Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a22af161ade4f2bccf81f9b009947a8b6c7ec579
https://github.com/galaxyproject/galaxy/commit/a22af161ade4f2bccf81f9b00994…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/test.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/pulsar/client/manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
For python2/3 compatibility, replace basestring with six's string_types, unicode with six's text_type.
Commit: fbc40f69f68f4e5d547019b561429fd958c237f8
https://github.com/galaxyproject/galaxy/commit/fbc40f69f68f4e5d547019b56142…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/pulsar/client/interface.py
Log Message:
-----------
use six's text_type
Commit: da9cd12ae69d584be222f7979f2b5c4567106a99
https://github.com/galaxyproject/galaxy/commit/da9cd12ae69d584be222f7979f2b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Use unicodify
Commit: 0028ac263634ee846b0fb9e0e134f6b771f50e1e
https://github.com/galaxyproject/galaxy/commit/0028ac263634ee846b0fb9e0e134…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
need binary type
Commit: 8ee38f64f33305753aa96fc230d97a8fabda4885
https://github.com/galaxyproject/galaxy/commit/8ee38f64f33305753aa96fc230d9…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/web/form_builder.py
Log Message:
-----------
Do not test if text_type instance before calling unicodify()
Commit: 6653bcb63bb36c450f4a3d0a6722b4a8c04a6ae8
https://github.com/galaxyproject/galaxy/commit/6653bcb63bb36c450f4a3d0a6722…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
remove unncessary if statements
Commit: 66bce36a4075a0b111fff9832f100bba3566447f
https://github.com/galaxyproject/galaxy/commit/66bce36a4075a0b111fff9832f10…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
Log Message:
-----------
Indentation fixes, import json_fix from galaxy.util.json
Commit: f706ed7e86244e183482ce18f68e71dcd6fcd5c3
https://github.com/galaxyproject/galaxy/commit/f706ed7e86244e183482ce18f68e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
properly encode column_filter
Commit: 92fe009f965700f1a3b4e61d33c67c5348084d2a
https://github.com/galaxyproject/galaxy/commit/92fe009f965700f1a3b4e61d33c6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-02-20 (Sat, 20 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
fix bad rebase
Commit: 1b25944a5d83bf8893d4969452db67a0b2e61ba0
https://github.com/galaxyproject/galaxy/commit/1b25944a5d83bf8893d4969452db…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-02-22 (Mon, 22 Feb 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/test.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/pulsar/client/interface.py
M lib/pulsar/client/manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Merge pull request #1731 from mvdbeek/python_2_3_string_handling
Python 2/3 string handling
Compare: https://github.com/galaxyproject/galaxy/compare/4e73d56bf1dd...1b25944a5d83
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8cf990bd7fd8c4941c36c841830f71da364d39c1
https://github.com/galaxyproject/galaxy/commit/8cf990bd7fd8c4941c36c841830f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-09 (Tue, 09 Feb 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/output_collection_def.py
M test/unit/tools/test_collect_primary_datasets.py
Log Message:
-----------
Revise dbkey handling for discovred datasets.
Newer style <discover_datasets>'s based discovery will default to using input_dbkey the way normal inputs do. Legacy, implicit filename based discovery will continue to use '?' as the default.
This should work for collections and individual extra outputs.
Fixes #1598.
Thanks to @gregvonkuster for finding this issue and documenting it so thoroughly.
Commit: d7eb315f721684f279f3a0d59c10fbcb7f20a5c7
https://github.com/galaxyproject/galaxy/commit/d7eb315f721684f279f3a0d59c10…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-19 (Fri, 19 Feb 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/output_collection_def.py
M test/unit/tools/test_collect_primary_datasets.py
Log Message:
-----------
Merge pull request #1610 from jmchilton/discovered_dataset_keys
Improve dbkey handling for discovered datasets.
