8ceaba96920cfb1be72c48f4974 https://github.com/galaxyproject/galaxy/commit/640cfb1e7d8be8ceaba96920cfb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam to BAM Commit: e519f4e7efcbb055a66a861588ceabd09e0b9b58 https://github.com/galaxyproject/galaxy/commit/e519f4e7efcbb055a66a861588ce… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rearrange sniffer Commit: 295e5712ee2c020292754ddcb75d6d5744c4ed10 https://github.com/galaxyproject/galaxy/commit/295e5712ee2c020292754ddcb75d… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- adjust tests Commit: 2b5b6cf74fb29eb4608318477c062982d8ad955c https://github.com/galaxyproject/galaxy/commit/2b5b6cf74fb29eb4608318477c06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix test and add datatypes to test/functional/tools/sample_datatypes_conf.xml This test is still failing because `CONVERTER_sam_to_bam` will be invoked instead of CONVERTER_sam_to_bam_native. Possibly becasue Bam inherits from BamNative, so this isn't strictly speaking wrong, though not what one would expect. Commit: a8b3d23f1438f31436b86d24b48868fd3e133dad https://github.com/galaxyproject/galaxy/commit/a8b3d23f1438f31436b86d24b488… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Adjust sniffer test for unsorted bam Commit: 43dd7910f4865c9c4205ad8eaa5e8f1a71b6b6c6 https://github.com/galaxyproject/galaxy/commit/43dd7910f4865c9c4205ad8eaa5e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #37 from mvdbeek/bam_native_tests Fix test and add datatypes to test/functional/tools/sample_datatypes_… Commit: 446643159540f8db67dfd0752560b387b63fc4b8 https://github.com/galaxyproject/galaxy/commit/446643159540f8db67dfd0752560… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- resort the converters so that the accepted_formats are infront Commit: 8928b34506c1ba1f4856fad82dc42aef0f7c68f6 https://github.com/galaxyproject/galaxy/commit/8928b34506c1ba1f4856fad82dc4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- implement priority converters Commit: b139726ed380192ecf03f10e91220a0488b573f3 https://github.com/galaxyproject/galaxy/commit/b139726ed380192ecf03f10e9122… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- fix spelling Commit: ea34bdc34d560962f3f149d9f019d0ac3a3c4f0a https://github.com/galaxyproject/galaxy/commit/ea34bdc34d560962f3f149d9f019… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #38 from bgruening/converter_resorting resort the converters so that the accepted_formats are infront Commit: 49dd02f4090b525beba735fc9ff16e32388b3fcd https://github.com/galaxyproject/galaxy/commit/49dd02f4090b525beba735fc9ff1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Keep header when converting sam to bam Otherwise the converted datasets are not valid BAM files. Commit: c32680733c8985d0db48a10d0b50fab7514dc4ff https://github.com/galaxyproject/galaxy/commit/c32680733c8985d0db48a10d0b50… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "fix spelling" This reverts commit b139726ed380192ecf03f10e91220a0488b573f3. Commit: 38c5f711983033bb01072a769e6a618528724955 https://github.com/galaxyproject/galaxy/commit/38c5f711983033bb01072a769e6a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "implement priority converters" This reverts commit 8928b34506c1ba1f4856fad82dc42aef0f7c68f6. Commit: 6b444f609d3a48d17a783e581dc077b0731673ca https://github.com/galaxyproject/galaxy/commit/6b444f609d3a48d17a783e581dc0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "resort the converters so that the accepted_formats are infront" This reverts commit 446643159540f8db67dfd0752560b387b63fc4b8. Commit: c2328e32eb18bd7a4a5c791306203b933fc73603 https://github.com/galaxyproject/galaxy/commit/c2328e32eb18bd7a4a5c79130620… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Move up sam_to_bam_native converter That should allow implicit conversion from sam to bam_native for tools that support bam_native. Commit: a36ebe35521e3e45c5c3301eef9535ebdf630f9d https://github.com/galaxyproject/galaxy/commit/a36ebe35521e3e45c5c3301eef95… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Enhance tests for sam_to_bam conversion This demonstrates that the `sam_to_bam` converter will be used for an input with `format="bam"`, and not `sam_to_bam_native`. Commit: d544adf5ee45557f2e40c2f1050f4f2a427d56e1 https://github.com/galaxyproject/galaxy/commit/d544adf5ee45557f2e40c2f1050f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/registry.py M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Merge pull request #39 from mvdbeek/bam_unsorted Fix tests and revert additional sorting of converters Commit: ae0c3524b87d1f14374ee04d452320ff0c091cf8 https://github.com/galaxyproject/galaxy/commit/ae0c3524b87d1f14374ee04d4523… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/grid/grid-model.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/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.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/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/gulpfile.js M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/user_preferences_extra_conf.yml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M doc/source/api/quickstart.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/jobs.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/biostar.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.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/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/router.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/vue.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/zh/locale.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.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/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A 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/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge branch 'dev' into bam_unsorted Commit: aaaf7b50a7a227e5344712f6441fce337a20d1ba https://github.com/galaxyproject/galaxy/commit/aaaf7b50a7a227e5344712f6441f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Enable conda_auto_init and conda_auto_install for framework tests Commit: 680bf685c2dfdc874277321e2c7d0673516bf62a https://github.com/galaxyproject/galaxy/commit/680bf685c2dfdc874277321e2c7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix datatype order Commit: 8ecc86cb677bc3971baa75bf0e8c1481d8e3aef4 https://github.com/galaxyproject/galaxy/commit/8ecc86cb677bc3971baa75bf0e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Simplify conda framework setup Thanks @nsoranzo! Commit: 8f65cd46b0ec7c1a92a305219f43c837cd2a471a https://github.com/galaxyproject/galaxy/commit/8f65cd46b0ec7c1a92a305219f43… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M scripts/functional_tests.py A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5180 from bgruening/bam_unsorted Add BamNative datatype Compare: https://github.com/galaxyproject/galaxy/compare/33bd54079be7...8f65cd46b0ec

