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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/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.

1 0

[galaxyproject/galaxy] 96d77b: More PRs, stub out proposed features.
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 96d77b0791592b35fb6e4201d011f5c223060cfe https://github.com/galaxyproject/galaxy/commit/96d77b0791592b35fb6e4201d011… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- More PRs, stub out proposed features. **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] ab6606: Add test for single and multi-input identifiers
by GitHub 30 Sep '18

30 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/a47887639d50...e226edc5ade7 **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] 565f61: Fix remaining selenium py3 erorrs
by GitHub 30 Sep '18

30 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/f0131eff8b0c...a47887639d50 **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] 364e7e: Update name of Workflow when updating StoredWorkfl...
by GitHub 29 Sep '18

29 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 364e7e1f1fc54565982cea2fa47062b610d7b5ae https://github.com/galaxyproject/galaxy/commit/364e7e1f1fc54565982cea2fa470… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Update name of Workflow when updating StoredWorkflow name Fixes https://github.com/galaxyproject/galaxy/issues/6773. Commit: 5bc3b2e16c315b97b18e794e4338f22ffd964dbf https://github.com/galaxyproject/galaxy/commit/5bc3b2e16c315b97b18e794e4338… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Provide a useful exception message for object store exceptions. Commit: a29c1e47a79a7e2f8dd1924ca4e79b27fea60a97 https://github.com/galaxyproject/galaxy/commit/a29c1e47a79a7e2f8dd1924ca4e7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #6799 from natefoo/better-object-store-logging [18.09] Provide a useful exception message for object store exceptions Commit: de794dd9051b5b9788cd6db7db81ccbe62eec4fa https://github.com/galaxyproject/galaxy/commit/de794dd9051b5b9788cd6db7db81… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6774 from mvdbeek/fix_old_wf_name [18.05] Update name of Workflow when updating StoredWorkflow name Commit: f0131eff8b0c8886135fc4f9854e0060352a0e6e https://github.com/galaxyproject/galaxy/commit/f0131eff8b0c8886135fc4f9854e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 4d915044b2fb9ab6d61a08636156a5b0aa96bdc4 https://github.com/galaxyproject/galaxy/commit/4d915044b2fb9ab6d61a08636156… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/95230337bc41...4d915044b2fb **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] 364e7e: Update name of Workflow when updating StoredWorkfl...
by GitHub 29 Sep '18

29 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 364e7e1f1fc54565982cea2fa47062b610d7b5ae https://github.com/galaxyproject/galaxy/commit/364e7e1f1fc54565982cea2fa470… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Update name of Workflow when updating StoredWorkflow name Fixes https://github.com/galaxyproject/galaxy/issues/6773. Commit: de794dd9051b5b9788cd6db7db81ccbe62eec4fa https://github.com/galaxyproject/galaxy/commit/de794dd9051b5b9788cd6db7db81… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6774 from mvdbeek/fix_old_wf_name [18.05] Update name of Workflow when updating StoredWorkflow name Commit: f0131eff8b0c8886135fc4f9854e0060352a0e6e https://github.com/galaxyproject/galaxy/commit/f0131eff8b0c8886135fc4f9854e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/a29c1e47a79a...f0131eff8b0c **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] 364e7e: Update name of Workflow when updating StoredWorkfl...
by GitHub 29 Sep '18

29 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 364e7e1f1fc54565982cea2fa47062b610d7b5ae https://github.com/galaxyproject/galaxy/commit/364e7e1f1fc54565982cea2fa470… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Update name of Workflow when updating StoredWorkflow name Fixes https://github.com/galaxyproject/galaxy/issues/6773. Commit: de794dd9051b5b9788cd6db7db81ccbe62eec4fa https://github.com/galaxyproject/galaxy/commit/de794dd9051b5b9788cd6db7db81… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6774 from mvdbeek/fix_old_wf_name [18.05] Update name of Workflow when updating StoredWorkflow name Compare: https://github.com/galaxyproject/galaxy/compare/9bc37c03b657...de794dd9051b **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] 8dbf14: Add a pgcleanup action to purge HDAs of purged his...
by GitHub 29 Sep '18

