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

[galaxyproject/galaxy] 019f08: Allow including paths in inputs json files.
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 019f088543736cecf74febd414782d7a207acd9c https://github.com/galaxyproject/galaxy/commit/019f088543736cecf74febd41478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow including paths in inputs json files. Commit: 6af48d90dbb64b9aa01b9876ae5b10cbe17e5f09 https://github.com/galaxyproject/galaxy/commit/6af48d90dbb64b9aa01b9876ae5b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- data_stype to data_style Commit: ce09f53e24ff992d7f39fc94d01b75a1cbcee1fe https://github.com/galaxyproject/galaxy/commit/ce09f53e24ff992d7f39fc94d01b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6468 from jmchilton/allow_including_paths_in_inputs_json Allow including paths in inputs json files. Compare: https://github.com/galaxyproject/galaxy/compare/60fc4baa4c3a...ce09f53e24ff **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] f9cadc: Update SnpEff build to 4.3+T.galaxy3
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f9cadc3a86a865fd95d60b4e4c6394156ce1df95 https://github.com/galaxyproject/usegalaxy-playbook/commit/f9cadc3a86a865fd… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 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: ----------- Update SnpEff build to 4.3+T.galaxy3 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 9454f7: Markdown missing code closing tag
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9454f715b8c2c9797fee64379c86164504a0788e https://github.com/galaxyproject/usegalaxy-playbook/commit/9454f715b8c2c979… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Markdown missing code closing tag Commit: 39e34574fa086c1ad0745da177ebf401585c73eb https://github.com/galaxyproject/usegalaxy-playbook/commit/39e34574fa086c1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M roles/galaxyproject.galaxy/README.md Log Message: ----------- Merge pull request #148 from eslerm/patch-1 Markdown missing code closing tag Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd52ea967973...… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 50602c: WIP Swarm Scale improvements
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 50602ce96c3f1b9486486f23217629537a9e7d51 https://github.com/galaxyproject/usegalaxy-playbook/commit/50602ce96c3f1b94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: A roles/usegalaxy_swarmscale/files/_inc_fail.yml M roles/usegalaxy_swarmscale/files/ansible.cfg R roles/usegalaxy_swarmscale/files/delete.yml A roles/usegalaxy_swarmscale/files/group_vars/all/spawn.yml M roles/usegalaxy_swarmscale/files/instance R roles/usegalaxy_swarmscale/files/inventory.head R roles/usegalaxy_swarmscale/files/inventory.spawn A roles/usegalaxy_swarmscale/files/inventory/openstack.yml R roles/usegalaxy_swarmscale/files/leave.yml A roles/usegalaxy_swarmscale/files/resume.yml A roles/usegalaxy_swarmscale/files/roles/docker/defaults/main.yml A roles/usegalaxy_swarmscale/files/roles/docker/handlers/main.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/install_debian.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/install_redhat.yml A roles/usegalaxy_swarmscale/files/roles/docker/tasks/main.yml R roles/usegalaxy_swarmscale/files/spawn.yml A roles/usegalaxy_swarmscale/files/suspend.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- WIP Swarm Scale improvements **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 97c344: Fix the --log-file option in the job handlers
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97c344a17a0188a687629103feefcdf03af8e768 https://github.com/galaxyproject/galaxy/commit/97c344a17a0188a687629103feef… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers Commit: b396d3d10788f752bce2ded0598fab2bd21e605b https://github.com/galaxyproject/galaxy/commit/b396d3d10788f752bce2ded0598f… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- PEP8 Commit: 60fc4baa4c3af7b32fd74dccd7aee1850196bc87 https://github.com/galaxyproject/galaxy/commit/60fc4baa4c3af7b32fd74dccd7ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6351 from dpryan79/fixHandlerLogging Fix the --log-file option in the job handlers Compare: https://github.com/galaxyproject/galaxy/compare/ce866b9e2396...60fc4baa4c3a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 06694e: Fix paths to clean scratch on Jetstream
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 06694e8a4aa8493ea5582db5ca16138444c75152 https://github.com/galaxyproject/infrastructure-playbook/commit/06694e8a4aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M env/jscommon/group_vars/controllers.yml Log Message: ----------- Fix paths to clean scratch on Jetstream **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a6173c: Fix bug noticed in sentry
by GitHub 09 Jul '18

09 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6173c023e4620430ffe3fc127750e0cb04355b1 https://github.com/galaxyproject/galaxy/commit/a6173c023e4620430ffe3fc12775… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Fix bug noticed in sentry Commit: ce866b9e2396da30f660206e10a7a375e244f583 https://github.com/galaxyproject/galaxy/commit/ce866b9e2396da30f660206e10a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Merge pull request #6474 from erasche/asdfasdf Fix bug noticed in sentry Compare: https://github.com/galaxyproject/galaxy/compare/068005fd6e1c...ce866b9e2396 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 0198df: Implement overall structure.
