- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 32b85e: Only permit yaml.safe_loading of data
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32b85ecb591d01acbbbb9ed1bedd1a48804a0837 https://github.com/galaxyproject/galaxy/commit/32b85ecb591d01acbbbb9ed1bedd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webhooks/__init__.py M scripts/grt/export.py M scripts/grt/upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Only permit yaml.safe_loading of data Event trusted data, belt + suspenders method. Commit: df41d4f4087f9b133750a2c350ea207753f30f54 https://github.com/galaxyproject/galaxy/commit/df41d4f4087f9b133750a2c350ea… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Remove some shell=True and fix commands Commit: cd6a1afaa9980d958ad324fa987a07e7608bf841 https://github.com/galaxyproject/galaxy/commit/cd6a1afaa9980d958ad324fa987a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Replace some os.system calls with subprocess Commit: 73337725bdd654904563dc54b04083a23e4a252d https://github.com/galaxyproject/galaxy/commit/73337725bdd654904563dc54b040… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Two more commands to list Commit: c85db3fd68590d3d2f61b0b3f88026773d9563a0 https://github.com/galaxyproject/galaxy/commit/c85db3fd68590d3d2f61b0b3f880… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- Some more command refactoring Commit: 670897ec5ca2284c7fad453c3d595defe3cca280 https://github.com/galaxyproject/galaxy/commit/670897ec5ca2284c7fad453c3d59… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/system.py Log Message: ----------- One more os command Commit: 9b8e76f9d9df0ae0ba6238d44a8f07b97fe34d6f https://github.com/galaxyproject/galaxy/commit/9b8e76f9d9df0ae0ba6238d44a8f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/managers/citations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py Log Message: ----------- Convert urllib to requests Which has built-in protection against urls like "file:///tmp/a" Commit: db0400298651f6d4c9d909406c3fe632d057bbf7 https://github.com/galaxyproject/galaxy/commit/db0400298651f6d4c9d909406c3f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Log Message: ----------- remove unused imports Commit: a68d6be3a1c6e6fd85c5ae94232467f193156d53 https://github.com/galaxyproject/galaxy/commit/a68d6be3a1c6e6fd85c5ae942324… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- reorder imports Commit: 93ffc4055b145811b86191dae8b865ea45b55fcb https://github.com/galaxyproject/galaxy/commit/93ffc4055b145811b86191dae8b8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- replace check_output with python processing and shell=False Commit: d79a2459a95dfda7856b9898d40d062f00456006 https://github.com/galaxyproject/galaxy/commit/d79a2459a95dfda7856b9898d40d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/webapps/config_manage.py Log Message: ----------- These we will revert to their original yaml.load It would be nice to fix them eventually, but we'll settle for an incremental improvement. Commit: b3261309843f8cfec1a5a589b4628e44e6bf76df https://github.com/galaxyproject/galaxy/commit/b3261309843f8cfec1a5a589b462… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- import ordering Commit: 8f4491bfffce5d13e2199df5d60e06e3672a08c1 https://github.com/galaxyproject/galaxy/commit/8f4491bfffce5d13e2199df5d60e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Consume stderr Commit: 0f7dd52988269dc4567bdbbd71be0fd273741efd https://github.com/galaxyproject/galaxy/commit/0f7dd52988269dc4567bdbbd71be… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Copy changes over Commit: 75df58ae86ff1796f0bb0ea975fc1d0d518c155a https://github.com/galaxyproject/galaxy/commit/75df58ae86ff1796f0bb0ea975fc… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds_3_sites.py Log Message: ----------- fix Commit: fd92ac3eedd145635a74530ba62bb7fea7c540f4 https://github.com/galaxyproject/galaxy/commit/fd92ac3eedd145635a74530ba62b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- revert this change Commit: 27beb7030d99a511a428ad59211a3137a2761559 https://github.com/galaxyproject/galaxy/commit/27beb7030d99a511a428ad59211a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- revert/sync Commit: 1a57c06d6a81dc6f92eb4843c89a7333f874bc32 https://github.com/galaxyproject/galaxy/commit/1a57c06d6a81dc6f92eb4843c89a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix import ordering Thanks @nsoranzo, I appreciate all the comments here. Commit: 290971ca7a28eb579dc2d40c9653b9e160253634 https://github.com/galaxyproject/galaxy/commit/290971ca7a28eb579dc2d40c9653… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/transfer_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py Log Message: ----------- more review comments Commit: 15c73233c52b29ed94066c06ebb1e10c935ae28d https://github.com/galaxyproject/galaxy/commit/15c73233c52b29ed94066c06ebb1… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M scripts/edam_mapping.py Log Message: ----------- fix lint Commit: 19d03edc7ff8384a5360d71365076a2594fb0b8b https://github.com/galaxyproject/galaxy/commit/19d03edc7ff8384a5360d7136507… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- refactor missed call Commit: 626a3dc2995f0d797232aa666f1bdf3e6a5d22dd https://github.com/galaxyproject/galaxy/commit/626a3dc2995f0d797232aa666f1b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- fix ordering Commit: 41574d022249bae4df4b89bfb50c3a599ee5585e https://github.com/galaxyproject/galaxy/commit/41574d022249bae4df4b89bfb50c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- swap for subprocess.call per @nsoranzo suggestion Commit: 0c6dfd7a41a8df8c000b133d8833eb9963ae183e https://github.com/galaxyproject/galaxy/commit/0c6dfd7a41a8df8c000b133d8833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4604 from erasche/hardening Various bits of hardening Compare: https://github.com/galaxyproject/galaxy/compare/9f2582e9fbed...0c6dfd7a41a8

