Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea36a627e48d71a5ef3482be36d64b3a57c10235 https://github.com/galaxyproject/galaxy/commit/ea36a627e48d71a5ef3482be36d64... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: A lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- first commit modeled off S3 adapter Commit: 596248ae0f2af5cb1a01dbb8de8f05c572c4bbcb https://github.com/galaxyproject/galaxy/commit/596248ae0f2af5cb1a01dbb8de8f0... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M templates/admin/impersonate.mako M templates/ind_share_base.mako M test/api/test_users.py M test/unit/managers/test_UserManager.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into azure-blob-objectstore Commit: c3a074faf044fa21e73ae060e4d5a1872d8b9475 https://github.com/galaxyproject/galaxy/commit/c3a074faf044fa21e73ae060e4d5a... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- added object_store_conf.xml.sample Commit: b217ecde14d80f211bc550cb56fa4524872e23f9 https://github.com/galaxyproject/galaxy/commit/b217ecde14d80f211bc550cb56fa4... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js A test/unit/datatypes/test_data.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: 0a49f17411dec1235226a8dc0fc7237bc4f6a40a https://github.com/galaxyproject/galaxy/commit/0a49f17411dec1235226a8dc0fc72... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M doc/source/lib/galaxy.objectstore.rst Log Message: ----------- Modified galaxy.objectstore.rst Not sure how RST works — would appreciate some guidance here. Commit: 3a3074134fd0bbdf81c269e127934d1c87b0d8bd https://github.com/galaxyproject/galaxy/commit/3a3074134fd0bbdf81c269e127934... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- fixed most lint errors Commit: cb44eb372ef71d856804c3747e0e282e14176702 https://github.com/galaxyproject/galaxy/commit/cb44eb372ef71d856804c3747e0e2... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/history/grid.mako M test/api/test_workflows.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: c668baeea5d4106e439ebbb39d406ccc1f4848f2 https://github.com/galaxyproject/galaxy/commit/c668baeea5d4106e439ebbb39d406... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R lib/galaxy/objectstore/azureObjectStore.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- better naming Commit: 8bc8e38b369115d9970586a24626d04b101c6952 https://github.com/galaxyproject/galaxy/commit/8bc8e38b369115d9970586a24626d... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- typo Commit: 4fa0c27bf1594a3f46209e3718d55fd7063bbbd9 https://github.com/galaxyproject/galaxy/commit/4fa0c27bf1594a3f46209e3718d55... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Another lint pass. Commit: 2405f558c8d3abc0cbbe1738208e682d9bc02502 https://github.com/galaxyproject/galaxy/commit/2405f558c8d3abc0cbbe1738208e6... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Oops.. Commit: a2c5e33d021f61b0e2efa95b12fc6a9d3e7ae82e https://github.com/galaxyproject/galaxy/commit/a2c5e33d021f61b0e2efa95b12fc6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: ebe83e21bd25c5fc9d4c4f8018401e5967d5cd66 https://github.com/galaxyproject/galaxy/commit/ebe83e21bd25c5fc9d4c4f8018401... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #1 from dannon/minor_azure_tweaks Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: d9d549299171364576e141710637283176fd6dd4 https://github.com/galaxyproject/galaxy/commit/d9d549299171364576e1417106372... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- more consistent naming. Commit: 4a8a14d8cf593b84cc338062d7361140f8410851 https://github.com/galaxyproject/galaxy/commit/4a8a14d8cf593b84cc338062d7361... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: ca79c905f83aa20be3a598da94ec09919457511a https://github.com/galaxyproject/galaxy/commit/ca79c905f83aa20be3a598da94ec0... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- oops again... Commit: 91081bf2802195f501595bca9a51b38b69c18669 https://github.com/galaxyproject/galaxy/commit/91081bf2802195f501595bca9a51b... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- added dependency to azure Commit: 7dcc6374ccf9ce9903cc82f11f146a1f5aefdc87 https://github.com/galaxyproject/galaxy/commit/7dcc6374ccf9ce9903cc82f11f146... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- oops =) Commit: d36162a389586ffa0d692a446be26c53b1e7741d https://github.com/galaxyproject/galaxy/commit/d36162a389586ffa0d692a446be26... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- fixes the lint error I think. Commit: e59602fed14e0f7bea81309407e47e600a24a529 https://github.com/galaxyproject/galaxy/commit/e59602fed14e0f7bea81309407e47... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Update check_azure_storage check, read the object store config to detect stores. Commit: 3199217448f7646c660c954c66e989f4a2e224fb https://github.com/galaxyproject/galaxy/commit/3199217448f7646c660c954c66e98... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove debug print Commit: 0da66864e491e7b8b1a5454ee12a3db1ba52e9e1 https://github.com/galaxyproject/galaxy/commit/0da66864e491e7b8b1a5454ee12a3... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #2 from dannon/azure-blob-objectstore Fixes azure_blob detection for conditional dependency resolution Commit: 0b1730fe7f94875edf378dec629f692da66c8ad3 https://github.com/galaxyproject/galaxy/commit/0b1730fe7f94875edf378dec629f6... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- trying this... Commit: e349aafe047ce0e419634b96c34acef8b60549af https://github.com/galaxyproject/galaxy/commit/e349aafe047ce0e419634b96c34ac... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix bug. Commit: 4dc8b7d8037defe9b29038ee05ab22b889cd2740 https://github.com/galaxyproject/galaxy/commit/4dc8b7d8037defe9b29038ee05ab2... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- clean things up a little... Commit: b4896bc341ab9d40a255c74a7a5fdeb0db37f72a https://github.com/galaxyproject/galaxy/commit/b4896bc341ab9d40a255c74a7a5fd... Author: Alexander Lenail <alexander.lenail@tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix lint Commit: c7caeb3c3959e87e55e791aa4f87de63e71a9032 https://github.com/galaxyproject/galaxy/commit/c7caeb3c3959e87e55e791aa4f87d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/object_store_conf.xml.sample M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge branch 'azure-blob-objectstore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4841b352140...c7caeb3c3959