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

[galaxyproject/usegalaxy-playbook] 61c8d1: Only run `make client-production-maps` on Test ins...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 61c8d1e2ef0776dfb0614330a689d3de213eeb94 https://github.com/galaxyproject/usegalaxy-playbook/commit/61c8d1e2ef0776df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M roles/usegalaxy_cvmfs/tasks/_inc_client_build.yml Log Message: ----------- Only run `make client-production-maps` on Test instead of `make client` per @martenson.

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[galaxyproject/usegalaxy-playbook] da54b7: Switch from cvmfs_config wipecache to cvmfs_talk r...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: da54b7136c3c811e7c5b280732eaf3c95e5012a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/da54b7136c3c811e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M env/common/_inc_snapshot.yml A roles/usegalaxy_cvmfs/tasks/flush_cache.yml M roles/usegalaxy_cvmfs/tasks/main.yml R roles/usegalaxy_cvmfs/tasks/wipecache.yml Log Message: ----------- Switch from cvmfs_config wipecache to cvmfs_talk remount sync Commit: 39baf637e13d0a87778d753ec7cc96e57dc8ffe4 https://github.com/galaxyproject/usegalaxy-playbook/commit/39baf637e13d0a87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/77742e182b54...…

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[galaxyproject/galaxy] b5945a: Add IdeasPre datatype subclassed from Rgenetics
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: b5945ad3e3a972acb41c87c2ddeeff222779020c https://github.com/galaxyproject/galaxy/commit/b5945ad3e3a972acb41c87c2ddee… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Add IdeasPre datatype subclassed from Rgenetics Commit: 3fdd4edc5c1954dc750dfeff03cb3205ee1b6042 https://github.com/galaxyproject/galaxy/commit/3fdd4edc5c1954dc750dfeff03cb… Author: greg <ghv2(a)psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Subclass IdeasPre from Html Commit: 7feef3dc0e6853fb3a0ded2056f39d1ff0f222e8 https://github.com/galaxyproject/galaxy/commit/7feef3dc0e6853fb3a0ded2056f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix "Go back to workflows list" link on workflow sharing interface. Commit: 9df2813524275b89e97f9dd6b8d4ae4e4b307947 https://github.com/galaxyproject/galaxy/commit/9df2813524275b89e97f9dd6b8d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix more workflow sharing broken links Commit: b463be78a5066c7e6c389c43af2bd863f05e4a80 https://github.com/galaxyproject/galaxy/commit/b463be78a5066c7e6c389c43af2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 977bbf1481b2fd36512f869c01f0af6ba4099a92 https://github.com/galaxyproject/galaxy/commit/977bbf1481b2fd36512f869c01f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: eba3fb4b35570fc704dbb9a70c733293a2ee4514 https://github.com/galaxyproject/galaxy/commit/eba3fb4b35570fc704dbb9a70c73… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh for galaxy tarballs Do not assume git is installed and the `.git` directory is present. Fix https://github.com/galaxyproject/galaxy/issues/5466 Commit: 3f50b45a4e3016a211dcbd0876bb95acb29cf900 https://github.com/galaxyproject/galaxy/commit/3f50b45a4e3016a211dcbd0876bb… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py Log Message: ----------- Merge pull request #5445 from gregvonkuster/add-ideaspre [18.01] Add support for the ideaspre datatype Commit: d91078024bf3e9404aaca1c8655a5bc2b451ebc8 https://github.com/galaxyproject/galaxy/commit/d91078024bf3e9404aaca1c8655a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone [18.01] Fix common_startup.sh for galaxy tarballs Commit: c5568a7b1ac07dd86f45801c2706173701b20dc2 https://github.com/galaxyproject/galaxy/commit/c5568a7b1ac07dd86f45801c2706… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #5467 from dannon/workflow_sharing_link_fixes [18.01] Workflow sharing link fixes Commit: ba3b3d5c180e318c26c8db7f0dff7f26115554df https://github.com/galaxyproject/galaxy/commit/ba3b3d5c180e318c26c8db7f0dff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- do not allow codefiles for TS tool loading 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: aefe0e14498d5e5bf5c5f9307ab28f05d0efb81c https://github.com/galaxyproject/galaxy/commit/aefe0e14498d5e5bf5c5f9307ab2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge pull request #5510 from martenson/ts-deny-codefile [18.01] do not allow codefiles for TS tool loading 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 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: b9ddec71a4632942534048069f7d0d474b2c8982 https://github.com/galaxyproject/galaxy/commit/b9ddec71a4632942534048069f7d… Author: Martin Cech <marten(a)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/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: 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. 