- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5ce771: Strip URL of download_file and download_by_url ins...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5ce771b70e44f28fde2e14bf963f97fed36bc2ae https://github.com/galaxyproject/galaxy/commit/5ce771b70e44f28fde2e14bf963f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip URL of download_file and download_by_url install actions. Commit: 4c815a7d0589a00df8c8fffba730a79030ad7791 https://github.com/galaxyproject/galaxy/commit/4c815a7d0589a00df8c8fffba730… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Compare: https://github.com/galaxyproject/galaxy/compare/5b720b4a0240...4c815a7d0589

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[galaxyproject/galaxy] 5ce771: Strip URL of download_file and download_by_url ins...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ce771b70e44f28fde2e14bf963f97fed36bc2ae https://github.com/galaxyproject/galaxy/commit/5ce771b70e44f28fde2e14bf963f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip URL of download_file and download_by_url install actions. Commit: f06b8205897a594b9d10e3f0aeb37f4858ca15c6 https://github.com/galaxyproject/galaxy/commit/f06b8205897a594b9d10e3f0aeb3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1775 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Compare: https://github.com/galaxyproject/galaxy/compare/4498c50f90c9...f06b8205897a

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[galaxyproject/galaxy] dbab6f: Workaround for #1739 - fixing up subworkflow inut ...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dbab6f5b979f19c33c3cd1aeb5c459dcc5612eec https://github.com/galaxyproject/galaxy/commit/dbab6f5b979f19c33c3cd1aeb5c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Workaround for #1739 - fixing up subworkflow inut connections. Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch. Commit: 5b720b4a02408a0601e7ecaf4fb2374c8c5753a7 https://github.com/galaxyproject/galaxy/commit/5b720b4a02408a0601e7ecaf4fb2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1774 from jmchilton/wf_fixes [16.01] Workaround for #1739 - fixing up subworkflow input connections. Compare: https://github.com/galaxyproject/galaxy/compare/b5e91d23779c...5b720b4a0240

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[galaxyproject/galaxy] aa27fc: better default than localhost
by GitHub 22 Feb '16

22 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa27fcf75bd8fe7bb0bcab5428ff80a6b750a41e https://github.com/galaxyproject/galaxy/commit/aa27fcf75bd8fe7bb0bcab5428ff… 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: ----------- better default than localhost Commit: 5d37f9b103af0d9f4773528eabb5e4a81ceaa704 https://github.com/galaxyproject/galaxy/commit/5d37f9b103af0d9f4773528eabb5… 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: ----------- missing quotes Commit: bad1aca5a9fded2547e43dd66f37500d64e22655 https://github.com/galaxyproject/galaxy/commit/bad1aca5a9fded2547e43dd66f37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Split out inspect and container_port_mapping / container_gateway_ip recovery, fix typo. Commit: e718e8ebac640109d0b1ed6f0c706705ab315d2d https://github.com/galaxyproject/galaxy/commit/e718e8ebac640109d0b1ed6f0c70… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- docstring fixes Commit: 4498c50f90c9113c793a45066b52ea4ba5b208fa https://github.com/galaxyproject/galaxy/commit/4498c50f90c9113c793a45066b52… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1770 from mvdbeek/fix_ies Use "Gateway" from docker inspect as default docker_hostname Compare: https://github.com/galaxyproject/galaxy/compare/1b25944a5d83...4498c50f90c9

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[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 19 Feb '16

19 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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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Commit: a0537762f2861247109ead028c33eaca2bd42dbc https://github.com/galaxyproject/galaxy/commit/a0537762f2861247109ead028c33… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M lib/galaxy/config.py M lib/tool_shed/util/encoding_util.py M static/maps/mvc/ui/popup-menu.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/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/68e6312a6410...a0537762f286

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Compare: https://github.com/galaxyproject/galaxy/compare/80a858a3afd9...3f34131ff506

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[galaxyproject/galaxy] 587d45: Fix installation of Tool Shed repositories contain...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Compare: https://github.com/galaxyproject/galaxy/compare/868acc362f6c...476734d86510

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[galaxyproject/usegalaxy-playbook] c9696f: install new MEME and bwa on Main
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c9696f8218c4e21051ae7e59daec2140dddd161e https://github.com/galaxyproject/usegalaxy-playbook/commit/c9696f8218c4e210… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- install new MEME and bwa on Main update Main mutable confs

