- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ce3d43: More Prs for the release notes.
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: ce3d43221a8d4e843a25c49c679a4ab75fd3756c https://github.com/galaxyproject/galaxy/commit/ce3d43221a8d4e843a25c49c679a… 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: ----------- More Prs for the release notes. **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] b7187f: Don't delete referenced Datasets when purging user...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b7187f0e62e172dd7d2db1bbd51f9c3f9a5058c5 https://github.com/galaxyproject/galaxy/commit/b7187f0e62e172dd7d2db1bbd51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Don't delete referenced Datasets when purging users. Commit: f6a5cae8e1af10003e3553cb27b2512977bc0c8e https://github.com/galaxyproject/galaxy/commit/f6a5cae8e1af10003e3553cb27b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #6809 from natefoo/purge-user-fix [18.05] Don't delete referenced Datasets when purging users Compare: https://github.com/galaxyproject/galaxy/compare/2aad3b2ced20...f6a5cae8e1af **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/usegalaxy-playbook] 8f60b3: Update Test
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f60b33abe9beae37c6f715713bb8238302570b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/8f60b33abe9beae3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 30fabb77ea09ec00fc132f09b171906c8a28f878 https://github.com/galaxyproject/usegalaxy-playbook/commit/30fabb77ea09ec00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/46388a8c46a4...… **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] 546459: Wrap onclick functions with a tooltip de-tipper fo...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 546459f3536ca7b1504550794e8d1d77e68985d0 https://github.com/galaxyproject/galaxy/commit/546459f3536ca7b1504550794e8d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Wrap onclick functions with a tooltip de-tipper for faIconButtons. Commit: 35b72ff508a860ed297780345d213c9155f014aa https://github.com/galaxyproject/galaxy/commit/35b72ff508a860ed297780345d21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Remove now-unnecessary tooltip dispose Commit: 3146c57b310fedc525aa6a5b8ab87d8bacf2784d https://github.com/galaxyproject/galaxy/commit/3146c57b310fedc525aa6a5b8ab8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Blur buttons onclick Commit: 7c290b1743b03c1eb1711df8218f5733a8f791c8 https://github.com/galaxyproject/galaxy/commit/7c290b1743b03c1eb1711df8218f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Set a reasonable nearby focus instead of blur, to prevent tabindex loss. Commit: 34d54558b3dc40d54a507128b8a45b691151f863 https://github.com/galaxyproject/galaxy/commit/34d54558b3dc40d54a507128b8a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Simplify wrapping logic, fix context. Commit: 7320752138dc186b96f53746b1811dcc2c212dc1 https://github.com/galaxyproject/galaxy/commit/7320752138dc186b96f53746b181… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Client formatting. Commit: fd6af5eb0e0ba79679f8395d9333cf3e7331ba05 https://github.com/galaxyproject/galaxy/commit/fd6af5eb0e0ba79679f8395d9333… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- No memory leaks here Commit: 74d82096d8eef3cbd05b52cf956d0dc654d05533 https://github.com/galaxyproject/galaxy/commit/74d82096d8eef3cbd05b52cf956d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Merge pull request #6745 from dannon/more-generic-tooltip-handling-for-fa-buttons [18.09] Generic tooltip hide for onclick faIconButtons Compare: https://github.com/galaxyproject/galaxy/compare/1a3e9ae17327...74d82096d8ee **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/usegalaxy-playbook] c7efaf: Manage static content on Pulsar servers with a loc...
by GitHub 01 Oct '18

01 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c7efaf25968e96096369eb073d7e476d815ea423 https://github.com/galaxyproject/usegalaxy-playbook/commit/c7efaf25968e9609… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/common/group_vars/pulsargalaxyservers.yml M env/common/update.yml Log Message: ----------- Manage static content on Pulsar servers with a local copy of Galaxy. They get a default config but it's needed for the conditional wheels step Commit: b4f0da6f91e4a159292e18ea5ed1d1593719ae70 https://github.com/galaxyproject/usegalaxy-playbook/commit/b4f0da6f91e4a159… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M CHANGELOG.md M env/common/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Bridges Conda fixes Commit: 46388a8c46a45c81ecb91e8fcb7c2cdf1d58be96 https://github.com/galaxyproject/usegalaxy-playbook/commit/46388a8c46a45c81… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 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: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ce796e2bf4be...… **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/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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