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. Commit: d7de19b072745ab96a68428281e186cd4c755e45 https://github.com/galaxyproject/galaxy/commit/d7de19b072745ab96a68428281e1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix toolbox filters Commit: adaacbc66508d1bb57376c5b43cac21b3d7c28bb https://github.com/galaxyproject/galaxy/commit/adaacbc66508d1bb57376c5b43ca… Author: Dannon Baker <dannon.baker(a)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/5ff6be93ed074485a60e56730924… Author: mvdbeek <m.vandenbeek(a)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: d5687bc418664bd05e4034a1beea603890128f5e https://github.com/galaxyproject/galaxy/commit/d5687bc418664bd05e4034a1beea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- PEP8 fixes. Commit: ea2bac8a12ad220d39f7e851f70821836da4bbdb https://github.com/galaxyproject/galaxy/commit/ea2bac8a12ad220d39f7e851f708… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- yes, the name is tool not tools :( Commit: 7120739230255c63bf9786fb735016292b57dcfd https://github.com/galaxyproject/galaxy/commit/7120739230255c63bf9786fb7350… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Shouldn't break backward compatiblity at all without it - but to get the outputs Pulsar requires an update (https://github.com/galaxyproject/pulsar/pull/159) as well. Commit: c20b68a5dd92e29c0e1a985f46fccae89efcac18 https://github.com/galaxyproject/galaxy/commit/c20b68a5dd92e29c0e1a985f46fc… Author: Nicola Soranzo <nsoranzo(a)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: 283ab0459fe25cc26606ccae86bdd99e1c6765b9 https://github.com/galaxyproject/galaxy/commit/283ab0459fe25cc26606ccae86bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Improve performance bugs and misleading summary info in history list. Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing. Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered. This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries. Commit: 7457ce426f0563464dff2313249381afa9378f28 https://github.com/galaxyproject/galaxy/commit/7457ce426f0563464dff23132493… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- optimize nonadmin and nonanon library list permission queries Before, the code would emit extra queries per each library to find out whether the current user has permissions on it. By pre-fetching all of them in one query and passing around as a dict object we should see a considerable speedup on Galaxies with many libraries. Commit: 296af58c3d3f6fdb19560f1c8ab58290c9742b8b https://github.com/galaxyproject/galaxy/commit/296af58c3d3f6fdb19560f1c8ab5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Merge pull request #5542 from martenson/optimize-nonadmin-nonanon-datalibs [18.01] optimize nonadmin and nonanon library list permission queries Commit: 755fb9fb21581f29ba96a1465ca73e72eb68b610 https://github.com/galaxyproject/galaxy/commit/755fb9fb21581f29ba96a1465ca7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less Log Message: ----------- style changes for history lists * include title for all state indicators * shorten title * change style of deleted indicator * comment out unused less variables Commit: 1ccd55a500e59c98a910f783e5fcc01913beef54 https://github.com/galaxyproject/galaxy/commit/1ccd55a500e59c98a910f783e5fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5535 from jmchilton/pulsar_error_handling_1 [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Commit: 42c12c51884454c60a8b109f1ae7e814eeeaf7a4 https://github.com/galaxyproject/galaxy/commit/42c12c51884454c60a8b109f1ae7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #5533 from jmchilton/history_list_opts [18.01] Improve performance bugs and misleading summary info in history list. Commit: 8c941ae35a37f8dd087222c6827c122ddfdcc966 https://github.com/galaxyproject/galaxy/commit/8c941ae35a37f8dd087222c6827c… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527 Commit: a269a95cf0aef62b1f1dbca8de698d7b2f61f52b https://github.com/galaxyproject/galaxy/commit/a269a95cf0aef62b1f1dbca8de69… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 6b0e20a7a9006aec997b9e60aae793d5d2fb8915 https://github.com/galaxyproject/galaxy/commit/6b0e20a7a9006aec997b9e60aae7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #5526 from bgruening/user_filter [18.01] fix toolbox filters Commit: fa93d4e04bccd31ba347bbb916b9c7b23b6c5c9d https://github.com/galaxyproject/galaxy/commit/fa93d4e04bccd31ba347bbb916b9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: 5488cf29eabc835e8e7ee994035557392471c586 https://github.com/galaxyproject/galaxy/commit/5488cf29eabc835e8e7ee9940355… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5552 from davebx/18.01 [18.01] Close tempfile handles. Commit: a63b0e7f857aa08a72acd667f22ddd84eca457f7 https://github.com/galaxyproject/galaxy/commit/a63b0e7f857aa08a72acd667f22d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M client/package.json M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/search/script.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/datatypes/genetics.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.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 M lib/tool_shed/tools/tool_validator.py M scripts/common_startup.sh M templates/webapps/galaxy/workflow/sharing.mako A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/2b3a2833acf8...a63b0e7f857a

