October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10 Commit: ae140949a8696a3b12aee83a9176e8091787a85d https://github.com/galaxyproject/galaxy/commit/ae140949a8696a3b12aee83a9176… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/54d3994131f2...ae140949a869

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[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/b04aafa8e871...34344a7563a3

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[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Compare: https://github.com/galaxyproject/galaxy/compare/f925ffe4b743...8e199a33cf25

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[galaxyproject/galaxy] d58809: Remove duplicate (invalid) return in form-paramete...
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d58809b16547ef2c37a5cb6347f303cb1f7b048f https://github.com/galaxyproject/galaxy/commit/d58809b16547ef2c37a5cb6347f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Remove duplicate (invalid) return in form-parameters.js Commit: 00c8c2d01389b799e9004ca9ca77941521901cb0 https://github.com/galaxyproject/galaxy/commit/00c8c2d01389b799e9004ca9ca77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Bundles Commit: be0541db9771e6ad1e8a78d1335fdde4b8060761 https://github.com/galaxyproject/galaxy/commit/be0541db9771e6ad1e8a78d1335f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #4826 from dannon/double_return_invalid Fix double return in form-parameters Compare: https://github.com/galaxyproject/galaxy/compare/2a2534789d6b...be0541db9771

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[galaxyproject/galaxy] 54357f: Write out registry.xml file in case jobs are missi...
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54357f38e9929f3f3a084f298bd644395976a91a https://github.com/galaxyproject/galaxy/commit/54357f38e9929f3f3a084f298bd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Write out registry.xml file in case jobs are missing this file Commit: 94540adda48fbc0c75ffd6b7caa56864b387b721 https://github.com/galaxyproject/galaxy/commit/94540adda48fbc0c75ffd6b7caa5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Clarify previous commit. Commit: a474822f3cbe232b82d23c48507e48f65b6f16c0 https://github.com/galaxyproject/galaxy/commit/a474822f3cbe232b82d23c48507e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #4728 from mvdbeek/fix_registry_missing [17.05] Fix metadata for deleted registry by Galaxy shutdown. Commit: e4518ff3e3d628f2cd47ea48217da6352ef11e30 https://github.com/galaxyproject/galaxy/commit/e4518ff3e3d628f2cd47ea48217d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: b5ded00eb50181f17b3c003e1b7c895098b85d25 https://github.com/galaxyproject/galaxy/commit/b5ded00eb50181f17b3c003e1b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: 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 Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 545d5556588dfe28c8a9857333366ba62dbcd2fd https://github.com/galaxyproject/galaxy/commit/545d5556588dfe28c8a985733336… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: 2f79351e3cdb1fe9705f00590038b11cba4b428e https://github.com/galaxyproject/galaxy/commit/2f79351e3cdb1fe9705f00590038… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 9fa9d42c5093ddd8f70193cc6a07ae0af0394f8c https://github.com/galaxyproject/galaxy/commit/9fa9d42c5093ddd8f70193cc6a07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix backport issues Commit: f925ffe4b743d080585bc6d151dc8ca98cc4f171 https://github.com/galaxyproject/galaxy/commit/f925ffe4b743d080585bc6d151dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 Commit: e60f324b66676cc5020aa74bfa011f886eaeca68 https://github.com/galaxyproject/galaxy/commit/e60f324b66676cc5020aa74bfa01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 Commit: ef268027191b526b8c8dfe69c3d8352c0412ce1d https://github.com/galaxyproject/galaxy/commit/ef268027191b526b8c8dfe69c3d8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__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/webhooks/__init__.py Log Message: ----------- Hardening backport differences from dev present in 16.10 but not 16.07 Commit: d70713d07a3c4d98b71df9247bbd8644ab6b2b40 