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

[galaxyproject/usegalaxy-playbook] 3ec46d: Updated DuNovo to 2.15
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ec46d06eb5b4ea551bc835cd920176ff3a8f974 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ec46d06eb5b4ea5… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Updated DuNovo to 2.15 **NOTE:** This service 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] 78d290: Do not install py2-ipaddress under Python 3
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78d290c9fbf26adc0a4621174502e50047bbd843 https://github.com/galaxyproject/galaxy/commit/78d290c9fbf26adc0a4621174502… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Do not install py2-ipaddress under Python 3 Commit: 662682c14818dfbc52579e96ff4aae4a8e047070 https://github.com/galaxyproject/galaxy/commit/662682c14818dfbc52579e96ff4a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- unicodify bytestrings from uwsgi.opt Fix the 2 following tracebacks: ``` added lib/ to pythonpath. Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 180, in uwsgi_app return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy") File "lib/galaxy/web/framework/webapp.py", line 968, in build_native_uwsgi_app app_kwds = get_app_kwds(config_section) File "lib/galaxy/web/stack/__init__.py", line 434, in get_app_kwds return application_stack_class().get_app_kwds(config_section, app_name=app_name) File "lib/galaxy/web/stack/__init__.py", line 260, in get_app_kwds has_ini_config = has_ini_config or (config_file and has_ext(config_file, "ini", aliases=True, ignore="sample")) File "lib/galaxy/util/path/__init__.py", line 290, in has_ext root, _ext = __splitext_ignore(path, ignore=ignore) File "lib/galaxy/util/path/__init__.py", line 387, in __splitext_ignore root, ext = __splitext_no_sep(path) File "lib/galaxy/util/path/__init__.py", line 381, in __splitext_no_sep return (path.rsplit(extsep, 1) + [''])[0:2] TypeError: a bytes-like object is required, not 'str' unable to load app 0 (mountpoint='') (callable not found or import error) ``` ``` galaxy.queue_worker INFO 2018-06-03 02:12:51,186 [p:2150,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1 Traceback (most recent call last): File "lib/galaxy/web/stack/__init__.py", line 456, in _do_uwsgi_postfork f(*args, **kwargs) File "lib/galaxy/webapps/galaxy/buildapp.py", line 190, in postfork_setup app.application_stack.log_startup() File "lib/galaxy/web/stack/__init__.py", line 351, in log_startup for s in UWSGIApplicationStack._serving_on(): File "lib/galaxy/web/stack/__init__.py", line 237, in _serving_on yield UWSGIApplicationStack._socket_opt_to_str(opt, val) File "lib/galaxy/web/stack/__init__.py", line 208, in _socket_opt_to_str if val.startswith('='): TypeError: startswith first arg must be bytes or a tuple of bytes, not str ``` Commit: e81931cd753e4c85e624d80e3901c97d6064f9e1 https://github.com/galaxyproject/galaxy/commit/e81931cd753e4c85e624d80e3901… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix loading of tools under Python 3 Tools containing a text parameter fail with a traceback like: ``` [pid: 2433|app: 0|req: 15/28] 127.0.0.1 () {42 vars in 905 bytes} [Sun Jun 3 02:24:59 2018] GET /api/tools/addValue/build?version=1.0.0&__identifer=nv6x1qdhzxo&tool_version=1.0.0 => generated 71 bytes in 58 msecs (HTTP/1.1 500) 3 headers in 143 bytes (1 switches on core 1) galaxy.web.framework.decorators ERROR 2018-06-03 02:25:01,999 [p:2433,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 281, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 113, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 1913, in to_json 'state_inputs' : params_to_strings(self.inputs, state_inputs, self.app), File "lib/galaxy/tools/parameters/__init__.py", line 207, in params_to_strings rval[key] = value if nested else str(dumps(value)) File "/usr/lib/python3.5/json/__init__.py", line 230, in dumps return _default_encoder.encode(obj) File "/usr/lib/python3.5/json/encoder.py", line 198, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python3.5/json/encoder.py", line 256, in iterencode return _iterencode(o, 0) File "/usr/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError: b'c1,c2' is not JSON serializable ``` Commit: b08455ecab5fa068b7f8b93fe08c9c552c8c25a0 https://github.com/galaxyproject/galaxy/commit/b08455ecab5fa068b7f8b93fe08c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #6265 from nsoranzo/python3 Python3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/2f6c184e6f5c...b08455ecab5f **NOTE:** This service 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] 825d7f: Allow from_param to reference a child collection