1 0

[galaxyproject/galaxy] 5554c2: Fix import by url for history archive import tool
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 5554c2f9b98b4192e106fdce52fa067945f431e8 https://github.com/galaxyproject/galaxy/commit/5554c2f9b98b4192e106fdce52fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: b82676b8eec35313896614aa0fb5fdeeddacf541 https://github.com/galaxyproject/galaxy/commit/b82676b8eec35313896614aa0fb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: b5d0030b3ed4bf08aa26c29b72c4f5757874669c https://github.com/galaxyproject/galaxy/commit/b5d0030b3ed4bf08aa26c29b72c4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 662440e730791318b5ff3a9346f1ee6243c56208 https://github.com/galaxyproject/galaxy/commit/662440e730791318b5ff3a9346f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 8fa785427cf8d41fd420092baaaf574825bb9d0b https://github.com/galaxyproject/galaxy/commit/8fa785427cf8d41fd420092baaaf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5344 from mvdbeek/history_import_fixes [17.09] History import fixes Compare: https://github.com/galaxyproject/galaxy/compare/3c85407ec801...8fa785427cf8

1 0

[galaxyproject/usegalaxy-playbook]
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/test_reenable_sentry Home: https://github.com/galaxyproject/usegalaxy-playbook

1 0

[galaxyproject/usegalaxy-playbook] 4480e3: Re-enable sentry on test
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4480e3199496563ddcf31c1aa2e88a5031700fc5 https://github.com/galaxyproject/usegalaxy-playbook/commit/4480e3199496563d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Re-enable sentry on test Commit: aa74d76efb826314c541203138e512eb523590a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa74d76efb826314… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge pull request #76 from galaxyproject/test_reenable_sentry Re-enable sentry on test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a7b84fe15f7e...…

1 0

[galaxyproject/usegalaxy-playbook] a7b84f: Update Test
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a7b84fe15f7ed8743880602e824d4ac157c36b98 https://github.com/galaxyproject/usegalaxy-playbook/commit/a7b84fe15f7ed874… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

