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

[galaxyproject/galaxy] 33ac7e: Drop E731 from flake8 enforcement (though we shoul...
by GitHub 12 Jan '16

12 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33ac7e391078bae9da2519c95ff44d152f1b2d92 https://github.com/galaxyproject/galaxy/commit/33ac7e391078bae9da2519c95ff4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M setup.cfg Log Message: ----------- Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) Commit: 89e7c3df95026071e3ea6ce11f3c78a1a275cc20 https://github.com/galaxyproject/galaxy/commit/89e7c3df95026071e3ea6ce11f3c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M test/casperjs/casperjs_runner.py Log Message: ----------- Address W503 and E721 errors now enforced by pep8 1.7. Commit: 0a6f6c3da43806aa7d47ed714ef2602761bc2c4b https://github.com/galaxyproject/galaxy/commit/0a6f6c3da43806aa7d47ed714ef2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1483 from dannon/fix_lint_new_flake8 Fix project linting for new pep8 Compare: https://github.com/galaxyproject/galaxy/compare/ea5c082e8895...0a6f6c3da438

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[galaxyproject/galaxy] a26c97: Remove IPython IE, which was replaced by Jupyter I...
by GitHub 12 Jan '16

12 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a26c975964a12b4b2643fd1db3a7848ea21a6fe2 https://github.com/galaxyproject/galaxy/commit/a26c975964a12b4b2643fd1db3a7… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb Log Message: ----------- Remove IPython IE, which was replaced by Jupyter IE. Commit: ea5c082e88951162b4bf3d7d0059aa13682bd905 https://github.com/galaxyproject/galaxy/commit/ea5c082e88951162b4bf3d7d0059… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb Log Message: ----------- Merge pull request #1402 from bgruening/remove_ipython Remove IPython IE, which was replaced by Jupyter IE. Compare: https://github.com/galaxyproject/galaxy/compare/5a2eb7d4739d...ea5c082e8895

