galaxy-commits October 2016

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[galaxyproject/galaxy] 5d294e: Fix GFF attribute filtering tool broken in #2983
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d294ea7d3a14561a15c30f3527dfcd21d517369 https://github.com/galaxyproject/galaxy/commit/5d294ea7d3a14561a15c30f3527d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Fix GFF attribute filtering tool broken in #2983 Commit: 32bc17cdaa636ba0ba2a97a372b37d518cdd6390 https://github.com/galaxyproject/galaxy/commit/32bc17cdaa636ba0ba2a97a372b3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Whitespace fix Commit: 0062eacfdf86fbfe8fda3de88b2b5b122cdc567e https://github.com/galaxyproject/galaxy/commit/0062eacfdf86fbfe8fda3de88b2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Merge pull request #3044 from blankenberg/gff-filter-tool-fix Fix GFF attribute filtering tool broken in #2983 Compare: https://github.com/galaxyproject/galaxy/compare/277727ada67d...0062eacfdf86

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[galaxyproject/galaxy] 77f78c: Change __all__ from list to tuple
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77f78cfbc79ddc345bc22277afc335f11e189491 https://github.com/galaxyproject/galaxy/commit/77f78cfbc79ddc345bc22277afc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.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/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Change __all__ from list to tuple Also fix import order and Python3 compatibility. Commit: 277727ada67d32404dc953d393716af8aa2aabdc https://github.com/galaxyproject/galaxy/commit/277727ada67d32404dc953d39371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.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/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #3041 from nsoranzo/flake8-import-order Change __all__ from list to tuple [1/2] Compare: https://github.com/galaxyproject/galaxy/compare/36ae57c6e028...277727ada67d

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[galaxyproject/galaxy] f6d5f3: Fix downloading tool tarball with boolean test inp...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/tool_tarball_fix Home: https://github.com/galaxyproject/galaxy Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc0153… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix downloading tool tarball with boolean test input values.

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[galaxyproject/galaxy] ba0795: Fix tabular filtering tool broken in #2983
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ba07956117e5e4527fa5d2837da2c267f6ab981d https://github.com/galaxyproject/galaxy/commit/ba07956117e5e4527fa5d2837da2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Fix tabular filtering tool broken in #2983 Commit: 36ae57c6e028fc814af1cd4740e9222dfcb56021 https://github.com/galaxyproject/galaxy/commit/36ae57c6e028fc814af1cd4740e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Merge pull request #3043 from blankenberg/fix-filter-tool Fix tabular filtering tool broken in #2983 Compare: https://github.com/galaxyproject/galaxy/compare/a22a4d0bd5a2...36ae57c6e028

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[galaxyproject/galaxy] 6c17d1: Remove outdated warning
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c17d1a823b4367b93fff61d7f2fbed23dc5de3b https://github.com/galaxyproject/galaxy/commit/6c17d1a823b4367b93fff61d7f2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove outdated warning After digging through the code I am not finding evidence that this was ever possible to do, at least not since sometime pre-2010. Commit: a22a4d0bd5a2376c130ad84e4bc0313b9f252e45 https://github.com/galaxyproject/galaxy/commit/a22a4d0bd5a2376c130ad84e4bc0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3046 from erasche/remove_warning Remove outdated warning on ID_SECRET Compare: https://github.com/galaxyproject/galaxy/compare/c6713e7c31d5...a22a4d0bd5a2

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[galaxyproject/galaxy] dcde64: Fix import order. Fix typos and improve readabilit...
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dcde64ce407b332072525c66885adf03a26eeb5e https://github.com/galaxyproject/galaxy/commit/dcde64ce407b332072525c66885a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Fix import order. Fix typos and improve readability Commit: 04bf2153b8f61c60288cb180d448e7c20352f6e7 https://github.com/galaxyproject/galaxy/commit/04bf2153b8f61c60288cb180d448… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- WorkflowSummary: add dict to map a job id to its representative job Fix #2742 introduced in commit 9ede8e556be1f6038361b579c1457068e50e951a . The representative job is the first in the returned query, so substantially random and not necessarily the one with the lowest job id. Mapping a job id to its representative job in extract_steps() makes it robust also against API requests with manually chosen collection job ids. Commit: c6713e7c31d5ffe576af5af7de56d3536d196786 https://github.com/galaxyproject/galaxy/commit/c6713e7c31d5ffe576af5af7de56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #3039 from nsoranzo/fix_for_2742 Fix workflow extraction API tests on PostgreSQL Compare: https://github.com/galaxyproject/galaxy/compare/1e2688f15785...c6713e7c31d5

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[galaxyproject/galaxy] 91bfec: Add documentation on optional ``multiple="true"`` ...
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91bfecea67b78f7e459a250a7844c6344154367f https://github.com/galaxyproject/galaxy/commit/91bfecea67b78f7e459a250a7844… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add documentation on optional ``multiple="true"`` data parameters. Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility). Rebased with indention requested by @nsoranzo and fixes for the test case tool. Commit: 1e2688f1578552ea03e7a601d927c4475b96fdd2 https://github.com/galaxyproject/galaxy/commit/1e2688f1578552ea03e7a601d927… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3024 from jmchilton/multi_optional_param Add documentation on optional ``multiple="true"`` data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/58d608b9060d...1e2688f15785

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[galaxyproject/usegalaxy-playbook] 15ce7b: Added 2 hour expiration to welcome images
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15ce7b388961f5602cb73ea3ef86369b9353bac4 https://github.com/galaxyproject/usegalaxy-playbook/commit/15ce7b388961f560… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M templates/nginx/galaxy_test.j2 M templates/nginx/usegalaxy.j2 Log Message: ----------- Added 2 hour expiration to welcome images

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[galaxyproject/usegalaxy-playbook] f5e6cf: Increase the job output limit to 200GB
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f5e6cf2545cabc406008bc52c378a51683b39859 https://github.com/galaxyproject/usegalaxy-playbook/commit/f5e6cf2545cabc40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase the job output limit to 200GB

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[galaxyproject/usegalaxy-playbook] b75611: Fix gzip content encoding regressions for Test/Mai...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b75611579b5fd15ff8b1f8d219e1b2daddb6b481 https://github.com/galaxyproject/usegalaxy-playbook/commit/b75611579b5fd15f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M production/group_vars/galaxywebservers.yml M stage/group_vars/galaxyservers.yml M templates/nginx/galaxy_test.j2 M templates/nginx/toolshed.j2 M templates/nginx/usegalaxy.j2 Log Message: ----------- Fix gzip content encoding regressions for Test/Main and Toolsheds

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galaxy-commits October 2016