Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b87d57aac7c15c0455e0936c0325a1a0b326407e https://github.com/galaxyproject/galaxy/commit/b87d57aac7c15c0455e0936c0325a... Author: mvdbeek <m.vandenbeek@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/349b25b74ae4de51ab567a0215054... Author: mvdbeek <m.vandenbeek@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/3b8a2f9edc93c45e5153896035f32... Author: mvdbeek <m.vandenbeek@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/321cd78ad82b2c686e515567c1506... Author: John Chilton <jmchilton@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 Commit: e73731f5528a08735a6b65bf419a6f7986c1c771 https://github.com/galaxyproject/galaxy/commit/e73731f5528a08735a6b65bf419a6... Author: John Chilton <jmchilton@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: b9ddec71a4632942534048069f7d0d474b2c8982 https://github.com/galaxyproject/galaxy/commit/b9ddec71a4632942534048069f7d0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- disable loading of webhooks in TS and reports apps Commit: 80a41f32744d2d76b74973663cd6d751daf8e8a5 https://github.com/galaxyproject/galaxy/commit/80a41f32744d2d76b74973663cd6d... Author: John Chilton <jmchilton@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#sqlalche...) 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: fd1ac05cdfb1dff01e17edcdfd7304803ece2201 https://github.com/galaxyproject/galaxy/commit/fd1ac05cdfb1dff01e17edcdfd730... Author: Martin Cech <marten@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. Commit: ed23cc652df321371ef6d66d32e7812406577f30 https://github.com/galaxyproject/galaxy/commit/ed23cc652df321371ef6d66d32e78... Author: Martin Cech <marten@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. Commit: adaacbc66508d1bb57376c5b43cac21b3d7c28bb https://github.com/galaxyproject/galaxy/commit/adaacbc66508d1bb57376c5b43cac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Merge pull request #5521 from martenson/webhooks-galaxy-only [18.01] disable loading of webhooks in TS and reports apps Commit: 5ff6be93ed074485a60e567309247e9dbf02db09 https://github.com/galaxyproject/galaxy/commit/5ff6be93ed074485a60e567309247... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Use profile="18.01" for BamNative converters This is because samtools writes to stderr when sorting/merging large files. Part of https://github.com/galaxyproject/galaxy/issues/5496#issuecomment-365458089. Commit: c20b68a5dd92e29c0e1a985f46fccae89efcac18 https://github.com/galaxyproject/galaxy/commit/c20b68a5dd92e29c0e1a985f46fcc... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Merge pull request #5532 from mvdbeek/bam_native_converter_fix [18.01] Use profile="18.01" for BamNative converters Commit: 043fe35e9521c20987cd995de90aaf1f01e94e63 https://github.com/galaxyproject/galaxy/commit/043fe35e9521c20987cd995de90aa... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.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 remote-tracking branch 'jmchilton/release_18.01' into dev_merge_0 Commit: 3de8593e19641ad1078dbb53a870876ec32c80e1 https://github.com/galaxyproject/galaxy/commit/3de8593e19641ad1078dbb53a8708... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.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 #5540 from jmchilton/dev_merge_0 Merge release_18.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/0b137669d7d2...3de8593e1964