June 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 8417a5: Switch to Ansible 2.4 dynamic task includes to avo...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/yaml-uwsgi Home: https://github.com/galaxyproject/ansible-galaxy Commit: 8417a5bf92da86c1fd1d8e19dce86c9eaf675701 https://github.com/galaxyproject/ansible-galaxy/commit/8417a5bf92da86c1fd1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M meta/main.yml M tasks/dependencies.yml M tasks/download.yml M tasks/main.yml Log Message: ----------- Switch to Ansible 2.4 dynamic task includes to avoid tons of skips when running the role in pieces. Commit: 719fa075397f562fb7c14bdb2f71d911c24fa527 https://github.com/galaxyproject/ansible-galaxy/commit/719fa075397f562fb7c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A .gitignore M README.md M defaults/main.yml A filter_plugins/uwsgi_yaml.py M tasks/clone.yml M tasks/errordocs.yml M tasks/static_setup.yml M templates/galaxy.ini.j2 A templates/galaxy.yml.j2 Log Message: ----------- Support for YAML galaxy config Compare: https://github.com/galaxyproject/ansible-galaxy/compare/8417a5bf92da^...719… **NOTE:** This service 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] 533ffa: Add gxy.io redirect for my slides
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 533ffaccc4277ee08ee2db631b8ce1d0cada5dd2 https://github.com/galaxyproject/infrastructure-playbook/commit/533ffaccc42… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M env/galaxy/templates/nginx/gxy.io.j2 Log Message: ----------- Add gxy.io redirect for my slides **NOTE:** This service 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] 8a55c4: Add dataselector component
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a55c4fd5467ed67650f543c4a1955316b569d04 https://github.com/galaxyproject/galaxy/commit/8a55c4fd5467ed67650f543c4a19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: A client/galaxy/scripts/components/DataSelector.vue Log Message: ----------- Add dataselector component Commit: 7cf17001efb8b9491b0e34c8fe063e31d16e1729 https://github.com/galaxyproject/galaxy/commit/7cf17001efb8b9491b0e34c8fe06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/components/DataSelector.vue Log Message: ----------- Use methods to show and hide dialog Commit: ea5d3d30c4bc356b4d2c1b39e07270e40ff6cb0a https://github.com/galaxyproject/galaxy/commit/ea5d3d30c4bc356b4d2c1b39e072… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Add shared data content access helper Commit: b657fbdd738a0aafb5112445e9aafbb6df9fa3cf https://github.com/galaxyproject/galaxy/commit/b657fbdd738a0aafb5112445e9aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: A client/galaxy/scripts/components/DataDialog.vue R client/galaxy/scripts/components/DataSelector.vue M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Remove surrounding div in dialog component Commit: f9e37d43091a61b2102283a57fff858bde8b9f51 https://github.com/galaxyproject/galaxy/commit/f9e37d43091a61b2102283a57fff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/layout/data.js Log Message: ----------- Append modal to body, display always -- we'll use/destroy() this. Commit: 8a9c6d32321908c6c1bd763cf9cdb91f4c899fc8 https://github.com/galaxyproject/galaxy/commit/8a9c6d32321908c6c1bd763cf9cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/layout/data.js Log Message: ----------- Add select field to shared data selector Commit: 8a34978decbe8fb70be9eece744aba1b3de03383 https://github.com/galaxyproject/galaxy/commit/8a34978decbe8fb70be9eece744a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Improve error handling, add spinner Commit: 30c42e62d6d724e79177c08ba5c46215a01c9f73 https://github.com/galaxyproject/galaxy/commit/30c42e62d6d724e79177c08ba5c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Hide second option while loading datasets Commit: 8a858b31bca3c7bd1b1cc7985ac83b89828a2111 https://github.com/galaxyproject/galaxy/commit/8a858b31bca3c7bd1b1cc7985ac8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add default error message, fix alert properties Commit: 6ab1bfbe218689794644d43123dd10021b2ebabe https://github.com/galaxyproject/galaxy/commit/6ab1bfbe218689794644d43123dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Revise error message handling Commit: 648caa48e49f7a086b20a39fa39cf438f103b9f8 https://github.com/galaxyproject/galaxy/commit/648caa48e49f7a086b20a39fa39c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Add comments Commit: 59461c2a8f7dbfffa6ed22f54c197a405f992aca https://github.com/galaxyproject/galaxy/commit/59461c2a8f7dbfffa6ed22f54c19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add history dataset id to option text Commit: e662c9754814559232fe0206b2f56548f2fde26c https://github.com/galaxyproject/galaxy/commit/e662c9754814559232fe0206b2f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Replace select field by table Commit: 1d94c6762e7b830710e5697f99bc2dd6ddeebbb8 https://github.com/galaxyproject/galaxy/commit/1d94c6762e7b830710e5697f99bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add event handlers, close modal Commit: 67c48378c54fc8da0666e88069ce9816c096218e https://github.com/galaxyproject/galaxy/commit/67c48378c54fc8da0666e88069ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Move search field into modal header Commit: ce76463527a61dc4dba40f4b578645df7693bb81 https://github.com/galaxyproject/galaxy/commit/ce76463527a61dc4dba40f4b5786… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Use default label and file icons Commit: b93e01a784b85d071c3b709de4186278c40a4a4a https://github.com/galaxyproject/galaxy/commit/b93e01a784b85d071c3b709de418… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Use different icons for datasets and collections Commit: d05f72f8e0648fc200e2707fafb9df31724e824c https://github.com/galaxyproject/galaxy/commit/d05f72f8e0648fc200e2707fafb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add no match notification Commit: cfc63ef24a06266ae9ee55955cce629be7a36558 https://github.com/galaxyproject/galaxy/commit/cfc63ef24a06266ae9ee55955cce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Remove debug statement Commit: d64bae64580e03a2dd8695a5471f3046323021ff https://github.com/galaxyproject/galaxy/commit/d64bae64580e03a2dd8695a5471f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Merge pull request #6195 from guerler/shared_data_selector Common dataset selector Compare: https://github.com/galaxyproject/galaxy/compare/2894dfc8928c...d64bae64580e **NOTE:** This service 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] 996763: Comma-separate tool names in missing tools error m...