https://github.com/galaxyproject/galaxy/commit/d70713d07a3c4d98b71df9247bbd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: fe9839bf7ca720061548ff3bcebdc79062e7adf5 https://github.com/galaxyproject/galaxy/commit/fe9839bf7ca720061548ff3bcebd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: 36b974c90514332c6cb732f9c376a66767100944 https://github.com/galaxyproject/galaxy/commit/36b974c90514332c6cb732f9c376… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 3bb5d825c13ae2dbd366f24dc316bcdaa7171eb9 https://github.com/galaxyproject/galaxy/commit/3bb5d825c13ae2dbd366f24dc316… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 8d573db729a92344ad9115b7657ace07a4718a21 https://github.com/galaxyproject/galaxy/commit/8d573db729a92344ad9115b7657a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 6d8f8ecb466ae75ca7d586496512cb70206a08f6 https://github.com/galaxyproject/galaxy/commit/6d8f8ecb466ae75ca7d586496512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: b04aafa8e871f4d2f3bf7a636ccf0ef432fda875 https://github.com/galaxyproject/galaxy/commit/b04aafa8e871f4d2f3bf7a636ccf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M .travis.yml M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M setup.cfg M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py M tox.ini Log Message: ----------- Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 Commit: 139ba7c13e38a98a090a91167e0538f259baa7c2 https://github.com/galaxyproject/galaxy/commit/139ba7c13e38a98a090a91167e05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 03087e5ee77701e410e7d9336a74cedf3206e3f3 https://github.com/galaxyproject/galaxy/commit/03087e5ee77701e410e7d9336a74… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: f9213b16f5bb26b2b7176d50602d852ea4e08562 https://github.com/galaxyproject/galaxy/commit/f9213b16f5bb26b2b7176d50602d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: 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 Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 7ad6182ef4952480354e4737b72c062fc75be93e https://github.com/galaxyproject/galaxy/commit/7ad6182ef4952480354e4737b72c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: b13f5d7f943106cf27670c7153e6c8967a749bcf https://github.com/galaxyproject/galaxy/commit/b13f5d7f943106cf27670c7153e6… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 24c8a26852aecdcc5d8d23300e551f282b90c628 https://github.com/galaxyproject/galaxy/commit/24c8a26852aecdcc5d8d23300e55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix backport issues Commit: 9955c4d24bff197b01f2ff6227fdfb06224d9ab9 https://github.com/galaxyproject/galaxy/commit/9955c4d24bff197b01f2ff6227fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 950f92627176068609fc5191c72f681e3e16fb22 https://github.com/galaxyproject/galaxy/commit/950f92627176068609fc5191c72f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: d8ee1a9a8d42f1287262a25fa282799d44d4f583 https://github.com/galaxyproject/galaxy/commit/d8ee1a9a8d42f1287262a25fa282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Revert ignoring I201 from 16.10 in 17.01 Commit: 25fc0982b75243e9c95a5312b56359f83bc72e87 https://github.com/galaxyproject/galaxy/commit/25fc0982b75243e9c95a5312b563… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Log Message: ----------- Merge branch 'release_16.10' into backport-hardening-17.01 Commit: 86929ff9f01201f0ef50429b96d4ab83a3887e8f https://github.com/galaxyproject/galaxy/commit/86929ff9f01201f0ef50429b96d4… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py Log Message: ----------- add augustus and snap datatypes Commit: 54d3994131f28963a1c3c4beccaf029a121d15b1 https://github.com/galaxyproject/galaxy/commit/54d3994131f28963a1c3c4beccaf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.