1 0

[galaxyproject/galaxy] 1fedf7: add maintenance.sh to simplify setting up a cleanu...
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fedf7e680ef287e81e7a55b668b74a0aefc5d77 https://github.com/galaxyproject/galaxy/commit/1fedf7e680ef287e81e7a55b668b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: A scripts/common_startup_variables.sh A scripts/maintenance.sh Log Message: ----------- add maintenance.sh to simplify setting up a cleanup cron job or run the cleanup scripts in general Commit: b372c3b4b9e339b8c4f81ae88e57fc4a37731769 https://github.com/galaxyproject/galaxy/commit/b372c3b4b9e339b8c4f81ae88e57… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M scripts/maintenance.sh Log Message: ----------- fix location of cleanup_datasets.py if executed outside of the root Commit: 33bd54079be7b7c27afa1ce8a1ff80d2cacfb0d3 https://github.com/galaxyproject/galaxy/commit/33bd54079be7b7c27afa1ce8a1ff… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: A scripts/common_startup_variables.sh A scripts/maintenance.sh Log Message: ----------- Merge pull request #4916 from scholtalbers/add_maintenance_script Add maintenance script.. Compare: https://github.com/galaxyproject/galaxy/compare/c8a7b7b07cad...33bd54079be7

1 0

[galaxyproject/galaxy] 1a43ef: Work around (temporarily) wrong getsize() output
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a43ef5b83d7378faa653451ebc38a54725a7481 https://github.com/galaxyproject/galaxy/commit/1a43ef5b83d7378faa653451ebc3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Work around (temporarily) wrong getsize() output I'm not sure how/why this happens, but this can be reproduced by copying a file to a location in one process, while checking the size in another process: Run this to copy a file indefinitely: ``` import os import shutil open('test').write("foo") while True: shutil.copy('test', 'test.file') os.remove('test.file') ``` In the same directory run this ``` import os count = 0 wrong_size = False while True: try: size = os.path.getsize('test.file') if size == 0: wrong_size = True wrong_count = count elif wrong_size and os.path.getsize('test.file') != 0: # We have seen the wrong size being reported, but now it's correct again print("Got wrong file size at %dnd try, was fixed in %dnd try" % (wrong_count, count)) break except Exception: pass count += 1 ``` It'll (probably) fail like this: ``` Got wrong file size at 0nd try, was fixed in 1nd try ``` or more often: ``` Got wrong file size at 31nd try, was fixed in 32nd try ``` This seems to be fixed when running os.path.getsize() another time, so we simply do that here. Commit: 16344a62d3a8f30f4c468b552ce49ca989a1f0b7 https://github.com/galaxyproject/galaxy/commit/16344a62d3a8f30f4c468b552ce4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Alternative fix for missing metadata on datasets that report output size 0 Commit: 161467513b3f911cde15b890c404ed373f4571f4 https://github.com/galaxyproject/galaxy/commit/161467513b3f911cde15b890c404… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Use a for loop when checking size in object store and adjust `empty()` to use the new code. Thanks @nsoranzo. Commit: c8a7b7b07cad174b0d8ed142be9fa3ec4a6ed997 https://github.com/galaxyproject/galaxy/commit/c8a7b7b07cad174b0d8ed142be9f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #5335 from mvdbeek/no_check_data Work around (temporarily) wrong getsize() output Compare: https://github.com/galaxyproject/galaxy/compare/4993249ab6b9...c8a7b7b07cad

1 0

[galaxyproject/galaxy] 7af638: Disable galaxy tour 'path' navigation -- this styl...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7af6381e24c8bcd8efc5c56491eaa02571ba8f17 https://github.com/galaxyproject/galaxy/commit/7af6381e24c8bcd8efc5c56491ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Disable galaxy tour 'path' navigation -- this style of tour nav behaves very poorly with Galaxy and it's pretty easy to get a tour completely *stuck* in reload loops from the user experience, forcing manual cache cleaning or the like to make Galaxy usable again. Commit: 4993249ab6b995026ad1db2ba22eb3014ee0e7c2 https://github.com/galaxyproject/galaxy/commit/4993249ab6b995026ad1db2ba22e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Merge pull request #5340 from dannon/tour_path_tweak Disable galaxy tour 'path' navigation Compare: https://github.com/galaxyproject/galaxy/compare/7659efc68c92...4993249ab6b9

