- 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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[galaxyproject/galaxy] bd5f71: Separate endpoints for form building and attribute...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd5f711bd272dba7fc032b894a7b6c50098e1d83 https://github.com/galaxyproject/galaxy/commit/bd5f711bd272dba7fc032b894a7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Separate endpoints for form building and attribute changes Commit: e09958fd8f9a386761f6ebe520a8323e7b5e4c0c https://github.com/galaxyproject/galaxy/commit/e09958fd8f9a386761f6ebe520a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor form building endpoint Commit: b451c6a13741e1f7f47d759edda67e49ec4e3983 https://github.com/galaxyproject/galaxy/commit/b451c6a13741e1f7f47d759edda6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Use consistent naming for input forms Commit: d7d8817a98bc176c53c44b0110b4aa2aba01985d https://github.com/galaxyproject/galaxy/commit/d7d8817a98bc176c53c44b0110b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use consistent input appending style, remove spaces Commit: 101c9b4b355fe6903296bbc7be2ac40464b746c6 https://github.com/galaxyproject/galaxy/commit/101c9b4b355fe6903296bbc7be2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix missing role handling Commit: 14c6622cac29d0396661101154698df3e4c0f796 https://github.com/galaxyproject/galaxy/commit/14c6622cac29d039666110115469… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Show attribute editing without tabs Commit: e191991242d2c4331ae1cf22da08cdb5b30e09c6 https://github.com/galaxyproject/galaxy/commit/e191991242d2c4331ae1cf22da08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Reconnect attributes endpoint Commit: 6c321dca3fe47e474ae5f68b72c88de4cd5db712 https://github.com/galaxyproject/galaxy/commit/6c321dca3fe47e474ae5f68b72c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Fix status message handling, use consistent message format Commit: 2eeafa72abdf80d7856de6bbba5f0f031e166e57 https://github.com/galaxyproject/galaxy/commit/2eeafa72abdf80d7856de6bbba5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Add error handler, fix datatype retrieval Commit: c100667d8d1875fd9893ae41edc81bf470ae5b28 https://github.com/galaxyproject/galaxy/commit/c100667d8d1875fd9893ae41edc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove three year old comments Commit: 4bb5813800edf01ed982e65452547c7a3614c2bb https://github.com/galaxyproject/galaxy/commit/4bb5813800edf01ed982e6545254… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use one-liner for message Commit: 7b969111adc2f2cb9bcc2d70e6e134b9e0e9a52b 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parse response to message handler Commit: bb33e65c61a68177a30779d4e690b7c4fa7be28b https://github.com/galaxyproject/galaxy/commit/bb33e65c61a68177a30779d4e690… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Reuse tab view, add area for info and annotation Commit: e45519c00ea4bf1a4901c710bfd61c483b36bad5 https://github.com/galaxyproject/galaxy/commit/e45519c00ea4bf1a4901c710bfd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix metadata name Commit: e257d0ec8a308692c92899bb8426446c151073d7 https://github.com/galaxyproject/galaxy/commit/e257d0ec8a308692c92899bb8426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Augment error handling Commit: 4b93fdf5f966251bb6c7a3eb2b8d78f5b6637263 https://github.com/galaxyproject/galaxy/commit/4b93fdf5f966251bb6c7a3eb2b8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Reduce render update to forms, do not re-render tabs Commit: 9a7150f645abe26bdeeb1d06ecfdbb177d725ae8 https://github.com/galaxyproject/galaxy/commit/9a7150f645abe26bdeeb1d06ecfd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Hide until data is available Commit: 589e83e909744ea79a78c3c6ede44f331da6a196 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M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adjust client message handler Commit: ce6f0a7f0daa5abe0109fa522be8e7fe6c2ea5ae https://github.com/galaxyproject/galaxy/commit/ce6f0a7f0daa5abe0109fa522be8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Encode/decode role ids, add support for permission handling Commit: 591873a132ea4b1c5c25cba362656082637f15e7 https://github.com/galaxyproject/galaxy/commit/591873a132ea4b1c5c25cba36265… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-default.