galaxy-commits September 2018

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179 discussions

[galaxyproject/galaxy] bddabe: Add missing route for API endpoint.
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Compare: https://github.com/galaxyproject/galaxy/compare/2a79ae0ce1bb...1dacc35332cf **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 545bd1: Handle queries returning 0 rows
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 545bd1e0fc09c451b27f98a743216167b51a201c https://github.com/galaxyproject/infrastructure-playbook/commit/545bd1e0fc0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Handle queries returning 0 rows **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ba4e7d: Make gro and top datatypes tabular subclasses
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: ba4e7d199b4bc080dcd741710d2241147bdbe745 https://github.com/galaxyproject/galaxy/commit/ba4e7d199b4bc080dcd741710d22… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make gro and top datatypes tabular subclasses I think that was the intention in https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Commit: 1f8c234c2be8baac9db94e17f4727e6c3c6c55ef https://github.com/galaxyproject/galaxy/commit/1f8c234c2be8baac9db94e17f472… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make top datatype inherit from Text. Commit: 17157dd0633b4deb91a39bbc76288dd2968423f5 https://github.com/galaxyproject/galaxy/commit/17157dd0633b4deb91a39bbc7628… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #9 from blankenberg/gro2 Make top datatype inherit from Text. Commit: 9657cd6b32ed0768d2c73dd9d63c38432afb4b71 https://github.com/galaxyproject/galaxy/commit/9657cd6b32ed0768d2c73dd9d63c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6695 from mvdbeek/fix_gro_top_datatypes [18.09] Make gro and top datatypes tabular subclasses Compare: https://github.com/galaxyproject/galaxy/compare/80266129fe3d...9657cd6b32ed **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c871a0: Patch update.sh
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c871a03e5b572cec0c67b6d6f59f72a8f4e83fe3 https://github.com/galaxyproject/galaxy/commit/c871a03e5b572cec0c67b6d6f59f… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Patch update.sh to address dependency update issues on a macOS. Commit: 5286a1e757deb89b5521935b31d062cee29a29a8 https://github.com/galaxyproject/galaxy/commit/5286a1e757deb89b5521935b31d0… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #6694 from VJalili/patch-5 Patch update.sh to address dependency update issues on a macOS. Compare: https://github.com/galaxyproject/galaxy/compare/0c9d02f96289...5286a1e757de **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4fc9fe: Fix target update for rule collection builder afte...
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Compare: https://github.com/galaxyproject/galaxy/compare/9217680ab6af...2a79ae0ce1bb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 471162: [18.09] Fix new extract dataset to perserve collec...
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 471162eadb4408318db534c6d24f7685bedb29eb https://github.com/galaxyproject/galaxy/commit/471162eadb4408318db534c6d24f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- [18.09] Fix new extract dataset to perserve collection element identifier. Commit: 80266129fe3d3d4b9657da0a3c5e8232bfa2a46b https://github.com/galaxyproject/galaxy/commit/80266129fe3d3d4b9657da0a3c5e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- Merge pull request #6692 from jmchilton/1809_fix_extract_name [18.09] Fix new extract dataset tool to preserve collection element identifier. Compare: https://github.com/galaxyproject/galaxy/compare/c8cb164ab8ad...80266129fe3d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] be0495: Update version to 18.09.rc1
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be04959cf311e0f495f5a10e84f6f1933594a38d https://github.com/galaxyproject/galaxy/commit/be04959cf311e0f495f5a10e84f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.rc1 Commit: c06464a78cbedeb2dd30d9547b2b799ad4666b5e https://github.com/galaxyproject/galaxy/commit/c06464a78cbedeb2dd30d9547b2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 19.01.dev Commit: 88c2130ed1a1f97fc66b78975595ca47f2152ea1 https://github.com/galaxyproject/galaxy/commit/88c2130ed1a1f97fc66b78975595… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Log Message: ----------- Merge branch 'version-18.09' into version-19.01.dev Commit: 0c9d02f9628945e5341314d88e69c84b2c76a38c https://github.com/galaxyproject/galaxy/commit/0c9d02f9628945e5341314d88e69… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #6688 from dannon/version-19.01.dev Version 19.01.dev Compare: https://github.com/galaxyproject/galaxy/compare/ebc5858f02e0...0c9d02f96289 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] be0495: Update version to 18.09.rc1
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: be04959cf311e0f495f5a10e84f6f1933594a38d https://github.com/galaxyproject/galaxy/commit/be04959cf311e0f495f5a10e84f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.rc1 Commit: c8cb164ab8ad4fe5d7ea9768e3f7e58051200525 https://github.com/galaxyproject/galaxy/commit/c8cb164ab8ad4fe5d7ea9768e3f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #6687 from dannon/version-18.09 Update version to 18.09.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/ebc5858f02e0...c8cb164ab8ad **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy]
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ec320d: Update `cloud` objectstore to adhere with cloudbri...
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec320d2bad5c327b625e66a13a22c941cac96c5d https://github.com/galaxyproject/galaxy/commit/ec320d2bad5c327b625e66a13a22… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Update `cloud` objectstore to adhere with cloudbridge v1 interface. Commit: d0e2820b4f2e35e5a15c96296c656e7c03ee44df https://github.com/galaxyproject/galaxy/commit/d0e2820b4f2e35e5a15c96296c65… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Log exception message failing to create bucket in cloud objectstore. Commit: a52b8a436523a6de040001d45f9773699e58445b https://github.com/galaxyproject/galaxy/commit/a52b8a436523a6de040001d45f97… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Catch a cloudbridge exception if a given bucket does not exist. Commit: 0956604e557bf1a3857fa870beee7f7f6f36d929 https://github.com/galaxyproject/galaxy/commit/0956604e557bf1a3857fa870beee… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud manager to adhere with v1 cloudbridge interface. Commit: 94fe62803b18151f4aa7830c27704fe6ab65cefb https://github.com/galaxyproject/galaxy/commit/94fe62803b18151f4aa7830c2770… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update cloudbridge version in conditional requirements. Commit: ae41b22113332d7cb11db4d64b9037da473d90ba https://github.com/galaxyproject/galaxy/commit/ae41b22113332d7cb11db4d64b90… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update dependencies using `make update-dependencies`. Commit: c95d995e9d980ced74ef0697b14c786a72369680 https://github.com/galaxyproject/galaxy/commit/c95d995e9d980ced74ef0697b14c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Fix pyinotify environment marker Remove outdated pin on boto. Commit: 11274995ca5a84f750000be724d770e77d9de990 https://github.com/galaxyproject/galaxy/commit/11274995ca5a84f750000be724d7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Rename bucket to bucket_name in cloud API and manager. Commit: 240074224f07d1a047e5560627e3f19fb02ae0e7 https://github.com/galaxyproject/galaxy/commit/240074224f07d1a047e5560627e3… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Rename bucket_obj to bucket. Commit: ebc5858f02e07585860b4adc26ccaff300e1154c https://github.com/galaxyproject/galaxy/commit/ebc5858f02e07585860b4adc26cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/managers/cloud.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Merge pull request #6660 from VJalili/upgrade_cloudbridge Upgrade CloudBridge to v1.0.1 Compare: https://github.com/galaxyproject/galaxy/compare/b8fe2fe294f1...ebc5858f02e0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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galaxy-commits September 2018