Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a3e28db774a51197e7000b0cb493a5741b24474 https://github.com/galaxyproject/galaxy/commit/5a3e28db774a51197e7000b0cb493... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Better encapsulation when queueing jobs. No need for the runner to know all these internals of the JobWrapper when it is just taking attributes on the job or job wrapper and calling job wrapper methods with them. Provides nice symmetry between queue/finish now also. Commit: 1b5dff11a738c8d01b457dedda80e5f533ad1127 https://github.com/galaxyproject/galaxy/commit/1b5dff11a738c8d01b457dedda80e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Setup objectstore for datasets in job handler instead of web thread. This is good for a few reasons * It speeds up the bottleneck that is the job creation code in the web thread (the job handler is much easier to parallelize). Skipping the flush for all those datasets and skipping the disk write per dataset should really speed things up nicely when submitting large numbers of jobs and jobs with a large number of inputs. * This prevents a disk slow down from grinding the web response to a halt. We don't want the handler to freeze up either - but if something is going to freeze it is a better user experience and easier to recover from the job handler freezing while their are disk problems. * This allows per-job-handler object store configurations - simply configure different job handlers with different object store configurations. This is cool and important and I can imagine some awesome applications but I will wait for them to materialize. Commit: 36019f93085d4c5c51c14b3eafa936d779096513 https://github.com/galaxyproject/galaxy/commit/36019f93085d4c5c51c14b3eafa93... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restructure JobWrapper/TaskWrapper for more unified initialization... ... especially after changes to set object store id in the job handler. This fixes the parallelism tests for those changes. Commit: c9d17545d843df5e3989185433b8419036fe8208 https://github.com/galaxyproject/galaxy/commit/c9d17545d843df5e3989185433b84... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Config rebuild, and a few typos. Commit: 561e0099bc22ce5593a3ca2b363cceb8a05fd6c6 https://github.com/galaxyproject/galaxy/commit/561e0099bc22ce5593a3ca2b363cc... Author: Dannon <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6550 from jmchilton/objectstore_setup Configure object store for datasets in job handler instead of web thread. Compare: https://github.com/galaxyproject/galaxy/compare/1f35d13db561...561e0099bc22 **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.