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 12 Jan '16

12 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.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/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 https://github.com/galaxyproject/galaxy/commit/6c9a82e142c5bf70ae4612f094b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for Section upgrade messages. Commit: 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 https://github.com/galaxyproject/galaxy/commit/2c0ad432f8485cb40719adfa8ecb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use test param label instead of param label in conditional upgrade missing message. Commit: 8334593de11e915389b1da58c3b5db26121c7bef https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6 https://github.com/galaxyproject/galaxy/commit/7923360dcec48b2e98d7c2a5bcae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator being cutoff by restoring height: 100% Commit: 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168 https://github.com/galaxyproject/galaxy/commit/3924a5a0e3d2c7d787e81fabc4e2… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed indentation errors Commit: 94b049926d844a8aa54017b6d7a9983b94203316 https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% Commit: 2be17071f35bb5db2298883aff107134a53701d1 https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 0d98cf8ab76a374362302547b5699fa024d5ce21 https://github.com/galaxyproject/galaxy/commit/0d98cf8ab76a374362302547b569… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Log a warning for missing tool whitelist file only if explicitly defined. Also fix the log message. Commit: a9034b5df3f3c80144727ebc161caa38b64ba7a1 https://github.com/galaxyproject/galaxy/commit/a9034b5df3f3c80144727ebc161c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection. Commit: b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec https://github.com/galaxyproject/galaxy/commit/b6e7b9a33b5dec7fdad2ad2f863b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Adjustments to sanitize_whitelist reloading. Commit: 2835aead8f949e3ac8b5c2ece0dc00c872950bde https://github.com/galaxyproject/galaxy/commit/2835aead8f949e3ac8b5c2ece0dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #2 from dannon/release_15.10_config Adjustments to sanitize_whitelist reloading. Commit: f13e9298de2eba4bee36ecb8336477a63345294b https://github.com/galaxyproject/galaxy/commit/f13e9298de2eba4bee36ecb83364… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1278 from nsoranzo/release_15.10_config [15.10] Log a warning for missing tool whitelist file only if explicitly defined. Commit: fba354cb87754450ac41e58252dd405ac073557d https://github.com/galaxyproject/galaxy/commit/fba354cb87754450ac41e58252dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #1282 from natefoo/kombu-el-cap [15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection Commit: 6a47d2d3a7f27b659e5de5fb1b37c7c1f9d04302 https://github.com/galaxyproject/galaxy/commit/6a47d2d3a7f27b659e5de5fb1b37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1239 from jmchilton/collection_outputs_hidden [15.10] "Fix" collection outputs to hide the HDAs in the history. Commit: 760c2b56bee664f2f874e2cc26d2129858da1bb1 https://github.com/galaxyproject/galaxy/commit/760c2b56bee664f2f874e2cc26d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly show and label hidden datasets on rerurn Commit: 66146ad5d0e17e35b6eee50699b0261422835000 https://github.com/galaxyproject/galaxy/commit/66146ad5d0e17e35b6eee50699b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns Commit: 989f961fb6351d1f63374b4fc40429c1e897b1e2 https://github.com/galaxyproject/galaxy/commit/989f961fb6351d1f63374b4fc404… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. Commit: 9b30b134d6ab93c2a84a856352f32a6713dd49cd https://github.com/galaxyproject/galaxy/commit/9b30b134d6ab93c2a84a856352f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Commit: 11eca70db129173ea20aac0040c9645049af189c https://github.com/galaxyproject/galaxy/commit/11eca70db129173ea20aac0040c9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Commit: 1b3ee81dbae9375443ea396280c1e418cae84876 https://github.com/galaxyproject/galaxy/commit/1b3ee81dbae9375443ea396280c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Commit: b0deead9c3260598f83d1ab2ec74b3c3e8974456 https://github.com/galaxyproject/galaxy/commit/b0deead9c3260598f83d1ab2ec74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Fix change handler association Commit: b4683fbce4cf7c133fdd8af6c6fef58a5bf3c76d https://github.com/galaxyproject/galaxy/commit/b4683fbce4cf7c133fdd8af6c6fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- raise and