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/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 Commit: 8fa7cc8a1dcc1ced376912692aa0162ea133de12 https://github.com/galaxyproject/galaxy/commit/8fa7cc8a1dcc1ced376912692aa0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- sniff snaphmm too Commit: deedb17caf66760855b4749771fa0e1655618dc0 https://github.com/galaxyproject/galaxy/commit/deedb17caf66760855b4749771fa… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/datatypes/annotation.py Log Message: ----------- edam terms Commit: 66820a46eba8f8adc0a573a8c2727e28e0de23e8 https://github.com/galaxyproject/galaxy/commit/66820a46eba8f8adc0a573a8c272… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-17 (Tue, 17 Oct 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/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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: ----------- Backport of hardening fixes to 17.05 Commit: 60b5abfa3e85502631fc922b231f51f63b118234 https://github.com/galaxyproject/galaxy/commit/60b5abfa3e85502631fc922b231f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix TDT's dependency Commit: 9241c9e3dbf67bb3f55fa89181c80a13e5466e0e https://github.com/galaxyproject/galaxy/commit/9241c9e3dbf67bb3f55fa89181c8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into backport-hardening-17.05 Commit: 7906a946f110ef8f55524121e3addb320982979c https://github.com/galaxyproject/galaxy/commit/7906a946f110ef8f55524121e3ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Merge pull request #4815 from anatskiy/release_17.09_tdt_fix Fix TDT's dependency Commit: c96e9945a613a27f4826baf3c0e61edda2dfa0bb https://github.com/galaxyproject/galaxy/commit/c96e9945a613a27f4826baf3c0e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Force absolute import in much of galaxy.util Commit: b15f5a74957ec154e7cd501f0a65936d11206aa0 https://github.com/galaxyproject/galaxy/commit/b15f5a74957ec154e7cd501f0a65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Merge pull request #4817 from dannon/backport_abs_import [17.09] Backport abs-import changes from util. Commit: ef203a69e95facee788086fc507b062528cbb638 https://github.com/galaxyproject/galaxy/commit/ef203a69e95facee788086fc507b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 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/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.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 #4816 from natefoo/backport-hardening-17.05 [17.05] Various bits of hardening from #4604 Commit: 136925087e08eaef706e38b35299d1daa1ca2266 https://github.com/galaxyproject/galaxy/commit/136925087e08eaef706e38b35299… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/annotation.py Log Message: ----------- Merge pull request #4808 from abretaud/augsnaptypes [17.09] Add augustus and snap datatypes Commit: 7fc354f11806208a074595455342e941f632fd00 https://github.com/galaxyproject/galaxy/commit/7fc354f11806208a074595455342… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Write out registry.xml file in case jobs are missing this file Commit: 7a2b7f27c51a883f89eed8ef4022d638d6acde1f https://github.com/galaxyproject/galaxy/commit/7a2b7f27c51a883f89eed8ef4022… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Clarify previous commit. Commit: 0f311470d9c2ce0a2de869b32c84143cd56acc6e https://github.com/galaxyproject/galaxy/commit/0f311470d9c2ce0a2de869b32c84… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-18 (Wed, 18 Oct 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/web/base/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: ----------- Backport of hardening fixes to 17.09 Commit: a3daa338b8941a1676d0e0f36b854c3c93f73fbe https://github.com/galaxyproject/galaxy/commit/a3daa338b8941a1676d0e0f36b85… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into backport-hardening-17.09 Commit: 07e58a1cdf181bb277ef322ce51af4b2cdc86d00 https://github.com/galaxyproject/galaxy/commit/07e58a1cdf181bb277ef322ce51a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-18 (Wed, 18 Oct 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/handler.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/web/base/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/galaxy_ext/metadata/set_metadata.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 #4824 from natefoo/backport-hardening-17.09 [17.09] Various bits of hardening from #4604 Commit: 2a2534789d6bf65525e984211540a8038c727029 https://github.com/galaxyproject/galaxy/commit/2a2534789d6bf65525e984211540… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/76d187ae9a81...2a2534789d6b