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0198df5406b385c80b0536b0905fee3f0719f635 https://github.com/galaxyproject/galaxy/commit/0198df5406b385c80b0536b0905f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: A lib/galaxy/managers/cloud_storages.py A lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Implement overall structure. Commit: bdc98d5569dabcf6b82b2d447e75821adb080d03 https://github.com/galaxyproject/galaxy/commit/bdc98d5569dabcf6b82b2d447e75… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add cloud storage api mapper. Commit: 645f74b6b6ae9ded06f8f073c08bae0519ed38c3 https://github.com/galaxyproject/galaxy/commit/645f74b6b6ae9ded06f8f073c08b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Capture invalid type of cloud storage api payload, & raise exception. Commit: 140a1f7a8ea8455e4a96fa6e2dbb5148ebb3fe0e https://github.com/galaxyproject/galaxy/commit/140a1f7a8ea8455e4a96fa6e2dbb… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Unbox payload & check if it contains all data required for cloud storage Commit: 15293d652c724635f294376cb5a23bf4e6d3419f https://github.com/galaxyproject/galaxy/commit/15293d652c724635f294376cb5a2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: A lib/galaxy/managers/cloud_storage.py R lib/galaxy/managers/cloud_storages.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Some refactoring: "Storages" -> "Storage" & "object" -> "obj" Commit: ca0bb57add1c66237e3e6ceff3a0afbac91ba26f https://github.com/galaxyproject/galaxy/commit/ca0bb57add1c66237e3e6ceff3a0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Add provider as a payload requirement to the cloud storage API. Commit: 164f8d8b1f6a3697ed18ba9b01c188ec688e72c9 https://github.com/galaxyproject/galaxy/commit/164f8d8b1f6a3697ed18ba9b01c1… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Renamed bucket to container to use more generic terminology. Commit: 76aa47f69be61c77a7322a91824675999617f345 https://github.com/galaxyproject/galaxy/commit/76aa47f69be61c77a7322a918246… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Cloud storage api now sends download request to cloud storage manager. Commit: 2e1fbedc7f692fd23eea24e646c6b0b1caa851a2 https://github.com/galaxyproject/galaxy/commit/2e1fbedc7f692fd23eea24e646c6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Fix a conditional assignment bug. Commit: c725b33ec25d67be1ca2b51faeec5a07186dcf36 https://github.com/galaxyproject/galaxy/commit/c725b33ec25d67be1ca2b51faeec… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Pass trans from cloud_storage api to cloud_storage_manager. Commit: f7d90706f922497d19c398d170c50ae1627fa836 https://github.com/galaxyproject/galaxy/commit/f7d90706f922497d19c398d170c5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M 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client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.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/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A 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test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.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 M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud-storage-api Commit: 6856b81db0f2f6913c7b1f98c4d54ccaaf022480 https://github.com/galaxyproject/galaxy/commit/6856b81db0f2f6913c7b1f98c4d5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- In cloud_storage, receive credentials and pass them to the manager. Commit: dc17e0285a6460c1ded477a976aaa316897caa13 https://github.com/galaxyproject/galaxy/commit/dc17e0285a6460c1ded477a976aa… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Download data from AWS S3 in cloud_storage manager. Commit: f56e4abb800d09956294323025827ee149e08ae2 https://github.com/galaxyproject/galaxy/commit/f56e4abb800d0995629432302582… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Call upload tool to persist the dataset copied from cloud-based storage. Commit: 8ceaae7a89457c6688375ddb324c0ecc2893c31c https://github.com/galaxyproject/galaxy/commit/8ceaae7a89457c6688375ddb324c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Linting fixes while reviewing cloud_storage Commit: a43de58c91e91a3e43aa1e80b7de78457c839491 https://github.com/galaxyproject/galaxy/commit/a43de58c91e91a3e43aa1e80b7de… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Merge pull request #5 from dannon/cloud-storage-api Linting fixes while reviewing cloud_storage Commit: 5e4b63bf7635eacf53a808e0c487a476ad1bee1b https://github.com/galaxyproject/galaxy/commit/5e4b63bf7635eacf53a808e0c487… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Add history_id to list of required fields of cloud storage API payload. Commit: ae527da165774d9ca2d7a1ac5b1649fef1ce6d49 