show specific exception and warning when no files detected Commit: 2d7c2019fba1b3de89a5a5183c7bd147a309f958 https://github.com/galaxyproject/galaxy/commit/2d7c2019fba1b3de89a5a5183c7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1360 from martenson/raise-specific-exception [15.10] datalibs: raise and show specific exception and warning when no files detected Commit: abd51e7f791c99a93062b9f2fee7827dea857c20 https://github.com/galaxyproject/galaxy/commit/abd51e7f791c99a93062b9f2fee7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association Commit: f042fe8548ec4a0f2f29b72d0c34736e2ff524f9 https://github.com/galaxyproject/galaxy/commit/f042fe8548ec4a0f2f29b72d0c34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 93c6d0542124c220e36c1e90d62e3e2aef607e9a https://github.com/galaxyproject/galaxy/commit/93c6d0542124c220e36c1e90d62e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd https://github.com/galaxyproject/galaxy/commit/ffb973477b02c4bc1cbfa95c7a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 641b275aa424421591833f6a3bce3ebd8b358017 https://github.com/galaxyproject/galaxy/commit/641b275aa424421591833f6a3bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 57a76065a54f63a47874158c121f002308648025 https://github.com/galaxyproject/galaxy/commit/57a76065a54f63a47874158c121f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: 2817eabf95a980a250e272c3917e5dcfc24743b2 https://github.com/galaxyproject/galaxy/commit/2817eabf95a980a250e272c3917e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: c3580da7b826b42de631017d4d2baf7e6ac3cfdf https://github.com/galaxyproject/galaxy/commit/c3580da7b826b42de631017d4d2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: 52b66d0dee8c026bfb8858671f900b862837fae5 https://github.com/galaxyproject/galaxy/commit/52b66d0dee8c026bfb8858671f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1385 from martenson/port-marius-ts-fix [15.10] Port marius TS fix Commit: 5d26f589cc475ff95b97ef2dcb34d5a290079e8b https://github.com/galaxyproject/galaxy/commit/5d26f589cc475ff95b97ef2dcb34… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M scripts/functional_tests.py M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1295 from jmchilton/test_fixes_backport_15_10 [15.10] Backport various testing fixes. Commit: 7b45f7b4047377dc1e5c622a3dc6449e3c68f9ad https://github.com/galaxyproject/galaxy/commit/7b45f7b4047377dc1e5c622a3dc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1259 from markiskander/reporter_fixes Fixed indentation errors for Reports Commit: 291d7751707d2382c1d3a24b01fafec4ae757748 https://github.com/galaxyproject/galaxy/commit/291d7751707d2382c1d3a24b01fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1430 from natefoo/version-16.01 [16.01] Update version to 16.01.rc1 Commit: 073609d005d2e5d109e7f55b839058dce005ca95 https://github.com/galaxyproject/galaxy/commit/073609d005d2e5d109e7f55b8390… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Fix casper tests. Commit: 5d32c9f8fc7ef8f287df2a1047dc1c394d9d791d https://github.com/galaxyproject/galaxy/commit/5d32c9f8fc7ef8f287df2a1047dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge pull request #1439 from jmchilton/backport_casper_fixes [16.01] Fix casper tests. Commit: 7a3cc410549474de18ff195c0e1dcd76fa92f64b https://github.com/galaxyproject/galaxy/commit/7a3cc410549474de18ff195c0e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix optional watchdog handling. Broken with 4086dd61dafe562ec01a8b1fce687a539aedbcfe. Thanks for bug report from @nsoranzo. Commit: e611b8fdb80beb87196a685924abe8e71bedcbea https://github.com/galaxyproject/galaxy/commit/e611b8fdb80beb87196a685924ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Use a more typical optional default value for optional import in watcher.py. Thanks to @nsoranzo for the advice - https://github.com/galaxyproject/galaxy/pull/1448#discussion_r49210125. Commit: d05ee507253901ef69a8892f6820b953c8d05725 https://github.com/galaxyproject/galaxy/commit/d05ee507253901ef69a8892f6820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Empty cherry-pick of 93c6d05 to cleanup merge. Commit: 47361f12ecaad83d5d563be763320ae1b17edc3b https://github.com/galaxyproject/galaxy/commit/47361f12ecaad83d5d563be76332… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: e8e01bdfb19cf1cc8f8cf485762c68d3f8e2f352 https://github.com/galaxyproject/galaxy/commit/e8e01bdfb19cf1cc8f8cf485762c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: 90bed00ebe8a5b4a7e0aeb61c23c991daae03fb8 https://github.com/galaxyproject/galaxy/commit/90bed00ebe8a5b4a7e0aeb61c23c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js Commit: dff94d743fd6e438f069deae5c9e8479357190cc