- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0c321c: removed config.ini parameter from cleanup scripts
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Compare: https://github.com/galaxyproject/galaxy/compare/393f055a2307...2d772d74b940

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[galaxyproject/galaxy] 2dfb48: Fix bug with remove workflow outputs from a node.
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2dfb4875bba0059a4b44bd77e7fadb7adf6af7d7 https://github.com/galaxyproject/galaxy/commit/2dfb4875bba0059a4b44bd77e7fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix bug with remove workflow outputs from a node. Fixes https://github.com/galaxyproject/galaxy/issues/5931. Commit: feb3e5688dd6d97402a201e77e0179ac6dc30670 https://github.com/galaxyproject/galaxy/commit/feb3e5688dd6d97402a201e77e01… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5935 from jmchilton/workflow_outputs_fix Fix bug with removing workflow outputs from a node. Compare: https://github.com/galaxyproject/galaxy/compare/5c3e6648519d...feb3e5688dd6

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[galaxyproject/ansible-galaxy] a8a01b: code block was supposed to end
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: a8a01bb5fe0d9a5ecbf72cd6b162b719c4428ff3 https://github.com/galaxyproject/ansible-galaxy/commit/a8a01bb5fe0d9a5ecbf7… Author: E. Rasche <hxr(a)hx42.org> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M README.md Log Message: ----------- code block was supposed to end

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[galaxyproject/galaxy] 89ff88: Improve dropdown click and highlighting behavior
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89ff880bcde0916c6ea3ae70fabb0e4366b3fdd0 https://github.com/galaxyproject/galaxy/commit/89ff880bcde0916c6ea3ae70fabb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Improve dropdown click and highlighting behavior Commit: 0881547bfcc0be8fbe101885543303c152103265 https://github.com/galaxyproject/galaxy/commit/0881547bfcc0be8fbe1018855433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'guerler/fix_drop_selection' into dev Commit: 5c3e6648519d6591bcf3e71b6d2b4e1ba2fe1170 https://github.com/galaxyproject/galaxy/commit/5c3e6648519d6591bcf3e71b6d2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/yarn.lock Log Message: ----------- Client format after merges. Compare: https://github.com/galaxyproject/galaxy/compare/e40c61b9a740...5c3e6648519d

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[galaxyproject/galaxy] df292f: Fix trackster links
by GitHub 21 Apr '18

21 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df292fbf0e8c3246ec518a58385ea5a1233f0d45 https://github.com/galaxyproject/galaxy/commit/df292fbf0e8c3246ec518a58385e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Fix trackster links Commit: e40c61b9a740974f3784b2cef90d1f973dabed52 https://github.com/galaxyproject/galaxy/commit/e40c61b9a740974f3784b2cef90d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Merge pull request #5916 from guerler/fix_trackster_link Fix trackster links Compare: https://github.com/galaxyproject/galaxy/compare/d51812b832db...e40c61b9a740

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[galaxyproject/galaxy] f6c00e: improve ux of various builder elements
by GitHub 21 Apr '18

