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

[galaxyproject/galaxy] 63f674: Add routes for workflow import view, apply consist...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63f674c26d371569a3aaf8887a53f97e8707f951 https://github.com/galaxyproject/galaxy/commit/63f674c26d371569a3aaf8887a53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes for workflow import view, apply consistent routes Commit: 962811b586e7e2cbf4213fbeff914aac0c66a755 https://github.com/galaxyproject/galaxy/commit/962811b586e7e2cbf4213fbeff91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: A client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Add vue component for workflow import form Commit: 20ce0e42d9ef5a26539de08e1749eb1617e2960a https://github.com/galaxyproject/galaxy/commit/20ce0e42d9ef5a26539de08e1749… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove legacy view Commit: e55f8c5f56fceae6d3ec2e53a019c43407b4dba3 https://github.com/galaxyproject/galaxy/commit/e55f8c5f56fceae6d3ec2e53a019… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add import workflow from file option to api endpoint Commit: f086080c65e98ed60794fae6e4f7e552d5c9c42c https://github.com/galaxyproject/galaxy/commit/f086080c65e98ed60794fae6e4f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused controller endpoint, and disabled legacy option Commit: 68af8c9e780417a4e34de1ca349b1e5ace7c8e58 https://github.com/galaxyproject/galaxy/commit/68af8c9e780417a4e34de1ca349b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary check Commit: 5173d6f222c684d132c05684aae3b6e0c47b6e0c https://github.com/galaxyproject/galaxy/commit/5173d6f222c684d132c05684aae3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore broken installed_repository_file option Commit: b6ee0a53ec5c116e2aacb4f9e8f47868ba76bb51 https://github.com/galaxyproject/galaxy/commit/b6ee0a53ec5c116e2aacb4f9e8f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary spacing and unused variable Commit: 8a51d02ce641184bdb9da51eb6017004cfdfd777 https://github.com/galaxyproject/galaxy/commit/8a51d02ce641184bdb9da51eb601… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix library usage, and parameter naming Fix file reading caller Avoid using bare except Fix file parameter name Add missing library Commit: e5a564ef17990ba4b7c6db6381ef8fb98cd5bab9 https://github.com/galaxyproject/galaxy/commit/e5a564ef17990ba4b7c6db6381ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add additional checks for installed repository handler, open files using with-block Commit: 6a57ba8d28fb2f7c95850411118adb9e17c23c72 https://github.com/galaxyproject/galaxy/commit/6a57ba8d28fb2f7c95850411118a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Use archive_source and not url Commit: 51e32b6beaabe35fbd8a1cbaf38200d46ce33e3f https://github.com/galaxyproject/galaxy/commit/51e32b6beaabe35fbd8a1cbaf382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix error message Commit: 4c483a884a0948f86ca47e4b32494fc40e6764b8 https://github.com/galaxyproject/galaxy/commit/4c483a884a0948f86ca47e4b3249… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Show warning if import was successful but has errors Commit: 12096d2a9fa4a7d177b419e0a7c7bbff9d1af982 https://github.com/galaxyproject/galaxy/commit/12096d2a9fa4a7d177b419e0a7c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix spacing in import block Commit: 3f34055e8ae3dccdaf8d235662b3e82591959bbd https://github.com/galaxyproject/galaxy/commit/3f34055e8ae3dccdaf8d235662b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to fix selenium tests Fix lint Commit: 368691624bc408bdad2383f04e6fb5c266e2ff4a https://github.com/galaxyproject/galaxy/commit/368691624bc408bdad2383f04e6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'exact_version_handling' into workflow_import Commit: 3a3c796fcf154e94d910f24e6e40b59afa999265 https://github.com/galaxyproject/galaxy/commit/3a3c796fcf154e94d910f24e6e40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix failing tests Commit: 8ba207de7199c66090f9526e451b8095751790d8 https://github.com/galaxyproject/galaxy/commit/8ba207de7199c66090f9526e451b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore error handling variation Commit: 2fa340842cca7b46da121743153f5d31afe16eea https://github.com/galaxyproject/galaxy/commit/2fa340842cca7b46da121743153f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove api flag check from workflow manager Commit: 8d5c1d08d8e3eb8a459343b2b4f4e4376407ea5d https://github.com/galaxyproject/galaxy/commit/8d5c1d08d8e3eb8a459343b2b4f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add source to workflow name Commit: 75c2c4f2494be66a459aece8e1707a6024e36e61 https://github.com/galaxyproject/galaxy/commit/75c2c4f2494be66a459aece8e170… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix import from myexperiment service Commit: 2cb4d52d4dbb1b3a74a5bcf01205cfa6cb3181f1 https://github.com/galaxyproject/galaxy/commit/2cb4d52d4dbb1b3a74a5bcf01205… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix default parameters for 3rd party workflow import controller Commit: fbd9d81409df888cd99c4d3f05875721b4505baf https://github.com/galaxyproject/galaxy/commit/fbd9d81409df888cd99c4d3f0587… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused variable Commit: ffe9c3bd294c55b4c4576dcc5187a3593d1bf9a1 https://github.com/galaxyproject/galaxy/commit/ffe9c3bd294c55b4c4576dcc5187… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused source identifier Commit: fe4bff1fb9d84c057b40f04a9285ca5ca4dfb5fc https://github.com/galaxyproject/galaxy/commit/fe4bff1fb9d84c057b40f04a9285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #5804 from guerler/workflow_import Use vue and api to handle workflow imports Compare: https://github.com/galaxyproject/galaxy/compare/679083c935c1...fe4bff1fb9d8