1 0

[galaxyproject/galaxy] c1debb: Refactor galaxy.ini.sample config comments toward ...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1debb7c63d9b61d7391bb8abbf474d6272be662 https://github.com/galaxyproject/galaxy/commit/c1debb7c63d9b61d7391bb8abbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Refactor galaxy.ini.sample config comments toward per-option docs. Commit: 025f92bb73c7347536bf23f2adcff833c3c7284c https://github.com/galaxyproject/galaxy/commit/025f92bb73c7347536bf23f2adcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Random fix for tool filters. Commit: cd30a3424f3e564f3729b083e6abbd642c0122fa https://github.com/galaxyproject/galaxy/commit/cd30a3424f3e564f3729b083e6ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- Don't read global configuration for reports - it doesn't use it. Commit: 6dd0684be3f8825676a7854b6f36faf874f03176 https://github.com/galaxyproject/galaxy/commit/6dd0684be3f8825676a7854b6f36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix ignoring ".sample" in newish path module. Required to correctly detect the extension of sample configuration files. Commit: 4a2a7e79459f65f1686c8814ca1a4a59bf829be5 https://github.com/galaxyproject/galaxy/commit/4a2a7e79459f65f1686c8814ca1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - allow printing comment header on sample description files. Generated from the desc field in the app schema. Commit: 87ace980d73ba7130dd29015145a09bd10f6dd68 https://github.com/galaxyproject/galaxy/commit/87ace980d73ba7130dd29015145a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - fix sample file generation for large default values. The various messages in the Galaxy config were being split across lines and generating invalid YAML. Commit: 146dfd21143774d5451b4417eb223d73cdc23573 https://github.com/galaxyproject/galaxy/commit/146dfd21143774d5451b4417eb22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - hack uWSGI section of sample file generation. Because uWSGI seems really bad at parsing fairly simple, entirely valid YAML. Commit: 72466136d148848b560827ac5b34945d308216ed https://github.com/galaxyproject/galaxy/commit/72466136d148848b560827ac5b34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - improve default value formatting in RST. Commit: 1b58157d003db7a663aa102994aea2873e2f7a7b https://github.com/galaxyproject/galaxy/commit/1b58157d003db7a663aa102994ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- config_manage.py - fix to generate YAML booleans in RST docs. The new default - might as well use that representation. Commit: 0ae21925b7c08c82a8daf4887e78ca66b06f38e9 https://github.com/galaxyproject/galaxy/commit/0ae21925b7c08c82a8daf4887e78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A tmp_config_convert/convert.py Log Message: ----------- convert_yaml - script to convert galaxy.ini.sample to config_schema.yml. Commit: 44341ba5c1ca11bf94eb97c9644d3ac11f1b0268 https://github.com/galaxyproject/galaxy/commit/44341ba5c1ca11bf94eb97c9644d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - setup copy of galaxy.ini.sample for conversion to work on. Commit: 3703f05c33b702bf4c27e14619bb6965f1d4e38f https://github.com/galaxyproject/galaxy/commit/3703f05c33b702bf4c27e14619bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - cleanup noise in conversion's copy of galaxy.ini.sample before conversion. Commit: f058370a98fa84f3b7bdf5286c4e16cd3b811947 https://github.com/galaxyproject/galaxy/commit/f058370a98fa84f3b7bdf5286c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- convert_yaml - run conversion to YAML. Commit: 2b12d0b605732f918e075ae52ea3518e15e61598 https://github.com/galaxyproject/galaxy/commit/2b12d0b605732f918e075ae52ea3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: R config/galaxy.ini.sample A lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- convert_yaml - make sample a schema. Commit: 6901fa9371be28584957fe14a06c73c221ed223b https://github.com/galaxyproject/galaxy/commit/6901fa9371be28584957fe14a06c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: R tmp_config_convert/convert.py R tmp_config_convert/galaxy.ini.sample Log Message: ----------- convert_yaml - remove tmp directory for converting yaml. Commit: 8a9dc5907d377819989d9c0165929c0f378d0559 https://github.com/galaxyproject/galaxy/commit/8a9dc5907d377819989d9c016592… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M Makefile A lib/galaxy/webapps/galaxy/uwsgi_schema.yml Log Message: ----------- yaml_config - Add entry points (e.g. Makefile) for dealing with Galaxy YAML configs. Commit: d08dc05d9588e24a31de3a4a1ba9a07b42ae2e2e https://github.com/galaxyproject/galaxy/commit/d08dc05d9588e24a31de3a4a1ba9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A config/galaxy.yml.sample Log Message: ----------- yaml_config - Generate Galaxy yaml sample. Commit: 4f4928b38677475fd3d70b0435bc9910154ccaba https://github.com/galaxyproject/galaxy/commit/4f4928b38677475fd3d70b0435bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst A doc/source/admin/options.rst M lib/galaxy/webapps/config_manage.py Log Message: ----------- yaml_config - Add RST docs for Galaxy options. Automatically generated from the new specification. Commit: 7bae23e105a46378b6042b6d00b1c61778349c0f https://github.com/galaxyproject/galaxy/commit/7bae23e105a46378b6042b6d00b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M .travis.yml M scripts/common_startup.sh M scripts/galaxy-main M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh Log Message: ----------- yaml_config - update code base for converting galaxy.ini.sample to YAML. Commit: ba35d474a012d2ef60a6191fbfe3ee03ed04e09c https://github.com/galaxyproject/galaxy/commit/ba35d474a012d2ef60a6191fbfe3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/authentication.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/reports.