1 0

[galaxyproject/galaxy] 54357f: Write out registry.xml file in case jobs are missi...
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 54357f38e9929f3f3a084f298bd644395976a91a https://github.com/galaxyproject/galaxy/commit/54357f38e9929f3f3a084f298bd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Write out registry.xml file in case jobs are missing this file Commit: 94540adda48fbc0c75ffd6b7caa56864b387b721 https://github.com/galaxyproject/galaxy/commit/94540adda48fbc0c75ffd6b7caa5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Clarify previous commit. Commit: a474822f3cbe232b82d23c48507e48f65b6f16c0 https://github.com/galaxyproject/galaxy/commit/a474822f3cbe232b82d23c48507e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #4728 from mvdbeek/fix_registry_missing [17.05] Fix metadata for deleted registry by Galaxy shutdown. Commit: e4518ff3e3d628f2cd47ea48217da6352ef11e30 https://github.com/galaxyproject/galaxy/commit/e4518ff3e3d628f2cd47ea48217d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: b5ded00eb50181f17b3c003e1b7c895098b85d25 https://github.com/galaxyproject/galaxy/commit/b5ded00eb50181f17b3c003e1b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: 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 Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 545d5556588dfe28c8a9857333366ba62dbcd2fd https://github.com/galaxyproject/galaxy/commit/545d5556588dfe28c8a985733336… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: 2f79351e3cdb1fe9705f00590038b11cba4b428e https://github.com/galaxyproject/galaxy/commit/2f79351e3cdb1fe9705f00590038… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 9fa9d42c5093ddd8f70193cc6a07ae0af0394f8c https://github.com/galaxyproject/galaxy/commit/9fa9d42c5093ddd8f70193cc6a07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix backport issues Commit: f925ffe4b743d080585bc6d151dc8ca98cc4f171 https://github.com/galaxyproject/galaxy/commit/f925ffe4b743d080585bc6d151dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4801 from natefoo/backport-hardening-16.07 [16.07] Various bits of hardening from #4604 Commit: e60f324b66676cc5020aa74bfa011f886eaeca68 https://github.com/galaxyproject/galaxy/commit/e60f324b66676cc5020aa74bfa01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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 M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into backport-hardening-16.10 Commit: ef268027191b526b8c8dfe69c3d8352c0412ce1d https://github.com/galaxyproject/galaxy/commit/ef268027191b526b8c8dfe69c3d8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__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/webhooks/__init__.py Log Message: ----------- Hardening backport differences from dev present in 16.10 but not 16.07 Commit: d70713d07a3c4d98b71df9247bbd8644ab6b2b40 https://github.com/galaxyproject/galaxy/commit/d70713d07a3c4d98b71df9247bbd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: fe9839bf7ca720061548ff3bcebdc79062e7adf5 https://github.com/galaxyproject/galaxy/commit/fe9839bf7ca720061548ff3bcebd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: 36b974c90514332c6cb732f9c376a66767100944 https://github.com/galaxyproject/galaxy/commit/36b974c90514332c6cb732f9c376… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 3bb5d825c13ae2dbd366f24dc316bcdaa7171eb9 https://github.com/galaxyproject/galaxy/commit/3bb5d825c13ae2dbd366f24dc316… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 8d573db729a92344ad9115b7657ace07a4718a21 https://github.com/galaxyproject/galaxy/commit/8d573db729a92344ad9115b7657a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 6d8f8ecb466ae75ca7d586496512cb70206a08f6 https://github.com/galaxyproject/galaxy/commit/6d8f8ecb466ae75ca7d586496512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: b04aafa8e871f4d2f3bf7a636ccf0ef432fda875 https://github.com/galaxyproject/galaxy/commit/b04aafa8e871f4d2f3bf7a636ccf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M .travis.yml M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M setup.cfg M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/unit/workflows/workflow_support.py M tox.ini Log Message: ----------- Merge pull request #4804 from natefoo/backport-hardening-16.10 [16.10] Various bits of hardening from #4604 Commit: 139ba7c13e38a98a090a91167e0538f259baa7c2 https://github.com/galaxyproject/galaxy/commit/139ba7c13e38a98a090a91167e05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 03087e5ee77701e410e7d9336a74cedf3206e3f3 https://github.com/galaxyproject/galaxy/commit/03087e5ee77701e410e7d9336a74… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Rebase hardening commits from dev Commit: f9213b16f5bb26b2b7176d50602d852ea4e08562 https://github.com/galaxyproject/galaxy/commit/f9213b16f5bb26b2b7176d50602d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: 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 Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 7ad6182ef4952480354e4737b72c062fc75be93e