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[galaxyproject/galaxy] caed7b: Use only latest publication
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: caed7b60aa98153049fa2e26f5855833e7cdfce0 https://github.com/galaxyproject/galaxy/commit/caed7b60aa98153049fa2e26f585… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Use only latest publication Commit: 9f2582e9fbed242498810aa67c508a26eb6196fa https://github.com/galaxyproject/galaxy/commit/9f2582e9fbed242498810aa67c50… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Merge pull request #4688 from nsoranzo/citation_fixes Use only latest publication Compare: https://github.com/galaxyproject/galaxy/compare/1c2c59526714...9f2582e9fbed

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[galaxyproject/galaxy] 0b1dd6: Selenium - bug fix for history test options.
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b1dd637a98c9b878972a3b7b0faf783a045f2b3 https://github.com/galaxyproject/galaxy/commit/0b1dd637a98c9b878972a3b7b0fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - bug fix for history test options. Wait on something useful instead of picking an arbitrary sleep time and praying. Commit: aa825d22aa8ec934fc4ec2a30f20fc821c8e3c0b https://github.com/galaxyproject/galaxy/commit/aa825d22aa8ec934fc4ec2a30f20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient issue with saved histories test. Commit: 76fe60180a4b9059d0fb110573e93bf6274be893 https://github.com/galaxyproject/galaxy/commit/76fe60180a4b9059d0fb110573e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Selenium - fix bug where snapshots might be used in tests before it is setup. Commit: 4a4d0498d6a371dc8ddaa226d33ff5cf0a897e69 https://github.com/galaxyproject/galaxy/commit/4a4d0498d6a371dc8ddaa226d33f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - better fix for upload build click before callback registered. Should fix this transient failure. https://jenkins.galaxyproject.org/job/selenium/568/artifact/568-test-errors… Commit: 6168e243b28cd85b8b8b719acc55d3e2108af43a https://github.com/galaxyproject/galaxy/commit/6168e243b28cd85b8b8b719acc55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_custom_builds.py Log Message: ----------- Selenium - fix rerunning test errors for test_custom_builds. Fixed similar problem for saved histories tests with 341667437ae718258a8d543c4e09d187f7f85326. Should fix this problem https://jenkins.galaxyproject.org/job/selenium/568/artifact/568-test-errors…. Commit: c90a84e1c211daf680b7e0a8c7aca246bc3152cf https://github.com/galaxyproject/galaxy/commit/c90a84e1c211daf680b7e0a8c7ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient error in history switching test. History sometimes takes longer than that second to switch in the GUI, so start a retry cycle on that assertion after a half a second. xref https://jenkins.galaxyproject.org/job/selenium/586/artifact/586-test-errors… Commit: 97cf3b94d1571401f3d57a83dd1a644ff356e772 https://github.com/galaxyproject/galaxy/commit/97cf3b94d1571401f3d57a83dd1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_anon_history.py Log Message: ----------- Selenium - fix transiently failing test caused by not waiting on anonymous history loading. After logging out - may need to a wait a second to give the UI and backend a chance to create a new history for the now anoymous user. Pause and let that happen. xref https://jenkins.galaxyproject.org/job/selenium/585/artifact/585-test-errors… Commit: 9d3ed321be4d0179616af7478eb96bb358b29607 https://github.com/galaxyproject/galaxy/commit/9d3ed321be4d0179616af7478eb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient history in test_saved_histories related to fetching history names. xref https://jenkins.galaxyproject.org/job/selenium/588/artifact/588-test-errors… Commit: 9f5309688eb17b92d4733a7f9752f97e5a4139db https://github.com/galaxyproject/galaxy/commit/9f5309688eb17b92d4733a7f9752… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Import order fix. Commit: 1c2c59526714b00fdf17dd854fe65719df976eba https://github.com/galaxyproject/galaxy/commit/1c2c59526714b00fdf17dd854fe6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4687 from jmchilton/selenium_fixes_34 Ever more Selenium fixes. Compare: https://github.com/galaxyproject/galaxy/compare/c20ac3c820c3...1c2c59526714

