- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] e10fcb: Update Main mutable configs
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e10fcb013f465822884f26bd8466302b56203082 https://github.com/galaxyproject/usegalaxy-playbook/commit/e10fcb013f465822… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update Main mutable configs **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] b4b49d: Add self help to error reporting interface.
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b4b49dc2028da2064fd34d7345b23b47150a1039 https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add self help to error reporting interface. Commit: 88bf3435775e94217bccfc46a5215311dea321aa https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Import Backbone consistently across the app Commit: 84d66bea6008dc534aa6a2331e824005b204da19 https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- h2!=h3 Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051 https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #6711 from dannon/error_help [18.09] Add self help to error reporting interface Compare: https://github.com/galaxyproject/galaxy/compare/9657cd6b32ed...32223161c7ca **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] f7c1d3: unquote the tool_version in the tools API
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Compare: https://github.com/galaxyproject/galaxy/compare/1dacc35332cf...f513594c31a3 **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] 17d148: Use tool_version instead of version parameter
by GitHub 14 Sep '18

14 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17d148eb8f40ed6f7046ad628e1bdcfbaa80f4bb https://github.com/galaxyproject/galaxy/commit/17d148eb8f40ed6f7046ad628e1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 33cac64546a7ef7b04f65196b0ce919ad8f94d93 https://github.com/galaxyproject/galaxy/commit/33cac64546a7ef7b04f65196b0ce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6710 from mvdbeek/change_version_parameter_to_tool_version Use tool_version instead of version parameter Compare: https://github.com/galaxyproject/galaxy/compare/d1352c4b274a...33cac64546a7 **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] 943e67: Test that newest version will be returned if tool ...
by GitHub 13 Sep '18

13 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 943e67e4e59beea726912dc013a30903827f6277 https://github.com/galaxyproject/galaxy/commit/943e67e4e59beea726912dc013a3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: 5de1c2c980343d031b81bbc16fcde43ee4909c60 https://github.com/galaxyproject/galaxy/commit/5de1c2c980343d031b81bbc16fcd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: f8430b110dccfe53f347757d2284b4329218cec4 https://github.com/galaxyproject/galaxy/commit/f8430b110dccfe53f347757d2284… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 56ed50400f94a04e88c3a6a09721903d571dc969 https://github.com/galaxyproject/galaxy/commit/56ed50400f94a04e88c3a6a09721… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: d1352c4b274a91722e55dae634a332803b8fdc6e https://github.com/galaxyproject/galaxy/commit/d1352c4b274a91722e55dae634a3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6702 from mvdbeek/fix_latest_version Fix wrong version being returned if requested version doesn't exist Compare: https://github.com/galaxyproject/galaxy/compare/5286a1e757de...d1352c4b274a **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/usegalaxy-playbook] ed28cd: Update galaxy to 1dacc35332cf956ed5631fe8c6fa8e231...
by GitHub 12 Sep '18

12 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed28cdc622c6a9552dc0d6bc11320afe1640b8a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed28cdc622c6a955… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update galaxy to 1dacc35332cf956ed5631fe8c6fa8e231dab663e via Ansible. **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] 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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