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[galaxyproject/infrastructure-playbook] 669ca9: Remove cvmfs_wipecache setuid binary
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 669ca93ed1e988e9159633abf51306b06617aecf https://github.com/galaxyproject/infrastructure-playbook/commit/669ca93ed1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M roles/cvmfs/tasks/client.yml M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Remove cvmfs_wipecache setuid binary

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[galaxyproject/galaxy] fa93d4: Close tempfile handles.
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fa93d4e04bccd31ba347bbb916b9c7b23b6c5c9d https://github.com/galaxyproject/galaxy/commit/fa93d4e04bccd31ba347bbb916b9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: 5488cf29eabc835e8e7ee994035557392471c586 https://github.com/galaxyproject/galaxy/commit/5488cf29eabc835e8e7ee9940355… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5552 from davebx/18.01 [18.01] Close tempfile handles. Compare: https://github.com/galaxyproject/galaxy/compare/6b0e20a7a900...5488cf29eabc

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[galaxyproject/usegalaxy-playbook] 77742e: Installed and updated a lot of tools.
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 77742e182b54e9df7664aa115b17631dea4ad107 https://github.com/galaxyproject/usegalaxy-playbook/commit/77742e182b54e9df… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.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: ----------- Installed and updated a lot of tools. Including but not limited to: - ideas_preprocessor - ideas - ideas_genome_tracks - snpEff - PlantTribes

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[galaxyproject/galaxy] d30811: fixed stale link
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d30811eea38f3bb535d52cb86dbb0db0aca5009d https://github.com/galaxyproject/galaxy/commit/d30811eea38f3bb535d52cb86dbb… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- fixed stale link Commit: c9c2e968daba29d15e574f148bbdcb06ee59ce3f https://github.com/galaxyproject/galaxy/commit/c9c2e968daba29d15e574f148bbd… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #5548 from bernt-matthias/topic/fix-obo-link fixed stale link Compare: https://github.com/galaxyproject/galaxy/compare/f7b505e68dad...c9c2e968daba

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[galaxyproject/infrastructure-playbook] ff1886: Commit missing key change
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ff188630f138398352f9a94c4cac19dd67fc553f https://github.com/galaxyproject/infrastructure-playbook/commit/ff188630f13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M common_env/group_vars/baseenv/vault.yml Log Message: ----------- Commit missing key change Commit: 550f81cbfb0745eeebfdeeb4342b09f9c34c54ed https://github.com/galaxyproject/infrastructure-playbook/commit/550f81cbfb0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M roles/cvmfs/defaults/main.yml A roles/cvmfs/files/cvmfs_remount_sync.c A roles/cvmfs/files/cvmfs_remount_sync.centos_6 A roles/cvmfs/files/cvmfs_remount_sync.centos_7 M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/stratum0.yml M roles/cvmfs/tasks/stratum1.yml M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Use new and improved cvmfs_talk remount sync functionality over cvmfs_config wipecache. Include a setuid binary for unprivileged users to call remount. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/db9646bca4…

