Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0198df5406b385c80b0536b0905fee3f0719f635 https://github.com/galaxyproject/galaxy/commit/0198df5406b385c80b0536b0905fe... Author: vahid <jalili.vahid@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/bdc98d5569dabcf6b82b2d447e758... Author: vahid <jalili.vahid@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/645f74b6b6ae9ded06f8f073c08ba... Author: vahid <jalili.vahid@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/140a1f7a8ea8455e4a96fa6e2dbb5... Author: vahid <jalili.vahid@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/15293d652c724635f294376cb5a23... Author: vjalili <jalili.vahid@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/ca0bb57add1c66237e3e6ceff3a0a... Author: vjalili <jalili.vahid@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/164f8d8b1f6a3697ed18ba9b01c18... Author: vjalili <jalili.vahid@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/76aa47f69be61c77a7322a9182467... Author: vjalili <jalili.vahid@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/2e1fbedc7f692fd23eea24e646c6b... Author: vjalili <jalili.vahid@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/c725b33ec25d67be1ca2b51faeec5... Author: vjalili <jalili.vahid@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/f7d90706f922497d19c398d170c50... Author: vjalili <jalili.vahid@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 client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M 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lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh M scripts/galaxy-main R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/1.csv A test-data/example-bag.zip A test-data/qname_sorted.bam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/multi_output_recurse.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/selenium_tests/framework.py M 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/6856b81db0f2f6913c7b1f98c4d54... Author: vjalili <jalili.vahid@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/dc17e0285a6460c1ded477a976aaa... Author: vjalili <jalili.vahid@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/f56e4abb800d09956294323025827... Author: vjalili <jalili.vahid@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/8ceaae7a89457c6688375ddb324c0... Author: Dannon Baker <dannon.baker@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/a43de58c91e91a3e43aa1e80b7de7... Author: Vahid <VJalili@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/5e4b63bf7635eacf53a808e0c487a... Author: vjalili <jalili.vahid@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/ae527da165774d9ca2d7a1ac5b164... Author: vjalili <jalili.vahid@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/ab8ca7055bf6d2599c2f3888d8619... Author: vjalili <jalili.vahid@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/a9d6cab52a5668b815942f1cf1889... Author: vjalili <jalili.vahid@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/651d4c7f2ae5861d896ba4ab44518... Author: vjalili <jalili.vahid@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/6e0fea91b3e05f0203b25f46a87b3... Author: vjalili <jalili.vahid@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/10644a86a95910d9106cd00fddd96... Author: vjalili <jalili.vahid@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/fb9656a1a0e7b00c1d9087988ed2e... Author: vjalili <jalili.vahid@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/547443d396f2c04c05396f3f37c8b... Author: vjalili <jalili.vahid@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/d9e5806070662e07dc66af4816b02... Author: vjalili <jalili.vahid@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/eb0df62df78f1b5625961137c20ff... Author: vjalili <jalili.vahid@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/23e1209851b16e01b8c9e1acbc36e... Author: vjalili <jalili.vahid@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/177fe583c5c8274850ab69138fb5e... Author: vjalili <jalili.vahid@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/532c5867a19679bfa1d2d8e999be3... Author: vjalili <jalili.vahid@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/9daa216b830c620ed6d5f8231ed08... Author: vjalili <jalili.vahid@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/70b669992b10682d45c519ef88566... Author: vjalili <jalili.vahid@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/9960e3bde1eb13506b4f01349fc95... Author: vjalili <jalili.vahid@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/c83194d9bddae4989296f6424f76d... Author: vjalili <jalili.vahid@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/61a1e7eb4c80fdb95c338695a38ef... Author: vjalili <jalili.vahid@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/907ef7b3ea67530bc41b601f975ed... Author: vjalili <jalili.vahid@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/55646658165aefd6cc48dcb216b8d... Author: vjalili <jalili.vahid@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/24a1a6bc906cdcbfdab74808c5ef7... Author: vjalili <jalili.vahid@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/a3de1c5a66e034637cb0cdfb9c996... Author: vjalili <jalili.vahid@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/c656f36ffd7df4d1586bf822cc03a... Author: vjalili <jalili.vahid@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/8302e574446a8719da430f1174762... Author: vjalili <jalili.vahid@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/6e11334fa7122858012c644038eb0... Author: vjalili <jalili.vahid@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/3e551cd9994e76820151bbd002ed7... Author: vjalili <jalili.vahid@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/cfe6a9a67757150d7fce0d42f992c... Author: vjalili <jalili.vahid@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/b61bb88daa3566c8b929d81e74f7c... Author: vjalili <jalili.vahid@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/068005fd6e1c6da73dd08a8c1f8e7... Author: Enis Afgan <afgane@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.