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/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add readonly support for select fields, remove custom readonly form Commit: 95200bbe4e3904f5bf8b20d77ba4128c257cf56f https://github.com/galaxyproject/galaxy/commit/95200bbe4e3904f5bf8b20d77ba4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use hidden type and labels for input messages Commit: 7435c464b07bdc4d7947daef7e15ceb7ff54911a https://github.com/galaxyproject/galaxy/commit/7435c464b07bdc4d7947daef7e15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-view.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/form/form-view.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/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/form/form-view.js Log Message: ----------- Add flag to specify editable forms Parse converter exception to client Commit: 5ecb2332ef79f8cac5c0c31e90a996d780fad3af https://github.com/galaxyproject/galaxy/commit/5ecb2332ef79f8cac5c0c31e90a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove html from error message Commit: e759b293795397ccbfb318e6244e55a166cdc30b https://github.com/galaxyproject/galaxy/commit/e759b293795397ccbfb318e6244e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix datatype form enabling Commit: 347d7805fe2e0d7e85b6edcf7aa5f8e30bdb30b3 https://github.com/galaxyproject/galaxy/commit/347d7805fe2e0d7e85b6edcf7aa5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.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 M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix former edit links and targets Fix flag handling for permissions Repack Commit: 71a3158421a4430364d91e1b7ec867fd82411778 https://github.com/galaxyproject/galaxy/commit/71a3158421a4430364d91e1b7ec8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M config/error_report.yml.sample M lib/galaxy/dataset_collections/type_description.py A lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M static/maps/mvc/upload/default/default-view.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/upload/default/default-view.js Log Message: ----------- Merge branch 'dev' into revise_dataset_attributes Commit: 9a4c76da767c6463dfc5b82c3e6220bebb5b67c8 https://github.com/galaxyproject/galaxy/commit/9a4c76da767c6463dfc5b82c3e62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.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-edit-attributes.js Log Message: ----------- Fix names, removes space from icon cls Commit: aea59ddda12877e501141b39cf1fead83ebbf64c https://github.com/galaxyproject/galaxy/commit/aea59ddda12877e501141b39cf1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refresh session for permissions Commit: a246510bd0cc859171f7876a141feb89b7499a03 https://github.com/galaxyproject/galaxy/commit/a246510bd0cc859171f7876a141f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix handling of multiple roles for dataset permissions Commit: 990d1aec844eca2c86188f9acc91ba0d3dbd2b8e https://github.com/galaxyproject/galaxy/commit/990d1aec844eca2c86188f9acc91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove debug message, fix spacing, remove unused library Commit: 966cc95f4030e7b9680de9ae6094f9ab84d42981 https://github.com/galaxyproject/galaxy/commit/966cc95f4030e7b9680de9ae6094… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Avoid naming conflict Commit: 470d1eee18a7508c0405ca0750deb9ab627ab7fc https://github.com/galaxyproject/galaxy/commit/470d1eee18a7508c0405ca0750de… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix anonymous access to edit attributes Commit: 90f9a50574f8e324a1b12f1100c669a3a71d6119 https://github.com/galaxyproject/galaxy/commit/90f9a50574f8e324a1b12f1100c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M static/maps/mvc/upload/upload-view.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/upload/upload-view.js M test/api/test_tools_upload.py M test/base/populators.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into revise_dataset_attributes Commit: dfb2cc2f363f29085e022e14b7c145c80c389d3d https://github.com/galaxyproject/galaxy/commit/dfb2cc2f363f29085e022e14b7c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-select-default.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/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4779 from guerler/revise_dataset_attributes Allow dataset attribute changes without refreshing the page Compare: https://github.com/galaxyproject/galaxy/compare/49f62e7a3577...dfb2cc2f363f