https://github.com/galaxyproject/galaxy/commit/dff94d743fd6e438f069deae5c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Conflicts: lib/galaxy/tools/actions/__init__.py Commit: 88a1e636b8dea04a0db7d557fa6eb1483097b69d https://github.com/galaxyproject/galaxy/commit/88a1e636b8dea04a0db7d557fa6e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #1448 from jmchilton/watcher_fix [16.01] Fix optional watchdog handling. Commit: e36d33ce74babd939b3e70f30f0bf84f3cd2e527 https://github.com/galaxyproject/galaxy/commit/e36d33ce74babd939b3e70f30f0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1451 from jmchilton/release_16.01_merge_0 [16.01] Empty cherry-pick of 93c6d05 to cleanup merge 15.10 -> 16.01 Commit: c13b1c088cfbb0c708b2ce1d9068c704aba6cc95 https://github.com/galaxyproject/galaxy/commit/c13b1c088cfbb0c708b2ce1d9068… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. Commit: f8a7ac082036995573f849b12f64f6d4fbfb8b6b https://github.com/galaxyproject/galaxy/commit/f8a7ac082036995573f849b12f64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge release_15.10 into release_16.01. Conflicts: eggs.ini lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/toolbox/base.py static/maps/mvc/collection/list-collection-creator.js.map static/maps/mvc/library/library-foldertoolbar-view.js.map static/maps/utils/uploadbox.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/library/library-foldertoolbar-view.js static/scripts/utils/uploadbox.js test/base/twilltestcase.py test/functional/tools/samples_tool_conf.xml Commit: bb8f0f75efb971471fa65c2cc6951bfaa00b0fd0 https://github.com/galaxyproject/galaxy/commit/bb8f0f75efb971471fa65c2cc695… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1455 from jmchilton/release_16.01_merge_1 [16.01] Merge #1314 forward into 16.01. Commit: 0403a3175cbbdf45c76b8db31549ae7ec734b1ce https://github.com/galaxyproject/galaxy/commit/0403a3175cbbdf45c76b8db31549… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Fix refactoring from 7587809b Commit: 71aef50d25646325aca1eefab79f5cfff93246c3 https://github.com/galaxyproject/galaxy/commit/71aef50d25646325aca1eefab79f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1461 from jmchilton/release_16.01 [16.01] Merge more of 15.10 forward. Commit: 252586f86cfe0467244472d75483cd182556bfef https://github.com/galaxyproject/galaxy/commit/252586f86cfe0467244472d75483… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-10 (Sun, 10 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- improve default tours Commit: 3dda415fb9f516630f360aba5a9cd562ee70e680 https://github.com/galaxyproject/galaxy/commit/3dda415fb9f516630f360aba5a9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4 Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: d2702e9e4448a008b8d49744f549c160c7023ee1 https://github.com/galaxyproject/galaxy/commit/d2702e9e4448a008b8d49744f549… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix spelling mistake spotted by Nicola Commit: 54dca064fafca929ccd16625797a1eafe21da391 https://github.com/galaxyproject/galaxy/commit/54dca064fafca929ccd16625797a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- UI, Multi-history: fix drop event handler to use dataTransfer of original event Commit: 107ce1986f62eaeb1fb26a49921d8e1cbc53c958 https://github.com/galaxyproject/galaxy/commit/107ce1986f62eaeb1fb26a49921d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #1464 from bgruening/tours+ Improve default tours Commit: cea1f9e617b9375e3a01b7b4bf7804d0d0117cee https://github.com/galaxyproject/galaxy/commit/cea1f9e617b9375e3a01b7b4bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge pull request #1468 from carlfeberhard/fix.multihistory-drop [16.01] UI, Multi-history: fix drop event handler to use dataTransfer of orig… Commit: 24cb97cdbf9672ea09748a58c3d6d14b97704958 https://github.com/galaxyproject/galaxy/commit/24cb97cdbf9672ea09748a58c3d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1462 from jmchilton/release_16.01_merge_4 [16.01] Full merge of 15.10 into 16.01. Commit: f939c4eab5b1a4fb1f9e6e4feec61017c508d67f https://github.com/galaxyproject/galaxy/commit/f939c4eab5b1a4fb1f9e6e4feec6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/library/library-foldertoolbar-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M test/api/test_tools.py M test/casperjs/modules/user.js Log Message: ----------- Merge from release to dev. Commit: 5a2eb7d4739dd183c4dd2263048c8913300a3b07 https://github.com/galaxyproject/galaxy/commit/5a2eb7d4739dd183c4dd2263048c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebundle post merge. Compare: https://github.com/galaxyproject/galaxy/compare/6e170e84b4bb...5a2eb7d4739d