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[galaxyproject/galaxy] afb2ea: Clean up some twilltestcase methods.
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afb2ea387d5a8c5b6794f3bf95940cce842aea2b https://github.com/galaxyproject/galaxy/commit/afb2ea387d5a8c5b6794f3bf9594… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 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 M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_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: ----------- Clean up some twilltestcase methods. Commit: b96bc82db610a58f2c3fabdd65fc2e99a42b6e45 https://github.com/galaxyproject/galaxy/commit/b96bc82db610a58f2c3fabdd65fc… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M test/functional/test_get_data.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py Log Message: ----------- Fix overly enthusiastic s///g. Commit: a941e88b04005f8f44338af65ee2212447181da7 https://github.com/galaxyproject/galaxy/commit/a941e88b04005f8f44338af65ee2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: 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_1410_update_manager.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Ensure that a valid login exists after cookies are cleared. Commit: 68e6312a6410b44edd7f52d629f422a62d2818ce https://github.com/galaxyproject/galaxy/commit/68e6312a6410b44edd7f52d629f4… Author: Aysam Guerler <aysam.guerler(a)gmail.com> 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 pull request #1742 from davebx/ttc_cleanup Clean up some twilltestcase methods. Compare: https://github.com/galaxyproject/galaxy/compare/f5277a654a04...68e6312a6410

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[galaxyproject/galaxy] 84de6b: Fix target or window.location when importing histo...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Compare: https://github.com/galaxyproject/galaxy/compare/aabc916ed20a...80a858a3afd9

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[galaxyproject/galaxy] c56635: Make api/tools return tool_shed_repository informa...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c56635ad2883df92575c85a5946726037ceef600 https://github.com/galaxyproject/galaxy/commit/c56635ad2883df92575c85a59467… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Make api/tools return tool_shed_repository information. Commit: f5277a654a048869d213f4941198ef43c03a46b6 https://github.com/galaxyproject/galaxy/commit/f5277a654a048869d213f4941198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1752 from mvdbeek/return_tsr_info_on_tools_api Make api/tools return tool_shed_repository information. Compare: https://github.com/galaxyproject/galaxy/compare/e3b1fc1bef99...f5277a654a04

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[galaxyproject/galaxy] 80f4a5: [PROCEDURES] Drop Ross from the committers group.
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80f4a5eaed2ec17e5ef97dc800707ea56a60d6dd https://github.com/galaxyproject/galaxy/commit/80f4a5eaed2ec17e5ef97dc80070… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Drop Ross from the committers group. Ross Lazarus has done a lot for Galaxy for a long time and has been a fantastic presence in the community. He is now retired and has no intention of touching the code or reviewing pull requests so I think it is best to remove him from the committers list. I have contacted him to confirm this and he has no problem with his removal from this group. Just to reiterate, this isn't a condemnation of any kind, from the organization policies - "Periodically, active members may review this group and request inactive members are removed - this should not be interpreted as a condemnation of these inactive members but merely as a reflection of a desire to keep this group focused enough to remain effective." Commit: e3b1fc1bef99bca281e6a86f927b44bbfa7fdaae https://github.com/galaxyproject/galaxy/commit/e3b1fc1bef99bca281e6a86f927b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1698 from jmchilton/ross [PROCEDURES] Drop Ross from the committers group. Compare: https://github.com/galaxyproject/galaxy/compare/b3296526da94...e3b1fc1bef99

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[galaxyproject/galaxy] b2da13: [PROCEDURES] Add Marius van den Beek to Galaxy com...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2da133e07c971afd35963c50b9b36eb5b24a358 https://github.com/galaxyproject/galaxy/commit/b2da133e07c971afd35963c50b9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Marius has been an indispensable member of the Galaxy community for a while - his contributions to tools, planemo, and ansible roles have been signficant and invaluable. However over the last several months he has taken a very active role on the Galaxy central code base itself. He has worked through a number of very intricate bugs to tool shed, tooling, and workflow code - consistently providing high quality and important bug fixes. Beyond that he has made signficant enhancements to the testing of Galaxy and workflow available to tool developers leveraging local tool sheds. He also is very active in the review of issues and pull requests, perhaps the most important role of Galaxy committer group members. Commit: b3296526da94cee8ffd1acdf3186548d967f075f https://github.com/galaxyproject/galaxy/commit/b3296526da94cee8ffd1acdf3186… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1699 from jmchilton/mvdbeek [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Compare: https://github.com/galaxyproject/galaxy/compare/8e5aa4ac6774...b3296526da94

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[galaxyproject/infrastructure-playbook] 1bd157: Change access lists for orval
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1bd1570dcd2376995d29468e5c67ea630ec8ef09 https://github.com/galaxyproject/infrastructure-playbook/commit/1bd1570dcd2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Change access lists for orval

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[galaxyproject/galaxy] 37b98b: Load whitelist regardless of whether the setting i...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Compare: https://github.com/galaxyproject/galaxy/compare/39ec09df4806...aabc916ed20a

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