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9967639bac92eb3f7103794663f41b88f11baa9c https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Comma-separate tool names in missing tools error message Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769 https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6378 from guerler/commaseperror [18.05] Comma-separate tool names in missing tools error message Compare: https://github.com/galaxyproject/galaxy/compare/d28ab2a4f31b...22d383c39842 **NOTE:** This service 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] 572f38: move the sanitization to the try/except block
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 572f38d1fb47e914ad10766007c855786e1643a2 https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- move the sanitization to the try/except block as it may fail (and it did, on Main) Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6377 from martenson/catch-sanitization-faults [18.05] Catch sanitization faults Compare: https://github.com/galaxyproject/galaxy/compare/6d5be41b3205...d28ab2a4f31b **NOTE:** This service 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] 9b195e: Swarmscale fixes for floating IPs
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9b195e9e8f4edb3a582841082cd5807b4eb23d7d https://github.com/galaxyproject/usegalaxy-playbook/commit/9b195e9e8f4edb3a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: A roles/usegalaxy_swarmscale/files/ansible.cfg M roles/usegalaxy_swarmscale/files/leave.yml M roles/usegalaxy_swarmscale/files/spawn.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- Swarmscale fixes for floating IPs **NOTE:** This service 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] 536c45: Optimizations for dynamic output files collection.
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 536c45dc1107640a2d0a2e9741f5b6a692ee4173 https://github.com/galaxyproject/galaxy/commit/536c45dc1107640a2d0a2e9741f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Optimizations for dynamic output files collection. During the set hid and update quota parts of this operation - skip a bunch of extra flushes and skip checking for extra files since these cannot be created in conjunction with dynamic file discovery currently. Cut this part of that operation from about 50 seconds to 7 when creating a collection with 1000 elements on my laptop against a local postgres database. Commit: 2894dfc8928ca1e232b76ae83a84155f7f06e687 https://github.com/galaxyproject/galaxy/commit/2894dfc8928ca1e232b76ae83a84… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6367 from jmchilton/finish_opt Optimizations for dynamic output file collection. Compare: https://github.com/galaxyproject/galaxy/compare/d1c063d6614f...2894dfc8928c **NOTE:** This service 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] 76dee1: Add gafa.sqlite datatype
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76dee1970aab5f124cea97fde5a44cd8d93b6d67 https://github.com/galaxyproject/galaxy/commit/76dee1970aab5f124cea97fde5a4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add gafa.sqlite datatype Generated by the GAFA tool: https://toolshed.g2.bx.psu.edu/view/earlhaminst/gafa/ Can be visualised with the Aequatus.js plugin (PR forthcoming). Work in collaboration with @anilthanki as part of the GeneSeqToFamily project: https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqTo… Commit: d1c063d6614f75191bb0f48f7ce2e9ddaacf1efc https://github.com/galaxyproject/galaxy/commit/d1c063d6614f75191bb0f48f7ce2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6372 from nsoranzo/add_gafa.sqlite_datatype Add gafa.sqlite datatype Compare: https://github.com/galaxyproject/galaxy/compare/7e826afecdf3...d1c063d6614f **NOTE:** This service 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] c6403a: Fix logging bug.
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c6403acd0f18196c0453a90fe89ccf861d7a28d6 https://github.com/galaxyproject/galaxy/commit/c6403acd0f18196c0453a90fe89c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix logging bug. Commit: 6d5be41b320510d6e2d163399a3a6e30d6f9bda0 https://github.com/galaxyproject/galaxy/commit/6d5be41b320510d6e2d163399a3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6366 from jmchilton/job_log_bug [18.05] Fix small bug in logging output name in job finish. Compare: https://github.com/galaxyproject/galaxy/compare/d0a0fa8319e5...6d5be41b3205 **NOTE:** This service 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] f950cf: Remove debug statement when creating certain kinds...
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f950cf9ac4334d973b5dd3f907d5a4518d656283 https://github.com/galaxyproject/galaxy/commit/f950cf9ac4334d973b5dd3f907d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Remove debug statement when creating certain kinds of collections. Commit: 7e826afecdf36f3d1719186c586f5391a5522809 https://github.com/galaxyproject/galaxy/commit/7e826afecdf36f3d1719186c586f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6371 from jmchilton/remove_bad_log_statement Remove debug statement when creating certain kinds of collections. Compare: https://github.com/galaxyproject/galaxy/compare/f89c6a408207...7e826afecdf3 **NOTE:** This service 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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