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

[galaxyproject/galaxy] 1568c0: fix title_default to work as a default and not an ...
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1568c0db809988599f10aebe1a24457087a49a1d https://github.com/galaxyproject/galaxy/commit/1568c0db809988599f10aebe1a24… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- fix title_default to work as a default and not an override Commit: 0ae86f59a1f491eaa022676cdac76fce251eb322 https://github.com/galaxyproject/galaxy/commit/0ae86f59a1f491eaa022676cdac7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Merge pull request #1429 from dannon/interactive_tours fix title_default to work as a default and not an override Compare: https://github.com/galaxyproject/galaxy/compare/ddc2a12eb18e...0ae86f59a1f4

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[galaxyproject/galaxy] 237ecc: Add form help class
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 237ecc77898f90d8d2d5d95741ff6fbaecc9e936 https://github.com/galaxyproject/galaxy/commit/237ecc77898f90d8d2d5d95741ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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/tool/tool-template.js M static/style/blue/base.css Log Message: ----------- Add form help class Commit: ddc2a12eb18e036e2e5cad072eb4ea99328ec7b2 https://github.com/galaxyproject/galaxy/commit/ddc2a12eb18e036e2e5cad072eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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/tool/tool-template.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1428 from guerler/add_pseudo_class_000 Add form help class Compare: https://github.com/galaxyproject/galaxy/compare/8bd293683bd2...ddc2a12eb18e

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[galaxyproject/galaxy] c41642: Remove dup NiceConfigParser from loadwsgi.py.
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c416426522c7cf8f684f12937a42354abd4ce875 https://github.com/galaxyproject/galaxy/commit/c416426522c7cf8f684f12937a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Remove dup NiceConfigParser from loadwsgi.py. We are really adopting pastescript as our own. Commit: 39f5c5d207f091f214b87d391a5aefb47402b9fc https://github.com/galaxyproject/galaxy/commit/39f5c5d207f091f214b87d391a5a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make docutils an optional dependency of galaxy-lib. Commit: 951b95e07964885e2fac88b685f498aca2f3e7fc https://github.com/galaxyproject/galaxy/commit/951b95e07964885e2fac88b685f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/multi_byte.py Log Message: ----------- Make wchartype an optional dependency of galaxy-lib. Commit: 8bd293683bd2144a877ec7206c003d52892c5796 https://github.com/galaxyproject/galaxy/commit/8bd293683bd2144a877ec7206c00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1427 from jmchilton/lib-deps Revise galaxy-lib dependencies. Compare: https://github.com/galaxyproject/galaxy/compare/0bad80ebdf2a...8bd293683bd2

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[galaxyproject/galaxy] 2be9aa: cram datatype: support for crai indexes via pysam
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2be9aa2569b35a86f4c593215189a07eb5dd62f0 https://github.com/galaxyproject/galaxy/commit/2be9aa2569b35a86f4c593215189… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai indexes via pysam Commit: d7eb84e57bbd119d788ca759e0d61a464a030c7a https://github.com/galaxyproject/galaxy/commit/d7eb84e57bbd119d788ca759e0d6… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai index (using built-in pysam) Commit: 78558beec3ebeca63a282e667948a18c2b21c508 https://github.com/galaxyproject/galaxy/commit/78558beec3ebeca63a282e667948… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype definition: flake8 correction Commit: 0bad80ebdf2a36ae23e05b1dee6152ee387b3b79 https://github.com/galaxyproject/galaxy/commit/0bad80ebdf2a36ae23e05b1dee61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1182 from yhoogstrate/bam_cram_index_via_pysam cram datatype: crai index via pysam Compare: https://github.com/galaxyproject/galaxy/compare/634a5b7fd9f2...0bad80ebdf2a

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[galaxyproject/galaxy] ce2795: Copy pastescript's NiceConfigParser into galaxy.ut...
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce2795d87ca4e5063ca699ad75cb6e4461fba30c https://github.com/galaxyproject/galaxy/commit/ce2795d87ca4e5063ca699ad75cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Copy pastescript's NiceConfigParser into galaxy.util.properties. This is used in galaxy-lib and by utilities such as galaxy/main.py which has no reason to depend on pastescript. Commit: 634a5b7fd9f289c09a963f19a9db36937fc301c9 https://github.com/galaxyproject/galaxy/commit/634a5b7fd9f289c09a963f19a9db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1413 from jmchilton/lib_0 Copy pastescript's NiceConfigParser into galaxy.util.properties. Compare: https://github.com/galaxyproject/galaxy/compare/6bd854ebe428...634a5b7fd9f2

