Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0fc0a49b4bb7de0f95bdd8f594a22515243cd4a7
https://github.com/galaxyproject/galaxy/commit/0fc0a49b4bb7de0f95bdd8f594a2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
change 'user' menu to login or register for anons
Commit: 1fa8c837accda3d8120538da98ef200ab0250453
https://github.com/galaxyproject/galaxy/commit/1fa8c837accda3d8120538da98ef…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
improve french localization of the new menu item
Commit: e842a265875909a0bead4e6e3e9f8006170067c3
https://github.com/galaxyproject/galaxy/commit/e842a265875909a0bead4e6e3e9f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Merge pull request #3955 from martenson/user-menu-ux
change 'user' menu to login or register for anons
Compare: https://github.com/galaxyproject/galaxy/compare/439579298acb...e842a2658759
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8599dff7a0098e121ddb244345a1c478f0a05cee
https://github.com/galaxyproject/galaxy/commit/8599dff7a0098e121ddb244345a1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Standardize usage of log.exception in datatypes registry.
Commit: d303cf5ffbea29ad9d0d96b167f20606a022a488
https://github.com/galaxyproject/galaxy/commit/d303cf5ffbea29ad9d0d96b167f2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
Log Message:
-----------
Strip exception strings from being included in log.exception statements across the project.
Commit: c46e36bdee354a879d2770b0ec9e22b00ec1c104
https://github.com/galaxyproject/galaxy/commit/c46e36bdee354a879d2770b0ec9e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Overhaul string templating in log.exception statements -- should apply to all logs, eventually.
Commit: d43d7aa140f399fbaa65308fe842c9afba8c44a3
https://github.com/galaxyproject/galaxy/commit/d43d7aa140f399fbaa65308fe842…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-14 (Fri, 14 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Fix E241, F841 from exception refactoring.
Commit: 386afbb4f6ac703c60d2ffd975a1c3740f67457b
https://github.com/galaxyproject/galaxy/commit/386afbb4f6ac703c60d2ffd975a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-21 (Fri, 21 Apr 2017)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
Log Message:
-----------
Merge pull request #3933 from dannon/exception_logging_fixes
Standardize usage of log.exception
Compare: https://github.com/galaxyproject/galaxy/compare/01b3eb42d88b...386afbb4f6ac
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff
https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_1.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Start work on a relabelling collection operation.
I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:
- Validate uniqueness of identifiers and provide nice messages if they are not unique.
- Validate that at least the required number of lines are present in the file and provide a nice message if not.
- Add strict mode to ensure exactly the correct number of lines is added.
- Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
- Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
- Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331
https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e987…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_2.txt
Log Message:
-----------
Add possibility to rename collection items from a tabular file
Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8
https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/relabel_from_file.xml
Log Message:
-----------
Fix failing test case in relable_from_file based on comment from @mvdbeek.
Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47
https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_bad_1.txt
Log Message:
-----------
Various improvements to relabel from file collection operation.
- Better error handling (check for bad characters when creating collections).
- Implement a strict mode parameter to do even more validation.
- Rework tabular vs txt mode to be explicit user choice.
- Mirror fix in release_17.01 for datasets not having a history,
Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8
https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
A test-data/new_labels_bad_2.txt
Log Message:
-----------
Fix relabel_from_file collection operation error handling if duplicate identifiers.
Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e
https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/relabel_from_file.xml
A test-data/filter_labels_1.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement collection operation for filtering lists from a file.
Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0
https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eec…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_from_file.xml
A lib/galaxy/tools/relabel_from_file.xml
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3940 from jmchilton/collection_op_filter_from_file
Collection Operation - Filtering from a File
Compare: https://github.com/galaxyproject/galaxy/compare/9f4fd7c44964...01b3eb42d88b