October 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 702870: Allow starting Galaxy under gunicorn when using ga...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 702870c17c9f27707db3c2f003356fe1b52529e0 https://github.com/galaxyproject/galaxy/commit/702870c17c9f27707db3c2f00335… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Allow starting Galaxy under gunicorn when using galaxy.ini and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`. Additional gunicorn cmdline arguments can be passed using `GUNICORN_CMD_ARGS`. In a first pass this will allow running planemo {server, test} under python 3, as Paste has some problems under python 3: ``` galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration ``` That said gunicorn is a nice pure-python alternative to paste going forward. Commit: 9f1e78d92f96499bc8409d7f5f1cfe0a652a1b92 https://github.com/galaxyproject/galaxy/commit/9f1e78d92f96499bc8409d7f5f1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Drop gulp plugin staging task from default (probably temporarily?), since it's all done in python at server start now. Commit: b64c82921e02d3be5de21a8a971c44279650399c https://github.com/galaxyproject/galaxy/commit/b64c82921e02d3be5de21a8a971c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Need quotes around export? Commit: 7622d128094d16775c8eb426b6debace070193ad https://github.com/galaxyproject/galaxy/commit/7622d128094d16775c8eb426b6de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Merge pull request #6808 from dannon/no_plugin_staging_gulp [18.09] Drop gulp plugin staging task from default tasks Commit: 176364ac80130ca439006c4b75fd393ac850681b https://github.com/galaxyproject/galaxy/commit/176364ac80130ca439006c4b75fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Move gunicorn to dev-requirements Commit: 1a3e9ae17327f3d77fc6f64ec85c4165d4c680ef https://github.com/galaxyproject/galaxy/commit/1a3e9ae17327f3d77fc6f64ec85c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support [18.09] Allow starting Galaxy under gunicorn when using galaxy.ini Commit: 260e37f2bc317a4dc8685b84da5a831d6c4c164a https://github.com/galaxyproject/galaxy/commit/260e37f2bc317a4dc8685b84da5a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/gulpfile.js M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/55c90960e9a6...260e37f2bc31 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 702870: Allow starting Galaxy under gunicorn when using ga...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 702870c17c9f27707db3c2f003356fe1b52529e0 https://github.com/galaxyproject/galaxy/commit/702870c17c9f27707db3c2f00335… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Allow starting Galaxy under gunicorn when using galaxy.ini and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`. Additional gunicorn cmdline arguments can be passed using `GUNICORN_CMD_ARGS`. In a first pass this will allow running planemo {server, test} under python 3, as Paste has some problems under python 3: ``` galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration ``` That said gunicorn is a nice pure-python alternative to paste going forward. Commit: b64c82921e02d3be5de21a8a971c44279650399c https://github.com/galaxyproject/galaxy/commit/b64c82921e02d3be5de21a8a971c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Need quotes around export? Commit: 176364ac80130ca439006c4b75fd393ac850681b https://github.com/galaxyproject/galaxy/commit/176364ac80130ca439006c4b75fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Move gunicorn to dev-requirements Commit: 1a3e9ae17327f3d77fc6f64ec85c4165d4c680ef https://github.com/galaxyproject/galaxy/commit/1a3e9ae17327f3d77fc6f64ec85c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support [18.09] Allow starting Galaxy under gunicorn when using galaxy.ini Compare: https://github.com/galaxyproject/galaxy/compare/7622d128094d...1a3e9ae17327 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9f1e78: Drop gulp plugin staging task from default (probab...