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[galaxyproject/galaxy] 0203a6: Tours.
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0203a69d88c854c1fe3a210c83ff3ee0d943f4df https://github.com/galaxyproject/galaxy/commit/0203a69d88c854c1fe3a210c83ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.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 A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako Log Message: ----------- Tours. Commit: 40382fb0c1d7ec38252413aa50b3cb24418d158e https://github.com/galaxyproject/galaxy/commit/40382fb0c1d7ec38252413aa50b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A config/plugins/tours/galaxy_ui.yaml Log Message: ----------- Add slightly modified intro tour from bjoern, mostly compatible. Commit: f107b17928bddbe4f87e757f2301d56b807253cf https://github.com/galaxyproject/galaxy/commit/f107b17928bddbe4f87e757f2301… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/webpack.config.js M static/maps/mvc/tours.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/tours.js Log Message: ----------- Refactor a bit, adjust textinsert action to trigger 'change' on the element. Commit: 1e5640163a36c12e5f9e719358a1653a0fb18401 https://github.com/galaxyproject/galaxy/commit/1e5640163a36c12e5f9e719358a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Tour shim in onload, check sessionStorage (or would local be more appropriate?) Commit: 7110a0cc5e411062b8c6e5857e04ce10f121ffdd https://github.com/galaxyproject/galaxy/commit/7110a0cc5e411062b8c6e5857e04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Document necessary tweak. Commit: 9e7eaaa7aaf9c9a6928edc08abecbc26a3a76004 https://github.com/galaxyproject/galaxy/commit/9e7eaaa7aaf9c9a6928edc08abec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Finish sessionStorage and restart of tours across multiple pages. Commit: 5a3524245b41f2978b81ee01176dcf1caa382d50 https://github.com/galaxyproject/galaxy/commit/5a3524245b41f2978b81ee01176d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Actually let people end a tour. Commit: ffede653023a49aabcfcc958816b20e0e183a4ba https://github.com/galaxyproject/galaxy/commit/ffede653023a49aabcfcc958816b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Debugging cruft. Commit: 8c1beb2af5633660efc8ec7caaa871416f2508ea https://github.com/galaxyproject/galaxy/commit/8c1beb2af5633660efc8ec7caaa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- title override, working on fixing style. Commit: 4efa8e73b3479f3914b6b54d6a8bc4651aec7ef4 https://github.com/galaxyproject/galaxy/commit/4efa8e73b3479f3914b6b54d6a8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Consolidate to standard options dict, minor refactorings. Commit: 38b3c6e97aa0d6fe595be0f6e9021109ddd17226 https://github.com/galaxyproject/galaxy/commit/38b3c6e97aa0d6fe595be0f6e902… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Build client, bundle. Commit: 9b14d515db16d3a769532740a9b807b37a1177bd https://github.com/galaxyproject/galaxy/commit/9b14d515db16d3a769532740a9b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M static/style/blue/bootstrap-tour.css M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Stylize! Commit: e8116b8bbf22373ae8e784e83cf55426fd5b60bc https://github.com/galaxyproject/galaxy/commit/e8116b8bbf22373ae8e784e83cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css Log Message: ----------- Flip global vars back, now that bootstrap-tours.css is included and will override. Commit: aecc5d864f8e211c6f60ea8717f726c5807a1a76 https://github.com/galaxyproject/galaxy/commit/aecc5d864f8e211c6f60ea8717f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object. Commit: 2c5241dc3bba2114b43fe7f7e6e2efb17b705a28 https://github.com/galaxyproject/galaxy/commit/2c5241dc3bba2114b43fe7f7e6e2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Full client rebuild. Commit: e325eba37c159e78a20895edbd6d521657f9b650 https://github.com/galaxyproject/galaxy/commit/e325eba37c159e78a20895edbd6d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/galaxy/api/tours.py M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here. Commit: 578e201d64aa33224a586fe7928a8be5b476d332 https://github.com/galaxyproject/galaxy/commit/578e201d64aa33224a586fe7928a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Launch tour on GET arg (?tour_id=core.galaxy_ui). Commit: 4322f5e9b9e152aec75339925228b90ef759b47b https://github.com/galaxyproject/galaxy/commit/4322f5e9b9e152aec75339925228… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: A config/plugins/tours/core.galaxy_ui.yaml R config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py Log Message: ----------- Force tour_id to be locked to filename, instead of allowing these to be out of sync. Commit: 401583d730a6d5d1e57c82bb08c3216b40856d8f https://github.com/galaxyproject/galaxy/commit/401583d730a6d5d1e57c82bb08c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Move TOURS.giveTour at the top level of the namespace instead of a method of the view. Commit: 603cb2f18dfc1f4518066e514f660f7db91eb45d https://github.com/galaxyproject/galaxy/commit/603cb2f18dfc1f4518066e514f66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: A config/plugins/tours/core.history.yaml Log Message: ----------- Add history tour from @bgruening Commit: d23541092070b3dff9ef18a56620fc93837d9233 