February 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a22af1: For python2/3 compatibility, replace basestring wi...
by GitHub 22 Feb '16

22 Feb '16

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

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[galaxyproject/galaxy] ecd6ca: Remove len(stderr), breaks on recent docker versio...
by GitHub 21 Feb '16

21 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ecd6ca8a2f9752e78a16e3a9da6c370dc379fe4b https://github.com/galaxyproject/galaxy/commit/ecd6ca8a2f9752e78a16e3a9da6c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-21 (Sun, 21 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: 4e73d56bf1dd31f3d8cf24d1b5d59dc3a058f17d https://github.com/galaxyproject/galaxy/commit/4e73d56bf1dd31f3d8cf24d1b5d5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-21 (Sun, 21 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1769 from mvdbeek/fix_ies Remove len(stderr), breaks on recent docker versions Compare: https://github.com/galaxyproject/galaxy/compare/d7eb315f7216...4e73d56bf1dd

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[galaxyproject/galaxy] 8cf990: Revise dbkey handling for discovred datasets.
by GitHub 19 Feb '16

19 Feb '16

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

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[galaxyproject/galaxy] 0ae21a: fix returning from versioned dataset view back to ...
by GitHub 19 Feb '16

19 Feb '16

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

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[galaxyproject/galaxy] cc943f: Add database table and API endpoint for metadata.
by GitHub 19 Feb '16

19 Feb '16

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

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[galaxyproject/galaxy] 4c0993: Fix updating in-memory tools for tool shed install...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c0993cc420bc5e6a1d315677962d41803a41cd3 https://github.com/galaxyproject/galaxy/commit/4c0993cc420bc5e6a1d315677962… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix updating in-memory tools for tool shed installs into sections. Commit: b4c823f2cd47bd0f75351c820651abfefa1a8472 https://github.com/galaxyproject/galaxy/commit/b4c823f2cd47bd0f75351c820651… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1758 from jmchilton/ts_section_fix [16.01] Fix updating in-memory tools for tool shed installs into sections. Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Commit: b5e91d23779cc6db491b7d7b1701b25cb10da6fb https://github.com/galaxyproject/galaxy/commit/b5e91d23779cc6db491b7d7b1701… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/util/__init__.py Commit: 975304ac5919369b08733bf6367f58b1ba8adf03 https://github.com/galaxyproject/galaxy/commit/975304ac5919369b08733bf6367f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5ff028a9d063...975304ac5919

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[galaxyproject/galaxy] ef9362: Fix pretty_print_time_interval for MySQL. Fix #161...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Commit: b5e91d23779cc6db491b7d7b1701b25cb10da6fb https://github.com/galaxyproject/galaxy/commit/b5e91d23779cc6db491b7d7b1701… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/b4c823f2cd47...b5e91d23779c

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[galaxyproject/galaxy] 7b8f67: Place logo into config, add masthead test cases
by GitHub 18 Feb '16

18 Feb '16

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

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[galaxyproject/galaxy] ef9362: Fix pretty_print_time_interval for MySQL. Fix #161...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Compare: https://github.com/galaxyproject/galaxy/compare/476734d86510...6c83fbe24dd0

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[galaxyproject/galaxy] 4c0993: Fix updating in-memory tools for tool shed install...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4c0993cc420bc5e6a1d315677962d41803a41cd3 https://github.com/galaxyproject/galaxy/commit/4c0993cc420bc5e6a1d315677962… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix updating in-memory tools for tool shed installs into sections. Commit: b4c823f2cd47bd0f75351c820651abfefa1a8472 https://github.com/galaxyproject/galaxy/commit/b4c823f2cd47bd0f75351c820651… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1758 from jmchilton/ts_section_fix [16.01] Fix updating in-memory tools for tool shed installs into sections. Compare: https://github.com/galaxyproject/galaxy/compare/3f34131ff506...b4c823f2cd47

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