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[galaxyproject/galaxy] 2573f0: Some tweaks to shed_util_common.
by GitHub 12 Jan '16

12 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2573f023c8b899bb994bab4cb669423113e1a0f4 https://github.com/galaxyproject/galaxy/commit/2573f023c8b899bb994bab4cb669… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Some tweaks to shed_util_common. Commit: d38e7a61a1b115099804647d256d67064af99ecb https://github.com/galaxyproject/galaxy/commit/d38e7a61a1b115099804647d256d… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Use built-in sort method. Commit: 72540179262d53e5080385fc3cab3243d984c0c1 https://github.com/galaxyproject/galaxy/commit/72540179262d53e5080385fc3cab… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct default behavior. Commit: 508c42536d2fcd4ecd5abc2ff828675b7ccdfbdc https://github.com/galaxyproject/galaxy/commit/508c42536d2fcd4ecd5abc2ff828… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Do not cast to string when formatting expects int. Commit: f2773b7b14f90b717a77159098a322e7645a7631 https://github.com/galaxyproject/galaxy/commit/f2773b7b14f90b717a77159098a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M .gitignore M .travis.yml M Makefile M lib/galaxy/tours/__init__.py M lib/tool_shed/dependencies/repository/relation_builder.py M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ts_revisions_refactor Commit: 0bdc0a48e9d94eb0087490b92d2b53693abe1171 https://github.com/galaxyproject/galaxy/commit/0bdc0a48e9d94eb0087490b92d2b… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix failing tests. Commit: 6e170e84b4bb551d2090cb5579fef697bb0cdec6 https://github.com/galaxyproject/galaxy/commit/6e170e84b4bb551d2090cb5579fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1452 from davebx/ts_revisions_refactor Some tweaks to shed_util_common. Compare: https://github.com/galaxyproject/galaxy/compare/092402e7d401...6e170e84b4bb