https://github.com/galaxyproject/galaxy/commit/d23541092070b3dff9ef18a56620… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove tour id from tour; unique and namespaced by filename and not a separate identifier. Commit: e243fe3bc1e66dfcb9de778e66ff99028c56f358 https://github.com/galaxyproject/galaxy/commit/e243fe3bc1e66dfcb9de778e66ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Slight refactoring, fix .yaml stripping bug. Commit: 0ef88e1e5397bc094a4a0f9f9683fdaffab35f48 https://github.com/galaxyproject/galaxy/commit/0ef88e1e5397bc094a4a0f9f9683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add tour reloading API endpoint. Commit: b9faf84b245a39780373545f778586bcc9ace916 https://github.com/galaxyproject/galaxy/commit/b9faf84b245a39780373545f7785… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: A test/api/test_tours.py Log Message: ----------- Stub an API test for tours so I can refactor a little. Commit: 01fed4b6d4d473d81fe2e89ee8199b00d0815a00 https://github.com/galaxyproject/galaxy/commit/01fed4b6d4d473d81fe2e89ee819… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Allow .yml extensions. Though not the "official" extension for YAML files, it is actually seen much more common in the wild. Commit: b35a39bd55d088fa25d2b3999fa482b83055f38a https://github.com/galaxyproject/galaxy/commit/b35a39bd55d088fa25d2b3999fa4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py Log Message: ----------- Prefer self.app to trans.app. See comments here https://github.com/galaxyproject/galaxy/pull/1392#commitcomment-15141262 for instance for argument why this is superior. Commit: da8b943f538d55c2d8290870eb19210c831cb627 https://github.com/galaxyproject/galaxy/commit/da8b943f538d55c2d8290870eb19… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.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/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tools/parameters/wrapped_json.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/topsort.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/onload.js.map M static/maps/utils/uploadbox.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/webapps/galaxy/galaxy.masthead.mako A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-app.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge. Commit: 7587809bb6f08a1ff4754b8d13b8ebfafaabc259 https://github.com/galaxyproject/galaxy/commit/7587809bb6f08a1ff4754b8d13b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Improve tour directory logic. - Refactor plugin framework logic for finding configuration directories out into util. - Rework tours to use the plugin framework logic to parse configuration directories. - Rework tour logic to allow multiple tour configuration directories. - Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does. Commit: c28d4d01eef483a2c8255f1ac14d636ab60351a7 https://github.com/galaxyproject/galaxy/commit/c28d4d01eef483a2c8255f1ac14d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Correctly specify default tour location. Commit: 4ef3e21c954a8bfe5b12758252ffcb5b303445f8 https://github.com/galaxyproject/galaxy/commit/4ef3e21c954a8bfe5b12758252ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix onclick handling broken w/ #1407 Commit: 5c765c08715c17c07c1916c8c7a484d8ef71a954 https://github.com/galaxyproject/galaxy/commit/5c765c08715c17c07c1916c8c7a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'dev' into interactive_tours Commit: 1d97e4271ef40969bb117e424691418ccecec7a2 https://github.com/galaxyproject/galaxy/commit/1d97e4271ef40969bb117e424691… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge dev to include menu/onclick fix. Commit: 1876ea6bb2565ccaf7f6475f9387e43f91e34bb5 https://github.com/galaxyproject/galaxy/commit/1876ea6bb2565ccaf7f6475f9387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/tours.py A test/api/test_tours.py Log Message: ----------- Merge pull request #8 from jmchilton/interactive_tours Minor tweaks to interactive tours backend. Commit: 5924857c2c7e012875b9840811ab22b9d4935cfa https://github.com/galaxyproject/galaxy/commit/5924857c2c7e012875b9840811ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Fix pre/postclick that got broken somewhere along the way w/ patches&merges. Commit: 9416e6f3f75513f8e86f741d5c2f322708abdb0b https://github.com/galaxyproject/galaxy/commit/9416e6f3f75513f8e86f741d5c2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge and resolve conflicts, rebuilding. Commit: 3d1b3f9806007e456ea5f409df5be96b69aabdb7 https://github.com/galaxyproject/galaxy/commit/3d1b3f9806007e456ea5f409df5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- How'd that get there? Commit: a1a549ea67b28679b079f4150cf6ce18bc87dd56 https://github.com/galaxyproject/galaxy/commit/a1a549ea67b28679b079f4150cf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js Log Message: ----------- Re-add identifiers to masthead, new ones for scratchbook (thanks @guerler) Commit: 6bd854ebe428a69f2e5664448330b8a4b2aafe77 https://github.com/galaxyproject/galaxy/commit/6bd854ebe428a69f2e5664448330… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py Log Message: ----------- Merge pull request #1422 from dannon/interactive_tours Interactive Tours Compare: https://github.com/galaxyproject/galaxy/compare/1730c12f8d3b...6bd854ebe428