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[galaxyproject/galaxy] 4311f5: nicer logging for sentry
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4311f5574dbf82574599b4947cc2721a1132675e https://github.com/galaxyproject/galaxy/commit/4311f5574dbf82574599b4947cc2… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- nicer logging for sentry Commit: c20ac3c820c30c70dfbe4de12b645350ec15cf7c https://github.com/galaxyproject/galaxy/commit/c20ac3c820c30c70dfbe4de12b64… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #4693 from erasche/ie-logging-patch-sentry Nicer logging message for sentry Compare: https://github.com/galaxyproject/galaxy/compare/70ba94763e85...c20ac3c820c3

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[galaxyproject/galaxy] 9f4c72: Un-pin flake8 deps for dev branch
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f4c72a345ff629ea4b1430026d15decddf38617 https://github.com/galaxyproject/galaxy/commit/9f4c72a345ff629ea4b1430026d1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Un-pin flake8 deps for dev branch Commit: 70ba94763e8547ed761d6ba42dc14ff72f5f8320 https://github.com/galaxyproject/galaxy/commit/70ba94763e8547ed761d6ba42dc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4689 from nsoranzo/unpin_flake8_deps Un-pin flake8 deps for dev branch Compare: https://github.com/galaxyproject/galaxy/compare/0c23d40b22b6...70ba94763e85

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[galaxyproject/galaxy] 2495ce: Remove overly chatty debug statement in workflow o...
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2495ceae267da873813d2dc1aae145b686d18672 https://github.com/galaxyproject/galaxy/commit/2495ceae267da873813d2dc1aae1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove overly chatty debug statement in workflow output cleanup -- this happens pretty often and much of the time is not a problem at all. If we have to track down any new issues with workflow output cleanup, it's easy enough to temporarily add this logging. Commit: 244fc834cd4dd3980cc3edb755d22ca5a9372421 https://github.com/galaxyproject/galaxy/commit/244fc834cd4dd3980cc3edb755d2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index. Commit: 832da6ca66cba8fe155adccd4d327289c9e04430 https://github.com/galaxyproject/galaxy/commit/832da6ca66cba8fe155adccd4d32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #4674 from natefoo/use-pypi [17.09] Explicitly include PyPI as an --extra-index-url to pip Commit: 74ad0acb52031355c7efe28b00d1d9b0205174f2 https://github.com/galaxyproject/galaxy/commit/74ad0acb52031355c7efe28b00d1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Remove repetition in Galaxy env setup in the job script and fix issues with remote metadata on Pulsar. Commit: 276af4db2ab5e81f4af8f35b7d09f48d9fed8dcd https://github.com/galaxyproject/galaxy/commit/276af4db2ab5e81f4af8f35b7d09… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Job script enhancements based on feedback. Commit: 53095d688be81a36c31b9721caebf58b383cfe72 https://github.com/galaxyproject/galaxy/commit/53095d688be81a36c31b9721caeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/metadata.py Log Message: ----------- Fix remote datatypes_conf.xml and registry.xml param rewriting with Pulsar Commit: db5185cca0bb9b5f59d8fcf218eb4c5d81cb5911 https://github.com/galaxyproject/galaxy/commit/db5185cca0bb9b5f59d8fcf218eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pulsar release was 0.8.0 not 0.7.5 Commit: 2669ab022ed2f90faac54c510014f87783efeaa0 https://github.com/galaxyproject/galaxy/commit/2669ab022ed2f90faac54c510014… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pass job output file unqualified names to Pulsar so that it can create them before running the job. Commit: 3344c77a188cd92ffb2e7150a4f4a2f4f7facedb https://github.com/galaxyproject/galaxy/commit/3344c77a188cd92ffb2e7150a4f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Bump pulsar lib version to 0.8.0 for output touch support. Commit: c7699cd3a0e16b9522af334cf2ea1a107fbe5f57 https://github.com/galaxyproject/galaxy/commit/c7699cd3a0e16b9522af334cf2ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix lint error Commit: 27a28e2c406d274e396cf3cb095576ebae9cd38c https://github.com/galaxyproject/galaxy/commit/27a28e2c406d274e396cf3cb0955… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #4662 from natefoo/pulsar-touch-outputs [17.09] Pass job output file unqualified names to Pulsar so that it can create them before running the job Commit: d1be9e6a8fa1a383b3f75d1ea5f1b0d486b69258 https://github.com/galaxyproject/galaxy/commit/d1be9e6a8fa1a383b3f75d1ea5f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #4622 from natefoo/pulsar-remote-metadata-fixes [17.09] Pulsar remote metadata fixes Commit: 7896413b2b6a55ea99958504134ab6027baefbe8 https://github.com/galaxyproject/galaxy/commit/7896413b2b6a55ea99958504134a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #4671 from dannon/remove_debug [17.09] Remove chatty debug statement Commit: 41013563e5e15745fd2bf796340578f6d758fbe8 https://github.com/galaxyproject/galaxy/commit/41013563e5e15745fd2bf7963405… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M CITATION Log Message: ----------- Update CITATION file with 2016 paper Commit: 3ae6318b02e61fcf997b6d2726f12851f51aa802 https://github.com/galaxyproject/galaxy/commit/3ae6318b02e61fcf997b6d2726f1… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Merge pull request #4686 from mvdbeek/citation_update Update CITATION file with 2016 paper Commit: 0c23d40b22b659abc3636b76a15fb7d392cbb92f https://github.com/galaxyproject/galaxy/commit/0c23d40b22b659abc3636b76a15f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9e4259192dd7...0c23d40b22b6