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- yaml_config - update admin docs for switch to YAML config. Commit: 14f0185b217fad83009f2f8822a75774af42ae42 https://github.com/galaxyproject/galaxy/commit/14f0185b217fad83009f2f8822a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- yaml_config - change test wrapper to work with either ini or yml in container. Commit: f06860a8fb200f01154e4822b3931f32c882a706 https://github.com/galaxyproject/galaxy/commit/f06860a8fb200f01154e4822b393… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- yaml_config - Don't parse YAML configurations as ini files. Commit: 60cbcfd1eeb07a8b93e96ce148e911f1dfddb22b https://github.com/galaxyproject/galaxy/commit/60cbcfd1eeb07a8b93e96ce148e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M .ci/first_startup.sh Log Message: ----------- yaml_config - Try to fix first startup CI job for uWSGI default. Commit: bce21ab3f3ef7948a53c251c45f36b386928a29e https://github.com/galaxyproject/galaxy/commit/bce21ab3f3ef7948a53c251c45f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Axe special amqp config handling not used by modern messaging stuff. It wasn't compatible with YAML config and looks unused as far as I can tell. xref https://github.com/galaxyproject/galaxy/commit/6b92bf6eb8ca8a5114fc2ecf7fda… Commit: 8f69d17e8612dd8f33355a4bfd7a46ba635f1403 https://github.com/galaxyproject/galaxy/commit/8f69d17e8612dd8f33355a4bfd7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Don't use uWSGI master mode by default. Fixes Ctrl+C on macOS and is really only important in production configs where you should be using a config file anyway. Commit: cec42d1656f9e6ea5f28b3fd02dbe3eb3f1bf078 https://github.com/galaxyproject/galaxy/commit/cec42d1656f9e6ea5f28b3fd02db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- yaml_config - Update Conda FAQ to link out to last .ini variant of docs for those who need them. Commit: 33abb94252544686b313e7c238e19882bdcbc2af https://github.com/galaxyproject/galaxy/commit/33abb94252544686b313e7c238e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Drop missing --safe-pidfile uWSGI arg until it is released. Commit: f5aa17df1893ed9901de629e602fa052c169fa25 https://github.com/galaxyproject/galaxy/commit/f5aa17df1893ed9901de629e602f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix the use of --set galaxy_config_file with uWSGI where the app name is the PasteDeploy default `app:main`. Commit: 8cd23970fbb1f6250a65f570c288579777464cbf https://github.com/galaxyproject/galaxy/commit/8cd23970fbb1f6250a65f570c288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix for None config_file in web stack stuff. Commit: c99b4ece5bfb0b2d30049796cc9e415e05ef2092 https://github.com/galaxyproject/galaxy/commit/c99b4ece5bfb0b2d30049796cc9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 0585efaaa7d7d63d54088e120e3d5a7cd7e6ef33 https://github.com/galaxyproject/galaxy/commit/0585efaaa7d7d63d54088e120e3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/cluster.md M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst Log Message: ----------- Update newer deployer config docs for switch to YAML config. Commit: 70ee8d00cc3708b866723de9fe784c9c6a2cda3c https://github.com/galaxyproject/galaxy/commit/70ee8d00cc3708b866723de9fe78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Begin config schema for Galaxy (just the new not-in-galaxy.ini logging option for now, the rest will be autogenerated from the sample) Commit: 0664921e00ba5dac623c19f1f5344a7f367aaa62 https://github.com/galaxyproject/galaxy/commit/0664921e00ba5dac623c19f1f534… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: A doc/source/admin/application_server.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst Log Message: ----------- WIP admin documentation updates Commit: 8cf649b33186838f1de2364b696d36f962bc99bf https://github.com/galaxyproject/galaxy/commit/8cf649b33186838f1de2364b696d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: R doc/source/admin/application_server.rst M doc/source/admin/config.rst M doc/source/admin/index.rst M doc/source/admin/reports.rst M doc/source/admin/scaling.md Log Message: ----------- WIP admin docs updates for 18.01 Commit: 5ae0c323ec1ef374a24e18efb59df423424aa80c https://github.com/galaxyproject/galaxy/commit/5ae0c323ec1ef374a24e18efb59d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/webapps/config_manage.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py Log Message: ----------- Expand number of parameters with custom conversion/linting for Galaxy. Add functionality and test case for converting parameter names (e.g. from allow_library_path_paste to allow_path_pate) during conversion. Commit: e8a9cc27ff9e7de6aa70aedc7005773d34d3d59d https://github.com/galaxyproject/galaxy/commit/e8a9cc27ff9e7de6aa70aedc7005… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Locate the Galaxy config file when multiple uWSGI --yaml/--json arguments are used. Commit: 542aa95fa40288b7b754d3908d87967a7ce92e34 https://github.com/galaxyproject/galaxy/commit/542aa95fa40288b7b754d3908d87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- uWSGI: Use --master when daemonizing (required when using http server w/ daemonization) and fix `run.sh --stop-daemon` Commit: 36ecca47e7c859a980c4e775db0ebedbb1c02cef https://github.com/galaxyproject/galaxy/commit/36ecca47e7c859a980c4e775db0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Major updates to the scaling doc for uWSGI Commit: 18b3599207b12ff3019d7d1032101b6bdb99eb75 https://github.com/galaxyproject/galaxy/commit/18b3599207b12ff3019d7d103210… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Remove emperor mode reference Commit: daa7845580c08f7ded43af2aa1ff183fc95c5a05 https://github.com/galaxyproject/galaxy/commit/daa7845580c08f7ded43af2aa1ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Add docstring to LOGGING_CONFIG_DEFAULT so that it is part of the autodoc generated docs, so that it can be linked from statically written docs. Commit: 9204916ac8ffbfb5dad3734275fa3d4843300d20 https://github.com/galaxyproject/galaxy/commit/9204916ac8ffbfb5dad3734275fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/config.rst Log Message: ----------- Galaxy config doc corrections Commit: e0891cac355d062711b645e5e4859cddd6f14cdd https://github.com/galaxyproject/galaxy/commit/e0891cac355d062711b645e5e485… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/conf.py Log Message: ----------- Add intersphinx mapping to the Python 2.7 