[galaxyproject/galaxy] e4518f: Rebase hardening commits from dev

14 Oct 2017

      Branch: refs/heads/release_16.10
  Home:   https://github.com/galaxyproject/galaxy
  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

Compare: https://github.com/galaxyproject/galaxy/compare/e178879c0f9f...b04aafa8e871

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