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[galaxyproject/galaxy] 410135: Update CITATION file with 2016 paper
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 41013563e5e15745fd2bf796340578f6d758fbe8 https://github.com/galaxyproject/galaxy/commit/41013563e5e15745fd2bf7963405… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M CITATION Log Message: ----------- Update CITATION file with 2016 paper Commit: 3ae6318b02e61fcf997b6d2726f12851f51aa802 https://github.com/galaxyproject/galaxy/commit/3ae6318b02e61fcf997b6d2726f1… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Merge pull request #4686 from mvdbeek/citation_update Update CITATION file with 2016 paper Compare: https://github.com/galaxyproject/galaxy/compare/7896413b2b6a...3ae6318b02e6

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[galaxyproject/galaxy]
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/afgane-patch-1 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy]
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/revert-4356-revert-4355-patch-wrong-folder-id Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 31e272: Selenium - handle potentially stale elements when ...
by GitHub 23 Sep '17

23 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31e2721aabf1eaec6f91c71e4f78ee7543da8f7f https://github.com/galaxyproject/galaxy/commit/31e2721aabf1eaec6f91c71e4f78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - handle potentially stale elements when fetching tags. https://jenkins.galaxyproject.org/job/selenium/529/artifact/529-test-errors… Commit: 9e6e340adc99884a88dc50a2d6d35cdbd3f74fc6 https://github.com/galaxyproject/galaxy/commit/9e6e340adc99884a88dc50a2d6d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Selenium - handle potentially stale search box on workflow index page. https://jenkins.galaxyproject.org/job/selenium/530/artifact/530-test-errors… Commit: 3ffdfc67e75a608c05b35086233d40d7c09440cd https://github.com/galaxyproject/galaxy/commit/3ffdfc67e75a608c05b35086233d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - catch popups fading out as transitions to retry various actions on. Previously we only detected transitions for retrying actions based on stale element exceptions, this expands that to include popups that may be fading out for instance. I think this is what is happening with the transiently failing test here https://jenkins.galaxyproject.org/job/selenium/528/artifact/528-test-errors…. The exception indicates that a click was not clickable because a modal element that was fading out - though it had been previously clickable. I think this should fix that. Commit: 77b61ba82d3eec55c5acd2ae4ad3ec9fde0cc9db https://github.com/galaxyproject/galaxy/commit/77b61ba82d3eec55c5acd2ae4ad3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_options.py Log Message: ----------- Selenium - attempted fix for transiently failing history options test. Comments inline about this - but the target failure I'm hoping this fixes is: https://jenkins.galaxyproject.org/job/selenium/528/artifact/528-test-errors… Commit: 17348a62fe92716ed80cac6f0925e5d5c3203deb https://github.com/galaxyproject/galaxy/commit/17348a62fe92716ed80cac6f0925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Selenium - more robust inline searching for published histories grid. Refactor recent search improvement for workflow management into a method that can be shared with published histories grid. Should address the transient failure test here: https://jenkins.galaxyproject.org/job/selenium/521/artifact/521-test-errors… Commit: cf037fcc0c0e1f8954361812ec36d14515c8f3ab