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 825d7f6fa74384d195739fe7ac0bf4e1d5b9c1cf https://github.com/galaxyproject/galaxy/commit/825d7f6fa74384d195739fe7ac0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: 50c98701b7682d8878cbc2fa1acdc3f28abdad0e https://github.com/galaxyproject/galaxy/commit/50c98701b7682d8878cbc2fa1acd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 99889af1d52a263737dca3c7461baa5ce4fe8ad7 https://github.com/galaxyproject/galaxy/commit/99889af1d52a263737dca3c7461b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: f690386f0b88fa4f5f94b83e4dea8c97f60747fd https://github.com/galaxyproject/galaxy/commit/f690386f0b88fa4f5f94b83e4dea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Drop unused COLLECTION_ATTRIBUTES Commit: 2f6c184e6f5c614e36f8100648b1a5f5a8f6ac94 https://github.com/galaxyproject/galaxy/commit/2f6c184e6f5c614e36f8100648b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6253 from mvdbeek/mapping_over_from_param_fixes Mapping over from_param fixes Compare: https://github.com/galaxyproject/galaxy/compare/9cf66df7a7af...2f6c184e6f5c **NOTE:** This service 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] 4c4aa1: Update @erasche's name
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c4aa11ad469a3a66c1bfa03fb6985a9b0033498 https://github.com/galaxyproject/galaxy/commit/4c4aa11ad469a3a66c1bfa03fb69… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update @erasche's name Commit: 73fb6785fd7ddd9cf14d41b1f5496b0a2f9a9563 https://github.com/galaxyproject/galaxy/commit/73fb6785fd7ddd9cf14d41b1f549… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clarify how +1 votes on PRs can be expressed Commit: 9cf66df7a7af0d28b627ad9f24b395a4579cc988 https://github.com/galaxyproject/galaxy/commit/9cf66df7a7af0d28b627ad9f24b3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #6171 from nsoranzo/pr_approval [PROCEDURES] Clarify how +1 votes on PRs can be expressed v.3 Compare: https://github.com/galaxyproject/galaxy/compare/1954c9dc633b...9cf66df7a7af **NOTE:** This service 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] e95052: add sbml datatype
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e950520ab0a5c47296d023d9f20ffbdc55125996 https://github.com/galaxyproject/galaxy/commit/e950520ab0a5c47296d023d9f20f… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- add sbml datatype Commit: 9c17828e9616161a63ea6c7dfd4ebf0fb64bcae9 https://github.com/galaxyproject/galaxy/commit/9c17828e9616161a63ea6c7dfd4e… Author: MONJEAUD Cyril <Cyril.Monjeaud(a)irisa.fr> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- Add edam format Commit: 21aa40addfb21c22dad676aebe041c77cc4ffd92 https://github.com/galaxyproject/galaxy/commit/21aa40addfb21c22dad676aebe04… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add edam data Commit: fcc5b207ab77a29e17ab13d0ba0d38a420ced659 https://github.com/galaxyproject/galaxy/commit/fcc5b207ab77a29e17ab13d0ba0d… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- fix conflicts Commit: e57ff42e2ef8e61dd5d49e7f91a9ecabcd484706 https://github.com/galaxyproject/galaxy/commit/e57ff42e2ef8e61dd5d49e7f91a9… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add blank line Commit: 1954c9dc633bdf72df446a16f7ec2f2150f92e60 https://github.com/galaxyproject/galaxy/commit/1954c9dc633bdf72df446a16f7ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- Merge pull request #6201 from cmonjeau/add_sbml_datatype New datatype: SBML Compare: https://github.com/galaxyproject/galaxy/compare/5ba71f580fc8...1954c9dc633b **NOTE:** This service 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/infrastructure-playbook] 1f3c6d: Add libGL on nodes for PyQt5 conda package
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1f3c6d7f6e442eb8d9015be1048a2f2e49cf7135 https://github.com/galaxyproject/infrastructure-playbook/commit/1f3c6d7f6e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Add libGL on nodes for PyQt5 conda package **NOTE:** This service 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] 30b5e5: Enable dynamic reload of dynamic job rules when co...