documentation Commit: db00f97175c2870300617a8de8a5adac16e7b0d5 https://github.com/galaxyproject/galaxy/commit/db00f97175c2870300617a8de8a5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M .gitignore M doc/Makefile M doc/source/admin/config_logging.rst Log Message: ----------- Finish Galaxy logging configuration documentation Commit: adcf2138ae2f2013bed9386356b2b7c5d2d53648 https://github.com/galaxyproject/galaxy/commit/adcf2138ae2f2013bed9386356b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M .gitignore Log Message: ----------- Add missing generated docs to .gitignore Commit: 1e275e84f8d1ce2d1afb5974d62d988ccc0e2bfe https://github.com/galaxyproject/galaxy/commit/1e275e84f8d1ce2d1afb5974d62d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Add loggging configuration to admin docs TOC and move the cluster docs after the scaling docs Commit: 35b1e2c9e7ce349f8cc37d363bb637b96a37266b https://github.com/galaxyproject/galaxy/commit/35b1e2c9e7ce349f8cc37d363bb6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/jobs.md M doc/source/admin/scaling.md Log Message: ----------- Correct the handlers section of the job conf documentation. Commit: 1daa2ae6e5b11843912e2c42af2a0040a32d6030 https://github.com/galaxyproject/galaxy/commit/1daa2ae6e5b11843912e2c42af2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Fix support for proxy prefix under uWSGI. Commit: 1b583fb851ebfc476f53daff7447b37ee8477561 https://github.com/galaxyproject/galaxy/commit/1b583fb851ebfc476f53daff7447… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M doc/source/admin/index.rst A doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/index.rst R doc/source/admin/special_topics/nginx.md Log Message: ----------- Update nginx documentation for uWSGI Commit: 5a0d60537cdf9417c347921f06ae9b22e577274c https://github.com/galaxyproject/galaxy/commit/5a0d60537cdf9417c347921f06ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: A doc/source/admin/apache.md M doc/source/admin/index.rst M doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/index.rst M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Update Apache documentation for uWSGI Commit: 78992968ecd0de1f95b99352b53ea2ecd246f954 https://github.com/galaxyproject/galaxy/commit/78992968ecd0de1f95b99352b53e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Correct documentation line endings Commit: f4131b8d2bcf75c1724e19265cf4ca93dfaefa73 https://github.com/galaxyproject/galaxy/commit/f4131b8d2bcf75c1724e19265cf4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Correct doc typos caught by @nsoranzo Commit: 5fcefe404f7d5cd5d2dbbf0628b265e9d24138f5 https://github.com/galaxyproject/galaxy/commit/5fcefe404f7d5cd5d2dbbf0628b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst M doc/source/admin/apache.md M doc/source/admin/nginx.md A doc/source/admin/proxy_package_layout.rst Log Message: ----------- Attempt to reduce duplication in the proxy documentation through the use of includes, move the multi-config-file discussion to a common page. Commit: efb061d4d4a88b491e77b52b670d18c1f28a81de https://github.com/galaxyproject/galaxy/commit/efb061d4d4a88b491e77b52b670d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Add a tiny bit about uwsgitop Commit: cdc6657bda6a70ecc036f53cf265f1815dc2badc https://github.com/galaxyproject/galaxy/commit/cdc6657bda6a70ecc036f53cf265… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Update galaxy.yml.sample uwsgi section from defaults in get_uwsgi_args.py Commit: 44c291bc663a94635d0b2b1f8e04529dcf307f9d https://github.com/galaxyproject/galaxy/commit/44c291bc663a94635d0b2b1f8e04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.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-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-model.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/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-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-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.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/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/gulpfile.js M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M config/user_preferences_extra_conf.yml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/api/quickstart.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/jobs.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/tools/repositories.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/biostar.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.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/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.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/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/vue.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.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/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml 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 M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config Commit: 3fdbaa3dec07078388ce63bdb1a6f9251ffeb3f1 https://github.com/galaxyproject/galaxy/commit/3fdbaa3dec07078388ce63bdb1a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Regenerate galaxy.yml.sample and documentation for newly added/documented config options. Commit: dd0aeec50013e172a0f49c1e5681cc73ed635213 https://github.com/galaxyproject/galaxy/commit/dd0aeec50013e172a0f49c1e5681… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Fix lint error Commit: 7659efc68c92948e5e8e00404e537752158061cb https://github.com/galaxyproject/galaxy/commit/7659efc68c92948e5e8e00404e53… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .gitignore M .travis.yml M Makefile R config/galaxy.ini.sample A config/galaxy.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/util/path/__init__.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/config_schema.yml A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py Log Message: ----------- Merge pull request #5105 from jmchilton/ini_to_yaml_config Convert options file to YAML and use uWSGI by default Compare: https://github.com/galaxyproject/galaxy/compare/b174dafa36f0...7659efc68c92