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[galaxyproject/galaxy] fc546c: allow admins to set any role for library datasets ...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc546cb1abd2060eea159cc1198e09b55fbaaf41 https://github.com/galaxyproject/galaxy/commit/fc546cb1abd2060eea159cc1198e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- allow admins to set any role for library datasets permissions this bug led to a funny problem where admins couldn't add themselves Commit: 51c05d7a28926a1257fb0b9b82d16f0a5b9d7ab2 https://github.com/galaxyproject/galaxy/commit/51c05d7a28926a1257fb0b9b82d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- modify checks that will never be true Commit: 7f9fcf99e403194558f5eb7a3f5545ee25a91c65 https://github.com/galaxyproject/galaxy/commit/7f9fcf99e403194558f5eb7a3f55… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- refactor the lib dataset update permissions process to mirror the library's Commit: 679083c935c10013dc4a24f9f2a8ead77651c567 https://github.com/galaxyproject/galaxy/commit/679083c935c10013dc4a24f9f2a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5899 from martenson/fix-admin-datalib-perms Fix admin datalib dataset perms Compare: https://github.com/galaxyproject/galaxy/compare/921fde4b8cdc...679083c935c1

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[galaxyproject/galaxy] bf4f43: Rough implentation of the DockerAPIInterface.
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4f43d96a4cf3bdf090d82822a688677600e3f2 https://github.com/galaxyproject/galaxy/commit/bf4f43d96a4cf3bdf090d82822a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Rough implentation of the DockerAPIInterface. Commit: 2e9c25da28535c268467e9dc5dc982b067ed14bc https://github.com/galaxyproject/galaxy/commit/2e9c25da28535c268467e9dc5dc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Create a general method for handling galaxy.containers param -> docker-py param mapping. Plus some cleanup. Commit: b7531593697175ad9c8f110e9943c9086c779ae4 https://github.com/galaxyproject/galaxy/commit/b7531593697175ad9c8f110e9943… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Corrections to Docker spec handling Commit: ac9fce9a3c5e6995bafa5fbac602c2b2a4ccb003 https://github.com/galaxyproject/galaxy/commit/ac9fce9a3c5e6995bafa5fbac602… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- WIP Docker Swarm API interface Commit: 0bba56d106dbeedfac2c67226a749bf6354df4e2 https://github.com/galaxyproject/galaxy/commit/0bba56d106dbeedfac2c67226a74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker API TLS support Commit: 26d265e0107143a62e7799ecf51ea85ac698696c https://github.com/galaxyproject/galaxy/commit/26d265e0107143a62e7799ecf51e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker service fixes Commit: c8ab4fae4db13b106dcd1dbc4f109cc66c305d8a https://github.com/galaxyproject/galaxy/commit/c8ab4fae4db13b106dcd1dbc4f10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Enable setting defaults for docker API data structures. Commit: 360e43095a5036c8cedd452a5809160780f361a8 https://github.com/galaxyproject/galaxy/commit/360e43095a5036c8cedd452a5809… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker swarm interface for the API Commit: 0e357ca73729f67f27a31b83a7df6c5c74c43c99 https://github.com/galaxyproject/galaxy/commit/0e357ca73729f67f27a31b83a7df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Lint fixes Commit: 2794a650f5cd885f684d79e5124e349ccdf09879 https://github.com/galaxyproject/galaxy/commit/2794a650f5cd885f684d79e5124e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Fixes for swarm manager. Commit: 806703a5e2ac679bcac496bb9acd36a9b248ce48 https://github.com/galaxyproject/galaxy/commit/806703a5e2ac679bcac496bb9acd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Move DockerVolume to containers lib model and fix bugs. Commit: 9cd589508d260a8e04191701aa86e98548e97def https://github.com/galaxyproject/galaxy/commit/9cd589508d260a8e04191701aa86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/util/__init__.py Log Message: ----------- More detailed swarm manager state logging Commit: 605a156d618b352c0755af0b3e6e9e0922c126f8 https://github.com/galaxyproject/galaxy/commit/605a156d618b352c0755af0b3e6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Attempt to handle "phantom" docker tasks Commit: 0d90235b1c5e6742bc65f270c5ac0e19b48ee1d0 https://github.com/galaxyproject/galaxy/commit/0d90235b1c5e6742bc65f270c5ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix lint/unit test errors Commit: 9de17e248feb2fa39e3a026727df75a5f42b7c59 https://github.com/galaxyproject/galaxy/commit/9de17e248feb2fa39e3a026727df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add some error handling to the Docker API interface Commit: 507fed9e3c2e2ea6a7fc9938400c7642701bc3ad https://github.com/galaxyproject/galaxy/commit/507fed9e3c2e2ea6a7fc9938400c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix lint error Commit: 10e0314e8fe8d378fdeb97bfa0b3466e95e35f07 