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 11 Jan '16

11 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.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/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 https://github.com/galaxyproject/galaxy/commit/6c9a82e142c5bf70ae4612f094b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for Section upgrade messages. Commit: 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 https://github.com/galaxyproject/galaxy/commit/2c0ad432f8485cb40719adfa8ecb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use test param label instead of param label in conditional upgrade missing message. Commit: 8334593de11e915389b1da58c3b5db26121c7bef https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6 https://github.com/galaxyproject/galaxy/commit/7923360dcec48b2e98d7c2a5bcae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator being cutoff by restoring height: 100% Commit: 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168 https://github.com/galaxyproject/galaxy/commit/3924a5a0e3d2c7d787e81fabc4e2… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed indentation errors Commit: 94b049926d844a8aa54017b6d7a9983b94203316 https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% Commit: 2be17071f35bb5db2298883aff107134a53701d1 https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 0d98cf8ab76a374362302547b5699fa024d5ce21 https://github.com/galaxyproject/galaxy/commit/0d98cf8ab76a374362302547b569… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Log a warning for missing tool whitelist file only if explicitly defined. Also fix the log message. Commit: a9034b5df3f3c80144727ebc161caa38b64ba7a1 https://github.com/galaxyproject/galaxy/commit/a9034b5df3f3c80144727ebc161c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection. Commit: b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec https://github.com/galaxyproject/galaxy/commit/b6e7b9a33b5dec7fdad2ad2f863b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Adjustments to sanitize_whitelist reloading. Commit: 2835aead8f949e3ac8b5c2ece0dc00c872950bde https://github.com/galaxyproject/galaxy/commit/2835aead8f949e3ac8b5c2ece0dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #2 from dannon/release_15.10_config Adjustments to sanitize_whitelist reloading. Commit: f13e9298de2eba4bee36ecb8336477a63345294b https://github.com/galaxyproject/galaxy/commit/f13e9298de2eba4bee36ecb83364… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1278 from nsoranzo/release_15.10_config [15.10] Log a warning for missing tool whitelist file only if explicitly defined. Commit: fba354cb87754450ac41e58252dd405ac073557d https://github.com/galaxyproject/galaxy/commit/fba354cb87754450ac41e58252dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #1282 from natefoo/kombu-el-cap [15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection Commit: 6a47d2d3a7f27b659e5de5fb1b37c7c1f9d04302 https://github.com/galaxyproject/galaxy/commit/6a47d2d3a7f27b659e5de5fb1b37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1239 from jmchilton/collection_outputs_hidden [15.10] "Fix" collection outputs to hide the HDAs in the history. Commit: 760c2b56bee664f2f874e2cc26d2129858da1bb1 https://github.com/galaxyproject/galaxy/commit/760c2b56bee664f2f874e2cc26d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly show and label hidden datasets on rerurn Commit: 66146ad5d0e17e35b6eee50699b0261422835000 https://github.com/galaxyproject/galaxy/commit/66146ad5d0e17e35b6eee50699b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns Commit: 989f961fb6351d1f63374b4fc40429c1e897b1e2 https://github.com/galaxyproject/galaxy/commit/989f961fb6351d1f63374b4fc404… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. Commit: 9b30b134d6ab93c2a84a856352f32a6713dd49cd https://github.com/galaxyproject/galaxy/commit/9b30b134d6ab93c2a84a856352f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Commit: 11eca70db129173ea20aac0040c9645049af189c https://github.com/galaxyproject/galaxy/commit/11eca70db129173ea20aac0040c9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Commit: 1b3ee81dbae9375443ea396280c1e418cae84876 https://github.com/galaxyproject/galaxy/commit/1b3ee81dbae9375443ea396280c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Commit: b0deead9c3260598f83d1ab2ec74b3c3e8974456 https://github.com/galaxyproject/galaxy/commit/b0deead9c3260598f83d1ab2ec74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Fix change handler association Commit: b4683fbce4cf7c133fdd8af6c6fef58a5bf3c76d https://github.com/galaxyproject/galaxy/commit/b4683fbce4cf7c133fdd8af6c6fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- raise and show specific exception and warning when no files detected Commit: 2d7c2019fba1b3de89a5a5183c7bd147a309f958 https://github.com/galaxyproject/galaxy/commit/2d7c2019fba1b3de89a5a5183c7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1360 from martenson/raise-specific-exception [15.10] datalibs: raise and show specific exception and warning when no files detected Commit: abd51e7f791c99a93062b9f2fee7827dea857c20 https://github.com/galaxyproject/galaxy/commit/abd51e7f791c99a93062b9f2fee7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association Commit: f042fe8548ec4a0f2f29b72d0c34736e2ff524f9 https://github.com/galaxyproject/galaxy/commit/f042fe8548ec4a0f2f29b72d0c34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 93c6d0542124c220e36c1e90d62e3e2aef607e9a https://github.com/galaxyproject/galaxy/commit/93c6d0542124c220e36c1e90d62e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd https://github.com/galaxyproject/galaxy/commit/ffb973477b02c4bc1cbfa95c7a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 641b275aa424421591833f6a3bce3ebd8b358017 https://github.com/galaxyproject/galaxy/commit/641b275aa424421591833f6a3bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 57a76065a54f63a47874158c121f002308648025 https://github.com/galaxyproject/galaxy/commit/57a76065a54f63a47874158c121f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: 2817eabf95a980a250e272c3917e5dcfc24743b2 https://github.com/galaxyproject/galaxy/commit/2817eabf95a980a250e272c3917e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: c3580da7b826b42de631017d4d2baf7e6ac3cfdf https://github.com/galaxyproject/galaxy/commit/c3580da7b826b42de631017d4d2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: 52b66d0dee8c026bfb8858671f900b862837fae5 https://github.com/galaxyproject/galaxy/commit/52b66d0dee8c026bfb8858671f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1385 from martenson/port-marius-ts-fix [15.10] Port marius TS fix Commit: 5d26f589cc475ff95b97ef2dcb34d5a290079e8b https://github.com/galaxyproject/galaxy/commit/5d26f589cc475ff95b97ef2dcb34… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M scripts/functional_tests.py M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1295 from jmchilton/test_fixes_backport_15_10 [15.10] Backport various testing fixes. Commit: 7b45f7b4047377dc1e5c622a3dc6449e3c68f9ad https://github.com/galaxyproject/galaxy/commit/7b45f7b4047377dc1e5c622a3dc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1259 from markiskander/reporter_fixes Fixed indentation errors for Reports Commit: 90bed00ebe8a5b4a7e0aeb61c23c991daae03fb8 https://github.com/galaxyproject/galaxy/commit/90bed00ebe8a5b4a7e0aeb61c23c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js Commit: c13b1c088cfbb0c708b2ce1d9068c704aba6cc95 https://github.com/galaxyproject/galaxy/commit/c13b1c088cfbb0c708b2ce1d9068… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. Commit: f8a7ac082036995573f849b12f64f6d4fbfb8b6b https://github.com/galaxyproject/galaxy/commit/f8a7ac082036995573f849b12f64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge release_15.10 into release_16.01. Conflicts: eggs.ini lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/toolbox/base.py static/maps/mvc/collection/list-collection-creator.js.map static/maps/mvc/library/library-foldertoolbar-view.js.map static/maps/utils/uploadbox.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/library/library-foldertoolbar-view.js static/scripts/utils/uploadbox.js test/base/twilltestcase.py test/functional/tools/samples_tool_conf.xml Commit: 3dda415fb9f516630f360aba5a9cd562ee70e680 https://github.com/galaxyproject/galaxy/commit/3dda415fb9f516630f360aba5a9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4 Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 24cb97cdbf9672ea09748a58c3d6d14b97704958 https://github.com/galaxyproject/galaxy/commit/24cb97cdbf9672ea09748a58c3d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1462 from jmchilton/release_16.01_merge_4 [16.01] Full merge of 15.10 into 16.01. Compare: https://github.com/galaxyproject/galaxy/compare/cea1f9e617b9...24cb97cdbf96