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9f1e78d92f96499bc8409d7f5f1cfe0a652a1b92 https://github.com/galaxyproject/galaxy/commit/9f1e78d92f96499bc8409d7f5f1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Drop gulp plugin staging task from default (probably temporarily?), since it's all done in python at server start now. Commit: 7622d128094d16775c8eb426b6debace070193ad https://github.com/galaxyproject/galaxy/commit/7622d128094d16775c8eb426b6de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Merge pull request #6808 from dannon/no_plugin_staging_gulp [18.09] Drop gulp plugin staging task from default tasks Compare: https://github.com/galaxyproject/galaxy/compare/87463f4be633...7622d128094d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 106fb7: Drop incorrect flex designation for panel inner; t...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 106fb79c8b7bd8d2faa69f9bd007efe504183012 https://github.com/galaxyproject/galaxy/commit/106fb79c8b7bd8d2faa69f9bd007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Drop incorrect flex designation for panel inner; these are generally single line styles with floats. Fixes header for "Published History" view, etc. Commit: 71df0e44652fca8755869248935dc2bdeba39208 https://github.com/galaxyproject/galaxy/commit/71df0e44652fca8755869248935d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- New integrity hashes for yarn? Typo, artifacts (which will be gone soon!) Commit: d0b6bc6ddc7391527e98a4ece4e33396229c2d25 https://github.com/galaxyproject/galaxy/commit/d0b6bc6ddc7391527e98a4ece4e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- panel-body will always be full height Commit: ab660686c26241ec4959711603919b80442d32a0 https://github.com/galaxyproject/galaxy/commit/ab660686c26241ec495971160391… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for single and multi-input identifiers test_identifier_map_over_input_in_conditional fails at the moment (same issue as in https://github.com/galaxyproject/galaxy/issues/6182) Commit: 73f8f3129b07cbe96c10da161a547bf2008706e2 https://github.com/galaxyproject/galaxy/commit/73f8f3129b07cbe96c10da161a54… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/tools/parameters/wrapped.py Log Message: ----------- Partially fix missing element identifier This makes sure that any toplevel `|__identifier__` is passed on to nested inputs. Commit: f8d9a9e33a994a97c537ef15f1993fbe5d5866ea https://github.com/galaxyproject/galaxy/commit/f8d9a9e33a994a97c537ef15f199… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to recover wrapper datasets Otherwise we create new wrappers that lack the element identifier. Commit: c6d915b8f2d470517dfa6504fa635c69cc546b64 https://github.com/galaxyproject/galaxy/commit/c6d915b8f2d470517dfa6504fa63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Parse length to integer When using the little up/down button we get strings instead of integers, and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800 Commit: 2d78dbb9ec1d4d1ba7240d384b27bb6bb83c24b5 https://github.com/galaxyproject/galaxy/commit/2d78dbb9ec1d4d1ba7240d384b27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Build client Commit: 565f611389e434b6df57d39ad5c01ae037e46e76 https://github.com/galaxyproject/galaxy/commit/565f611389e434b6df57d39ad5c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix remaining selenium py3 erorrs Commit: 2e7adfbee4835f1374dffe7ba49760cfc19fdb0e https://github.com/galaxyproject/galaxy/commit/2e7adfbee4835f1374dffe7ba497… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Cast to bytestring in md5 function Commit: a47887639d50b2e5da55d9121b8d8e55509a9cd3 https://github.com/galaxyproject/galaxy/commit/a47887639d50b2e5da55d9121b8d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/web/framework/helpers/__init__.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #6803 from mvdbeek/finish_py3_selenium [18.09] Fix remaining selenium py3 errors Commit: e226edc5ade76dd0ec2e3d8db2e799567e8c11d7 https://github.com/galaxyproject/galaxy/commit/e226edc5ade76dd0ec2e3d8db2e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/util/__init__.py M test/api/test_tools.py A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6798 from mvdbeek/fix_element_identifier_for_non_multiple_true_mapover_in_conditionals [18.09] Fix element identifier for non multiple true mapover in conditionals Commit: d3ab953be3c553cfd71347322538c3adab6d7515 https://github.com/galaxyproject/galaxy/commit/d3ab953be3c553cfd71347322538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/scss/base.scss M client/yarn.lock M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6791 from dannon/flex-style-fixes [18.09] Flex-related style fixes Commit: 2aad3b2ced20189ab4e500bd501797a876089ee9 