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

[galaxyproject/galaxy] 070889: Better logging for a broad swath of workflow API t...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07088907d3c2ba58986e1025dc1fea6fc6ed0911 https://github.com/galaxyproject/galaxy/commit/07088907d3c2ba58986e1025dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Better logging for a broad swath of workflow API tests. I did a few of these test conversions with 0ff639a29c6179e530c977b358cebf229c76139d but this covers many more the workflow API tests. The idea is to switch to this with statement and context manager that does a better job managing test histories including summarizing the history when problems occur (this summary will include job information after #5697). Commit: 2ace504daea607cc482d29d1bbdfefe53504d748 https://github.com/galaxyproject/galaxy/commit/2ace504daea607cc482d29d1bbdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #5699 from jmchilton/workflow_api_logging Better logging for a large number of workflow API tests. Compare: https://github.com/galaxyproject/galaxy/compare/1d9d39867c38...2ace504daea6

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[galaxyproject/galaxy] e806a3: Fix for running Yarn in Docker for tests that do n...
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e806a3d0e55cee2e72c59a87dba511583d2934a0 https://github.com/galaxyproject/galaxy/commit/e806a3d0e55cee2e72c59a87dba5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix for running Yarn in Docker for tests that do not need it. Commit: 1d9d39867c3842f9218a52eb15c9636342eeb4f1 https://github.com/galaxyproject/galaxy/commit/1d9d39867c3842f9218a52eb15c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5690 from jmchilton/skip_client_build_docker Fix for running Yarn in Docker for tests that do not need it. Compare: https://github.com/galaxyproject/galaxy/compare/c6993caabff5...1d9d39867c38

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[galaxyproject/usegalaxy-playbook] 2f2df6: Switch swarmscale to use new image
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f2df6a844b0185c88482e2eb770b8acbce89959 https://github.com/galaxyproject/usegalaxy-playbook/commit/2f2df6a844b0185c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Switch swarmscale to use new image

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[galaxyproject/infrastructure-playbook] 9146d1: New Jetstream docker image
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9146d1938f4bfa8b4d894295f3a68e7f709792de https://github.com/galaxyproject/infrastructure-playbook/commit/9146d1938f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: A env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml Log Message: ----------- New Jetstream docker image