Compare: https://github.com/galaxyproject/galaxy/compare/040fb8185be6...d7eb315f7216
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0ae21aeb62029465bd87451c5432d4aed6ef5bae
https://github.com/galaxyproject/galaxy/commit/0ae21aeb62029465bd87451c5432…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M static/maps/galaxy.library.js.map
M static/scripts/galaxy.library.js
Log Message:
-----------
fix returning from versioned dataset view back to the latest
Commit: fcca59c70fc28330faa8472112e705dcd32b13e8
https://github.com/galaxyproject/galaxy/commit/fcca59c70fc28330faa8472112e7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
refactor; mainly the templates
Commit: 8f8da0105e488550546ac91ab65113c59ae27ff1
https://github.com/galaxyproject/galaxy/commit/8f8da0105e488550546ac91ab651…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M static/maps/galaxy.library.js.map
M static/scripts/galaxy.library.js
Log Message:
-----------
fix router returning from dataset permissions back to dataset
Commit: 3d9d822da3f20cac8ce33d958ec5681d3fa13a24
https://github.com/galaxyproject/galaxy/commit/3d9d822da3f20cac8ce33d958ec5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M static/maps/mvc/library/library-dataset-view.js.map
Log Message:
-----------
fix importing dataset into history
broken because of a change in the Galaxy modal object
Commit: 535b689cbc66d7607e2ddaa38804557403bafbc8
https://github.com/galaxyproject/galaxy/commit/535b689cbc66d7607e2ddaa38804…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
style the toolbar of dataset view templates
Commit: e28f329008ed088d47a049dd9edde1fb102896c3
https://github.com/galaxyproject/galaxy/commit/e28f329008ed088d47a049dd9edd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/style/less/library.less
M static/maps/mvc/library/library-dataset-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
add selects for dataset genome build and extension
minor stylistic fix for column width
Commit: b50cf13379306bbddfa4ec6f84f93465f467238b
https://github.com/galaxyproject/galaxy/commit/b50cf13379306bbddfa4ec6f84f9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
refactor library dataset permissions API to use role manager
fix a bug in making dataset private (when you called it multiple
times it would always add a new datasetpermission)
various refactorings of JS and py
Commit: 3371a96cffcc48415b6908be3e102634c25ea09a
https://github.com/galaxyproject/galaxy/commit/3371a96cffcc48415b6908be3e10…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
flake8 fixes
Commit: 2f26bdce3f6f16360bb5a761948452b1aa295f6d
https://github.com/galaxyproject/galaxy/commit/2f26bdce3f6f16360bb5a7619484…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
allow setting library dataset permissions with POSTing JSON
Commit: 879dffdd69b1dccee24647e8304def690a28b5af
https://github.com/galaxyproject/galaxy/commit/879dffdd69b1dccee24647e8304d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-17 (Wed, 17 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
correct the naming of variables and docs from Role.name to Role.id
Commit: 040fb8185be6bea64538963958d30218d4a575e3
https://github.com/galaxyproject/galaxy/commit/040fb8185be6bea64538963958d3…
Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2016-02-19 (Fri, 19 Feb 2016)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/style/less/library.less
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M static/maps/galaxy.library.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/galaxy.library.js
M static/scripts/mvc/library/library-dataset-view.js
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge pull request #1751 from martenson/libraries-refactor
various libraries refactoring and bugfixes
Compare: https://github.com/galaxyproject/galaxy/compare/0988a6e7d701...040fb8185be6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: cc943f240f70c880840548c45034fe377d18cc3c
https://github.com/galaxyproject/galaxy/commit/cc943f240f70c880840548c45034…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-22 (Fri, 22 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
A lib/galaxy/webapps/tool_shed/model/migrate/versions/0026_repository_dependency_table.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Add database table and API endpoint for metadata.
- Table tracks repository dependencies and is populated when metadata is generated.
- API endpoint returns a json dictionary of the requested metadata revision, recursively retrieving repository and tool dependencies it references.