1 0

[galaxyproject/usegalaxy-playbook] 73e398: Use IU for swarm communication since all the nodes...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 73e398cfa4693852eccccfe8d864c894842d4c38 https://github.com/galaxyproject/usegalaxy-playbook/commit/73e398cfa4693852… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Use IU for swarm communication since all the nodes are there anyway

1 0

[galaxyproject/galaxy] 3681a4: Move the client build for selenium to run_tests.sh...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3681a4b77f29a9bbb6cbbd6841fc0a9c8a41106e https://github.com/galaxyproject/galaxy/commit/3681a4b77f29a9bbb6cbbd6841fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Move the client build for selenium to run_tests.sh instead of in the external jenkins job configuration. Has the added benefit of skipping the client build when we don't want to run it. Commit: e61d5cdadfdd17b8879b6ec9a74937cb3eac3479 https://github.com/galaxyproject/galaxy/commit/e61d5cdadfdd17b8879b6ec9a749… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Build sourcemaps for the jenkins selenium tests -- I don't know that this actually gets resolved, but it doesn't have a huge impact on build time anyway Commit: b174dafa36f08b7903a3469856672f85cf88e2ec https://github.com/galaxyproject/galaxy/commit/b174dafa36f08b7903a346985667… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #5333 from dannon/jenkins_client_build_tweak Move the client build for selenium to in-repo script Compare: https://github.com/galaxyproject/galaxy/compare/a48d0e9a7faa...b174dafa36f0