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[galaxyproject/galaxy] 54dca0: UI, Multi-history: fix drop event handler to use d...
by GitHub 11 Jan '16

11 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 54dca064fafca929ccd16625797a1eafe21da391 https://github.com/galaxyproject/galaxy/commit/54dca064fafca929ccd16625797a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- UI, Multi-history: fix drop event handler to use dataTransfer of original event Commit: cea1f9e617b9375e3a01b7b4bf7804d0d0117cee https://github.com/galaxyproject/galaxy/commit/cea1f9e617b9375e3a01b7b4bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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/history/history-view-edit.js Log Message: ----------- Merge pull request #1468 from carlfeberhard/fix.multihistory-drop [16.01] UI, Multi-history: fix drop event handler to use dataTransfer of orig… Compare: https://github.com/galaxyproject/galaxy/compare/107ce1986f62...cea1f9e617b9

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[galaxyproject/galaxy] 252586: improve default tours
by GitHub 11 Jan '16

11 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 252586f86cfe0467244472d75483cd182556bfef https://github.com/galaxyproject/galaxy/commit/252586f86cfe0467244472d75483… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-10 (Sun, 10 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- improve default tours Commit: d2702e9e4448a008b8d49744f549c160c7023ee1 https://github.com/galaxyproject/galaxy/commit/d2702e9e4448a008b8d49744f549… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix spelling mistake spotted by Nicola Commit: 107ce1986f62eaeb1fb26a49921d8e1cbc53c958 https://github.com/galaxyproject/galaxy/commit/107ce1986f62eaeb1fb26a49921d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #1464 from bgruening/tours+ Improve default tours Compare: https://github.com/galaxyproject/galaxy/compare/71aef50d2564...107ce1986f62

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[galaxyproject/galaxy]
by GitHub 11 Jan '16

11 Jan '16

Branch: refs/heads/conda_install_fix Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] dff94d: "Fix" collection outputs to hide the HDAs in the h...
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dff94d743fd6e438f069deae5c9e8479357190cc https://github.com/galaxyproject/galaxy/commit/dff94d743fd6e438f069deae5c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Conflicts: lib/galaxy/tools/actions/__init__.py Commit: 71aef50d25646325aca1eefab79f5cfff93246c3 https://github.com/galaxyproject/galaxy/commit/71aef50d25646325aca1eefab79f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1461 from jmchilton/release_16.01 [16.01] Merge more of 15.10 forward. Compare: https://github.com/galaxyproject/galaxy/compare/0403a3175cbb...71aef50d2564

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[galaxyproject/galaxy] 0403a3: Fix refactoring from 7587809b
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0403a3175cbbdf45c76b8db31549ae7ec734b1ce https://github.com/galaxyproject/galaxy/commit/0403a3175cbbdf45c76b8db31549… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Fix refactoring from 7587809b

1 0