Commit: e6bc65e0da0f35e28abfc2870246736cc1138000
https://github.com/galaxyproject/galaxy/commit/e6bc65e0da0f35e28abfc2870246…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-22 (Fri, 22 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0026_repository_dependency_table.py
Log Message:
-----------
Fix certain travis errors.
Commit: f0a35fe73516b00cfe439427f1dcb8902e8870e9
https://github.com/galaxyproject/galaxy/commit/f0a35fe73516b00cfe439427f1dc…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-25 (Mon, 25 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0026_repository_dependency_table.py
M lib/tool_shed/metadata/repository_metadata_manager.py
Log Message:
-----------
Code cleanup, foreign key constraints.
Commit: 3d0e16a896d7455a30027da1f878b15187dae387
https://github.com/galaxyproject/galaxy/commit/3d0e16a896d7455a30027da1f878…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-25 (Mon, 25 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/metadata/repository_metadata_manager.py
Log Message:
-----------
Correct linting errors again.
Commit: dff50c36ca23c41b7c58c901d6927d3af10cafb5
https://github.com/galaxyproject/galaxy/commit/dff50c36ca23c41b7c58c901d692…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-26 (Tue, 26 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
R lib/galaxy/webapps/tool_shed/model/migrate/versions/0026_repository_dependency_table.py
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Eliminate the database table and migration.
This results in slightly reduced performance, but eliminates a source of potential error.
Commit: 09bc98587389bfbe27fd3fb104ad5f6cba13d987
https://github.com/galaxyproject/galaxy/commit/09bc98587389bfbe27fd3fb104ad…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-26 (Tue, 26 Jan 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/mapping.py
Log Message:
-----------
Don't try to import removed classes.
Commit: 8206cf1d499705b33cfa29be703a5be16016632f
https://github.com/galaxyproject/galaxy/commit/8206cf1d499705b33cfa29be703a…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-26 (Tue, 26 Jan 2016)
Changed paths:
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Remove obsolete code.
Commit: d113d21c4e7b3619a04d907a9c59e577cf510e90
https://github.com/galaxyproject/galaxy/commit/d113d21c4e7b3619a04d907a9c59…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-26 (Tue, 26 Jan 2016)
Changed paths:
M lib/tool_shed/metadata/repository_metadata_manager.py
Log Message:
-----------
Remove more obsolete code.
Commit: be5d8f1ed9c54dd54e5ae42f3305f9c6458322cb
https://github.com/galaxyproject/galaxy/commit/be5d8f1ed9c54dd54e5ae42f3305…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-29 (Fri, 29 Jan 2016)
Changed paths:
M .travis.yml
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/style/less/tour.less
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
M doc/source/project/issues.rst
A doc/source/releases/16.01.rst
M doc/source/releases/16.01_announce.rst
A doc/source/releases/16.04_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/interval.py
A lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/histories.py
A lib/galaxy/managers/history_contents.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M scripts/bootstrap_history.py
M scripts/common_startup.sh
R static/maps/libs/backbone/backbone.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-view.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
R static/scripts/libs/backbone/backbone.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-view.js
M static/style/blue/base.css
M templates/show_params.mako
M test/api/test_workflows.py
M test/api/workflows_format_2/converter.py
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/for_workflows/1.bam
A test/functional/tools/for_workflows/mapper.xml
A test/functional/tools/for_workflows/pileup.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ts_api_all_metadata
Commit: a271602f0ef36a6a8d33b959a2376e47c479a914
https://github.com/galaxyproject/galaxy/commit/a271602f0ef36a6a8d33b959a237…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-01-29 (Fri, 29 Jan 2016)
Changed paths:
M lib/tool_shed/util/metadata_util.py
Log Message:
-----------
Also return valid tools.