https://github.com/galaxyproject/galaxy/commit/7ad6182ef4952480354e4737b72c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Fix additional uses of subprocess shell=True Commit: b13f5d7f943106cf27670c7153e6c8967a749bcf https://github.com/galaxyproject/galaxy/commit/b13f5d7f943106cf27670c7153e6… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Rebase script integrity check improvements (#4720) from dev Commit: 24c8a26852aecdcc5d8d23300e551f282b90c628 https://github.com/galaxyproject/galaxy/commit/24c8a26852aecdcc5d8d23300e55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix backport issues Commit: 9955c4d24bff197b01f2ff6227fdfb06224d9ab9 https://github.com/galaxyproject/galaxy/commit/9955c4d24bff197b01f2ff6227fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Ignore I201 errors in 16.10 Commit: 950f92627176068609fc5191c72f681e3e16fb22 https://github.com/galaxyproject/galaxy/commit/950f92627176068609fc5191c72f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Add missing backport of hardening to scripts/grt.py Commit: d8ee1a9a8d42f1287262a25fa282799d44d4f583 https://github.com/galaxyproject/galaxy/commit/d8ee1a9a8d42f1287262a25fa282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-14 (Sat, 14 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Revert ignoring I201 from 16.10 in 17.01 Commit: 25fc0982b75243e9c95a5312b56359f83bc72e87 https://github.com/galaxyproject/galaxy/commit/25fc0982b75243e9c95a5312b563… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Log Message: ----------- Merge branch 'release_16.10' into backport-hardening-17.01 Commit: 54d3994131f28963a1c3c4beccaf029a121d15b1 https://github.com/galaxyproject/galaxy/commit/54d3994131f28963a1c3c4beccaf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.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/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/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.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/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4807 from natefoo/backport-hardening-17.01 [17.01] Various bits of hardening from #4604 Commit: 66820a46eba8f8adc0a573a8c2727e28e0de23e8 https://github.com/galaxyproject/galaxy/commit/66820a46eba8f8adc0a573a8c272… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-17 (Tue, 17 Oct 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/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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/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: ----------- Backport of hardening fixes to 17.05 Commit: 9241c9e3dbf67bb3f55fa89181c80a13e5466e0e https://github.com/galaxyproject/galaxy/commit/9241c9e3dbf67bb3f55fa89181c8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M scripts/grt.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into backport-hardening-17.05 Commit: ef203a69e95facee788086fc507b062528cbb638 https://github.com/galaxyproject/galaxy/commit/ef203a69e95facee788086fc507b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-17 (Tue, 17 Oct 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/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.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.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 #4816 from natefoo/backport-hardening-17.05 [17.05] Various bits of hardening from #4604 Commit: 7fc354f11806208a074595455342e941f632fd00 https://github.com/galaxyproject/galaxy/commit/7fc354f11806208a074595455342… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Write out registry.xml file in case jobs are missing this file Commit: 7a2b7f27c51a883f89eed8ef4022d638d6acde1f https://github.com/galaxyproject/galaxy/commit/7a2b7f27c51a883f89eed8ef4022… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Clarify previous commit. Commit: 0f311470d9c2ce0a2de869b32c84143cd56acc6e https://github.com/galaxyproject/galaxy/commit/0f311470d9c2ce0a2de869b32c84… Author: E Rasche <hxr(a)hx42.org> Date: 2017-10-18 (Wed, 18 Oct 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/web/base/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: ----------- Backport of hardening fixes to 17.09 Commit: a3daa338b8941a1676d0e0f36b854c3c93f73fbe https://github.com/galaxyproject/galaxy/commit/a3daa338b8941a1676d0e0f36b85… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into backport-hardening-17.09 Commit: 07e58a1cdf181bb277ef322ce51af4b2cdc86d00 https://github.com/galaxyproject/galaxy/commit/07e58a1cdf181bb277ef322ce51a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-18 (Wed, 18 Oct 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/handler.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/web/base/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/galaxy_ext/metadata/set_metadata.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 #4824 from natefoo/backport-hardening-17.09 [17.09] Various bits of hardening from #4604 Compare: https://github.com/galaxyproject/galaxy/compare/136925087e08...07e58a1cdf18

