Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32b85ecb591d01acbbbb9ed1bedd1a48804a0837 https://github.com/galaxyproject/galaxy/commit/32b85ecb591d01acbbbb9ed1bedd1... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webhooks/__init__.py M scripts/grt/export.py M scripts/grt/upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Only permit yaml.safe_loading of data Event trusted data, belt + suspenders method. Commit: df41d4f4087f9b133750a2c350ea207753f30f54 https://github.com/galaxyproject/galaxy/commit/df41d4f4087f9b133750a2c350ea2... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Remove some shell=True and fix commands Commit: cd6a1afaa9980d958ad324fa987a07e7608bf841 https://github.com/galaxyproject/galaxy/commit/cd6a1afaa9980d958ad324fa987a0... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Replace some os.system calls with subprocess Commit: 73337725bdd654904563dc54b04083a23e4a252d https://github.com/galaxyproject/galaxy/commit/73337725bdd654904563dc54b0408... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Two more commands to list Commit: c85db3fd68590d3d2f61b0b3f88026773d9563a0 https://github.com/galaxyproject/galaxy/commit/c85db3fd68590d3d2f61b0b3f8802... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- Some more command refactoring Commit: 670897ec5ca2284c7fad453c3d595defe3cca280 https://github.com/galaxyproject/galaxy/commit/670897ec5ca2284c7fad453c3d595... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/system.py Log Message: ----------- One more os command Commit: 9b8e76f9d9df0ae0ba6238d44a8f07b97fe34d6f https://github.com/galaxyproject/galaxy/commit/9b8e76f9d9df0ae0ba6238d44a8f0... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/managers/citations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py Log Message: ----------- Convert urllib to requests Which has built-in protection against urls like "file:///tmp/a" Commit: db0400298651f6d4c9d909406c3fe632d057bbf7 https://github.com/galaxyproject/galaxy/commit/db0400298651f6d4c9d909406c3fe... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Log Message: ----------- remove unused imports Commit: a68d6be3a1c6e6fd85c5ae94232467f193156d53 https://github.com/galaxyproject/galaxy/commit/a68d6be3a1c6e6fd85c5ae9423246... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- reorder imports Commit: 93ffc4055b145811b86191dae8b865ea45b55fcb https://github.com/galaxyproject/galaxy/commit/93ffc4055b145811b86191dae8b86... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- replace check_output with python processing and shell=False Commit: d79a2459a95dfda7856b9898d40d062f00456006 https://github.com/galaxyproject/galaxy/commit/d79a2459a95dfda7856b9898d40d0... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/webapps/config_manage.py Log Message: ----------- These we will revert to their original yaml.load It would be nice to fix them eventually, but we'll settle for an incremental improvement. Commit: b3261309843f8cfec1a5a589b4628e44e6bf76df https://github.com/galaxyproject/galaxy/commit/b3261309843f8cfec1a5a589b4628... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- import ordering Commit: 8f4491bfffce5d13e2199df5d60e06e3672a08c1 https://github.com/galaxyproject/galaxy/commit/8f4491bfffce5d13e2199df5d60e0... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Consume stderr Commit: 0f7dd52988269dc4567bdbbd71be0fd273741efd https://github.com/galaxyproject/galaxy/commit/0f7dd52988269dc4567bdbbd71be0... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Copy changes over Commit: 75df58ae86ff1796f0bb0ea975fc1d0d518c155a https://github.com/galaxyproject/galaxy/commit/75df58ae86ff1796f0bb0ea975fc1... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds_3_sites.py Log Message: ----------- fix Commit: fd92ac3eedd145635a74530ba62bb7fea7c540f4 https://github.com/galaxyproject/galaxy/commit/fd92ac3eedd145635a74530ba62bb... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- revert this change Commit: 27beb7030d99a511a428ad59211a3137a2761559 https://github.com/galaxyproject/galaxy/commit/27beb7030d99a511a428ad59211a3... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- revert/sync Commit: 1a57c06d6a81dc6f92eb4843c89a7333f874bc32 https://github.com/galaxyproject/galaxy/commit/1a57c06d6a81dc6f92eb4843c89a7... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix import ordering Thanks @nsoranzo, I appreciate all the comments here. Commit: 290971ca7a28eb579dc2d40c9653b9e160253634 https://github.com/galaxyproject/galaxy/commit/290971ca7a28eb579dc2d40c9653b... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/transfer_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py Log Message: ----------- more review comments Commit: 15c73233c52b29ed94066c06ebb1e10c935ae28d https://github.com/galaxyproject/galaxy/commit/15c73233c52b29ed94066c06ebb1e... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M scripts/edam_mapping.py Log Message: ----------- fix lint Commit: 19d03edc7ff8384a5360d71365076a2594fb0b8b https://github.com/galaxyproject/galaxy/commit/19d03edc7ff8384a5360d71365076... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- refactor missed call Commit: 626a3dc2995f0d797232aa666f1bdf3e6a5d22dd https://github.com/galaxyproject/galaxy/commit/626a3dc2995f0d797232aa666f1bd... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- fix ordering Commit: 41574d022249bae4df4b89bfb50c3a599ee5585e https://github.com/galaxyproject/galaxy/commit/41574d022249bae4df4b89bfb50c3... Author: E Rasche <hxr@hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- swap for subprocess.call per @nsoranzo suggestion Commit: 0c6dfd7a41a8df8c000b133d8833eb9963ae183e https://github.com/galaxyproject/galaxy/commit/0c6dfd7a41a8df8c000b133d8833e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4604 from erasche/hardening Various bits of hardening Compare: https://github.com/galaxyproject/galaxy/compare/9f2582e9fbed...0c6dfd7a41a8