[galaxy-commits] [galaxyproject/galaxy] e3b63e: Add migration script for cloudauthz table.

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3b63e16d08fe08556bc690eaf5eec3e00b8aaae https://github.com/galaxyproject/galaxy/commit/e3b63e16d08fe08556bc690eaf5ee... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: A lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py Log Message: ----------- Add migration script for cloudauthz table. Commit: c25e69253f105b9f20ed1b114e5bfdeecad60310 https://github.com/galaxyproject/galaxy/commit/c25e69253f105b9f20ed1b114e5bf... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add CloudAuthz class to model. Commit: dd9e8a5e6258ab14c7481691c3b5e6ef54c00836 https://github.com/galaxyproject/galaxy/commit/dd9e8a5e6258ab14c7481691c3b5e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Add CloudAuthz to mapping. Commit: 14288a2b150d49e46577c2e8238e93d927548202 https://github.com/galaxyproject/galaxy/commit/14288a2b150d49e46577c2e8238e9... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py Log Message: ----------- Add authn_id and user_id to cloudauthz. Commit: 7f5a59d1347af33285b7e6df5955cedf9d456221 https://github.com/galaxyproject/galaxy/commit/7f5a59d1347af33285b7e6df5955c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: A lib/galaxy/managers/cloudauthzs.py A lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add cloudauthz api and manger, and define a route for API calls. Commit: c6af14ba28e1f36fef4008b57595e90e1282e5cd https://github.com/galaxyproject/galaxy/commit/c6af14ba28e1f36fef4008b57595e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Add CloudAuthz summary view serializer. Commit: ee255be84748748bfd01e6862fed0c2970f55ac2 https://github.com/galaxyproject/galaxy/commit/ee255be84748748bfd01e6862fed0... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Fix a bug in CloudAuthz summary view serializer. Commit: 5bf003011a5efc8eb9d02d61170e23bbd1481c81 https://github.com/galaxyproject/galaxy/commit/5bf003011a5efc8eb9d02d61170e2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update CloudAuthz index; return all the cloudauthz records for a user. Commit: 6f043824978bccdc208929c84ac7ca83f00ca9f5 https://github.com/galaxyproject/galaxy/commit/6f043824978bccdc208929c84ac7c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Change router for cloudauthz index. Commit: 8a980b1f7f7e2aa3b16ce66e1852be14e2d784c1 https://github.com/galaxyproject/galaxy/commit/8a980b1f7f7e2aa3b16ce66e1852b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Refactoring *thzs -> *thz; remove (s). Commit: 7760c98953524e6e5355f7ca678759dd7f2977d9 https://github.com/galaxyproject/galaxy/commit/7760c98953524e6e5355f7ca67875... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Assess cloudauthz config type in API before passing it to its manager. Commit: 193b73f26ecb661a4fb180a64806a0c7f0c6a2ba https://github.com/galaxyproject/galaxy/commit/193b73f26ecb661a4fb180a64806a... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Fix a wrong order of imports. Commit: 0585f73384221cc024a62ecb1857f53670ced091 https://github.com/galaxyproject/galaxy/commit/0585f73384221cc024a62ecb1857f... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update cloudauthz API documentation. Commit: afa31d8b0978010e91724e86e2b08e9ffe698796 https://github.com/galaxyproject/galaxy/commit/afa31d8b0978010e91724e86e2b08... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update exception handling in cloudauthz to leverage Galaxy.exceptions. Commit: bff2f9f9f72988ffec9b9f92b935f48e39b79423 https://github.com/galaxyproject/galaxy/commit/bff2f9f9f72988ffec9b9f92b935f... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Decode and assert `authn_id` in cloudauthz API. Commit: 70a90c47a65660f5fabb233cb3859755d097edab https://github.com/galaxyproject/galaxy/commit/70a90c47a65660f5fabb233cb3859... 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M test/galaxy_selenium/smart_components.py M test/integration/test_scripts.