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[galaxyproject/usegalaxy-playbook] b1a247: Add data managers on Test
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b1a2477ec7e0867432df1c0923e5b54822a3b297 https://github.com/galaxyproject/usegalaxy-playbook/commit/b1a2477ec7e08674… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add data managers on Test

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[galaxyproject/galaxy] 884b1d: Change scratchbook close icon
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 884b1d42db8ca46dc5613e398cc22015a5384935 https://github.com/galaxyproject/galaxy/commit/884b1d42db8ca46dc5613e398cc2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Change scratchbook close icon Commit: 1730c12f8d3ba9d7e32bfbd1625835ab0d7dae53 https://github.com/galaxyproject/galaxy/commit/1730c12f8d3ba9d7e32bfbd16258… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge pull request #1425 from guerler/fix_close_icon_000 Change scratchbook close icon Compare: https://github.com/galaxyproject/galaxy/compare/099f1447a666...1730c12f8d3b

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[galaxyproject/galaxy] 62b80d: Fix onclick broken in #1407
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62b80dfcc5e00ee92c2be83bbd89911158b9f9b4 https://github.com/galaxyproject/galaxy/commit/62b80dfcc5e00ee92c2be83bbd89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix onclick broken in #1407 Commit: 099f1447a66631250f61f5b61920f9b11018daa2 https://github.com/galaxyproject/galaxy/commit/099f1447a66631250f61f5b61920… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1424 from dannon/fix_onclick Fix masthead/menu.js onclick functionality Compare: https://github.com/galaxyproject/galaxy/compare/c97053a5e844...099f1447a666

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[galaxyproject/galaxy] 6cea51: Fix conda installation in debug mode
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6cea5121b1159a1966647dafb8d7930e9c5ee53c https://github.com/galaxyproject/galaxy/commit/6cea5121b1159a1966647dafb8d7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix conda installation in debug mode Commit: c97053a5e844ff19b628f65282a1392c86240b0a https://github.com/galaxyproject/galaxy/commit/c97053a5e844ff19b628f65282a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #1421 from galaxyproject/conda_install_fix Fix conda installation in debug mode Compare: https://github.com/galaxyproject/galaxy/compare/5a441044fbc1...c97053a5e844

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