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[galaxyproject/galaxy] c83c38: Add basic structure to support chunked file upload...
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c83c38c723d76e4dd0f87b2c2fca08e88c515d87 https://github.com/galaxyproject/galaxy/commit/c83c38c723d76e4dd0f87b2c2fca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add basic structure to support chunked file uploads Commit: 2eb4fa5e4e06455a7fa6b079211b342b85aec808 https://github.com/galaxyproject/galaxy/commit/2eb4fa5e4e06455a7fa6b079211b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix debug statements Commit: 6de335391b9422b45b8bfc59f7d5860e6508623a https://github.com/galaxyproject/galaxy/commit/6de335391b9422b45b8bfc59f7d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove debugging script, submit actual data Commit: 96d3e8076d67adcfb18969ae5939e5b760f8ad6e https://github.com/galaxyproject/galaxy/commit/96d3e8076d67adcfb18969ae5939… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Modify progress handler to accomodate chunks Commit: 313f165c4a42303dbdcf795f62dfc705ffbcd4fe https://github.com/galaxyproject/galaxy/commit/313f165c4a42303dbdcf795f62df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use let instead of var for for-loops Commit: afe0b6a90e8a358dafc0f0700149cfaa3f3296d8 https://github.com/galaxyproject/galaxy/commit/afe0b6a90e8a358dafc0f0700149… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use regular debug statements instead of logger Commit: d9c9482685c040a03ba954ddd89818bd1e1ca0d7 https://github.com/galaxyproject/galaxy/commit/d9c9482685c040a03ba954ddd898… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse submission helper Commit: 309dfbf355c207b3b626076b5f9194e277bd8ec3 https://github.com/galaxyproject/galaxy/commit/309dfbf355c207b3b626076b5f91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove redundant log Commit: 8805d09c07b5eb8128283f7c205106592a9a29d2 https://github.com/galaxyproject/galaxy/commit/8805d09c07b5eb8128283f7c2051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add file data name parameter Commit: ca2382576227d078cd5e95b1f9778f121fed9e5a https://github.com/galaxyproject/galaxy/commit/ca2382576227d078cd5e95b1f977… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix for collection handler Commit: ca2c300d943f9df45744ba3b02da23d245e0cfb4 https://github.com/galaxyproject/galaxy/commit/ca2c300d943f9df45744ba3b02da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reduce chunk size for testing, remove debug output Commit: 09bd90845677c9b36881bbaf6f84be63049bf00a https://github.com/galaxyproject/galaxy/commit/09bd90845677c9b36881bbaf6f84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix chunk sizes Commit: 5e26c0322a5338d0096abab1559f54227d75b6b0 https://github.com/galaxyproject/galaxy/commit/5e26c0322a5338d0096abab1559f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix comment Commit: 975bd2f36714622b2b34e06422c9bb93ecd33e45 https://github.com/galaxyproject/galaxy/commit/975bd2f36714622b2b34e06422c9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Submit file segments in request body, use header parameters Commit: c5337fe04a89cc6a3716469f13b0c7a5777ad5bc https://github.com/galaxyproject/galaxy/commit/c5337fe04a89cc6a3716469f13b0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Parse file and chunk data to post helper Commit: 488ce62aa3c870c4dd524ad7d07efc9f27acbafe https://github.com/galaxyproject/galaxy/commit/488ce62aa3c870c4dd524ad7d07e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use template literal, fix session id parsing Commit: 0f69eafc9d7ca185a505a7c75e5ffce14cb48e49 https://github.com/galaxyproject/galaxy/commit/0f69eafc9d7ca185a505a7c75e5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Rename header parameter Commit: b56bec033d111be265102deef262127cb574906e https://github.com/galaxyproject/galaxy/commit/b56bec033d111be265102deef262… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix template string Commit: 2b18782598848f109b58efa9b5364b9afccaee7e https://github.com/galaxyproject/galaxy/commit/2b18782598848f109b58efa9b536… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Parse nginx upload directory to client Commit: 39512626d2f35083d554d99d86030bf79f826844 https://github.com/galaxyproject/galaxy/commit/39512626d2f35083d554d99d8603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse existing request helper for whole file submission Commit: 937fe619e61023b4fe786e4a7c2bfcbb52da7cfa https://github.com/galaxyproject/galaxy/commit/937fe619e61023b4fe786e4a7c2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix success response parsing Commit: bd9ce253383c8833a387e3895d032ad10fd0729d https://github.com/galaxyproject/galaxy/commit/bd9ce253383c8833a387e3895d03… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comments Commit: ceedcb550fb23b045db0b1e32938df32e8d79be7 https://github.com/galaxyproject/galaxy/commit/ceedcb550fb23b045db0b1e32938… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Consolidate helpers Commit: dee0cef80f6e5e2a480a8a41a2ed6b2bcb7ca92f 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lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml 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 R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/new_tags_1.txt M test/api/test_visualizations.py M test/base/interactor.