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

[galaxyproject/galaxy] 80a41f: Optimize public grid database interactions.
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 80a41f32744d2d76b74973663cd6d751daf8e8a5 https://github.com/galaxyproject/galaxy/commit/80a41f32744d2d76b74973663cd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Optimize public grid database interactions. For all four grid types (histories, viz, workflows, and pages), this computes rating average on the server and prefetches any annotations. This eliminates at least two extra queries for response element in the grid. See comment in the history controller for why I am fairly confident this is a good idea for annotations but tags are less obvious - these grids still go back to the postgres server multiple times per rendered item to render tags. I'm confident we should either subqueryload, joinedload, or upgrade to sqlalchemy 2.2 and selectinload (http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalch…) the tags as well - but I'm not sure which without being able to hack on a usegalaxy.org. This also brings in less of the user model (only username instead of all of it) to reduce over-the-wire transmission of unneeded data from postgres to Galaxy. For workflows we were LEFT OUTER JOIN-ing on the steps of the latest workflow - so we were bringing back a lot of extra rows for data that was completely unused. In light of this, it makes perfect sense to me why published workflows were the slowest of these and I suspect they will all be equally performant after this change (modulo the number of rows in the tables and the number of rows rendered). Commit: ed23cc652df321371ef6d66d32e7812406577f30 https://github.com/galaxyproject/galaxy/commit/ed23cc652df321371ef6d66d32e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5514 from jmchilton/optimize_public_grids [18.01] Optimize public grid database interactions. Compare: https://github.com/galaxyproject/galaxy/compare/fd1ac05cdfb1...ed23cc652df3

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[galaxyproject/galaxy] e73731: Optimize database interaction for user workflow li...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: e73731f5528a08735a6b65bf419a6f7986c1c771 https://github.com/galaxyproject/galaxy/commit/e73731f5528a08735a6b65bf419a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Optimize database interaction for user workflow list. Don't LEFT OUTER JOIN workflow against its steps to produce step count - this causes a lot of duplicated workflow data and fetches step data not needed to just produce a step count. Tweak pre-fetching for workflows shared with user also. Commit: fd1ac05cdfb1dff01e17edcdfd7304803ece2201 https://github.com/galaxyproject/galaxy/commit/fd1ac05cdfb1dff01e17edcdfd73… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5515 from jmchilton/optimize_workflow_list [18.01] Optimize database interaction for user workflow list. Compare: https://github.com/galaxyproject/galaxy/compare/321cd78ad82b...fd1ac05cdfb1

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[galaxyproject/usegalaxy-playbook] d7d51f: Use the sha1 hash filter for supervisor passwords ...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7d51f525b4d4eccf23572c180175b150767729c https://github.com/galaxyproject/usegalaxy-playbook/commit/d7d51f525b4d4ecc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M common_roles M env/common/group_vars/toolshedservers/common_vars.yml M env/common/group_vars/toolshedservers/common_vault.yml M env/main/group_vars/supervisorservers/vars.yml M env/main/group_vars/supervisorservers/vault.yml M env/test/group_vars/supervisorservers/vars.yml M env/test/group_vars/supervisorservers/vault.yml Log Message: ----------- Use the sha1 hash filter for supervisor passwords rather than requiring the admin to hash it themselves Commit: 41c84e4b7b851700448c785e479a319ac565c5ad https://github.com/galaxyproject/usegalaxy-playbook/commit/41c84e4b7b851700… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M env/common/stack.yml M env/common/update_shed.yml A env/testtoolshed/stack_extras.yml A env/testtoolshed/templates/toolshed/shedctl.j2 A env/testtoolshed/templates/toolshed/supervisorctl.j2 A env/testtoolshed/templates/toolshed/supervisord.conf.j2 M roles/usegalaxy_admin/tasks/main.yml Log Message: ----------- Shed stack missing pieces Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/526019280e50...…

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[galaxyproject/usegalaxy-playbook] 07fc7a: Update roles
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 07fc7a99e5b717cc9d0fc6b22b253e746e5acc73 https://github.com/galaxyproject/usegalaxy-playbook/commit/07fc7a99e5b717cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M roles/galaxyproject.galaxy/meta/.galaxy_install_info M roles/galaxyproject.galaxy/tasks/dependencies.yml M roles/galaxyproject.galaxy_toolshed/meta/.galaxy_install_info M roles/galaxyproject.galaxy_toolshed/tasks/database.yml Log Message: ----------- Update roles Commit: 526019280e502f8b430a6b0002eabe5c3ff0a507 https://github.com/galaxyproject/usegalaxy-playbook/commit/526019280e502f8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: A env/common/_inc_client_build.yml M env/common/update_shed.yml A env/testtoolshed/_inc_client_build.yml Log Message: ----------- TTS client build support Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/10df88a24d90...…

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[galaxyproject/ansible-galaxy]
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/tags/0.7.5 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 8e8a95: Include PyPI in conditional dependency sources.
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 8e8a950d11fe42bcc1d98ee3cbe06b4688359aae https://github.com/galaxyproject/ansible-galaxy/commit/8e8a950d11fe42bcc1d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Include PyPI in conditional dependency sources.

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[galaxyproject/usegalaxy-playbook] 10df88: Fix automatic (Python) dependency installation on ...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 10df88a24d903a2f0a1bbadd6d95992f67358f9b https://github.com/galaxyproject/usegalaxy-playbook/commit/10df88a24d903a2f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M env/common/update_shed.yml Log Message: ----------- Fix automatic (Python) dependency installation on TS updates

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[galaxyproject/galaxy] b87d57: Make galaxy compatible with pysam 0.14
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b87d57aac7c15c0455e0936c0325a1a0b326407e https://github.com/galaxyproject/galaxy/commit/b87d57aac7c15c0455e0936c0325… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Make galaxy compatible with pysam 0.14 Commit: 349b25b74ae4de51ab567a0215054d854af9a934 https://github.com/galaxyproject/galaxy/commit/349b25b74ae4de51ab567a021505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minimize duplication of BAM set_meta code Commit: 3b8a2f9edc93c45e5153896035f321bd23c7ec1a https://github.com/galaxyproject/galaxy/commit/3b8a2f9edc93c45e5153896035f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin pysam to 0.14 Commit: 321cd78ad82b2c686e515567c15062cc2ef92aec https://github.com/galaxyproject/galaxy/commit/321cd78ad82b2c686e515567c150… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5512 from mvdbeek/fix_new_pysam [18.01] Make galaxy compatible with pysam 0.14 Compare: https://github.com/galaxyproject/galaxy/compare/aefe0e14498d...321cd78ad82b

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[galaxyproject/usegalaxy-playbook] f61a0a: Update TTS
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f61a0acbc72a25dd139c8539d3dbe03d1f99089b https://github.com/galaxyproject/usegalaxy-playbook/commit/f61a0acbc72a25dd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS

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[galaxyproject/galaxy] 007ae8: Default slow request tracking to disabled; this is...
by GitHub 12 Feb '18

12 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 007ae8f9377666ab84599aee20fce2a63cc03fbc https://github.com/galaxyproject/galaxy/commit/007ae8f9377666ab84599aee20fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Default slow request tracking to disabled; this is only used in Galaxy and should fix TS/reports error. Commit: 39fd5fdc05e81918df322d1b84b444864d67174d https://github.com/galaxyproject/galaxy/commit/39fd5fdc05e81918df322d1b84b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #5513 from dannon/fix_non_gxy_sentry_middleware Default slow request tracking to disabled; Compare: https://github.com/galaxyproject/galaxy/compare/201d76568f75...39fd5fdc05e8

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