- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f50826: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: f5082604f7282587bb8385dbdb3bb91905bee87b https://github.com/galaxyproject/galaxy/commit/f5082604f7282587bb8385dbdb3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: c9fdb6e3efd2721dc193ea5f1d5cfe6c014ad94e https://github.com/galaxyproject/galaxy/commit/c9fdb6e3efd2721dc193ea5f1d5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper Compare: https://github.com/galaxyproject/galaxy/compare/02a8a7da0a0f...c9fdb6e3efd2

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[galaxyproject/galaxy] 10d276: Do not wrap __class__ attribute of SafeStringWrapp...
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10d27609af607208e182b7ce18b0447281de942c https://github.com/galaxyproject/galaxy/commit/10d27609af607208e182b7ce18b0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: b4475ba9df9b9425b5791e15c8c070b638768286 https://github.com/galaxyproject/galaxy/commit/b4475ba9df9b9425b5791e15c8c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3429 from nsoranzo/release_16.10_fix_3353 [16.10] Do not wrap __class__ attribute of SafeStringWrapper Compare: https://github.com/galaxyproject/galaxy/compare/4071b3eb79e4...b4475ba9df9b

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[galaxyproject/galaxy] 7f62eb: Fix history sharing test broken with #3417.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f62eb0c83c18949fdf945c4c194b89d74e66cae https://github.com/galaxyproject/galaxy/commit/7f62eb0c83c18949fdf945c4c194… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Fix history sharing test broken with #3417. Commit: 6fdd0014d38ac8455f26e12b9f44b55d46bc9ee6 https://github.com/galaxyproject/galaxy/commit/6fdd0014d38ac8455f26e12b9f44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Remove debugging "assert False" in workflow editor test. Commit: e1612d24eaf67f7dd517caa210131a54f141d2cd https://github.com/galaxyproject/galaxy/commit/e1612d24eaf67f7dd517caa21013… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Update URL used by Selenium tests that changed with a recent commit. Commit: 4071b3eb79e49806a6cd8df141be452366ba1942 https://github.com/galaxyproject/galaxy/commit/4071b3eb79e49806a6cd8df141be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #3440 from jmchilton/selenium_fixes_1 Fix most broken Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/c4f5a2cfb8b7...4071b3eb79e4

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[galaxyproject/galaxy] b00887: Fixup circular dependency in #3427.
by GitHub 19 Jan '17

19 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b00887b9d7e471c65155740db548effd75dc4703 https://github.com/galaxyproject/galaxy/commit/b00887b9d7e471c65155740db548… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fixup circular dependency in #3427. Unfortunately the "root" of the problem is that galaxy.tools.deps.requirements.ToolRequirement should be importable without importing galaxy.tools - but it cannot be currently just because of the way things are structured. Commit: c4f5a2cfb8b7a34faf05367a5f4d8073ab229b98 https://github.com/galaxyproject/galaxy/commit/c4f5a2cfb8b7a34faf05367a5f4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3447 from jmchilton/ts_import_cycle Fixup circular dependency in #3427. Compare: https://github.com/galaxyproject/galaxy/compare/94150df087b2...c4f5a2cfb8b7

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[galaxyproject/galaxy] 4a3c6c: Add nice css to error email
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a3c6c871d75a2e457b5ceb6cd081df827d60425 https://github.com/galaxyproject/galaxy/commit/4a3c6c871d75a2e457b5ceb6cd08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Add nice css to error email Apparently you have to inline it for certain web email clients to show it.. Commit: 94150df087b29810111952853a03fdb6ddd34631 https://github.com/galaxyproject/galaxy/commit/94150df087b29810111952853a03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #3445 from erasche/email-template-css Inline CSS in error report email Compare: https://github.com/galaxyproject/galaxy/compare/9646d264a1a9...94150df087b2