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[galaxyproject/infrastructure-playbook] e4378d: Mail OOM killer reports every hour during "busines...
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e4378df86507d569e54fa60ecaca161dbf6fadca https://github.com/galaxyproject/infrastructure-playbook/commit/e4378df8650… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: A taccenv/files/monitoring/mailoom.py M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Mail OOM killer reports every hour during "business hours"

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[galaxyproject/galaxy] 3259ec: Fix two invalid targets in dataset list item (top ...
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3259ecb7893d6d610b88e5d0840646971e53c4d3 https://github.com/galaxyproject/galaxy/commit/3259ecb7893d6d610b88e5d08406… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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/dataset/dataset-li-edit.js Log Message: ----------- Fix two invalid targets in dataset list item (top vs _top -- caused new window instead of nav; eventually this'll just be router when everything is compatible) Commit: 76d187ae9a81c4f2acbb6eb36b58346118b25f89 https://github.com/galaxyproject/galaxy/commit/76d187ae9a81c4f2acbb6eb36b58… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.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/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #4823 from dannon/toptoptop Fix two invalid targets in dataset list item Compare: https://github.com/galaxyproject/galaxy/compare/5a1f925143cd...76d187ae9a81

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[galaxyproject/galaxy] d3fc03: A few typos in galaxy_architecture slides.
by GitHub 18 Oct '17

18 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3fc03b0a04ed7d926ab04914ce0081f96213e73 https://github.com/galaxyproject/galaxy/commit/d3fc03b0a04ed7d926ab04914ce0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- A few typos in galaxy_architecture slides. Commit: 19160ec942d39989105c23cc0fb6333fc481ff2e https://github.com/galaxyproject/galaxy/commit/19160ec942d39989105c23cc0fb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- I don't know what this was trying to say before. Commit: 5a1f925143cd553aebdbd5fdc3e1c419195d9b25 https://github.com/galaxyproject/galaxy/commit/5a1f925143cd553aebdbd5fdc3e1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- Merge pull request #4822 from dannon/architecture_typos Minor architecture slides typos/grammar. Compare: https://github.com/galaxyproject/galaxy/compare/ee39e61fe9de...5a1f925143cd

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[galaxyproject/galaxy] 1bd7d3: Add prettier.
by GitHub 17 Oct '17

17 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1bd7d3b9c175df8716bc64f27eaefbd591ba68a3 https://github.com/galaxyproject/galaxy/commit/1bd7d3b9c175df8716bc64f27eae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Add prettier. Commit: ea2a68d405735bfb25b0906998f118ba69bce07e https://github.com/galaxyproject/galaxy/commit/ea2a68d405735bfb25b0906998f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Initial prettier npm script target Commit: 7f9c480b8035f3b7ab029d8fb787df1fd2bccc6d https://github.com/galaxyproject/galaxy/commit/7f9c480b8035f3b7ab029d8fb787… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Fix exclusion of libs for prettier. Commit: 0f15436e85392bb8ba32667196298e04ee09a79f https://github.com/galaxyproject/galaxy/commit/0f15436e85392bb8ba3266719629… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/yarn.lock Log Message: ----------- Previous commit left out the yarn lock Commit: 7e821b823f5d07b0dfd3bc0098dfe967b46c2ed8 https://github.com/galaxyproject/galaxy/commit/7e821b823f5d07b0dfd3bc0098df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Prettier version bump. Commit: 2c26532c3a2765ad4eec53fbeff79ebc65d1fa95 https://github.com/galaxyproject/galaxy/commit/2c26532c3a2765ad4eec53fbeff7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/package.json Log Message: ----------- Swap from flow to babylon parser for prettier. Commit: 87873c5e2f4e6b97fe0f2084bfca0295fcd471de https://github.com/galaxyproject/galaxy/commit/87873c5e2f4e6b97fe0f2084bfca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js 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/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/levenshtein.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.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/visualization.js M client/galaxy/scripts/viz/viz_views.js M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/generic-nav-view.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/modal.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/layout/router.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/webhooks.js.map M static/maps/nls/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Make it prettier, rebuild Commit: 5b2928f851bd5ea3b9c2a04abf2cee9ff0bc54cc https://github.com/galaxyproject/galaxy/commit/5b2928f851bd5ea3b9c2a04abf2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: 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/layout/menu.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-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/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-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/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.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-ftp.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/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.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-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.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-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.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-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/package.json M static/maps/layout/menu.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-li.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/job/job-params.js.map M static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-queue-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/shed-list-view.js.map M static/maps/mvc/toolshed/toolshed-model.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adjust prettier glob, rerun/rebuild. Commit: ee39e61fe9de4854590aa061bc8c79689d68dd45 https://github.com/galaxyproject/galaxy/commit/ee39e61fe9de4854590aa061bc8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.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/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/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js 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static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #4436 from dannon/prettier Prettier javascript formatting. Compare: https://github.com/galaxyproject/galaxy/compare/709779b1dfe9...ee39e61fe9de

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