Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 54357f38e9929f3f3a084f298bd644395976a91a https://github.com/galaxyproject/galaxy/commit/54357f38e9929f3f3a084f298bd64... Author: mvdbeek <m.vandenbeek@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/94540adda48fbc0c75ffd6b7caa56... Author: John Chilton <jmchilton@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/a474822f3cbe232b82d23c48507e4... Author: Nate Coraor <nate@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/e4518ff3e3d628f2cd47ea48217da... Author: E Rasche <hxr@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/b5ded00eb50181f17b3c003e1b7c8... Author: John Chilton <jmchilton@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/545d5556588dfe28c8a9857333366... Author: Nate Coraor <nate@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/2f79351e3cdb1fe9705f00590038b... Author: E Rasche <hxr@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/9fa9d42c5093ddd8f70193cc6a07a... Author: Nate Coraor <nate@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/f925ffe4b743d080585bc6d151dc8... Author: Nicola Soranzo <nsoranzo@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/e60f324b66676cc5020aa74bfa011... Author: Nate Coraor <nate@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/ef268027191b526b8c8dfe69c3d83... Author: E Rasche <hxr@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/d70713d07a3c4d98b71df9247bbd8... Author: Nicola Soranzo <nicola.soranzo@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/fe9839bf7ca720061548ff3bcebdc... Author: Nicola Soranzo <nicola.soranzo@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/36b974c90514332c6cb732f9c376a... Author: John Chilton <jmchilton@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/3bb5d825c13ae2dbd366f24dc316b... Author: Nate Coraor <nate@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/8d573db729a92344ad9115b7657ac... Author: Nicola Soranzo <nicola.soranzo@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/6d8f8ecb466ae75ca7d586496512c... Author: Nate Coraor <nate@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/b04aafa8e871f4d2f3bf7a636ccf0... Author: Nicola Soranzo <nsoranzo@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/139ba7c13e38a98a090a91167e053... Author: John Chilton <jmchilton@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/03087e5ee77701e410e7d9336a74c... Author: E Rasche <hxr@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/f9213b16f5bb26b2b7176d50602d8... Author: John Chilton <jmchilton@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/7ad6182ef4952480354e4737b72c0... Author: Nate Coraor <nate@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/b13f5d7f943106cf27670c7153e6c... Author: E Rasche <hxr@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/24c8a26852aecdcc5d8d23300e551... Author: Nate Coraor <nate@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/9955c4d24bff197b01f2ff6227fdf... Author: Nate Coraor <nate@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/950f92627176068609fc5191c72f6... Author: Nate Coraor <nate@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/d8ee1a9a8d42f1287262a25fa2827... Author: Nate Coraor <nate@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/25fc0982b75243e9c95a5312b5635... Author: Nate Coraor <nate@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/54d3994131f28963a1c3c4beccaf0... Author: Nicola Soranzo <nsoranzo@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/66820a46eba8f8adc0a573a8c2727... Author: E Rasche <hxr@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/9241c9e3dbf67bb3f55fa89181c80... Author: Nate Coraor <nate@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/ef203a69e95facee788086fc507b0... Author: Nicola Soranzo <nsoranzo@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/7fc354f11806208a074595455342e... Author: mvdbeek <m.vandenbeek@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/7a2b7f27c51a883f89eed8ef4022d... Author: John Chilton <jmchilton@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/0f311470d9c2ce0a2de869b32c841... Author: E Rasche <hxr@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/a3daa338b8941a1676d0e0f36b854... Author: Nate Coraor <nate@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/07e58a1cdf181bb277ef322ce51af... Author: Nicola Soranzo <nsoranzo@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