https://github.com/galaxyproject/galaxy/commit/10e0314e8fe8d378fdeb97bfa0b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/util/json.py Log Message: ----------- Move json format function to galaxy.util.json Commit: 8369d88295554639926ad5ddac445a20e449a0e4 https://github.com/galaxyproject/galaxy/commit/8369d88295554639926ad5ddac44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional docker dependency for containers interface Commit: 5537ce1fa748422a27aea062165095cfba07c754 https://github.com/galaxyproject/galaxy/commit/5537ce1fa748422a27aea0621650… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Handle the case where a node claims a task exists but the tasks/services API disagrees Commit: 559fb9df9ba0379b975aaa2b5df7ac963c18f037 https://github.com/galaxyproject/galaxy/commit/559fb9df9ba0379b975aaa2b5df7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Allow docker client callers to pass in a test function that the client wrapper will call on certain types of expected failures. If the function returns a truthy value, it is returned instead. This is useful for state-altering changes where the request may have succeeded but the response failed. Commit: 9db3d23eaca5ce7270a9480038acd52f52951298 https://github.com/galaxyproject/galaxy/commit/9db3d23eaca5ce7270a9480038ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py Log Message: ----------- Use consistent whitespace in containers lib classes Commit: c42d642233d962fc513c1039771acb00718d7348 https://github.com/galaxyproject/galaxy/commit/c42d642233d962fc513c1039771a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Containers: - Improve documentation of docker API param mapping - Improve sample containers config file - Fix constraints - A couple other minor bug/logging fixes Commit: b205956b3882a4b1dbc0529742ba8f5aafddafe5 https://github.com/galaxyproject/galaxy/commit/b205956b3882a4b1dbc0529742ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker: Don't retry 4xx errors indefinitely. Possibly need to do this for more APIErrors. Commit: 9e2ada9a008addbfbcf1d764d80d216dca6978a0 https://github.com/galaxyproject/galaxy/commit/9e2ada9a008addbfbcf1d764d80d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Infinite loop retry is probably bad. This should help with surviving transient errors. Commit: ca7b3fd59355df39304d37972f46940e88f1a975 https://github.com/galaxyproject/galaxy/commit/ca7b3fd59355df39304d37972f46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix tests due to missing name in mock module Commit: 91a25d0a08b969c9d6b7161fae6f34eff1c66f59 https://github.com/galaxyproject/galaxy/commit/91a25d0a08b969c9d6b7161fae6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py Log Message: ----------- Support manager failover for Docker Swarm mode Commit: 5127fd29570171f55d41e7458a5e2d7cec9a9837 https://github.com/galaxyproject/galaxy/commit/5127fd29570171f55d41e7458a5e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Swarm manager: log services that do not have tasks on any node. Commit: e651b34156a3af022bac250464d92ca6394c3d85 https://github.com/galaxyproject/galaxy/commit/e651b34156a3af022bac250464d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py A scripts/docker_swarm_manager.py Log Message: ----------- Remove swarm manager from lib Commit: d3038f859a03ad4b29eb6143ea9d88f915cfaac2 https://github.com/galaxyproject/galaxy/commit/d3038f859a03ad4b29eb6143ea9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Load containers interface on app load if enable_beta_containers_interface is set. Commit: 860aaf8241759f915501dba221a49b80a18a4e3e https://github.com/galaxyproject/galaxy/commit/860aaf8241759f915501dba221a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix docker interface failover by making the docker.APIClient wrapper use class vars, since we only ever want callers to use one APIClient. Commit: 564f7ecafe61d0c890cb9cde58640ce221935067 https://github.com/galaxyproject/galaxy/commit/564f7ecafe61d0c890cb9cde5864… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M scripts/docker_swarm_manager.py Log Message: ----------- Make the swarm manager recover on uncaught exceptions. It should do a better job of catching them in the application, but this is good enough for the moment. Commit: feb3e9ddf039e56f972149e7338138fb662745b4 https://github.com/galaxyproject/galaxy/commit/feb3e9ddf039e56f972149e73381… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix lint error Commit: 921fde4b8cdce2ab32846ba473846f1388b0592a https://github.com/galaxyproject/galaxy/commit/921fde4b8cdce2ab32846ba47384… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/app.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/util/__init__.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py A scripts/docker_swarm_manager.py Log Message: ----------- Merge pull request #5861 from natefoo/containers-docker-lib Implement the API version of the Docker containers interface Compare: https://github.com/galaxyproject/galaxy/compare/881dc3601823...921fde4b8cdc