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[galaxyproject/galaxy] e0990e: extend API version information
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0990e2ab58895e9667438aa3207f1a15e9ec3bf https://github.com/galaxyproject/galaxy/commit/e0990e2ab58895e9667438aa3207… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- extend API version information extend API version information #1907 https://github.com/galaxyproject/galaxy/issues/1907 output json file contents with version_major ``` {"extra": {"user_tag": "_fix_job_runner_issue", "commit-id": "abcde123"}, "version_major": "16.10"} ``` First check environment value GALAXY_VERSION_JSON_FILE. if it's not set, try "galaxy root direcotory"/version.json. if json file is not find, extra set empty. Commit: c2d1a2a1897ba05e5067433fcecdfcd60c761009 https://github.com/galaxyproject/galaxy/commit/c2d1a2a1897ba05e5067433fcecd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: 0c0e58d5fb6c48418c36e547e976dde1dfd79942 https://github.com/galaxyproject/galaxy/commit/0c0e58d5fb6c48418c36e547e976… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: 8c34293602ec99b7deb128f60e2086f89f25e64a https://github.com/galaxyproject/galaxy/commit/8c34293602ec99b7deb128f60e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- More idiomatic Python for extended version information. - Eliminate the use of a bare except. - Use a ``with`` to ensure file handling is cleaned up. Commit: 9646d264a1a9d9d9107c2311deb4e6f319bb417d https://github.com/galaxyproject/galaxy/commit/9646d264a1a9d9d9107c2311deb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #3411 from manabuishii/extend_api_version extend API version information Compare: https://github.com/galaxyproject/galaxy/compare/29cdd6007fa3...9646d264a1a9

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[galaxyproject/galaxy] 9373b6: Fix bug with job re-submission introduced in 34f0b...
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9373b69f8b6dd93f747d5b12bea7e4f75aef3add https://github.com/galaxyproject/galaxy/commit/9373b69f8b6dd93f747d5b12bea7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c. Commit: 29cdd6007fa333e8e9caa85a1fc58ae389405cf2 https://github.com/galaxyproject/galaxy/commit/29cdd6007fa333e8e9caa85a1fc5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3439 from jmchilton/fix_resubmissions Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c Compare: https://github.com/galaxyproject/galaxy/compare/d2e019844471...29cdd6007fa3

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[galaxyproject/galaxy] bf3a48: Fix import order and Python3 compatibility for lib...
by GitHub 17 Jan '17

17 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf3a487f2017d248317e9ea70e567f57a70d9cc9 https://github.com/galaxyproject/galaxy/commit/bf3a487f2017d248317e9ea70e56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.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/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/tools/ xref. #1715 Commit: d2e019844471ee29f9b2433e0f90f53ea54a7b7f https://github.com/galaxyproject/galaxy/commit/d2e019844471ee29f9b2433e0f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.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/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #3431 from nsoranzo/python3 Fix import order and Python3 compatibility for lib/galaxy/tools/ Compare: https://github.com/galaxyproject/galaxy/compare/910bbdfc54fe...d2e019844471

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[galaxyproject/galaxy] 9f4add: Bug fix in mulled.py
by GitHub 17 Jan '17

17 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f4add70d0967ccb6ddf1bd2d1393685ef639e97 https://github.com/galaxyproject/galaxy/commit/9f4add70d0967ccb6ddf1bd2d139… Author: Abdulrahman Azab <eng.azab(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Bug fix in mulled.py This bug was causing running docker with sudo while it should not Commit: 910bbdfc54fe4a84e16ebe9ed9bc7fe0eed28dc6 https://github.com/galaxyproject/galaxy/commit/910bbdfc54fe4a84e16ebe9ed9bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Merge pull request #3434 from abdulrahmanazab/patch-4 Bug fix in mulled.py Compare: https://github.com/galaxyproject/galaxy/compare/dd2ab483c095...910bbdfc54fe