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 M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: d95337bde017cf15eceee8b989aee01c9707fca4 https://github.com/galaxyproject/galaxy/commit/d95337bde017cf15eceee8b989ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/tools/parameters/grouping.py M static/style/blue/base.css Log Message: ----------- Add tool submission request Commit: c04bb8c2479a739d7bfeec2fd9ec7bec2b91a79a https://github.com/galaxyproject/galaxy/commit/c04bb8c2479a739d7bfeec2fd9ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Increase chunksize Commit: afd5c8d1c5b9e34fd7861b40c6ca78cbe4804490 https://github.com/galaxyproject/galaxy/commit/afd5c8d1c5b9e34fd7861b40c6ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add warning notification Commit: ba859bf603240caa385358e05529beca323a30a8 https://github.com/galaxyproject/galaxy/commit/ba859bf603240caa385358e05529… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix state handling, show warning message Commit: 42e7cebe43eaa57a9538a689dbe7f4700e52cfee https://github.com/galaxyproject/galaxy/commit/42e7cebe43eaa57a9538a689dbe7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix function declarations Commit: ecac866a26d80f32d329fb0c2be345caac62a2a0 https://github.com/galaxyproject/galaxy/commit/ecac866a26d80f32d329fb0c2be3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix debug statement, increase chunk size to 50MB Commit: 99d20ae69f637ac9f0483c457c43c8aa0b707c8c https://github.com/galaxyproject/galaxy/commit/99d20ae69f637ac9f0483c457c43… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Resume uploads if server or nginx proxy reload Commit: 4ac01cd50b6470a7641b009f857f04fc8f0099ff https://github.com/galaxyproject/galaxy/commit/4ac01cd50b6470a7641b009f857f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove/fix debug statements Commit: b50ca79fe8b7bcb9066ce710eba9c43649d504e5 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----------- Remove dependency from nginx variables, only pass session id Commit: 789c41c550e406b2d9cc27f33df49e2da647d208 https://github.com/galaxyproject/galaxy/commit/789c41c550e406b2d9cc27f33df4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Raise proper value error if session id is invalid Commit: 97f0530a866ad3160d4e35f75721087fda55ce1c https://github.com/galaxyproject/galaxy/commit/97f0530a866ad3160d4e35f75721… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M lib/galaxy/managers/configuration.py Log Message: ----------- Fix naming conflict between regular upload path and nginx path Commit: 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test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: ecc6ac5dbf58c351e71a10835641c988ec1d0d48 https://github.com/galaxyproject/galaxy/commit/ecc6ac5dbf58c351e71a10835641… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/managers/configuration.py Log Message: ----------- Default to 100 in configuration manager Commit: d6a3964c5b41f0a9a268a1c5182fa23798526a55 https://github.com/galaxyproject/galaxy/commit/d6a3964c5b41f0a9a268a1c5182f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Add additional checks, use join Commit: 3f56aeb3cf1e2d5f6eba961f1a6925b35e836cb4 https://github.com/galaxyproject/galaxy/commit/3f56aeb3cf1e2d5f6eba961f1a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Re-use regex to validate session id Commit: 51a135bbaaee7a65619a802e5506ecd1fd27df8b https://github.com/galaxyproject/galaxy/commit/51a135bbaaee7a65619a802e5506… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Read chunks of chunks when writing target file Commit: 529e98ef04e67a5068b55efd54d946aca126527f https://github.com/galaxyproject/galaxy/commit/529e98ef04e67a5068b55efd54d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Rely on automated file closing, add new line Commit: a4287f1212050c7ff068ad161ce2d17cd65bd7cb https://github.com/galaxyproject/galaxy/commit/a4287f1212050c7ff068ad161ce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/config.py M test/base/driver_util.py Log Message: ----------- Test chunked uploads Commit: a137420c42206fdf9482615ff292ba3d1546f22f https://github.com/galaxyproject/galaxy/commit/a137420c42206fdf9482615ff292… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use ceil instead of floor Commit: 2dba72fb2f850c9fb7ab940be7ae7bef5626acd9 https://github.com/galaxyproject/galaxy/commit/2dba72fb2f850c9fb7ab940be7ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Align chunk size check Commit: 22dd4a8a64820711abe91b6e1f75d2da52144b8a https://github.com/galaxyproject/galaxy/commit/22dd4a8a64820711abe91b6e1f75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Fix lint Commit: 7589bbbb4dd556e41988ff6a6327e004b53e5ef9 https://github.com/galaxyproject/galaxy/commit/7589bbbb4dd556e41988ff6a6327… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/uploads.py M test/base/driver_util.py Log Message: ----------- Specify chunk size in bytes instead of megabytes Commit: 71c88092c0a4fcd3ccb02e652c024591e004e7f8 https://github.com/galaxyproject/galaxy/commit/71c88092c0a4fcd3ccb02e652c02… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove unused import Commit: 8d1e0fccc2f116674250a1b977168beef2cbd238 https://github.com/galaxyproject/galaxy/commit/8d1e0fccc2f116674250a1b97716… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add chunk size config option to schema Commit: 941017b04a3092556d525130e40c8e242860d828 https://github.com/galaxyproject/galaxy/commit/941017b04a3092556d525130e40c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Moderate chunk size for upload tests Commit: 759511479f86b95575ca8b5f3bcf06d6acecf56f https://github.com/galaxyproject/galaxy/commit/759511479f86b95575ca8b5f3bcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix typo Commit: fcd00166e279cdd216deee8921449070192b19b9 https://github.com/galaxyproject/galaxy/commit/fcd00166e279cdd216deee892144… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Client format Commit: c6993caabff5aa0dcdbb2150a2f18fb9566aae84 https://github.com/galaxyproject/galaxy/commit/c6993caabff5aa0dcdbb2150a2f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'chunk_uploads' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5f73d7fbbd2c...c6993caabff5