29 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dbf140ccea8b951edff2b0c42bc5dfbe0df2715 https://github.com/galaxyproject/galaxy/commit/8dbf140ccea8b951edff2b0c42bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Add a pgcleanup action to purge HDAs of purged histories Commit: 95230337bc41b740027382ec531e0c775b8ac140 https://github.com/galaxyproject/galaxy/commit/95230337bc41b740027382ec531e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6801 from natefoo/pgcleanup-unpurged-hdas Add a pgcleanup action to purge HDAs of purged histories Compare: https://github.com/galaxyproject/galaxy/compare/ad76a0d57f17...95230337bc41 **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] 5bc3b2: Provide a useful exception message for object stor...
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5bc3b2e16c315b97b18e794e4338f22ffd964dbf https://github.com/galaxyproject/galaxy/commit/5bc3b2e16c315b97b18e794e4338… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Provide a useful exception message for object store exceptions. Commit: a29c1e47a79a7e2f8dd1924ca4e79b27fea60a97 https://github.com/galaxyproject/galaxy/commit/a29c1e47a79a7e2f8dd1924ca4e7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #6799 from natefoo/better-object-store-logging [18.09] Provide a useful exception message for object store exceptions Compare: https://github.com/galaxyproject/galaxy/compare/1e7677c3b2d7...a29c1e47a79a **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/usegalaxy-playbook] ce796e: Added From Peaks To Genese slide.
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ce796e2bf4be3bdcbeef57bc2baebad300e289b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce796e2bf4be3bdc… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: A env/common/files/galaxy/static/welcome_img/peaks-to-genes-300.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Added From Peaks To Genese slide. **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] 0743c7: All extracted datasets should be visible
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493 https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- All extracted datasets should be visible Commit: bf0370c1929def91bc69e1ab252dc0e8bfc2a387 https://github.com/galaxyproject/galaxy/commit/bf0370c1929def91bc69e1ab252d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix __encode_invocation signature and passthrough to manager that I busted in merging 18.05 forward Commit: da3b6a1566dc0bb2665b2781cdb3c76551d68613 https://github.com/galaxyproject/galaxy/commit/da3b6a1566dc0bb2665b2781cdb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- encode_invocation defers to manager and doesn't require trans passing anymore Commit: becb922dc1e8c2d48e03a2badcb940ab1661e247 https://github.com/galaxyproject/galaxy/commit/becb922dc1e8c2d48e03a2badcb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Strip all control characters from rules Similar to 366701cfb23d8de31eac3c4312c6accca2e74ef1, which is valid on its own, but here we just apply it to all rules. Commit: b44379c3d9da4b7916b3c5a4fdf5eff39ee2267d https://github.com/galaxyproject/galaxy/commit/b44379c3d9da4b7916b3c5a4fdf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6780 from mvdbeek/visible_extracted_datasets [18.09] All extracted datasets should be visible Commit: f54cba043354aa8fac339052462f7302613ca24a https://github.com/galaxyproject/galaxy/commit/f54cba043354aa8fac339052462f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge [18.09] Fix __encode_invocation signature Commit: 53b062f804c6d495b187656c84597f953210a2b0 https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Add bam upload test `test_upload_bam_file` fails on release_18.09 but passes on 18.05. Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata spontaneuosly reverting Similar to https://github.com/galaxyproject/galaxy/pull/6631/files. This fixes https://github.com/galaxyproject/galaxy/issues/6769 Commit: c5a325d01535d9b46e28165c531a119d5f51b2d6 https://github.com/galaxyproject/galaxy/commit/c5a325d01535d9b46e28165c531a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Merge pull request #6785 from mvdbeek/escape_all_rules [18.09] Strip all control characters from rules Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6 https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- allow making all datasets within history public, when sharing this is a one-off operation so notable behavior is that if you create a new dataset in the shared history, it still won't be public when there are default permissions set on history Commit: 70e325574cb82be62b1be8090e714ce44441686b https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use with statement for all file uploads Commit: e4399021520440a8f58e33dbae161f031f8da9eb https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/web/base/controller.py Log Message: ----------- show warning to user if some of the items within were not published Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664 https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6789 from mvdbeek/fix_bam_upload [18.09] Fix bam upload resulting in 'auto' datatype Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6793 from martenson/fix-sharing-by-link [18.09] allow making all datasets within history public, when sharing Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: ac46d21ece75c4fce57836758f566eda8c878166 https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 9bc37c03b6572072bffabc797ea44f7816890103 https://github.com/galaxyproject/galaxy/commit/9bc37c03b6572072bffabc797ea4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 1e7677c3b2d7a5063a7340255140c3c8aa42129a https://github.com/galaxyproject/galaxy/commit/1e7677c3b2d7a5063a7340255140… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: ad76a0d57f1740d512826ad0749244af361fade1 https://github.com/galaxyproject/galaxy/commit/ad76a0d57f1740d512826ad07492… 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 lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/root.py M test/api/test_tools_upload.py A test/unit/test_utils.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3cd71b4864d2...ad76a0d57f17 **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] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: ac46d21ece75c4fce57836758f566eda8c878166 https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 9bc37c03b6572072bffabc797ea44f7816890103 https://github.com/galaxyproject/galaxy/commit/9bc37c03b6572072bffabc797ea4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 1e7677c3b2d7a5063a7340255140c3c8aa42129a https://github.com/galaxyproject/galaxy/commit/1e7677c3b2d7a5063a7340255140… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/29a3b6bbfbde...1e7677c3b2d7 **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] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: ac46d21ece75c4fce57836758f566eda8c878166 https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 9bc37c03b6572072bffabc797ea44f7816890103 https://github.com/galaxyproject/galaxy/commit/9bc37c03b6572072bffabc797ea4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/cf62a1dafd90...9bc37c03b657 **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] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: ac46d21ece75c4fce57836758f566eda8c878166 https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/71b561512db9...ac46d21ece75 **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] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/e25b086dc13e...40cecf6ff421 **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] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/d80e60ce74aa...c4150d200214 **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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