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[galaxyproject/galaxy] cdaa20: Add whoami API
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cdaa20858a4b20f0080a851c6380c41e610f1346 https://github.com/galaxyproject/galaxy/commit/cdaa20858a4b20f0080a851c6380… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add whoami API Commit: b242dc3ab18c003bd3c8219305730be22d0729e9 https://github.com/galaxyproject/galaxy/commit/b242dc3ab18c003bd3c821930573… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Fix docs concerns Commit: 8c46cd5afcb63ece8d37b5051be723a359c1cc71 https://github.com/galaxyproject/galaxy/commit/8c46cd5afcb63ece8d37b5051be7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Correct API path Commit: dd2ab483c095848a372a57de3ce4f08677c402fb https://github.com/galaxyproject/galaxy/commit/dd2ab483c095848a372a57de3ce4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3423 from erasche/whoami Add whoami API Compare: https://github.com/galaxyproject/galaxy/compare/8cb61626811d...dd2ab483c095

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[galaxyproject/galaxy] 68f5bc: Reapply ui-misc.Message changes post-reversion. F...
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2 https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2 https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap form-view to use the new UnescapedMessage Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8 https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Name function appropriately for Javascript instead of being stuck in Python. Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24 https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html Commit: 8cb61626811d51afef0f7e27e9713fa98e6b664a https://github.com/galaxyproject/galaxy/commit/8cb61626811d51afef0f7e27e971… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/maps/mvc/ui/ui-misc.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-misc.js Compare: https://github.com/galaxyproject/galaxy/compare/ebf18440ac09...8cb61626811d

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[galaxyproject/galaxy] 68f5bc: Reapply ui-misc.Message changes post-reversion. F...
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2 https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2 https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap form-view to use the new UnescapedMessage Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8 https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Name function appropriately for Javascript instead of being stuck in Python. Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24 https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html Compare: https://github.com/galaxyproject/galaxy/compare/c94ccb3f28cd...02a8a7da0a0f

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[galaxyproject/galaxy] 537d6e: Fix "exact" property for merged conda dependencies...
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 537d6e645ae142962cdf59e6365299b8c99706bf https://github.com/galaxyproject/galaxy/commit/537d6e645ae142962cdf59e63652… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix "exact" property for merged conda dependencies. This was broken with there initial commit as part of #3391. Commit: 2ed131d206dbf73a141b7baf76c5ffcce6fef206 https://github.com/galaxyproject/galaxy/commit/2ed131d206dbf73a141b7baf76c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix display of repository dependency status that broke with the introduction of the all-at-once dependency resolution in #3391 and addresses in part #3398. I have only restored the (collapsed) display of dependencies for all requirements in a repository, so breaking the information out on a per tool basis remains on the TODO list. Commit: ebf18440ac09c364fa1fb6b1cdd1640808ffd593 https://github.com/galaxyproject/galaxy/commit/ebf18440ac09c364fa1fb6b1cdd1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3427 from mvdbeek/fix_dependency_display_and_api Fix dependency display and api Compare: https://github.com/galaxyproject/galaxy/compare/b2cf773befd6...ebf18440ac09

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[galaxyproject/galaxy] a5c445: Swap the client's ui-misc.Message to escape by def...
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.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 A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Commit: b2cf773befd655ccae204c358703c9061916a32f https://github.com/galaxyproject/galaxy/commit/b2cf773befd655ccae204c358703… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A static/maps/libs/showdown.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.map A static/scripts/libs/showdown.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1f9812b5d522...b2cf773befd6

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[galaxyproject/galaxy] 422cf1: Switch to Miniconda3.
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 422cf1917e97b612e972b3824fcf831c510dc535 https://github.com/galaxyproject/galaxy/commit/422cf1917e97b612e972b3824fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Switch to Miniconda3. It is the platformed used by bioconda for testing and will be supported longer than the older Python 2 variant. This shouldn't require Python 3 be installed on the host running Galaxy. Commit: d66d3a1a308a94dd548f29448b479c9d9b66a239 https://github.com/galaxyproject/galaxy/commit/d66d3a1a308a94dd548f29448b47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Add a log message to explain long pause during startup. When conda_auto_init is used. Commit: 1f9812b5d522118f79a304e3c4f5f69e28661b05 https://github.com/galaxyproject/galaxy/commit/1f9812b5d522118f79a304e3c4f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3419 from jmchilton/conda_tweaks Target Miniconda3 when installing Conda. Compare: https://github.com/galaxyproject/galaxy/compare/e573826e02e8...1f9812b5d522

