Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7bab16ef71c850b3cefab3686beeaee3708e1480
https://github.com/galaxyproject/galaxy/commit/7bab16ef71c850b3cefab3686bee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Preserve advanced search visibility
Commit: ee4c8e2afac1d16b386c4dc9afa9b0817a0c9325
https://github.com/galaxyproject/galaxy/commit/ee4c8e2afac1d16b386c4dc9afa9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Fix filters
Commit: 114997dca6af7483d3ed3f34fafd0f66e3583afc
https://github.com/galaxyproject/galaxy/commit/114997dca6af7483d3ed3f34fafd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-model.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Prevent search tag duplication
Commit: 706741f30b2ee0a1733e49cafa8c0d0e6b78385a
https://github.com/galaxyproject/galaxy/commit/706741f30b2ee0a1733e49cafa8c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-model.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Merge pull request #4449 from guerler/fix_grid_search
Fixes for advanced grid search
Compare: https://github.com/galaxyproject/galaxy/compare/68e8abc89aba...706741f30b2e
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0fa287f76a675c49c2702681ac4404f050b77130
https://github.com/galaxyproject/galaxy/commit/0fa287f76a675c49c2702681ac44…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A .ci/autopep8.sh
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/utils.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/middleware/xforwardedhost.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M test/casperjs/casperjs_runner.py
M test/galaxy_selenium/driver_factory.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M tools/data_source/upload.py
Log Message:
-----------
Add autopep8 script to help rebasing branches after #4440.
Fixes a few more PEP8 issues as part of the autopep8'ing as well.
Commit: 68e8abc89aba1263f82c643d1bde89da53d70bc9
https://github.com/galaxyproject/galaxy/commit/68e8abc89aba1263f82c643d1bde…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
A .ci/autopep8.sh
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/odict.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/sleeper.py
M lib/galaxy/util/ucsc.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/utils.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/middleware/xforwardedhost.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M test/casperjs/casperjs_runner.py
M test/galaxy_selenium/driver_factory.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #4447 from jmchilton/autopep8
Add autopep8 script to help rebasing branches after #4440.
Compare: https://github.com/galaxyproject/galaxy/compare/8c225ecf3d92...68e8abc89aba
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5cebb086b2849f92ac8da10d7e776e4334c28ff5
https://github.com/galaxyproject/galaxy/commit/5cebb086b2849f92ac8da10d7e77…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.psp
Log Message:
-----------
Add support for the MEME psp format
Commit: 806370123b028eb0728e05fff2f9f9853c5cd6c5
https://github.com/galaxyproject/galaxy/commit/806370123b028eb0728e05fff2f9…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
fix XML error
Commit: 7dae650fdbde77336250341832c928f604b41bab
https://github.com/galaxyproject/galaxy/commit/7dae650fdbde77336250341832c9…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.memepsp
R lib/galaxy/datatypes/test/1.psp
Log Message:
-----------
Change Psp to MemePsp and misc fixes per initial review
Commit: 3026bf56c9662f47062fbd37904803156a4fe0db
https://github.com/galaxyproject/galaxy/commit/3026bf56c9662f47062fbd379048…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Remove strange import - no idea from where it originated
Commit: 2b94fa3b890a00bbe170ac1bec68d29e8d19c75a
https://github.com/galaxyproject/galaxy/commit/2b94fa3b890a00bbe170ac1bec68…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2017-08-16 (Wed, 16 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Fix MemePsp sniff entry
Commit: 5799fbc3d13ae6ec41ef5a17e55faf6f58059ae3
https://github.com/galaxyproject/galaxy/commit/5799fbc3d13ae6ec41ef5a17e55f…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
change file_ext to be inline with memexml and co
Commit: cca1f9e9bcf455b4b655fe9c54707bc34d3c6c32
https://github.com/galaxyproject/galaxy/commit/cca1f9e9bcf455b4b655fe9c5470…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-08-17 (Thu, 17 Aug 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.memepsp
Log Message:
-----------
Merge pull request #4430 from gregvonkuster/psp_format
Add support for the MEME psp format
Compare: https://github.com/galaxyproject/galaxy/compare/35ab7457b903...cca1f9e9bcf4