21 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6c00e79217501b7622c151bac119726f8004a64 https://github.com/galaxyproject/galaxy/commit/f6c00e79217501b7622c151bac11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- improve ux of various builder elements Commit: f0e0b5c9fc88119ee5f2d380d38b0aa3e89079e1 https://github.com/galaxyproject/galaxy/commit/f0e0b5c9fc88119ee5f2d380d38b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix rule source edit cancel button. Commit: c4ad1f55e49c374eac8724d7ffbb787e5ac37c15 https://github.com/galaxyproject/galaxy/commit/c4ad1f55e49c374eac8724d7ffbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Disable reorient button. Commit: 1df00bfb51afbbf5969429aae274a88315e40d51 https://github.com/galaxyproject/galaxy/commit/1df00bfb51afbbf5969429aae274… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/package.json M client/webpack.config.js Log Message: ----------- Add bootstrap vue as a dependency. Commit: 847695a16248986b8f2d798f420f887f127b6d6a https://github.com/galaxyproject/galaxy/commit/847695a16248986b8f2d798f420f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Use bootstrap-vue to add many new tooltips to rule builder. Commit: 798d7d86795fd9dbee51f3551a051245111129ab https://github.com/galaxyproject/galaxy/commit/798d7d86795fd9dbee51f3551a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- bootstrap-vue popover describing regex. Commit: 5e78c00824b6ba2e97cd46b671133de9cec43ad1 https://github.com/galaxyproject/galaxy/commit/5e78c00824b6ba2e97cd46b67113… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- various UX and style improvements Commit: 34689c7629d7c1a2c00afb5d43ca22a62e76b4c9 https://github.com/galaxyproject/galaxy/commit/34689c7629d7c1a2c00afb5d43ca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge branch 'ux-stylechanges' of github.com:jmchilton/galaxy into ux-stylechanges Commit: 909075c67839830207bda14c455139eecaf979b8 https://github.com/galaxyproject/galaxy/commit/909075c67839830207bda14c4551… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - tweak tooltip placement so it doesn't overlap menu. Fixes test cases. Commit: d94cd0a9c20b497e17b7bfe3a5d059513d367e16 https://github.com/galaxyproject/galaxy/commit/d94cd0a9c20b497e17b7bfe3a5d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder Another tweak to fix test cases. Commit: d51812b832dbd1268e6ac76a1c22af05880d4525 https://github.com/galaxyproject/galaxy/commit/d51812b832dbd1268e6ac76a1c22… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/package.json M client/webpack.config.js Log Message: ----------- Merge pull request #5940 from jmchilton/ux-stylechanges More Rule Builder Style Changes Compare: https://github.com/galaxyproject/galaxy/compare/13661adcad91...d51812b832db

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[galaxyproject/galaxy] f6066d: RuleBuilder style fixes - bs4 branch fallout.
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6066d34fa403cf10cabdcaa58e420d6b7cc83b6 https://github.com/galaxyproject/galaxy/commit/f6066d34fa403cf10cabdcaa58e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder style fixes - bs4 branch fallout. Commit: 5bd45837dd3f044e72e8abbe90ea701be4627e80 https://github.com/galaxyproject/galaxy/commit/5bd45837dd3f044e72e8abbe90ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Set a minimum width for column selectors. Commit: 63620ba4007e81799606e91ef0549f32905fe791 https://github.com/galaxyproject/galaxy/commit/63620ba4007e81799606e91ef054… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve styling, validation of Build button in rule upload table. Commit: 20c8260108e3829425cd2b7dfb75ca8ddc1d1356 https://github.com/galaxyproject/galaxy/commit/20c8260108e3829425cd2b7dfb75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Redo footer inputs for rule builder. Gives more space for name and genome - dynamically resizes to space given with some reasonable minimum and maximum widths for widgets. Commit: f2d6a2d6b43ae32ce1302c7b2e0d5e0c9296ef94 https://github.com/galaxyproject/galaxy/commit/f2d6a2d6b43ae32ce1302c7b2e0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix click handler for BS4 changes. Commit: b59ea1633f4ec9724acf133ad8095bf9e8e6c99f https://github.com/galaxyproject/galaxy/commit/b59ea1633f4ec9724acf133ad809… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Proper bootstrap 4 dropdown menus in the RuleBuilder. Commit: 13661adcad91e99a9fc029fab7324194a63db605 https://github.com/galaxyproject/galaxy/commit/13661adcad91e99a9fc029fab732… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5909 from jmchilton/rule_builder_styling Rule builder styling fixes. Compare: https://github.com/galaxyproject/galaxy/compare/c2467f27ae54...13661adcad91