1 0

[galaxyproject/galaxy] a847db: Fix tool report submission
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a847dbd3d5e312b13cfe8a90844c8f88d3aedc78 https://github.com/galaxyproject/galaxy/commit/a847dbd3d5e312b13cfe8a90844c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix tool report submission Commit: a6e9504dde8b5c96f6f5fc183c56d9458b996588 https://github.com/galaxyproject/galaxy/commit/a6e9504dde8b5c96f6f5fc183c56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5303 from mvdbeek/sentry_hotfix [17.09] Fix tool report submission with sentry Commit: 6bef1fcbaa1df5690658f7b14512d212c115a0e5 https://github.com/galaxyproject/galaxy/commit/6bef1fcbaa1df5690658f7b14512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- remove an extra F from the folder ID Commit: c3d145ce995e9e5f8e54dd7e81333bcc712bf4ab https://github.com/galaxyproject/galaxy/commit/c3d145ce995e9e5f8e54dd7e8133… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge pull request #5327 from martenson/fix-structured-lib-link [17.09] fix link to library from history structure view Commit: d94148ff7999e0ecee9b617c4daec24da28ea1a5 https://github.com/galaxyproject/galaxy/commit/d94148ff7999e0ecee9b617c4dae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Prevent reloading when data table is being modified Fixes https://github.com/galaxyproject/galaxy/issues/4783. Commit: 8c1807c2879950ef47ccd162b6a7eebc83bc892b https://github.com/galaxyproject/galaxy/commit/8c1807c2879950ef47ccd162b6a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Trigger reload for each modified data table In unindeted one level too much in the previous commit, which would only reload the last table (thanks @dannon). The alternative would be to reload all tables, but I think this is more efficient. Commit: 8f91ae0db9f0ebdc06e6e284fb2fb254db553181 https://github.com/galaxyproject/galaxy/commit/8f91ae0db9f0ebdc06e6e284fb2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Reload tool data tables for 'undeclared_tables' Thanks @nsoranzo! Commit: 3c85407ec80186166a6cb58f35bcb6eda6cc739b https://github.com/galaxyproject/galaxy/commit/3c85407ec80186166a6cb58f35bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #5331 from mvdbeek/data_manager_reload_fix [17.09] Prevent reloading when data table is being modified Commit: a48d0e9a7faabe79045011117f060fd655adc510 https://github.com/galaxyproject/galaxy/commit/a48d0e9a7faabe79045011117f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/toolbox/watcher.py M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bf2c9bab344c...a48d0e9a7faa

1 0

[galaxyproject/galaxy] d94148: Prevent reloading when data table is being modifie...
by GitHub 18 Jan '18

18 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d94148ff7999e0ecee9b617c4daec24da28ea1a5 https://github.com/galaxyproject/galaxy/commit/d94148ff7999e0ecee9b617c4dae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Prevent reloading when data table is being modified Fixes https://github.com/galaxyproject/galaxy/issues/4783. Commit: 8c1807c2879950ef47ccd162b6a7eebc83bc892b https://github.com/galaxyproject/galaxy/commit/8c1807c2879950ef47ccd162b6a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Trigger reload for each modified data table In unindeted one level too much in the previous commit, which would only reload the last table (thanks @dannon). The alternative would be to reload all tables, but I think this is more efficient. Commit: 8f91ae0db9f0ebdc06e6e284fb2fb254db553181 https://github.com/galaxyproject/galaxy/commit/8f91ae0db9f0ebdc06e6e284fb2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Reload tool data tables for 'undeclared_tables' Thanks @nsoranzo! Commit: 3c85407ec80186166a6cb58f35bcb6eda6cc739b https://github.com/galaxyproject/galaxy/commit/3c85407ec80186166a6cb58f35bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #5331 from mvdbeek/data_manager_reload_fix [17.09] Prevent reloading when data table is being modified Compare: https://github.com/galaxyproject/galaxy/compare/c3d145ce995e...3c85407ec801

1 0