https://github.com/galaxyproject/galaxy/commit/cf037fcc0c0e1f8954361812ec36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Selenium - more robust modal checking in test_workflow_editor. During this transient failure: https://jenkins.galaxyproject.org/job/selenium/519/artifact/519-test-errors… the workflow was still loading when an assertion about the resulting modal text was issued. Avoiding the arbitrary sleep and instead just retrying the assertion until it holds true or times out is more robust and should prevent that. Commit: 341667437ae718258a8d543c4e09d187f7f85326 https://github.com/galaxyproject/galaxy/commit/341667437ae718258a8d543c4e09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix selenium test retrying of tests in test_saved_histories. The automatic retrying of tests only runs for methods - not for the full test case (if that makes sense) - so setUp() isn't rerun. By refactoring the login action out of the setUp method and into the test function for these cases - when the test is retried the user should be logged back in again as well. Commit: 3014b1068bc4b7dc42d3f4c0754f6eed881b453f https://github.com/galaxyproject/galaxy/commit/3014b1068bc4b7dc42d3f4c0754f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- remove unused import Commit: 9e4259192dd705e5c1b5a21a55b46ea685caad52 https://github.com/galaxyproject/galaxy/commit/9e4259192dd705e5c1b5a21a55b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4676 from jmchilton/selenium_fixes_33 Another round of small Selenium fixes. Compare: https://github.com/galaxyproject/galaxy/compare/22930eb56853...9e4259192dd7

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[galaxyproject/galaxy] 2495ce: Remove overly chatty debug statement in workflow o...
by GitHub 23 Sep '17

23 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 2495ceae267da873813d2dc1aae145b686d18672 https://github.com/galaxyproject/galaxy/commit/2495ceae267da873813d2dc1aae1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove overly chatty debug statement in workflow output cleanup -- this happens pretty often and much of the time is not a problem at all. If we have to track down any new issues with workflow output cleanup, it's easy enough to temporarily add this logging. Commit: 7896413b2b6a55ea99958504134ab6027baefbe8 https://github.com/galaxyproject/galaxy/commit/7896413b2b6a55ea99958504134a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #4671 from dannon/remove_debug [17.09] Remove chatty debug statement Compare: https://github.com/galaxyproject/galaxy/compare/d1be9e6a8fa1...7896413b2b6a

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[galaxyproject/galaxy] 8fa1f9: Small tweaks to fixup #2866.
by GitHub 22 Sep '17

22 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8fa1f9a2fea0e15213bfc4c666feaff472076225 https://github.com/galaxyproject/galaxy/commit/8fa1f9a2fea0e15213bfc4c666fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/reports/config.py M scripts/common_startup_functions.sh Log Message: ----------- Small tweaks to fixup #2866. Commit: 22930eb56853067bdcb1e4eec6abcb72f483426a https://github.com/galaxyproject/galaxy/commit/22930eb56853067bdcb1e4eec6ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/reports/config.py M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #4679 from jmchilton/yaml_config_fixes [17.09] Small tweaks to configuration and static assets Compare: https://github.com/galaxyproject/galaxy/compare/2c7bdbfe53d8...22930eb56853

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[galaxyproject/galaxy] 74ad0a: Remove repetition in Galaxy env setup in the job s...
by GitHub 22 Sep '17