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30b5e50ba0079a7dd24d3334cacbde2e4b9c07dc https://github.com/galaxyproject/galaxy/commit/30b5e50ba0079a7dd24d3334cacb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Enable dynamic reload of dynamic job rules when configured, using watchdog notifications. Commit: 91dbeebf5f4ea2fd94586a883616e6fc148940ae https://github.com/galaxyproject/galaxy/commit/91dbeebf5f4ea2fd94586a883616… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Fix non-Galaxy webapp unit tests Commit: 41a601d5375669bfb612b6a98e289fccd4eac8a9 https://github.com/galaxyproject/galaxy/commit/41a601d5375669bfb612b6a98e28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Watch any objects in job rule directories that are not python bytecode, rather than only watching python source. Commit: 8bd856da5120eb15053e1d32f1964aaa851626ad https://github.com/galaxyproject/galaxy/commit/8bd856da5120eb15053e1d32f196… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Ignore change events for dot files. This could be configurable if it's needed but I can't imagine when it would be. Prevents reloading on vim swapfile writes. Commit: 73ea1189e9fae103e367955fc62916e497074b38 https://github.com/galaxyproject/galaxy/commit/73ea1189e9fae103e367955fc629… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Avoid using builtins for variable names. file->file_path, dir->dir_path in generic watcher functions Commit: 1652c4221eacfac2a04955ee6fd4004c84f97ae6 https://github.com/galaxyproject/galaxy/commit/1652c4221eacfac2a04955ee6fd4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Merge pull request #8 from dannon/dynamic-rule-dynamic-reload Avoid using builtins for variable names. Commit: 5ba71f580fc861be9c924991a762f0917811b720 https://github.com/galaxyproject/galaxy/commit/5ba71f580fc861be9c924991a762… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload Enable automatic reload of dynamic job rules on change Compare: https://github.com/galaxyproject/galaxy/compare/a5594551c092...5ba71f580fc8 **NOTE:** This service 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] ba5e54: Enable cgroup metric on main
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ba5e549e1d61e9730825daea40aecbf701101e05 https://github.com/galaxyproject/usegalaxy-playbook/commit/ba5e549e1d61e973… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M env/main/files/galaxy/config/job_metrics_conf.xml Log Message: ----------- Enable cgroup metric on main **NOTE:** This service 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] c1614b: Pause jobs with invalid inputs
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1614be1ef5abaab241bf9739fb99390a8954343 https://github.com/galaxyproject/galaxy/commit/c1614be1ef5abaab241bf9739fb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Pause jobs with invalid inputs Otherwise these jobs may hang around forever/until the admin does a cleanup. This is probably preferable for users as well, as the pause message gives a hint of why their job didn't start running. Fixes https://github.com/galaxyproject/galaxy/issues/6022 and would minimize maintenance as outlined in https://github.com/galaxyproject/galaxy/issues/5944. I'm working on tests, but one easy way to test this is create a collection through the list builder interface, then delete the source HDAs. Then run a workflow on the collection and without this commit the outputs get created but the job just hangs around indefinetely. With the PR the steps consuming the collection and the subsequent jobs will be paused. Set to paused Commit: 0e31f97269586b061ce58a9eac75743590e310a3 https://github.com/galaxyproject/galaxy/commit/0e31f97269586b061ce58a9eac75… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add a testcase for pausing jobs with deleted input Fix test Commit: ed0b087926c53f4c2c4293ff6443f997fafa9526 https://github.com/galaxyproject/galaxy/commit/ed0b087926c53f4c2c4293ff6443… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Fail jobs with purged inputs We can't resume these jobs anyway, so better to set them to failed. Also resets the info field for datasets produced by resumed jobs. Commit: f9a65a10eb10fd2942ca3306b461ba7dbae4aa09 https://github.com/galaxyproject/galaxy/commit/f9a65a10eb10fd2942ca3306b461… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Display the info field for paused jobs Commit: f8cc653b3051b93cea446317194fcdd88d1aa674 https://github.com/galaxyproject/galaxy/commit/f8cc653b3051b93cea446317194f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M test/api/test_workflows.py Log Message: ----------- Pause job if input dataset state is paused Commit: ca31222cf87a471648876575f068f4e5ac3cba92 https://github.com/galaxyproject/galaxy/commit/ca31222cf87a471648876575f068… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Optimize job resume function Commit: c401f5a713c1774e2dd8d817de04d48e2864e40f https://github.com/galaxyproject/galaxy/commit/c401f5a713c1774e2dd8d817de04… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Use info style when displaying the reason for pausing a dataset Commit: a5594551c09250db0dac799711a0d5676817038c https://github.com/galaxyproject/galaxy/commit/a5594551c09250db0dac799711a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6036 from mvdbeek/kill_jobs_with_invalid_input Pause jobs with invalid inputs Compare: https://github.com/galaxyproject/galaxy/compare/f19f09b30f60...a5594551c092 **NOTE:** This service 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] bac416: Rename disabled flag for consistency with existing...