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[galaxyproject/galaxy] e06b44: Add labels to collection flattening operation to a...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e06b44437b46a82402e43c8e4c26d21af765fb3f https://github.com/galaxyproject/galaxy/commit/e06b44437b46a82402e43c8e4c26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/tools/flatten_collection.xml Log Message: ----------- Add labels to collection flattening operation to avoid confusion Commit: 49f62e7a3577c214bcfc16e7f2c21c594e387162 https://github.com/galaxyproject/galaxy/commit/49f62e7a3577c214bcfc16e7f2c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/tools/flatten_collection.xml Log Message: ----------- Merge pull request #4791 from guerler/fix_flatten_label Add labels to selection options of the collection flattening tool Compare: https://github.com/galaxyproject/galaxy/compare/e02faa35f918...49f62e7a3577

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[galaxyproject/galaxy] bce4da: Add another upload test this time with no dbkey pa...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bce4da7bc8837b35854e08b7ffbd9258219c709f https://github.com/galaxyproject/galaxy/commit/bce4da7bc8837b35854e08b7ffbd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Add another upload test this time with no dbkey param. Works fine... Commit: e02faa35f918b3417680eb27e8a2aae8a84d7b8c https://github.com/galaxyproject/galaxy/commit/e02faa35f918b3417680eb27e8a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge pull request #4790 from jmchilton/upload_test_no_dbkey Add another upload test this time with no dbkey param. Compare: https://github.com/galaxyproject/galaxy/compare/643be6463ddf...e02faa35f918

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[galaxyproject/galaxy] 4a2aa7: Always send dbkey during upload.
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a2aa7cab51c81023cf04b3575e47a2f06f4f165 https://github.com/galaxyproject/galaxy/commit/4a2aa7cab51c81023cf04b3575e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.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/upload/upload-view.js Log Message: ----------- Always send dbkey during upload. Seems to be needed on test.galaxyproject.org and for Selenium tests but not just running on my local laptop. This does seem to fix the problems though: A passing selenium suite with this change: https://jenkins.galaxyproject.org/view/All/job/jmchilton-selenium/172/. Commit: 82f671d3eeb64f9afc3ca79edee5a859b5b9cbe4 https://github.com/galaxyproject/galaxy/commit/82f671d3eeb64f9afc3ca79edee5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use initial dbkey and file_type to specify defaults Commit: 32e10a2e30dd5ab6b9159212ae8dd96d881a156d https://github.com/galaxyproject/galaxy/commit/32e10a2e30dd5ab6b9159212ae8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.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/upload/upload-view.js Log Message: ----------- Use ? and auto as defaults Commit: 627fb407ed90bebb714e12b400b85fe7bd06d495 https://github.com/galaxyproject/galaxy/commit/627fb407ed90bebb714e12b400b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.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/upload/upload-view.js Log Message: ----------- Merge pull request #59 from guerler/selenium_fix_000 Use initial dbkey and file_type to specify defaults Commit: 643be6463ddf0489936b1f0e7882e36fd1932d22 https://github.com/galaxyproject/galaxy/commit/643be6463ddf0489936b1f0e7882… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.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/upload/upload-view.js Log Message: ----------- Merge pull request #4789 from jmchilton/selenium_fix Always send dbkey during upload from UI. Compare: https://github.com/galaxyproject/galaxy/compare/5bf08cf01765...643be6463ddf

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[galaxyproject/galaxy] 500a7a: test case to fix mothur.freq sniffer
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 500a7aee64708717a187ee87b4351d1295c48a6a https://github.com/galaxyproject/galaxy/commit/500a7aee64708717a187ee87b435… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq Log Message: ----------- test case to fix mothur.freq sniffer Commit: 787c3e575371b0969f57592a6f522d7d2634e2bc https://github.com/galaxyproject/galaxy/commit/787c3e575371b0969f57592a6f52… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- test case to fix mothur.freq sniffer Commit: 6dd59d9d2dcf6241506cf7720729145874e66121 https://github.com/galaxyproject/galaxy/commit/6dd59d9d2dcf6241506cf7720729… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- flake Commit: 03fe2a9779dfe51659f021b6856a74cac6c44ba3 https://github.com/galaxyproject/galaxy/commit/03fe2a9779dfe51659f021b6856a… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- addresses comments Commit: 5bf08cf017659de3026d9ca17c7ebeb0f7257ccb https://github.com/galaxyproject/galaxy/commit/5bf08cf017659de3026d9ca17c7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq Log Message: ----------- Merge pull request #4781 from yhoogstrate/mothur_freq_fix Mothur.freq sniffer more stringent Compare: https://github.com/galaxyproject/galaxy/compare/d3345d9feedf...5bf08cf01765