22 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 74ad0acb52031355c7efe28b00d1d9b0205174f2 https://github.com/galaxyproject/galaxy/commit/74ad0acb52031355c7efe28b00d1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Remove repetition in Galaxy env setup in the job script and fix issues with remote metadata on Pulsar. Commit: 276af4db2ab5e81f4af8f35b7d09f48d9fed8dcd https://github.com/galaxyproject/galaxy/commit/276af4db2ab5e81f4af8f35b7d09… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Job script enhancements based on feedback. Commit: 53095d688be81a36c31b9721caebf58b383cfe72 https://github.com/galaxyproject/galaxy/commit/53095d688be81a36c31b9721caeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/metadata.py Log Message: ----------- Fix remote datatypes_conf.xml and registry.xml param rewriting with Pulsar Commit: db5185cca0bb9b5f59d8fcf218eb4c5d81cb5911 https://github.com/galaxyproject/galaxy/commit/db5185cca0bb9b5f59d8fcf218eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pulsar release was 0.8.0 not 0.7.5 Commit: c7699cd3a0e16b9522af334cf2ea1a107fbe5f57 https://github.com/galaxyproject/galaxy/commit/c7699cd3a0e16b9522af334cf2ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix lint error Commit: d1be9e6a8fa1a383b3f75d1ea5f1b0d486b69258 https://github.com/galaxyproject/galaxy/commit/d1be9e6a8fa1a383b3f75d1ea5f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #4622 from natefoo/pulsar-remote-metadata-fixes [17.09] Pulsar remote metadata fixes Compare: https://github.com/galaxyproject/galaxy/compare/27a28e2c406d...d1be9e6a8fa1

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[galaxyproject/galaxy] 2669ab: Pass job output file unqualified names to Pulsar s...
by GitHub 22 Sep '17

22 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 2669ab022ed2f90faac54c510014f87783efeaa0 https://github.com/galaxyproject/galaxy/commit/2669ab022ed2f90faac54c510014… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Pass job output file unqualified names to Pulsar so that it can create them before running the job. Commit: 3344c77a188cd92ffb2e7150a4f4a2f4f7facedb https://github.com/galaxyproject/galaxy/commit/3344c77a188cd92ffb2e7150a4f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Bump pulsar lib version to 0.8.0 for output touch support. Commit: 27a28e2c406d274e396cf3cb095576ebae9cd38c https://github.com/galaxyproject/galaxy/commit/27a28e2c406d274e396cf3cb0955… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #4662 from natefoo/pulsar-touch-outputs [17.09] Pass job output file unqualified names to Pulsar so that it can create them before running the job Compare: https://github.com/galaxyproject/galaxy/compare/832da6ca66cb...27a28e2c406d

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[galaxyproject/usegalaxy-playbook] dd9ab8: Make swarmscale a bit heartier
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd9ab853788639b2b2916a215a8d955258d55e98 https://github.com/galaxyproject/usegalaxy-playbook/commit/dd9ab853788639b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/common/stack.yml M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyswarmscaleservers/vault.yml M roles/usegalaxy_swarmscale/files/delete.yml M roles/usegalaxy_swarmscale/files/inc_spawn.yml M roles/usegalaxy_swarmscale/files/instance A roles/usegalaxy_swarmscale/files/leave.yml M roles/usegalaxy_swarmscale/files/spawn.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- Make swarmscale a bit heartier

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[galaxyproject/galaxy] 244fc8: Explicitly include PyPI as an --extra-index-url to...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 244fc834cd4dd3980cc3edb755d22ca5a9372421 https://github.com/galaxyproject/galaxy/commit/244fc834cd4dd3980cc3edb755d2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index. Commit: 832da6ca66cba8fe155adccd4d327289c9e04430 https://github.com/galaxyproject/galaxy/commit/832da6ca66cba8fe155adccd4d32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #4674 from natefoo/use-pypi [17.09] Explicitly include PyPI as an --extra-index-url to pip Compare: https://github.com/galaxyproject/galaxy/compare/4dbadc26e4bb...832da6ca66cb

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[galaxyproject/galaxy] 4ee180: Fix Selenium tests outright broken in #4669.
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ee18019e0750a363ba34ae5acece4faa8aec850 https://github.com/galaxyproject/galaxy/commit/4ee18019e0750a363ba34ae5acec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix Selenium tests outright broken in #4669. Way to go @jmchilton. Commit: 2c7bdbfe53d8cdf3bbbbc1b3061a873c99c1b42e https://github.com/galaxyproject/galaxy/commit/2c7bdbfe53d8cdf3bbbbc1b3061a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4673 from jmchilton/selenium_fixes_32 Fix Selenium tests outright broken in #4669. Compare: https://github.com/galaxyproject/galaxy/compare/41b13f6d8551...2c7bdbfe53d8