https://github.com/galaxyproject/galaxy/commit/2aad3b2ced20189ab4e500bd5017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6802 from mvdbeek/fix_int_parsing_rules [18.05] Cast rule.length to int when parsing rules Commit: 87463f4be6334849b0e121bd534fada090aeb1d8 https://github.com/galaxyproject/galaxy/commit/87463f4be6334849b0e121bd534f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 55c90960e9a69e8576489ffffba7a0c482748c60 https://github.com/galaxyproject/galaxy/commit/55c90960e9a69e8576489ffffba7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/style/scss/base.scss M client/yarn.lock M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/helpers/__init__.py M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/test_tools.py A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4c0a20853c61...55c90960e9a6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c6d915: Parse length to integer
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c6d915b8f2d470517dfa6504fa635c69cc546b64 https://github.com/galaxyproject/galaxy/commit/c6d915b8f2d470517dfa6504fa63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Parse length to integer When using the little up/down button we get strings instead of integers, and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800 Commit: 2d78dbb9ec1d4d1ba7240d384b27bb6bb83c24b5 https://github.com/galaxyproject/galaxy/commit/2d78dbb9ec1d4d1ba7240d384b27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Build client Commit: 2aad3b2ced20189ab4e500bd501797a876089ee9 https://github.com/galaxyproject/galaxy/commit/2aad3b2ced20189ab4e500bd5017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6802 from mvdbeek/fix_int_parsing_rules [18.05] Cast rule.length to int when parsing rules Commit: 87463f4be6334849b0e121bd534fada090aeb1d8 https://github.com/galaxyproject/galaxy/commit/87463f4be6334849b0e121bd534f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/d3ab953be3c5...87463f4be633 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c6d915: Parse length to integer
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c6d915b8f2d470517dfa6504fa635c69cc546b64 https://github.com/galaxyproject/galaxy/commit/c6d915b8f2d470517dfa6504fa63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Parse length to integer When using the little up/down button we get strings instead of integers, and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800 Commit: 2d78dbb9ec1d4d1ba7240d384b27bb6bb83c24b5 https://github.com/galaxyproject/galaxy/commit/2d78dbb9ec1d4d1ba7240d384b27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Build client Commit: 2aad3b2ced20189ab4e500bd501797a876089ee9 https://github.com/galaxyproject/galaxy/commit/2aad3b2ced20189ab4e500bd5017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6802 from mvdbeek/fix_int_parsing_rules [18.05] Cast rule.length to int when parsing rules Compare: https://github.com/galaxyproject/galaxy/compare/de794dd9051b...2aad3b2ced20 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 3d772d: Add 6791
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 3d772dc03bf0ffa1c6d010596488c5cd3a26901d https://github.com/galaxyproject/galaxy/commit/3d772dc03bf0ffa1c6d010596488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6791 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] b5201e: Revise usage of styles for structured history view
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5201ebbd696f95b5fb32f8e11db09d2fad22e7b https://github.com/galaxyproject/galaxy/commit/b5201ebbd696f95b5fb32f8e11db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M lib/galaxy/util/create_history_template.py M static/style/blue/base.css Log Message: ----------- Revise usage of styles for structured history view Commit: 12c6475c61d4fa4b2d0fb02f398a77d868c6e845 https://github.com/galaxyproject/galaxy/commit/12c6475c61d4fa4b2d0fb02f398a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/admin/BaseGrid.vue Log Message: ----------- Use card instead of legacy tool form style for admin tables Commit: 4c0a20853c614134b7574d75df836e4ef15d4a71 https://github.com/galaxyproject/galaxy/commit/4c0a20853c614134b7574d75df83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M lib/galaxy/util/create_history_template.py M static/style/blue/base.css Log Message: ----------- Merge pull request #6790 from guerler/toolform_style Remove legacy tool form styles from structure history view and admin tables Compare: https://github.com/galaxyproject/galaxy/compare/7b9a21403ca1...4c0a20853c61 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 106fb7: Drop incorrect flex designation for panel inner; t...