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[galaxyproject/galaxy] 07806e: Another fix for Selenium testing on Jenkins.
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07806e628adf164e95543393a9f37a187acb9a0e https://github.com/galaxyproject/galaxy/commit/07806e628adf164e95543393a9f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Another fix for Selenium testing on Jenkins. Turns out that random sleep for 30 seconds was every bit as brittle as it seemed. This is a bit better. Commit: e573826e02e822abd63fe452b065efd690e277da https://github.com/galaxyproject/galaxy/commit/e573826e02e822abd63fe452b065… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Merge pull request #3422 from jmchilton/selenium_fixes_0 Another fix for Selenium testing on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/ec425007b11f...e573826e02e8

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[galaxyproject/galaxy] cc4cd5: Fix RStudio login
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Compare: https://github.com/galaxyproject/galaxy/compare/2d69909218b2...c94ccb3f28cd

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[galaxyproject/galaxy] f9b9eb: Expose anyway if the user is an admin user
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9b9ebdd38cf2ee1634bf7daab171a25a8cec953 https://github.com/galaxyproject/galaxy/commit/f9b9ebdd38cf2ee1634bf7daab17… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Expose anyway if the user is an admin user Commit: 7c02ed7a9d1ab2c5101fbc4753ae7ee35d770c14 https://github.com/galaxyproject/galaxy/commit/7c02ed7a9d1ab2c5101fbc4753ae… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Mirror change in #3250 Fixes #3372 Commit: 6fc538837bc541ea9ad46fefc3e54ca676526bc9 https://github.com/galaxyproject/galaxy/commit/6fc538837bc541ea9ad46fefc3e5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Remove extraneous tag Commit: ec425007b11fd871b473a488e5321bb4450bccbf https://github.com/galaxyproject/galaxy/commit/ec425007b11fd871b473a488e532… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #3417 from erasche/fix-3372 Fix accidental email exposure Compare: https://github.com/galaxyproject/galaxy/compare/4946313fc9dc...ec425007b11f

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[galaxyproject/galaxy] 890107: Reversion of ui-misc messagebox changes.
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Compare: https://github.com/galaxyproject/galaxy/compare/45a9d586b6e1...2d69909218b2

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[galaxyproject/galaxy] a5c445: Swap the client's ui-misc.Message to escape by def...
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.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 A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/b0ac7daecdda...45a9d586b6e1

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[galaxyproject/galaxy]
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support." Commit: 4946313fc9dc27d2bc2e3d0464682d8308b8702c https://github.com/galaxyproject/galaxy/commit/4946313fc9dc27d2bc2e3d046468… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3408 from galaxyproject/revert-3399-markdown Revert "Markdown datatype support." Compare: https://github.com/galaxyproject/galaxy/compare/7bb8376490a2...4946313fc9dc

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[galaxyproject/galaxy] a60b7d: fix typo
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a60b7da85e2b9ef83aa86a0593dd5b810802ddf3 https://github.com/galaxyproject/galaxy/commit/a60b7da85e2b9ef83aa86a0593dd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix typo Commit: 7bb8376490a251573252177ab4112caba64b4684 https://github.com/galaxyproject/galaxy/commit/7bb8376490a251573252177ab411… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #3409 from manabuishii/patch-4 fix typo Compare: https://github.com/galaxyproject/galaxy/compare/a87feb11ff61...7bb8376490a2

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support."