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[galaxyproject/galaxy] 313a0f: check that source before trying to move
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 313a0ff2973c8f528b88013d17761df449fd174b https://github.com/galaxyproject/galaxy/commit/313a0ff2973c8f528b88013d1776… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- check that source before trying to move Commit: aecbdac334a18ff1f82494fc6c0b58de90ad610c https://github.com/galaxyproject/galaxy/commit/aecbdac334a18ff1f82494fc6c0b… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/__init__.py Log Message: ----------- move the dir existance check out of move_merge Commit: c2467f27ae547b05513f011868c0d4a2d456c606 https://github.com/galaxyproject/galaxy/commit/c2467f27ae547b05513f011868c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5922 from abretaud/movemerge Fix error with data managers when trying to move_merge inexistant extra_files dir Compare: https://github.com/galaxyproject/galaxy/compare/33a28b8b8b6d...c2467f27ae54

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[galaxyproject/galaxy] c5e19d: Improves handling of existing k8s jobs on restart, ...
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5e19d4a532be11d695a12d3b3dca42d877057a8 https://github.com/galaxyproject/galaxy/commit/c5e19d4a532be11d695a12d3b3dc… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of existing k8s jobs on restart, and avoids clashes with jobs of previous instances, establishing an optional trust mechanism. Commit: 46b51944c68f65f8da5151ace54d2bcaeed353cd https://github.com/galaxyproject/galaxy/commit/46b51944c68f65f8da5151ace54d… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- PEP style fixes k8s runner. Commit: dc563eae75cc4394aafdeef5ae9cd04213326225 https://github.com/galaxyproject/galaxy/commit/dc563eae75cc4394aafdeef5ae9c… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-04-15 (Sun, 15 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds timeout behaviour for k8s existing job deletion Commit: 33a28b8b8b6d36e7ab972c9f3241ce92bd4fbc2b https://github.com/galaxyproject/galaxy/commit/33a28b8b8b6d36e7ab972c9f3241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #5761 from phnmnl/galaxy-prs/k8s-improves-job-handling-existing-jobs Kubernetes: Improves handling of existing jobs on Galaxy restart. Compare: https://github.com/galaxyproject/galaxy/compare/09fcf13aafb5...33a28b8b8b6d

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[galaxyproject/galaxy] de5ac4: more tolerant sanitizing
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de5ac42fa9672d6bcf1b7e0c958c13adff2dafa8 https://github.com/galaxyproject/galaxy/commit/de5ac42fa9672d6bcf1b7e0c958c… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- more tolerant sanitizing Commit: 16f9e58af5cceb9eb7f969a581bbf66316a99986 https://github.com/galaxyproject/galaxy/commit/16f9e58af5cceb9eb7f969a581bb… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- quotes Commit: bb9963dddce6e1287785ae4452f3883229ed7a6c https://github.com/galaxyproject/galaxy/commit/bb9963dddce6e1287785ae4452f3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- fix quote escaping Commit: 0b191abaf18271b9a51f21a13808e2b74c6cf0b1 https://github.com/galaxyproject/galaxy/commit/0b191abaf18271b9a51f21a13808… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- pass the condition by a json file instead of arg Commit: dc4902353f3254aa962f8efe1ea4e2af5f7499ab https://github.com/galaxyproject/galaxy/commit/dc4902353f3254aa962f8efe1ea4… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.xml Log Message: ----------- add test case for fixed bug Commit: dadb4fcda723ab14421b07cb4b1747aa3e8b325d https://github.com/galaxyproject/galaxy/commit/dadb4fcda723ab14421b07cb4b17… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- change back version Commit: 09fcf13aafb5dd6aa1f3b31446af91c7ca2ea3a6 https://github.com/galaxyproject/galaxy/commit/09fcf13aafb5dd6aa1f3b31446af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #5872 from abretaud/filter_sanitize Filter tool: fix too strict sanitizing Compare: https://github.com/galaxyproject/galaxy/compare/b9fe69fb8b46...09fcf13aafb5

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