- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b861b9: implement basic cache on toolbox to_dict objects
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b861b9ad4d693000ba8cf492ce6b1ff057db3d34 https://github.com/galaxyproject/galaxy/commit/b861b9ad4d693000ba8cf492ce6b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- implement basic cache on toolbox to_dict objects base the cache on absence of filters allow cache for users that don't opt in for filters Commit: 8a88cb9827b68e6795cf00496008e1aa189185ad https://github.com/galaxyproject/galaxy/commit/8a88cb9827b68e6795cf00496008… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: a90c3a1d3f2c2a12f285f3c21e91ca364f81853e https://github.com/galaxyproject/galaxy/commit/a90c3a1d3f2c2a12f285f3c21e91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5583 from martenson/backport-toolbox-cache [18.01] Backport toolbox cache Compare: https://github.com/galaxyproject/galaxy/compare/50cd159d4c21...a90c3a1d3f2c

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[galaxyproject/galaxy] 93d5c5: Optimize count query in grids (part 1).
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 93d5c54946e992112841df3461512bbeb6f5c7e9 https://github.com/galaxyproject/galaxy/commit/93d5c54946e992112841df346151… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Optimize count query in grids (part 1). Many grid operations execute a complex query twice - once to produce the total number of rows and once to iterate through the selected parts of the data. This can be more optimal in many ways - this starts us down the path to addressing that by doing two things. The first thing it does is eliminates the query all together if paging is enabled but the user has opted to see "all" the rows. There was never a reason to execute the query in that case I don't think. The second thing it does is move the calculation of the count query until after the data has been generated - this isn't more optimal by itself but it allows us to potentially calculate the count as part of the main query. I've implemented this in a broken way @ https://github.com/galaxyproject/galaxy/commit/ea404721585b5f78da1b91e57e31… but I realized it was too broad an approach and doesn't work if certain kinds of joins are used in the initial query - but a more targetted approach on a per-grid basis could work I think and moving this code after allow us to potentially do that more easily in subsequent commits. Additionally I added a note - that I think it would be best to just return None as the number of pages and issue a second query to the same endpoint with the same arguments but with count_only=true added as a query request parameter so we can render the main grid faster and then render the paging elements after the second query finishes. This would feel more responsive I think. Commit: 50cd159d4c212a36b8d3861295125ef055a296d9 https://github.com/galaxyproject/galaxy/commit/50cd159d4c212a36b8d386129512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5574 from jmchilton/optimize_count_query_1 [18.01] Optimize count query in grids (Part 1). Compare: https://github.com/galaxyproject/galaxy/compare/d8585f6a6f87...50cd159d4c21

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[galaxyproject/galaxy] c00e77: Fix lack of feedback when slow grids are loading d...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server. Fixes #5473 (after numerous other backend optimizations also). Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. Compare: https://github.com/galaxyproject/galaxy/compare/c8407786f25c...d8585f6a6f87

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[galaxyproject/usegalaxy-playbook] dd4b14: Main mutable configs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd4b1410d020827dde11de761d7c7ad575f4ba1e https://github.com/galaxyproject/usegalaxy-playbook/commit/dd4b1410d020827d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 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: ----------- Main mutable configs

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[galaxyproject/usegalaxy-playbook] 9de278: Test mutable configs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9de278cf3019b47e753bd6e5dfa660c8b67997d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9de278cf3019b47e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs

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[galaxyproject/usegalaxy-playbook] 0088bb: Mutable configs for new tool installs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0088bb471eedd62aade63ebe54bfd958e67887c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/0088bb471eedd62a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs for new tool installs

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[galaxyproject/usegalaxy-playbook] 95baed: Updated lastz.
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 95baede7590b49cc84b4ce2d105b924091e56bc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/95baede7590b49cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz.

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[galaxyproject/usegalaxy-playbook] a3feca: update MTS
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a3feca909a532438a65302bb71c927bc44188393 https://github.com/galaxyproject/usegalaxy-playbook/commit/a3feca909a532438… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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[galaxyproject/usegalaxy-playbook] c72e72: update tts
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c72e7203b1cbb8419957e56c4bf0f67abbd772f0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c72e7203b1cbb841… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update tts Commit: f2054837373e14d18ad4dcf0399ea085bc19c68d https://github.com/galaxyproject/usegalaxy-playbook/commit/f2054837373e14d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c3fd2231c3a6...…

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[galaxyproject/usegalaxy-playbook] c3fd22: Remove packed static route from TTS nginx
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3fd2231c3a6d4bb14457ab057716a928f2aec55 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3fd2231c3a6d4bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Remove packed static route from TTS nginx

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