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[galaxyproject/galaxy] 8833d1: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 8833d1a8a49d7b6d4a9c849b0335d3260564b351 https://github.com/galaxyproject/galaxy/commit/8833d1a8a49d7b6d4a9c849b0335… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn

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[galaxyproject/galaxy] 73e61f: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e57… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5688 from martenson/security-rn [18.01] backport add security announcement to the release notes Compare: https://github.com/galaxyproject/galaxy/compare/0182d8d0bec3...ebb7be8d0ec3

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[galaxyproject/galaxy] 085393: Remove input cloning in form section handler
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0853932d42df64f43f8531710947d50a9766d320 https://github.com/galaxyproject/galaxy/commit/0853932d42df64f43f8531710947… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Remove input cloning in form section handler Commit: 009305fb79fe7986e55266993f06047b5bebaf02 https://github.com/galaxyproject/galaxy/commit/009305fb79fe7986e55266993f06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js Log Message: ----------- Use flat copy for context when traversing input elements Commit: e76397970bd510d10822de3b44d160903c42aedd https://github.com/galaxyproject/galaxy/commit/e76397970bd510d10822de3b44d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use flex feature instead of manual size adjustment Commit: 37eb36a60c4749f9cae7e7fe3166dfe56a5ef48f https://github.com/galaxyproject/galaxy/commit/37eb36a60c4749f9cae7e7fe3166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js Log Message: ----------- Generalize scrolling behavior to highlight errors in tool forms Commit: 51a3a6d5ee6ebe255424a2beb433053801fe60ac https://github.com/galaxyproject/galaxy/commit/51a3a6d5ee6ebe255424a2beb433… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.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/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M static/style/blue/base.css M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into workflow_run_performance Commit: 31a3d5eab231302f8bd256bdcb20b1bdb6925d71 https://github.com/galaxyproject/galaxy/commit/31a3d5eab231302f8bd256bdcb20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-11 (Sun, 11 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into workflow_run_performance Commit: 5f73d7fbbd2c71c48f49fca5a0c1c4736a5de5de https://github.com/galaxyproject/galaxy/commit/5f73d7fbbd2c71c48f49fca5a0c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #5646 from guerler/workflow_run_performance Avoid producing deep-copies of tool input dictionaries Compare: https://github.com/galaxyproject/galaxy/compare/7bcd16d4cc58...5f73d7fbbd2c

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[galaxyproject/galaxy] 73e61f: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: 7bcd16d4cc5845a60223212067254f83dabf3f97 https://github.com/galaxyproject/galaxy/commit/7bcd16d4cc5845a6022321206725… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5685 from martenson/security-rn [18.01] add security announcement to the release notes Compare: https://github.com/galaxyproject/galaxy/compare/a53fb19f1628...7bcd16d4cc58

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[galaxyproject/galaxy] 3e033b: Prefill column selector for datasets which are not...
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e033bf896918d9e468f2d54dc98e068c3ded6ba https://github.com/galaxyproject/galaxy/commit/3e033bf896918d9e468f2d54dc98… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Prefill column selector for datasets which are not ready yet Commit: 895a858ded2533bf188edba7fa8f4d1cbe1337d4 https://github.com/galaxyproject/galaxy/commit/895a858ded2533bf188edba7fa8f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit loop, use map instead Commit: 7b6321e4a84794471c346d82054d810e274a3e4e https://github.com/galaxyproject/galaxy/commit/7b6321e4a84794471c346d82054d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use list comprehension instead of map Commit: a53fb19f16285caebb3552393cadc570eeb8b22b https://github.com/galaxyproject/galaxy/commit/a53fb19f16285caebb3552393cad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #5680 from guerler/fix_column_selector Populate column selector for datasets which are not ready yet Compare: https://github.com/galaxyproject/galaxy/compare/4558ad64f0bc...a53fb19f1628

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