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

[galaxyproject/usegalaxy-playbook] c8a4e8: Update Test and Main
by GitHub 16 Oct '17

16 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c8a4e8696c0309c8cd8174e86fdeb3d44907b442 https://github.com/galaxyproject/usegalaxy-playbook/commit/c8a4e8696c0309c8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/galaxyservers/vars.yml M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test and Main Commit: 2cf30a7c4b35f5a1090899dd71d7250ade2bc162 https://github.com/galaxyproject/usegalaxy-playbook/commit/2cf30a7c4b35f5a1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 705e049ebbdcf3b3ee38912f52ef429362b47934 https://github.com/galaxyproject/usegalaxy-playbook/commit/705e049ebbdcf3b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 8af5d97205bf1ec406cf91c309737fdf6fe8ff6b https://github.com/galaxyproject/usegalaxy-playbook/commit/8af5d97205bf1ec4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix Jetstream autosubmission, Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0e510520722c...…

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[galaxyproject/galaxy] e4518f: Rebase hardening commits from dev
by GitHub 14 Oct '17

14 Oct '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/e178879c0f9f...b04aafa8e871

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[galaxyproject/galaxy] d65a06: Fix to respect galaxy.json supplied metadata for e...
by GitHub 13 Oct '17

13 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d65a060b06b8d0a4dda95a9694e6006aba5e58af https://github.com/galaxyproject/galaxy/commit/d65a060b06b8d0a4dda95a9694e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py A test/functional/tools/empty_datasets.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix to respect galaxy.json supplied metadata for empty outputs. With a test case to verify this and a empty datasets in general (e.g. collecting empty datasets from work dir). Commit: f4d45549cf9e59a6b3fe00b44744ef69683a149a https://github.com/galaxyproject/galaxy/commit/f4d45549cf9e59a6b3fe00b44744… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py A test/functional/tools/empty_datasets.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4722 from jmchilton/empty_datasets Fix to respect galaxy.json supplied metadata for empty outputs. Compare: https://github.com/galaxyproject/galaxy/compare/73b4629a0be4...f4d45549cf9e

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[galaxyproject/galaxy] e4518f: Rebase hardening commits from dev
by GitHub 13 Oct '17

13 Oct '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/2ffeedfa723c...f925ffe4b743

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[galaxyproject/galaxy] d1bc98: Python3: fix remaining print statements
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1bc98dfcb617cf022070b96ee74f437cfe5c207 https://github.com/galaxyproject/galaxy/commit/d1bc98dfcb617cf022070b96ee74… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M contrib/galaxy_config_merger.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/jstree.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/library_upload_dir.py M scripts/api/workflow_import.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/extract_toolbox_sections.py M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/update_shed_config_path.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py Log Message: ----------- Python3: fix remaining print statements Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations. Commit: 73b4629a0be4956da976e0e7758f8b189c485821 https://github.com/galaxyproject/galaxy/commit/73b4629a0be4956da976e0e7758f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M contrib/galaxy_config_merger.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/jstree.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/library_upload_dir.py M scripts/api/workflow_import.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/extract_toolbox_sections.py M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/update_shed_config_path.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py Log Message: ----------- Merge pull request #4799 from nsoranzo/python3 Python3: fix remaining print statements Compare: https://github.com/galaxyproject/galaxy/compare/16843cee9ac2...73b4629a0be4