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[galaxyproject/galaxy] d5b714: Remove unused concept of dataset children.
by GitHub 11 Oct '17

11 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5b71415f62d97487ef898934875da65a2b29c47 https://github.com/galaxyproject/galaxy/commit/d5b71415f62d97487ef898934875… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove unused concept of dataset children. We didn't really have any corresponding to active tools, we know if they are present they break multiple different parts of Galaxy. Lots of database loads and complexity we are not using and that is broken. Commit: d3345d9feedff9469239d7e0e6cec647f934a4d1 https://github.com/galaxyproject/galaxy/commit/d3345d9feedff9469239d7e0e6ce… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4771 from jmchilton/copy_children Remove unused concept of dataset children. Compare: https://github.com/galaxyproject/galaxy/compare/490dea3d267c...d3345d9feedf

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[galaxyproject/galaxy] fb7015: Bug fix for XML warning during tool loads.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy 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. Compare: https://github.com/galaxyproject/galaxy/compare/2b18a0b8d5f7...fd8e2e1927f0

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[galaxyproject/galaxy] cbb119: pin flake and pydocstyle in tox
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbb119ebcd7bccc390eaae3874759b5e1091a86e https://github.com/galaxyproject/galaxy/commit/cbb119ebcd7bccc390eaae387475… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- pin flake and pydocstyle in tox Commit: 490dea3d267c1f5f7f5cc87cda759e31d3e4524b https://github.com/galaxyproject/galaxy/commit/490dea3d267c1f5f7f5cc87cda75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4787 from martenson/pin-tox pin flake and pydocstyle in tox Compare: https://github.com/galaxyproject/galaxy/compare/eab8f8e43f70...490dea3d267c

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[galaxyproject/usegalaxy-playbook] 0e5105: Removed PEAR from test and main.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e510520722c7dd8ff5675f4dc123976c32b5412 https://github.com/galaxyproject/usegalaxy-playbook/commit/0e510520722c7dd8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Removed PEAR from test and main.

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[galaxyproject/galaxy] 065c08: Bugfix - do not initiate empty FTP uploads.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 065c08dd903211e73b9cb90e9061a0959b31fa13 https://github.com/galaxyproject/galaxy/commit/065c08dd903211e73b9cb90e9061… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-view.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/upload/default/default-view.js Log Message: ----------- Bugfix - do not initiate empty FTP uploads. Broken with #4513. Commit: eab8f8e43f702898ca22f27e33ecdec0894d5aeb https://github.com/galaxyproject/galaxy/commit/eab8f8e43f702898ca22f27e33ec… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-view.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/upload/default/default-view.js Log Message: ----------- Merge pull request #4778 from jmchilton/no_empty_upload Bugfix - do not initiate empty FTP uploads. Compare: https://github.com/galaxyproject/galaxy/compare/f608753e2add...eab8f8e43f70

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[galaxyproject/galaxy] 1c9ff9: Load dataset edit attributes without page refresh
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.09 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/27e3e724cded...2b18a0b8d5f7

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[galaxyproject/galaxy] 4cd6df: PEP-8 fixes in doctests.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cd6dffe328169daad3d3d060b6966c3c8b7ae41 https://github.com/galaxyproject/galaxy/commit/4cd6dffe328169daad3d3d060b69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- PEP-8 fixes in doctests. Rebased with " ]" and "[ " fixes pointed out by @nsoranzo. Commit: f608753e2addf1cfbd8ff31186b9d29d6b1dab68 https://github.com/galaxyproject/galaxy/commit/f608753e2addf1cfbd8ff31186b9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #4764 from jmchilton/pep8_doctests PEP-8 fixes in random doctests. Compare: https://github.com/galaxyproject/galaxy/compare/f307490c11c6...f608753e2add

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[galaxyproject/galaxy] 012aaf: Pin pydocstyle...
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/a0f63b671f29...27e3e724cded

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[galaxyproject/galaxy] 012aaf: Pin pydocstyle...
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/81ece2551cea...1635f46430b1

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[galaxyproject/galaxy]
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy

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