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[galaxyproject/usegalaxy-playbook] 4a1dc0: Update Test
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a1dc0b405ad802fffc2b2d2d743f76aeedbc30f https://github.com/galaxyproject/usegalaxy-playbook/commit/4a1dc0b405ad802f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] d7de19: fix toolbox filters
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d7de19b072745ab96a68428281e186cd4c755e45 https://github.com/galaxyproject/galaxy/commit/d7de19b072745ab96a68428281e1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix toolbox filters Commit: d5687bc418664bd05e4034a1beea603890128f5e https://github.com/galaxyproject/galaxy/commit/d5687bc418664bd05e4034a1beea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- PEP8 fixes. Commit: ea2bac8a12ad220d39f7e851f70821836da4bbdb https://github.com/galaxyproject/galaxy/commit/ea2bac8a12ad220d39f7e851f708… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- yes, the name is tool not tools :( Commit: 7120739230255c63bf9786fb735016292b57dcfd https://github.com/galaxyproject/galaxy/commit/7120739230255c63bf9786fb7350… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Shouldn't break backward compatiblity at all without it - but to get the outputs Pulsar requires an update (https://github.com/galaxyproject/pulsar/pull/159) as well. Commit: 283ab0459fe25cc26606ccae86bdd99e1c6765b9 https://github.com/galaxyproject/galaxy/commit/283ab0459fe25cc26606ccae86bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Improve performance bugs and misleading summary info in history list. Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing. Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered. This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries. Commit: 7457ce426f0563464dff2313249381afa9378f28 https://github.com/galaxyproject/galaxy/commit/7457ce426f0563464dff23132493… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- optimize nonadmin and nonanon library list permission queries Before, the code would emit extra queries per each library to find out whether the current user has permissions on it. By pre-fetching all of them in one query and passing around as a dict object we should see a considerable speedup on Galaxies with many libraries. Commit: 296af58c3d3f6fdb19560f1c8ab58290c9742b8b https://github.com/galaxyproject/galaxy/commit/296af58c3d3f6fdb19560f1c8ab5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Merge pull request #5542 from martenson/optimize-nonadmin-nonanon-datalibs [18.01] optimize nonadmin and nonanon library list permission queries Commit: 755fb9fb21581f29ba96a1465ca73e72eb68b610 https://github.com/galaxyproject/galaxy/commit/755fb9fb21581f29ba96a1465ca7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less Log Message: ----------- style changes for history lists * include title for all state indicators * shorten title * change style of deleted indicator * comment out unused less variables Commit: 1ccd55a500e59c98a910f783e5fcc01913beef54 https://github.com/galaxyproject/galaxy/commit/1ccd55a500e59c98a910f783e5fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5535 from jmchilton/pulsar_error_handling_1 [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Commit: 42c12c51884454c60a8b109f1ae7e814eeeaf7a4 https://github.com/galaxyproject/galaxy/commit/42c12c51884454c60a8b109f1ae7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #5533 from jmchilton/history_list_opts [18.01] Improve performance bugs and misleading summary info in history list. Commit: 8c941ae35a37f8dd087222c6827c122ddfdcc966 https://github.com/galaxyproject/galaxy/commit/8c941ae35a37f8dd087222c6827c… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527 Commit: a269a95cf0aef62b1f1dbca8de698d7b2f61f52b https://github.com/galaxyproject/galaxy/commit/a269a95cf0aef62b1f1dbca8de69… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 6b0e20a7a9006aec997b9e60aae793d5d2fb8915 https://github.com/galaxyproject/galaxy/commit/6b0e20a7a9006aec997b9e60aae7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #5526 from bgruening/user_filter [18.01] fix toolbox filters Commit: f7b505e68dad6cee53ba884dce258f659d7da33a https://github.com/galaxyproject/galaxy/commit/f7b505e68dad6cee53ba884dce25… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/history.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a54681e8c67c...f7b505e68dad

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