1 0

[galaxyproject/galaxy] 73f689: Add permissions operation to role grid
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73f6891a39888323912433a6bd3a0b614cf56ea1 https://github.com/galaxyproject/galaxy/commit/73f6891a39888323912433a6bd3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add permissions operation to role grid Commit: df8b933837b919b9fc09af9455d00b9b8a9689f8 https://github.com/galaxyproject/galaxy/commit/df8b933837b919b9fc09af9455d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Revise labels Commit: b211a5c6fd3bfa4428c7afca97870d4bd7d8820a https://github.com/galaxyproject/galaxy/commit/b211a5c6fd3bfa4428c7afca9787… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Sort by last updated by default for roles Commit: 0a1b7dd433aae305aef579dad4ca45a6ced90879 https://github.com/galaxyproject/galaxy/commit/0a1b7dd433aae305aef579dad4ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add analog label and operation to groups grid Commit: 7507a882571a06da8cc494b8158a361122977f09 https://github.com/galaxyproject/galaxy/commit/7507a882571a06da8cc494b8158a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add manage information to user operations Commit: e9856dec958a6dd67f41adc7b8b4271546671648 https://github.com/galaxyproject/galaxy/commit/e9856dec958a6dd67f41adc7b8b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Restore sorting by name Commit: 16843cee9ac209aa68558c0a860de5671a3c835a https://github.com/galaxyproject/galaxy/commit/16843cee9ac209aa68558c0a860d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #4792 from guerler/roles_friendliness Add operations to roles, groups and user grids Compare: https://github.com/galaxyproject/galaxy/compare/06f6fdd580ff...16843cee9ac2

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[galaxyproject/galaxy] 54357f: Write out registry.xml file in case jobs are missi...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/release_17.05 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. Compare: https://github.com/galaxyproject/galaxy/compare/a83123ef5e38...a474822f3cbe

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[galaxyproject/galaxy] 1c9ff9: Load dataset edit attributes without page refresh
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c9ff98b81a803de48eafa5deb6f9d5e95733c9d https://github.com/galaxyproject/galaxy/commit/1c9ff98b81a803de48eafa5deb6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Load dataset edit attributes without page refresh Commit: dcad663cee2ce50f7b35871e51e50554b0d9b727 https://github.com/galaxyproject/galaxy/commit/dcad663cee2ce50f7b35871e51e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 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: ----------- Load dataset errors without page refresh Commit: ecd0dc4244cff688491dec7f2404ef65d1e1d861 https://github.com/galaxyproject/galaxy/commit/ecd0dc4244cff688491dec7f2404… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyles for stable release. Commit: 012aaf832027ba905b492645ebdeea9d903b6726 https://github.com/galaxyproject/galaxy/commit/012aaf832027ba905b492645ebde… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Pin pydocstyle... Commit: 220fdccd57cda5268d2beb482c1d4469cb8b5d94 https://github.com/galaxyproject/galaxy/commit/220fdccd57cda5268d2beb482c1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 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: ----------- Do not rely on the existence of the analysis app router Commit: a0f63b671f29f41d078c23b0421b981b3ac0bcdd https://github.com/galaxyproject/galaxy/commit/a0f63b671f29f41d078c23b0421b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4775 from jmchilton/pin_pydocstyle [17.09] Pin pydocstyles for stable release. Commit: f64b7fcfb124756ed8dc65bbfdfbe6b2f0cb66e0 https://github.com/galaxyproject/galaxy/commit/f64b7fcfb124756ed8dc65bbfdfb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4777 from jmchilton/release_17.01_pydocstyle_ping [17.01] Pin linting functions in tox.ini. Commit: 1635f46430b176f03b7c3982f4d02287e7d4a5e1 https://github.com/galaxyproject/galaxy/commit/1635f46430b176f03b7c3982f4d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 27e3e724cded1b5c99cc902dc478653feb84e505 https://github.com/galaxyproject/galaxy/commit/27e3e724cded1b5c99cc902dc478… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 2b18a0b8d5f7316e8a5e5fbc84e9c1062e519fa2 https://github.com/galaxyproject/galaxy/commit/2b18a0b8d5f7316e8a5e5fbc84e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #4773 from guerler/fix_edit_reload.000 [17.09] Load dataset attribute editing and errors without page refresh Commit: fb7015bf70aaf3468b34f9d5a464df18edcae7ac https://github.com/galaxyproject/galaxy/commit/fb7015bf70aaf3468b34f9d5a464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Bug fix for XML warning during tool loads. Commit: fd8e2e1927f0c6248e6d7ae4c5338015328bf9a0 https://github.com/galaxyproject/galaxy/commit/fd8e2e1927f0c6248e6d7ae4c533… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #4784 from jmchilton/tool_xml_warning [17.09] Bug fix for XML warning during tool loads. Commit: 24308fb6053dcecbf20d6e7a8a8e9b7d96fe07db https://github.com/galaxyproject/galaxy/commit/24308fb6053dcecbf20d6e7a8a8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Fix listify import in show_params.mako This fixes a problem reported on the [mailing list](http://dev.list.galaxyproject.org/Show-history-structure-Error-Undefi…. I am not sure why importing at the top of the file is not enough though. Commit: a83123ef5e384f95778a1293f293e4b9a919054b https://github.com/galaxyproject/galaxy/commit/a83123ef5e384f95778a1293f293… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #4794 from mvdbeek/fix_listify_import_in_show_params [17.05][BUG] Fix listify import in show params Commit: ebdadb68ad7caaa4afbde544e46ad57b4ab49dba https://github.com/galaxyproject/galaxy/commit/ebdadb68ad7caaa4afbde544e46a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 7ceaec4a22f0e30752877c8d235d4f4904896f94 https://github.com/galaxyproject/galaxy/commit/7ceaec4a22f0e30752877c8d235d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/package-lock.json M lib/galaxy/tools/parser/xml.py M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js M templates/show_params.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Commit: 06f6fdd580ff7e53576eee154c4731946c505dcf https://github.com/galaxyproject/galaxy/commit/06f6fdd580ff7e53576eee154c47… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/package-lock.json M lib/galaxy/tools/parser/xml.py M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/router.js M static/scripts/mvc/dataset/dataset-li-edit.js M templates/show_params.mako Log Message: ----------- Merge pull request #4796 from dannon/dev Merges 17.09 -> dev Compare: https://github.com/galaxyproject/galaxy/compare/dfb2cc2f363f...06f6fdd580ff