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[galaxyproject/galaxy] a3ff12: Explicitly write registry.xml when creating a job ...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3ff1297435721d3f687052382b75a2a2f2f9b25 https://github.com/galaxyproject/galaxy/commit/a3ff1297435721d3f687052382b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Explicitly write registry.xml when creating a job for the upload tool Commit: d980dfa162b340423ffd8822ac9dcdf6f1997e80 https://github.com/galaxyproject/galaxy/commit/d980dfa162b340423ffd8822ac9d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Write registry.xml for all tools that require galaxy's python env This should cover the upload and data_source tools. Commit: b7b3ffb1813f31b7811bdbb35602743294356f66 https://github.com/galaxyproject/galaxy/commit/b7b3ffb1813f31b7811bdbb35602… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Fix unit test failure Commit: 7fd6813dd7fcf373cc09a3da6fd6f4bf5c8b0863 https://github.com/galaxyproject/galaxy/commit/7fd6813dd7fcf373cc09a3da6fd6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M tox.ini Log Message: ----------- pin flake8 deps for release Commit: a25b6e5b0eb5ed97e789e1b4b8643be775a55e05 https://github.com/galaxyproject/galaxy/commit/a25b6e5b0eb5ed97e789e1b4b864… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4648 from martenson/version-17.09 [17.09]Update version to 17.09.rc1 Commit: f46a5c1797fb4c1f3fc663addf83ce9a411beac6 https://github.com/galaxyproject/galaxy/commit/f46a5c1797fb4c1f3fc663addf83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4650 from martenson/release_17.09 [17.09] pin flake8 deps for release Commit: ee6b8b1af8c997d874a9ad7213231582b69cf82c https://github.com/galaxyproject/galaxy/commit/ee6b8b1af8c997d874a9ad721323… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M tox.ini Log Message: ----------- pin the last flake8 thanks @nsoranzo :eagle: :eyes: Commit: 0e89935460a54fa846dff53041fcfe3b8e7e9ecd https://github.com/galaxyproject/galaxy/commit/0e89935460a54fa846dff53041fc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4652 from martenson/release_17.09 [17.09] pin the last missing flake8 Commit: 5404f7cda7ca4f3b9a2c423bdd29898fb7d8c911 https://github.com/galaxyproject/galaxy/commit/5404f7cda7ca4f3b9a2c423bdd29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M templates/display_base.mako M templates/display_common.mako Log Message: ----------- Small (temporary, mako is going away) layer to support modern routes in old display_base pages (workflow, history, etc). Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: c9aead91d75a1e0e636cf08ba725a8c2f8ff300a https://github.com/galaxyproject/galaxy/commit/c9aead91d75a1e0e636cf08ba725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M templates/display_base.mako M templates/display_common.mako Log Message: ----------- Merge pull request #4656 from dannon/display_link_fixes [17.09] Fix links on workflow, history items. Commit: 5d7b524b5785fcb483dbc7381c871595a070b1b0 https://github.com/galaxyproject/galaxy/commit/5d7b524b5785fcb483dbc7381c87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure [17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 706a5b2cd2bdac4c30a5b4d86aaf73a9e4ffa291 https://github.com/galaxyproject/galaxy/commit/706a5b2cd2bdac4c30a5b4d86aaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: cfabe37d69549e919d3fce15cbcca108fdcf1597 https://github.com/galaxyproject/galaxy/commit/cfabe37d69549e919d3fce15cbcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 4dbadc26e4bb4e40ca04ef746247abc504e98ca2 https://github.com/galaxyproject/galaxy/commit/4dbadc26e4bb4e40ca04ef746247… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 41b13f6d855180746576a40e0e209333746a4a8a https://github.com/galaxyproject/galaxy/commit/41b13f6d855180746576a40e0e20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M templates/display_base.mako M templates/display_common.mako M test/unit/jobs/test_job_wrapper.py M tox.ini Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/00677fc0f62c...41b13f6d8551