https://github.com/galaxyproject/galaxy/commit/ae527da165774d9ca2d7a1ac5b16… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Decode history ID and validate it in cloud storage API. Commit: ab8ca7055bf6d2599c2f3888d8619da9d6bb57dd https://github.com/galaxyproject/galaxy/commit/ab8ca7055bf6d2599c2f3888d861… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Specify a history to the upload tool in cloud storage manager. Commit: a9d6cab52a5668b815942f1cf18891ee1ef7e7a6 https://github.com/galaxyproject/galaxy/commit/a9d6cab52a5668b815942f1cf188… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Merge remote-tracking branch 'origin/cloud-storage-api' into cloud-storage-api Commit: 651d4c7f2ae5861d896ba4ab44518fcd6b33a582 https://github.com/galaxyproject/galaxy/commit/651d4c7f2ae5861d896ba4ab4451… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py M lib/galaxy/webapps/galaxy/api/cloud_storage.py Log Message: ----------- Transaction response is returned in standard http response codes. Commit: 6e0fea91b3e05f0203b25f46a87b375ad93897a8 https://github.com/galaxyproject/galaxy/commit/6e0fea91b3e05f0203b25f46a87b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud_storage.py Log Message: ----------- Name dataset with the same name as of the object being downloaded. Commit: 10644a86a95910d9106cd00fddd9632fd1a0d1ee https://github.com/galaxyproject/galaxy/commit/10644a86a95910d9106cd00fddd9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: A lib/galaxy/managers/cloud.py R lib/galaxy/managers/cloud_storage.py A lib/galaxy/webapps/galaxy/api/cloud.py R lib/galaxy/webapps/galaxy/api/cloud_storage.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor "CloudStorage" & "cloud_storage" to "Cloud" & "cloud" resp. Commit: fb9656a1a0e7b00c1d9087988ed2efbcf1255595 https://github.com/galaxyproject/galaxy/commit/fb9656a1a0e7b00c1d9087988ed2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Delete from-cloud-downloaded staged file after upload job is created. Commit: 547443d396f2c04c05396f3f37c8bc13bd7ed8fd https://github.com/galaxyproject/galaxy/commit/547443d396f2c04c05396f3f37c8… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Verify credentials when initializing a cloud provider. Commit: d9e5806070662e07dc66af4816b02ed77e1d56bf https://github.com/galaxyproject/galaxy/commit/d9e5806070662e07dc66af4816b0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add support for Azure to cloud storage manager. Commit: eb0df62df78f1b5625961137c20ffde0e11437c3 https://github.com/galaxyproject/galaxy/commit/eb0df62df78f1b5625961137c20f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Check for provider-specific missing (None) required credentials. Commit: 23e1209851b16e01b8c9e1acbc36e8070310ab38 https://github.com/galaxyproject/galaxy/commit/23e1209851b16e01b8c9e1acbc36… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Store supported provides name in a constant. Commit: 177fe583c5c8274850ab69138fb5e664f0bcef2f https://github.com/galaxyproject/galaxy/commit/177fe583c5c8274850ab69138fb5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Throw NotImplementedError for cloud api & manager upload functionality. Commit: 532c5867a19679bfa1d2d8e999be324c76dbdcd5 https://github.com/galaxyproject/galaxy/commit/532c5867a19679bfa1d2d8e999be… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud-api Commit: 9daa216b830c620ed6d5f8231ed0852a337882b2 https://github.com/galaxyproject/galaxy/commit/9daa216b830c620ed6d5f8231ed0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove some blank lines and fixed an import. Commit: 70b669992b10682d45c519ef885667ddf52f381c https://github.com/galaxyproject/galaxy/commit/70b669992b10682d45c519ef8856… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud Download API documentation. Commit: 9960e3bde1eb13506b4f01349fc95d12880ad705 https://github.com/galaxyproject/galaxy/commit/9960e3bde1eb13506b4f01349fc9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Leverage _future_expose_api for the expose_api decorator in cloud api. Commit: c83194d9bddae4989296f6424f76d59abf3eab54 https://github.com/galaxyproject/galaxy/commit/c83194d9bddae4989296f6424f76… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace explicit dict errors in cloud API with Galaxy.exceptions. Commit: 61a1e7eb4c80fdb95c338695a38efa4e0fba0f5e https://github.com/galaxyproject/galaxy/commit/61a1e7eb4c80fdb95c338695a38e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Return summary view of datasets created for data downloaded from cloud. Commit: 907ef7b3ea67530bc41b601f975eda3d2dad0b02 https://github.com/galaxyproject/galaxy/commit/907ef7b3ea67530bc41b601f975e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace returning http err code in cloud manager with Galaxy Exceptions. Commit: 