Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac581a5453e6f43a4900d55d67a3c1bd75081f47 https://github.com/galaxyproject/galaxy/commit/ac581a5453e6f43a4900d55d67a3c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M run_tests.sh M test/base/api.py M test/base/integration_util.py M test/integration/test_resolvers.py Log Message: ----------- Improved documentation and design of integration tests. - Allow running through ``run_tests.sh``. - Enable more verbose test errors for Conda tests. - Refactor how integration tests depend on API testing (use a Mixin instead of subclassing conceptually conflicting TestCase classes). Commit: 00c6ee17b7f742efdd895fae44771edacba77c4b https://github.com/galaxyproject/galaxy/commit/00c6ee17b7f742efdd895fae44771... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh Log Message: ----------- Fix Jenkins script test for integration tests. Commit: b78287f1508db2c06f0c309ed8d3747adb4d17fa https://github.com/galaxyproject/galaxy/commit/b78287f1508db2c06f0c309ed8d37... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/base/driver_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/integration/retry_jobs_job_conf.xml A test/integration/retry_jobs_job_resource_parameters_conf.xml A test/integration/retry_runner.py A test/integration/test_retry_jobs.py M test/unit/jobs/test_mapper.py Log Message: ----------- Integration test for advanced job runner stuff. Set of test cases that cover job resource handlers and resubmit job destinations. Commit: 0559cff6e94b250ddd98275b119ab51b36491e34 https://github.com/galaxyproject/galaxy/commit/0559cff6e94b250ddd98275b119ab... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py R test/integration/retry_jobs_job_conf.xml R test/integration/retry_jobs_job_resource_parameters_conf.xml R test/integration/retry_runner.py A test/integration/test_job_resubmission.py R test/integration/test_retry_jobs.py Log Message: ----------- Implement resubmit on unknown failures. Commit: 7d52b28ab2ab0314cd4fa31108a6750cb9750ef3 https://github.com/galaxyproject/galaxy/commit/7d52b28ab2ab0314cd4fa31108a67... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/integration/resubmission_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Allow expressions in job_conf resubmission conditions. Since we allow dynamic job runners clearly job_conf.xml must be considered a trusted document. Still I know that some are uneasy with eval generally so I only allow a very safe subset of Python expressions in this job_conf document. Commit: 949d1224892861bd27207dd0799e2b356576c2cb https://github.com/galaxyproject/galaxy/commit/949d1224892861bd27207dd0799e2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Fix preservation of resubmits for resubmitted jobs. Create an abstraction for the explicit handling of resubmits that is done during job recovery at startup. xref https://github.com/galaxyproject/galaxy/commit/5539a083e21b601bfd2f87fa3417f... Commit: 7e338d790964f594ae67b33e6a72e1777e774b8c https://github.com/galaxyproject/galaxy/commit/7e338d790964f594ae67b33e6a72e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add attempt to resubmission expression language. Commit: 325b0354754815d32ed458d212d8c1c192630b0b https://github.com/galaxyproject/galaxy/commit/325b0354754815d32ed458d212d8c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M test/integration/resubmission_job_conf.xml Log Message: ----------- Add a self re-submission test. Commit: 18eb1c8d0e4c3f7616d44fd177c90943695b7053 https://github.com/galaxyproject/galaxy/commit/18eb1c8d0e4c3f7616d44fd177c90... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_job_resource_parameters_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add seconds_running and seconds_since_queued to condition expression langauge. Commit: 334dfe1b116775466ef772a9d7a98d6247959ed0 https://github.com/galaxyproject/galaxy/commit/334dfe1b116775466ef772a9d7a98... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Allow (and test) using expressions in job re-submission delays. So you can backoff re-submission with ``delay="attempt * 30"`` for instance - which will cause a re-submission delay to increase by 30 seconds for each resubmission of a job. Commit: 521a585a23459714e9723903363ffa495918cc60 https://github.com/galaxyproject/galaxy/commit/521a585a23459714e9723903363ff... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M test/integration/resubmission_runners.py Log Message: ----------- Two lint fixes for #3291. Commit: 498dddb03fe33df71ec887a9c53311ce53069e31 https://github.com/galaxyproject/galaxy/commit/498dddb03fe33df71ec887a9c5331... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M run_tests.sh M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/unit/jobs/test_mapper.py Log Message: ----------- Merge pull request #3291 from jmchilton/integration_tests_0 Ready Integration Testing for Prime Time Compare: https://github.com/galaxyproject/galaxy/compare/ed4e87ecad31...498dddb03fe3