Commit: cc7594575437a3b2705ef0d7fd686d068b3fc775
https://github.com/galaxyproject/galaxy/commit/cc7594575437a3b2705ef0d7fd68…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
A .ci/first_startup.sh
M .ci/flake8_blacklist.txt
M .travis.yml
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/onload.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/phinch/config/phinch.ini.sample
A config/plugins/interactive_environments/phinch/config/phinch.xml
A config/plugins/interactive_environments/phinch/static/js/phinch.js
A config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/tool_conf.xml.sample
M doc/source/admin/framework_dependencies.rst
M doc/source/project/organization.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
A lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
R lib/galaxy/metadata
M lib/galaxy/model/__init__.py
A lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/none_like.py
A lib/galaxy/util/ucsc.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/histories.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/libraries.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M scripts/binary_compatibility.py
M scripts/common_startup.sh
R scripts/set_metadata.py
R set_metadata.sh
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/onload.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/onload.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/username.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/tool_shed/repository/common.mako
M test-data/3.bam
A test/functional/tools/paths_as_file.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools_support.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/phenotype_association/linkToDavid.xml
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.py
R tools/plotting/plot_filter.py
R tools/plotting/plotter.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/sr_mapping/srma_wrapper.xml
M tools/stats/aggregate_scores_in_intervals.py
R tools/validation/fix_errors.py
R tools/validation/fix_errors.xml
R tools/validation/fix_errors_code.py
R tools/validation/validate.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_all_metadata
Commit: 5ace08f4595cbe5f98af69a7dee57b9d5753a8d2
https://github.com/galaxyproject/galaxy/commit/5ace08f4595cbe5f98af69a7dee5…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M test/base/twilltestcase.py
M test/functional/test_admin_features.py
M test/functional/test_data_security.py
M test/functional/test_dataset_features.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_tags.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
R test/tool_shed/functional/test_1085_repository_dependency_handling.py
R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
A test/tool_shed/functional/test_1090_repository_dependency_handling.py
R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1130_datatype_converters.py
A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
R test/tool_shed/functional/test_1140_tool_help_images.py
A test/tool_shed/functional/test_1150_datatype_converters.py
R test/tool_shed/functional/test_1150_prior_installation_required.py
R test/tool_shed/functional/test_1160_circular_prior_installation_required.py
A test/tool_shed/functional/test_1160_tool_help_images.py
R test/tool_shed/functional/test_1170_complex_prior_installation_required.py
A test/tool_shed/functional/test_1170_prior_installation_required.py
A test/tool_shed/functional/test_1180_circular_prior_installation_required.py
A test/tool_shed/functional/test_1190_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_all_metadata
Commit: fa3c19e51e77bb17e36ec9cc5f4e625b8fb169b8
https://github.com/galaxyproject/galaxy/commit/fa3c19e51e77bb17e36ec9cc5f4e…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/shed_util_common.py
M test/tool_shed/base/twilltestcase.py
A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
A test/tool_shed/test_data/tool_dependencies.xml
Log Message:
-----------
Remove unused methods, add test for API endpoint.
Commit: ee1f76eadc7f75d319a5acf4f07ac278ca5a846f
https://github.com/galaxyproject/galaxy/commit/ee1f76eadc7f75d319a5acf4f07a…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M test/tool_shed/base/twilltestcase.py
R test/tool_shed/test_data/tool_dependencies.xml
Log Message:
-----------
Remove debugging and stray tool dependency definition.
Commit: 9b147414fb242b1f57107093de22a2619c14064d
https://github.com/galaxyproject/galaxy/commit/9b147414fb242b1f57107093de22…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
Log Message:
-----------
Remove json import that was used for debugging.
Commit: 8132d5bfe47bf78ee9c189fe063d358d7f0ddc30
https://github.com/galaxyproject/galaxy/commit/8132d5bfe47bf78ee9c189fe063d…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-02-19 (Fri, 19 Feb 2016)
Changed paths:
M test/tool_shed/base/twilltestcase.py
Log Message:
-----------
Fix failing test.
Commit: 0988a6e7d7012e3bb0a033f938e13a18c8ec2dfe
https://github.com/galaxyproject/galaxy/commit/0988a6e7d7012e3bb0a033f938e1…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-19 (Fri, 19 Feb 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/util/metadata_util.py
M test/tool_shed/base/twilltestcase.py
A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
Log Message:
-----------
Merge pull request #1565 from davebx/ts_api_all_metadata
Add API endpoint for fetching all metadata for a repository.