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[galaxyproject/galaxy] 24308f: Fix listify import in show_params.mako
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 24308fb6053dcecbf20d6e7a8a8e9b7d96fe07db https://github.com/galaxyproject/galaxy/commit/24308fb6053dcecbf20d6e7a8a8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Fix listify import in show_params.mako This fixes a problem reported on the [mailing list](http://dev.list.galaxyproject.org/Show-history-structure-Error-Undefi…. I am not sure why importing at the top of the file is not enough though. Commit: a83123ef5e384f95778a1293f293e4b9a919054b https://github.com/galaxyproject/galaxy/commit/a83123ef5e384f95778a1293f293… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #4794 from mvdbeek/fix_listify_import_in_show_params [17.05][BUG] Fix listify import in show params Commit: ebdadb68ad7caaa4afbde544e46ad57b4ab49dba https://github.com/galaxyproject/galaxy/commit/ebdadb68ad7caaa4afbde544e46a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/fd8e2e1927f0...ebdadb68ad7c

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[galaxyproject/galaxy] 24308f: Fix listify import in show_params.mako
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 24308fb6053dcecbf20d6e7a8a8e9b7d96fe07db https://github.com/galaxyproject/galaxy/commit/24308fb6053dcecbf20d6e7a8a8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Fix listify import in show_params.mako This fixes a problem reported on the [mailing list](http://dev.list.galaxyproject.org/Show-history-structure-Error-Undefi…. I am not sure why importing at the top of the file is not enough though. Commit: a83123ef5e384f95778a1293f293e4b9a919054b https://github.com/galaxyproject/galaxy/commit/a83123ef5e384f95778a1293f293… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #4794 from mvdbeek/fix_listify_import_in_show_params [17.05][BUG] Fix listify import in show params Compare: https://github.com/galaxyproject/galaxy/compare/1635f46430b1...a83123ef5e38

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