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[galaxyproject/galaxy] 5ab4ae: Changes for Fastq Compression.
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab4ae4f2f630ea12c8b4e82e90cd8dca2758a6f https://github.com/galaxyproject/galaxy/commit/5ab4ae4f2f630ea12c8b4e82e90c… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Changes for Fastq Compression. Commit: 7597da61e5de1796f0cf4ce2f6ea577cb390f311 https://github.com/galaxyproject/galaxy/commit/7597da61e5de1796f0cf4ce2f6ea… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Updated sequence.py and datatypes_conf.xml Commit: aabfa4283d396ba01ea42b47ab0b8601122096bd https://github.com/galaxyproject/galaxy/commit/aabfa4283d396ba01ea42b47ab0b… Author: ashok <ashvark(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M tools/data_source/upload.py Log Message: ----------- Changes to keep the compressed fastq file as it is with out decompressing. Commit: 7d4840ce6b46a2b51f0d5332d72e7b4d956ac808 https://github.com/galaxyproject/galaxy/commit/7d4840ce6b46a2b51f0d5332d72e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- For fastq.gz support inherit from Fastq and Binary and enhance FastQ format to be gzip aware. Commit: 10f1bb5459c4d27ca9142c0f4da1c8502ac9f1b2 https://github.com/galaxyproject/galaxy/commit/10f1bb5459c4d27ca9142c0f4da1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py A test-data/1.fastqsanger.gz A test/functional/tools/compressed_fastq_conversion.xml A test/functional/tools/compressed_fastq_no_conversion.xml Log Message: ----------- Create a BaseFastq class and add test tools Having a BaseFastq class allows Fastq and FastqGz classes to inherit from BaseFastq. FastqGz is therfor not a Fastq datatype and goes through the converter. Also add 2 tools to demonstrate that compressed fastq will be converted to uncompressed fastq if the tool specifies `format="fastq"`, while `format="fastq.gz"` leaves files compressed. The tool test can be run with: ``` planemo test --galaxy_root . test/functional/tools/compressed_fastq_no_conversion.xml planemo test --galaxy_root . test/functional/tools/compressed_fastq_conversion.xml ``` Note that fastq conversion appears to required a galaxy user session, and planemo testing fails. Interactive testing with `planemo serve` is not affected and works fine. Commit: b44a977e649e3c6ac7cfc0bc519c242139296789 https://github.com/galaxyproject/galaxy/commit/b44a977e649e3c6ac7cfc0bc519c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Quote paths in converters Commit: bcf08f630d40b45b852db56e4a59c362c3cfc2bf https://github.com/galaxyproject/galaxy/commit/bcf08f630d40b45b852db56e4a59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Ensure closing of open files Commit: 304c05f3a3a99a9d450c06145bf3985f72f8b7db https://github.com/galaxyproject/galaxy/commit/304c05f3a3a99a9d450c06145bf3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Remove deprecated page attribute Commit: 99a037d5b92828cbef097ae8434e1d172df3c888 https://github.com/galaxyproject/galaxy/commit/99a037d5b92828cbef097ae8434e… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- add fastq(*).bz2 datatypes and converters Commit: 833f2c3dbef2469fe7437e8939e329ddff8d2793 https://github.com/galaxyproject/galaxy/commit/833f2c3dbef2469fe7437e8939e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #1 from abretaud/bz2 Add fastq(*).bz2 datatypes and converters Commit: 500ed949e66cb0ddec757022cae8be230722d755 https://github.com/galaxyproject/galaxy/commit/500ed949e66cb0ddec757022cae8… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix indentation and import (#2) * fix indentation and import * import fix * refix indentation * better looking imports Commit: b327523c3011c81e164f12833ff010eb411d963e https://github.com/galaxyproject/galaxy/commit/b327523c3011c81e164f12833ff0… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- wrong import name (#3) Commit: 7d8bbd599a2528a3e0e9264d64d0da3e494b5016 https://github.com/galaxyproject/galaxy/commit/7d8bbd599a2528a3e0e9264d64d0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 43abc55284fd4a1d7ea62535797d29f9977ef0af https://github.com/galaxyproject/galaxy/commit/43abc55284fd4a1d7ea62535797d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 296889d0dfa767c3649c6331a911ba0fd904f9fd https://github.com/galaxyproject/galaxy/commit/296889d0dfa767c3649c6331a911… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- lint fix Commit: a87feb11ff61dc0a8ea2657c8afe99cd115d1eda https://github.com/galaxyproject/galaxy/commit/a87feb11ff61dc0a8ea2657c8afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #3145 from mvdbeek/fastqgz Support for gzipped fastq formats Compare: https://github.com/galaxyproject/galaxy/compare/34458725b826...a87feb11ff61

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