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz Commit: 4a944cebe9bf94579cd06eb3a4f5d4a46004f2ab https://github.com/galaxyproject/galaxy/commit/4a944cebe9bf94579cd06eb3a4f5d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Check if an `authn_id` exist & if user it belongs to the logged-in user. Commit: 900f88e87784a7a80901af1fa2d72b16f0a4e394 https://github.com/galaxyproject/galaxy/commit/900f88e87784a7a80901af1fa2d72... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Fix a typo: "og" -> "log" Commit: fd269464a154aa03b70dc55cb1bd996c81218052 https://github.com/galaxyproject/galaxy/commit/fd269464a154aa03b70dc55cb1bd9... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add a method to authnz manager to request CloudAuthz cloud access token. Commit: 3933b44627258cb68f4c16c2499f84f3f2c8837d https://github.com/galaxyproject/galaxy/commit/3933b44627258cb68f4c16c2499f8... 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templates/tagging_common.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.tiff A test-data/11.tabular A test-data/configfile.json A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M 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M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py M test/unit/test_objectstore.py M test/unit/test_remote_shell.py M test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/filters/cutWrapper.pl M tools/filters/random_lines_two_pass.py M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz Commit: 3c9b852faf3150692b954c5e3d52911346d4aa10 https://github.com/galaxyproject/galaxy/commit/3c9b852faf3150692b954c5e3d529... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: R lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py Log Message: ----------- Update the migration script number. Commit: e0e02c2e1d75790874c423d48fc4edfb325c20b3 https://github.com/galaxyproject/galaxy/commit/e0e02c2e1d75790874c423d48fc4e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add a method to authnz manager to get cloud access credentials. Commit: e510f07528221ddf325dcced890db2432a4cb7db https://github.com/galaxyproject/galaxy/commit/e510f07528221ddf325dcced890db... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-12 (Sun, 12 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace credentials with authz_id in the upload API of cloud storage. Commit: 841f04400003ddc44465e5c2c1c0ef1a86cf6e18 https://github.com/galaxyproject/galaxy/commit/841f04400003ddc44465e5c2c1c0e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-12 (Sun, 12 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud upload manager to use authz id instead of credentials. Commit: e1da0471604498ee207e7cae4f563f063d81b34b https://github.com/galaxyproject/galaxy/commit/e1da0471604498ee207e7cae4f563... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Configure AWS using temporary credentials generated by CloudAuthz. Commit: 64f3b3db526105e023c990a6a1ebf074e4df92c8 https://github.com/galaxyproject/galaxy/commit/64f3b3db526105e023c990a6a1ebf... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug calling different function from authnz manager. Commit: 123785ef2510e1ed185a28b4c6423de2cd018e0d https://github.com/galaxyproject/galaxy/commit/123785ef2510e1ed185a28b4c6423... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update the upload manager to adhere with latest CB interface changes. Commit: e292b2b38a7f448de3a060a3ec4ac1ae5803cbc3 https://github.com/galaxyproject/galaxy/commit/e292b2b38a7f448de3a060a3ec4ac... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- In cloud API: accept encoded authz id, and decode it. Commit: e6b93a090be676501ab418eb7e59da201fcbc307 https://github.com/galaxyproject/galaxy/commit/e6b93a090be676501ab418eb7e59d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Assert if user can assume a specific authz. Commit: 8d9f86b7fb285c7543cf30021a81be62e10e3644 https://github.com/galaxyproject/galaxy/commit/8d9f86b7fb285c7543cf30021a81b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Handle item cloudauthn accessibility in its manager rather than API. Commit: be882841e15545923f1af63338951ff2ff572823 https://github.com/galaxyproject/galaxy/commit/be882841e15545923f1af63338951... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Check for accessibility and availability of authz config. Commit: f36d5b549cb41547e816c7c7a37014cd5ae830f4 https://github.com/galaxyproject/galaxy/commit/f36d5b549cb41547e816c7c7a3701... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Make a func in cloudauthz manager static. Commit: a77971bce9694ba307197cbbc51b40bd1cb4d49e https://github.com/galaxyproject/galaxy/commit/a77971bce9694ba307197cbbc51b4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Update exception messages to avoid exposing decoded IDs in Authz manager Commit: cba657b7f6ddd8cca5ba8f31b016ee55281cfd58 https://github.com/galaxyproject/galaxy/commit/cba657b7f6ddd8cca5ba8f31b016e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M templates/webapps/galaxy/workflow/editor.mako M tools/stats/filtering.xml Log Message: ----------- Merge remote-tracking branch 'origin/refresh_token' into cloudauthz Commit: 3f2f8fd3e04530d5ed76ae5122a0eb32550605e5 https://github.com/galaxyproject/galaxy/commit/3f2f8fd3e04530d5ed76ae5122a0e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Move the on_the_fly_config func to module level. Commit: 12ef351cd2821291a4d90ff7a882dde40e6140b4 https://github.com/galaxyproject/galaxy/commit/12ef351cd2821291a4d90ff7a882d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Pass strategy requesting ID token in get_cloud_access_credentials. Commit: 34484e9e1eb92b8955943e95d8a36b63f983a7ea https://github.com/galaxyproject/galaxy/commit/34484e9e1eb92b8955943e95d8a36... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- pass trans when asking for cloud access credentials. Commit: e4ea4af05676d6c28e639d9404dc29e6a523ef90 https://github.com/galaxyproject/galaxy/commit/e4ea4af05676d6c28e639d9404dc2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Define a mapping connecting a user instance with its cloud authzs. Commit: c97313e0eb951ed56de39b534ac4669dfc33d03f https://github.com/galaxyproject/galaxy/commit/c97313e0eb951ed56de39b534ac46... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Implement equals, eq & ne for CloudAuthz type. Commit: d2fbff164b56a6249916d9ab36ae595c269982c1 https://github.com/galaxyproject/galaxy/commit/d2fbff164b56a6249916d9ab36ae5... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Avoid two cloud authz configuration with exact same config. Commit: 50876622fb7dc2503183dd8062846e8669fd4228 https://github.com/galaxyproject/galaxy/commit/50876622fb7dc2503183dd8062846... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Move a function from cloudauthzs to authnz manager. Commit: 7e68a992d3772ccd8ebbfb6a52f19fea6efbd78b https://github.com/galaxyproject/galaxy/commit/7e68a992d3772ccd8ebbfb6a52f19... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Move the logic of getting authnz config from manager to authnz/managers. Commit: e1d014939fe752cfcf99debc60e5756efe211fbf https://github.com/galaxyproject/galaxy/commit/e1d014939fe752cfcf99debc60e57... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Change a deepcopy of cloudauthz config, instead of the reference. Commit: 764ba3cdcedde28c0d96bfdb15e6321e096ea3cd https://github.com/galaxyproject/galaxy/commit/764ba3cdcedde28c0d96bfdb15e63... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Encapsulate getting cloud authz credentials in a try-catch block. Commit: 2915a2989a79742beb7e9a8bb31fcb422c3759f1 https://github.com/galaxyproject/galaxy/commit/2915a2989a79742beb7e9a8bb31fc... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Use _future_expose_api in cloudauthz APIs for better exception handling. Commit: c8e5427e5d48c98a2075648c7ff97040e0e8300f https://github.com/galaxyproject/galaxy/commit/c8e5427e5d48c98a2075648c7ff97... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Encapsulate can_user_assume_authn in a try-catch block. Commit: d223baa37ce4d61dd54e3b0dc29bf279d637fde9 https://github.com/galaxyproject/galaxy/commit/d223baa37ce4d61dd54e3b0dc29bf... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Move getting cloudauthz by id from cloud API to authnz manager. Commit: 656fe5512765a636375380ef78dedc53cd73ad0f https://github.com/galaxyproject/galaxy/commit/656fe5512765a636375380ef78ded... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update the get_cloud_access_credentials doc-string. Commit: 49976cb900c669a43b51d485475642e6b067d058 https://github.com/galaxyproject/galaxy/commit/49976cb900c669a43b51d48547564... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update the try_get_authz_config doc-string. Commit: c934165b1df40f0487cf0e7a58c5f812dfa13856 https://github.com/galaxyproject/galaxy/commit/c934165b1df40f0487cf0e7a58c5f... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Extend cloudauthz as per provider requirements. Commit: e448a4e167957004611cd0f770dc233c0352ee99 https://github.com/galaxyproject/galaxy/commit/e448a4e167957004611cd0f770dc2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Refactor a method name, and fix a bug in authnz manager. Commit: 9c8e1c41ddc25a60d80b87cfe10ff6cb4ec9a595 https://github.com/galaxyproject/galaxy/commit/9c8e1c41ddc25a60d80b87cfe10ff... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update doc string of upload manager. 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tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz # Conflicts: # lib/galaxy/managers/cloud.py Commit: f399d2981565d7395a02a80574a2d9c0dc12d950 https://github.com/galaxyproject/galaxy/commit/f399d2981565d7395a02a80574a2d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add cloudauthz to the requirements, and update-dependencies. Commit: b679bc038d1f9faf88590e1fdd0789142efbaa00 https://github.com/galaxyproject/galaxy/commit/b679bc038d1f9faf88590e1fdd078... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update requirements with patch in #6694 and manually revert dropping pyinotify. Commit: 13cf6615c6e1c5b4a105b45a2e1619dc4e95c6ec https://github.com/galaxyproject/galaxy/commit/13cf6615c6e1c5b4a105b45a2e161... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Fix lint issues in cloudauthz api. Commit: afed829a73131e158e3c4c08e19f8aedc2867631 https://github.com/galaxyproject/galaxy/commit/afed829a73131e158e3c4c08e19f8... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Fix lint issues with authnz/managers.py Commit: ba566a30563855f05f2fb667c3966afb4cd70334 https://github.com/galaxyproject/galaxy/commit/ba566a30563855f05f2fb667c3966... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Upgrade to Cloudauthz v0.2.0. Commit: c0a36ca20d0f95b56898ba06a6dd705b3c1afaea https://github.com/galaxyproject/galaxy/commit/c0a36ca20d0f95b56898ba06a6dd7... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Raise an exception if cannot get/refresh an ID token in cloudauthz. Commit: cc2fa14932ae1b3029865dcd8200bbb9fe72660c https://github.com/galaxyproject/galaxy/commit/cc2fa14932ae1b3029865dcd8200b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not surround getting cloud access credentials in a try-catch block. Commit: 915fc9ef024980917af1198f691ecdc4602e6baa https://github.com/galaxyproject/galaxy/commit/915fc9ef024980917af1198f691ec... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Catch CloudAuthz exceptions. Commit: d7c26f33527b9ce2adfe5ef79432608dfcd8d4cb https://github.com/galaxyproject/galaxy/commit/d7c26f33527b9ce2adfe5ef794326... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an extra `objects` in getting objects from a bucket. Commit: 4ceab06486d6eb3adeedc86da64c260ff4adcd7e https://github.com/galaxyproject/galaxy/commit/4ceab06486d6eb3adeedc86da64c2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Fix lint issues. Commit: 60f08316ec9b66a6ebbd8a224b09cb0fb89825ae https://github.com/galaxyproject/galaxy/commit/60f08316ec9b66a6ebbd8a224b09c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not assert credentials using cloudbridge. Commit: af6ded604dfe5fa2898e616820edf7948eca1261 https://github.com/galaxyproject/galaxy/commit/af6ded604dfe5fa2898e616820edf... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update exception message (and log it) in a cloud object is not found. Commit: e792480c74faf0500b2d1328a99c788482baa7ec https://github.com/galaxyproject/galaxy/commit/e792480c74faf0500b2d1328a99c7... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround downloading datasets to cloud in a try-catch to capture issues such as invalid credentials. Commit: e4184188323996513fba84794e80bfb86f4d122d https://github.com/galaxyproject/galaxy/commit/e4184188323996513fba84794e80b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Report both successfully and unsuccessfully downloaded datasets to cloud Commit: cfb77903293ded0e829064da2786058463a3bfce https://github.com/galaxyproject/galaxy/commit/cfb77903293ded0e829064da27860... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- log unsuccessful cloud downloads as `debug` not `exception`. Commit: aecf9929027df8d6d3d348815acfc698c9661e7c https://github.com/galaxyproject/galaxy/commit/aecf9929027df8d6d3d348815acfc... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-16 (Sun, 16 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix lint issues in cloud manager. Commit: 386eee076268964fe89299b82d5551ab0d08f75d https://github.com/galaxyproject/galaxy/commit/386eee076268964fe89299b82d555... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove a confusing debug log message. Commit: 00d883f2913767298c7616c4357048f6a8ae5d22 https://github.com/galaxyproject/galaxy/commit/00d883f2913767298c7616c435704... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an unused `user` argument from cloud connection config method. Commit: 9bba80a322b85f12a9950f583eab39a4aa830215 https://github.com/galaxyproject/galaxy/commit/9bba80a322b85f12a9950f583eab3... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Add more logging to cloudauthz api. Commit: 64d7418aae31cfee91f22112ac17d4f76f0f1276 https://github.com/galaxyproject/galaxy/commit/64d7418aae31cfee91f22112ac17d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Import Params in cloud manager. Commit: 0eb7892130b4b2099c2800919ad9cfb5c09a2cf7 https://github.com/galaxyproject/galaxy/commit/0eb7892130b4b2099c2800919ad9c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py Log Message: ----------- Add a description field to cloudauthz. Commit: f97c2550ec10d99a91cfe28dd3be96d1214d4499 https://github.com/galaxyproject/galaxy/commit/f97c2550ec10d99a91cfe28dd3be9... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Read cloudauthz description from api payload. Commit: 46183c91ec3d43927b4c9c83e297c7b3f2482635 https://github.com/galaxyproject/galaxy/commit/46183c91ec3d43927b4c9c83e297c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Remove provider from cloud upload api, leverage authnz.provider instead. Commit: 5e8cf269163773acf5674e8565615b9bd2b66b8d https://github.com/galaxyproject/galaxy/commit/5e8cf269163773acf5674e8565615... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Reuse a retrieved cloudauthz. Commit: 8f9a2c7c073b8d265f33b851467a6a4e906d86a4 https://github.com/galaxyproject/galaxy/commit/8f9a2c7c073b8d265f33b851467a6... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor authz -> cloudauthz. Commit: 6d4163ae966a5d27753f2cd22cd43e341713aec4 https://github.com/galaxyproject/galaxy/commit/6d4163ae966a5d27753f2cd22cd43... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug using undefined variable in cloud manager. Commit: cd571144b3ef74230bb68a19debe419cf8622249 https://github.com/galaxyproject/galaxy/commit/cd571144b3ef74230bb68a19debe4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update a function doc-string in authnz manager. Commit: 5355fe9877eadd1c26fe120169c5fe3dc0611332 https://github.com/galaxyproject/galaxy/commit/5355fe9877eadd1c26fe120169c5f... Author: Enis Afgan <afgane@gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/cloud.py A lib/galaxy/managers/cloudauthzs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/webapps/galaxy/api/cloud.py A lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5903 from VJalili/cloudauthz Tested this by creating an authorization and, after creating an appropriate role in the AWS IAM dashboard, uploading some data from a private S3 bucket - works as expected. Some useful requests are available in the (newly created) Postman team for the Galaxy project (ping me for an invite): https://galaxyproject.postman.co/ Compare: https://github.com/galaxyproject/galaxy/compare/1549aaa169a7...5355fe9877ea **NOTE:** This service has 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.