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bac4169d178eeace51cfdf62d979f8a14ce04101 https://github.com/galaxyproject/galaxy/commit/bac4169d178eeace51cfdf62d979… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Rename disabled flag for consistency with existing naming Commit: 5ae57e28667524086595483ff04674b010d067b1 https://github.com/galaxyproject/galaxy/commit/5ae57e28667524086595483ff046… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Use new collapsible flag in rules editor Commit: fb6dbb27026abfa8832dc821633214882e8ee6e9 https://github.com/galaxyproject/galaxy/commit/fb6dbb27026abfa8832dc8216332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse unmodified options Commit: 292a2096424a207a943457d00bf6540fc84e6a3d https://github.com/galaxyproject/galaxy/commit/292a2096424a207a943457d00bf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js Log Message: ----------- Remove input specific options handling, unify input update mechanism Commit: d0187ac206219c0fb0cb4767f6c1b5d0dcc68e1f https://github.com/galaxyproject/galaxy/commit/d0187ac206219c0fb0cb4767f6c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js Log Message: ----------- Adjust update handler for list inputs Commit: f3ccf42cab1cca514d4e8e159b4b1338090beaea https://github.com/galaxyproject/galaxy/commit/f3ccf42cab1cca514d4e8e159b4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Adjust handling in text select field Commit: 94220c0ac1c0c2273213355343b7164832d31a1a https://github.com/galaxyproject/galaxy/commit/94220c0ac1c0c2273213355343b7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Adjust update caller in rules editor Commit: c8afba470be865acc96af1d532876b580e1739a6 https://github.com/galaxyproject/galaxy/commit/c8afba470be865acc96af1d53287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Move options handling into selection fields Commit: 3df2a94dbd9d37c99bde75ef637866683a231618 https://github.com/galaxyproject/galaxy/commit/3df2a94dbd9d37c99bde75ef6378… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Fix library dataset selector Commit: 0bad91c59295626bd577662ac2c80f16868a6a6b https://github.com/galaxyproject/galaxy/commit/0bad91c59295626bd577662ac2c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse data as is to select field Commit: 0022615418af51ea6d8b1b00a12855ad4191177c https://github.com/galaxyproject/galaxy/commit/0022615418af51ea6d8b1b00a128… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Handle alternative option formatting in text select wrapper Commit: cb98bb23f3121708efa8d948b5e3e39426f2b773 https://github.com/galaxyproject/galaxy/commit/cb98bb23f3121708efa8d948b5e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js Log Message: ----------- Adjust drilldown handler Commit: 5c65012f9c2e41b328483fc28b685ae736cc500a https://github.com/galaxyproject/galaxy/commit/5c65012f9c2e41b328483fc28b68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix list parameter style Commit: f19f09b30f607c3af922fcba16ebe0ab95996d2f https://github.com/galaxyproject/galaxy/commit/f19f09b30f607c3af922fcba16eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6248 from guerler/form_fix Align input element update mechanism Compare: https://github.com/galaxyproject/galaxy/compare/53d2664b0b7b...f19f09b30f60 **NOTE:** This service 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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