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[galaxyproject/galaxy] a3ff12: Explicitly write registry.xml when creating a job ...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a3ff1297435721d3f687052382b75a2a2f2f9b25 https://github.com/galaxyproject/galaxy/commit/a3ff1297435721d3f687052382b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Explicitly write registry.xml when creating a job for the upload tool Commit: d980dfa162b340423ffd8822ac9dcdf6f1997e80 https://github.com/galaxyproject/galaxy/commit/d980dfa162b340423ffd8822ac9d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Write registry.xml for all tools that require galaxy's python env This should cover the upload and data_source tools. Commit: b7b3ffb1813f31b7811bdbb35602743294356f66 https://github.com/galaxyproject/galaxy/commit/b7b3ffb1813f31b7811bdbb35602… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Fix unit test failure Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 5d7b524b5785fcb483dbc7381c871595a070b1b0 https://github.com/galaxyproject/galaxy/commit/5d7b524b5785fcb483dbc7381c87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure [17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 706a5b2cd2bdac4c30a5b4d86aaf73a9e4ffa291 https://github.com/galaxyproject/galaxy/commit/706a5b2cd2bdac4c30a5b4d86aaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: cfabe37d69549e919d3fce15cbcca108fdcf1597 https://github.com/galaxyproject/galaxy/commit/cfabe37d69549e919d3fce15cbcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 4dbadc26e4bb4e40ca04ef746247abc504e98ca2 https://github.com/galaxyproject/galaxy/commit/4dbadc26e4bb4e40ca04ef746247… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/c9aead91d75a...4dbadc26e4bb

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[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 706a5b2cd2bdac4c30a5b4d86aaf73a9e4ffa291 https://github.com/galaxyproject/galaxy/commit/706a5b2cd2bdac4c30a5b4d86aaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: cfabe37d69549e919d3fce15cbcca108fdcf1597 https://github.com/galaxyproject/galaxy/commit/cfabe37d69549e919d3fce15cbcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/5d7b524b5785...cfabe37d6954

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[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 706a5b2cd2bdac4c30a5b4d86aaf73a9e4ffa291 https://github.com/galaxyproject/galaxy/commit/706a5b2cd2bdac4c30a5b4d86aaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/a9facdc7568f...706a5b2cd2bd

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[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/14ceb6d91b57...e178879c0f9f

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[galaxyproject/galaxy] aa68d3: Improve robustness of published workflow display t...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa68d38735acda43a078a3412afef3c604d2e205 https://github.com/galaxyproject/galaxy/commit/aa68d38735acda43a078a3412afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Improve robustness of published workflow display test case. Failed twice in different ways here https://jenkins.galaxyproject.org/job/selenium/484/ - this should address both cases. Commit: 00677fc0f62cc37732528f2af5ac964ce4239fad https://github.com/galaxyproject/galaxy/commit/00677fc0f62cc37732528f2af5ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4653 from jmchilton/selenium_fixes_28 Improve robustness of published workflow display test case. Compare: https://github.com/galaxyproject/galaxy/compare/35cd9339453d...00677fc0f62c

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[galaxyproject/galaxy] 01eb5f: Aggressively retry buggy submit_login() function i...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 01eb5f04e6661d389d8c8f681373b5c50fe259b9 https://github.com/galaxyproject/galaxy/commit/01eb5f04e6661d389d8c8f681373… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Aggressively retry buggy submit_login() function in Selenium tests. I don't get why when we click submit the user does not actually get logged in, but based on the last round of improved error messages this seems to be the case. You might think there is some callback in the login form that doesn't get registered by the time Selenium clicks the submit button - but this doesn't seem to be the case - I don't see any jquery magic happening in login.mako. Should fix failures like this: https://jenkins.galaxyproject.org/job/selenium/482/testReport/junit/seleniu… I'd say at this point this is the most common problem in the Selenium tests. This also introduces a framework for taking state snapshots of the Galaxy interface during tests that will only get written out if the tests fail. We now take screenshots before and after submitting the login form but this is a general purpose debugging mechanism that could be used other places. Commit: 35cd9339453dd245ab4c317517ea1dfafb6af147 https://github.com/galaxyproject/galaxy/commit/35cd9339453dd245ab4c317517ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4655 from jmchilton/selenium_fixes_29 Aggressively retry buggy submit_login() function in Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/24557fdeaab2...35cd9339453d

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[galaxyproject/galaxy] a45e7e: Fix transiently failing saved histories due to suc...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a45e7e196b03b6467ddea0bcacac9914830f0bb9 https://github.com/galaxyproject/galaxy/commit/a45e7e196b03b6467ddea0bcacac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix transiently failing saved histories due to success message disappearing. Commit: 24557fdeaab24ca8a763478ca5d5a2303f00243f https://github.com/galaxyproject/galaxy/commit/24557fdeaab24ca8a763478ca5d5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4669 from jmchilton/selenium_fixes_31 Fix transiently failing saved histories due to success message disappearing. Compare: https://github.com/galaxyproject/galaxy/compare/98f2c108238e...24557fdeaab2

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