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 106fb79c8b7bd8d2faa69f9bd007efe504183012 https://github.com/galaxyproject/galaxy/commit/106fb79c8b7bd8d2faa69f9bd007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Drop incorrect flex designation for panel inner; these are generally single line styles with floats. Fixes header for "Published History" view, etc. Commit: 71df0e44652fca8755869248935dc2bdeba39208 https://github.com/galaxyproject/galaxy/commit/71df0e44652fca8755869248935d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- New integrity hashes for yarn? Typo, artifacts (which will be gone soon!) Commit: d0b6bc6ddc7391527e98a4ece4e33396229c2d25 https://github.com/galaxyproject/galaxy/commit/d0b6bc6ddc7391527e98a4ece4e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- panel-body will always be full height Commit: d3ab953be3c553cfd71347322538c3adab6d7515 https://github.com/galaxyproject/galaxy/commit/d3ab953be3c553cfd71347322538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/scss/base.scss M client/yarn.lock M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6791 from dannon/flex-style-fixes [18.09] Flex-related style fixes Compare: https://github.com/galaxyproject/galaxy/compare/e226edc5ade7...d3ab953be3c5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ebcad5: First untested attempt at CLI plugin for LSF
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebcad566da836dd1e3c7c7362a022688cb352ac8 https://github.com/galaxyproject/galaxy/commit/ebcad566da836dd1e3c7c7362a02… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: A lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- First untested attempt at CLI plugin for LSF Commit: d70fa8171aa67878f3fac6b23360d018e42bfc1a https://github.com/galaxyproject/galaxy/commit/d70fa8171aa67878f3fac6b23360… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Example for LSF CLI Plugin for job_conf advanced. Commit: d6ea1509bfba4c544af9d43ef849a7576623929f https://github.com/galaxyproject/galaxy/commit/d6ea1509bfba4c544af9d43ef849… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- More job states Commit: 346ac61dbb683d6609dd3eb5688333302f33f390 https://github.com/galaxyproject/galaxy/commit/346ac61dbb683d6609dd3eb56883… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Nasty parsing required for bsub outputs given CLI expectations. Commit: b1a08ba128cca7f688d21a11fe7502c741e72641 https://github.com/galaxyproject/galaxy/commit/b1a08ba128cca7f688d21a11fe75… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Simplifies status parsing and avoids handling headers that are not there. Commit: ae1695b4c76b102a3a043c1d4dcdb70a0ba30f7e https://github.com/galaxyproject/galaxy/commit/ae1695b4c76b102a3a043c1d4dcd… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Switches memory with argmap mapping Commit: e4b28fe7ef7958d0ff1eb44c3dd417e022d3c4db https://github.com/galaxyproject/galaxy/commit/e4b28fe7ef7958d0ff1eb44c3dd4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- bkill instead of bstop for deleting jobs Commit: 33115f66ebfc92467b0f55fe5e2ca6a0604616a7 https://github.com/galaxyproject/galaxy/commit/33115f66ebfc92467b0f55fe5e2c… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Returns OK when not found. Commit: f09f333766900e4d571d77d0aa4b6213db1e82f3 https://github.com/galaxyproject/galaxy/commit/f09f333766900e4d571d77d0aa4b… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Offending white spaces for PEP Commit: b75b36efa9b454b6e785798431ae708d0b14fa75 https://github.com/galaxyproject/galaxy/commit/b75b36efa9b454b6e785798431ae… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- s/id/job_id/ in parse_status to avoid masking Commit: 7b9a21403ca1714b86e5d4d131a7ecdef9de3aa2 https://github.com/galaxyproject/galaxy/commit/7b9a21403ca1714b86e5d4d131a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Merge pull request #6788 from pcm32/feature/lsf-cli-plugin CLI plugin for LSF Compare: https://github.com/galaxyproject/galaxy/compare/4d915044b2fb...7b9a21403ca1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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