Compare: https://github.com/galaxyproject/galaxy/compare/975304ac5919...0988a6e7d701
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7b8f6751720a2caaa5b13f7089d1aa1c98fbedf6
https://github.com/galaxyproject/galaxy/commit/7b8f6751720a2caaa5b13f7089d1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M lib/galaxy/managers/configuration.py
M static/maps/layout/masthead.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/masthead.js
M templates/webapps/galaxy/galaxy.masthead.mako
M test/qunit/tests/masthead_tests.js
Log Message:
-----------
Place logo into config, add masthead test cases
Commit: 580895af1d642a52559e0bfa1788808a7c790b05
https://github.com/galaxyproject/galaxy/commit/580895af1d642a52559e0bfa1788…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/scripts/mvc/workflow/workflow-view-node.js
Log Message:
-----------
Revision
Commit: 7ea4668ff732f22c0d686ed35fd6ff1a0c431736
https://github.com/galaxyproject/galaxy/commit/7ea4668ff732f22c0d686ed35fd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/utils/utils.js
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/utils/utils.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/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/utils/utils.js
M test/qunit/tests/masthead_tests.js
Log Message:
-----------
Remove former populate_state
Commit: 032ecd1e6edc8075de5b3ad0c7a815b46099a1de
https://github.com/galaxyproject/galaxy/commit/032ecd1e6edc8075de5b3ad0c7a8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Remove former update state
Commit: 25c6eda06e75353c904f4e42864b72a30e35df62
https://github.com/galaxyproject/galaxy/commit/25c6eda06e75353c904f4e42864b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Remove regular tool handling from editor_form_post
Commit: 89759a00c15e567e6e01ba47d28237d62605aaaa
https://github.com/galaxyproject/galaxy/commit/89759a00c15e567e6e01ba47d282…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Remove DummyDataset
Commit: 6ffa104cb3931a60a484a4a42808e57a64dfbdd6
https://github.com/galaxyproject/galaxy/commit/6ffa104cb3931a60a484a4a42808…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use visit inputs to set runtime config, remove conflicting booleans
Commit: 9423283e83f756f79dd6167c39c47a38557075a0
https://github.com/galaxyproject/galaxy/commit/9423283e83f756f79dd6167c39c4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix ftp handling
Commit: 664ae0c8dfa61fac9147675d6da2a32128ea7136
https://github.com/galaxyproject/galaxy/commit/664ae0c8dfa61fac9147675d6da2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/util/workflow_util.py
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M test/api/test_tools.py
M test/unit/tools/test_execution.py
Log Message:
-----------
Attempt to strip legacy collection handling, fixes
Commit: 5a8246878473b988a163606d21bbd6b5ab0edaf4
https://github.com/galaxyproject/galaxy/commit/5a8246878473b988a163606d21bb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Use regular dataset matching for selected values
Commit: 5041c80d85ba5686f3d5f815349263ed4f8f0150
https://github.com/galaxyproject/galaxy/commit/5041c80d85ba5686f3d5f8153492…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
Fix optional column parameter handling and accept_default tag
Commit: 5ff028a9d0636e1e7f0e4bab02d40c98666a4ed8
https://github.com/galaxyproject/galaxy/commit/5ff028a9d0636e1e7f0e4bab02d4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/utils/utils.js
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/util/workflow_util.py
M static/maps/layout/masthead.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/utils/utils.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/layout/masthead.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/utils/utils.js
M templates/webapps/galaxy/galaxy.masthead.mako
M test/api/test_tools.py
M test/qunit/tests/masthead_tests.js
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
Merge pull request #1711 from guerler/revise_states_000
Revise tool parameter handling, remove redundancies
Compare: https://github.com/galaxyproject/galaxy/compare/a0537762f286...5ff028a9d063