55646658165aefd6cc48dcb216b8de4d3ac29963 https://github.com/galaxyproject/galaxy/commit/55646658165aefd6cc48dcb216b8… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- close staging file used in cloud api. Commit: 24a1a6bc906cdcbfdab74808c5ef7e116005cb2b https://github.com/galaxyproject/galaxy/commit/24a1a6bc906cdcbfdab74808c5ef… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Describe functions in cloud manager. Commit: a3de1c5a66e034637cb0cdfb9c99617823ab2eec https://github.com/galaxyproject/galaxy/commit/a3de1c5a66e034637cb0cdfb9c99… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Support OpenStack in the cloud download manager. Commit: c656f36ffd7df4d1586bf822cc03a387764ff020 https://github.com/galaxyproject/galaxy/commit/c656f36ffd7df4d1586bf822cc03… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Change OpenStack required credentials field names. Commit: 8302e574446a8719da430f1174762bf98f8200fe https://github.com/galaxyproject/galaxy/commit/8302e574446a8719da430f117476… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Refactor `container` to `bucket` in cloud API and manager. Commit: 6e11334fa7122858012c644038eb0bf58de7e6f2 https://github.com/galaxyproject/galaxy/commit/6e11334fa7122858012c644038eb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor cloud download api and use only one handle to the staging file. Commit: 3e551cd9994e76820151bbd002ed782e36c23a69 https://github.com/galaxyproject/galaxy/commit/3e551cd9994e76820151bbd002ed… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename the cloud storage APIs from Download and Upload to Copy-from and Copy-To, respectively. Commit: cfe6a9a67757150d7fce0d42f992cd1065cac9ee https://github.com/galaxyproject/galaxy/commit/cfe6a9a67757150d7fce0d42f992… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update documentation of the cloud copy from/to APIs reflecting previous refactoring. Commit: b61bb88daa3566c8b929d81e74f7cc9710875026 https://github.com/galaxyproject/galaxy/commit/b61bb88daa3566c8b929d81e74f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor api access to the cloud storage index. Commit: 068005fd6e1c6da73dd08a8c1f8e7c1fdbefe871 https://github.com/galaxyproject/galaxy/commit/068005fd6e1c6da73dd08a8c1f8e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A lib/galaxy/managers/cloud.py A lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5835 from VJalili/cloud-api Copy data from a cloud-based storage to a Galaxy history Compare: https://github.com/galaxyproject/galaxy/compare/3b3c18e0de83...068005fd6e1c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6c2bee: Update cliff and other related dependencies
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c2bee5ea464a6740c7f8c93b3699c6f824a70a4 https://github.com/galaxyproject/galaxy/commit/6c2bee5ea464a6740c7f8c93b369… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update cliff and other related dependencies cliff now has a universal wheel. Remove unused Pipfile.lock files. Skip broken lxml 4.2.2, see https://github.com/lxml/lxml/pull/265 . Fix more oscillating environment markers. Commit: 3b3c18e0de83b535c2cd0235307eaeb821300196 https://github.com/galaxyproject/galaxy/commit/3b3c18e0de83b535c2cd0235307e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #6469 from nsoranzo/update_dependencies Update cliff and other related dependencies Compare: https://github.com/galaxyproject/galaxy/compare/d65789880024...3b3c18e0de83 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fddc78: Let data managers also use conda python.
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fddc7899c1f09bf20f36369883f091199db0edd0 https://github.com/galaxyproject/galaxy/commit/fddc7899c1f09bf20f36369883f0… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Let data managers also use conda python. Since data managers only return a json object, there is no need for them to use the galaxy python. Commit: 3f2b2f81fa2dfafee4c2a861b9d1f451b843bd23 https://github.com/galaxyproject/galaxy/commit/3f2b2f81fa2dfafee4c2a861b9d1… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Style fix Commit: 8e1813b53d00946f298baf1eea86599fb45f7973 https://github.com/galaxyproject/galaxy/commit/8e1813b53d00946f298baf1eea86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use profile version to determine if data managers should preserve python env Commit: d6578988002416f95e10ed3751e22b9ed287f565 https://github.com/galaxyproject/galaxy/commit/d6578988002416f95e10ed3751e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6466 from rhpvorderman/patch-2 Let data managers also use conda python. Compare: https://github.com/galaxyproject/galaxy/compare/8df7cafe3ac6...d65789880024 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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