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[galaxyproject/infrastructure-playbook] dd951a: Block a specific pervasive spam message
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dd951a455bd8adada7a7d7246a33614239853ed5 https://github.com/galaxyproject/infrastructure-playbook/commit/dd951a455bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/galaxy/inventory M roles/postfix/templates/local.cf.j2 Log Message: ----------- Block a specific pervasive spam message

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[galaxyproject/usegalaxy-playbook] 2e8637: Replaced sbtas_se with btman
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e8637f67c843a5c23eb0f98aaadaf7461c26396 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e8637f67c843a5c… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Replaced sbtas_se with btman

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[galaxyproject/infrastructure-playbook] 968bc9: Correct slurm_user format (why didn't this cause f...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 968bc99aa90fdd56959e7af6ea73e6e86e083893 https://github.com/galaxyproject/infrastructure-playbook/commit/968bc99aa90… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/slurmclients/vars.yml Log Message: ----------- Correct slurm_user format (why didn't this cause failures?) Commit: be0fb386736f8999433559cc0d2403ca59f98529 https://github.com/galaxyproject/infrastructure-playbook/commit/be0fb386736… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/all.yml Log Message: ----------- Add mount definition for switching NFS servers as needed Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/654ae08ccf…

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[galaxyproject/galaxy] 5522c7: Add `index` to OIDC controller to list authnzs ass...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5522c78d9d1ebcb490285528a8587ff7157a6d6d https://github.com/galaxyproject/galaxy/commit/5522c78d9d1ebcb490285528a858… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Add `index` to OIDC controller to list authnzs associated with a user. Commit: 68dad22d1e15a30d8ee49f2f8002cdd7d7dfc723 https://github.com/galaxyproject/galaxy/commit/68dad22d1e15a30d8ee49f2f8002… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add router to authnz index. Commit: 881dc3601823da61c3a883f17907132f07afd0bd https://github.com/galaxyproject/galaxy/commit/881dc3601823da61c3a883f17907… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #5908 from VJalili/oidc_index OIDC controller index Compare: https://github.com/galaxyproject/galaxy/compare/b71a163a8ce8...881dc3601823

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[galaxyproject/galaxy] 100904: Add OIDC and OAuth2.0 config to authentication doc...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10090476267c1a2cec8103c4d3844057e682c730 https://github.com/galaxyproject/galaxy/commit/10090476267c1a2cec8103c4d384… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Add OIDC and OAuth2.0 config to authentication docs Commit: b71a163a8ce84403cec829e12265573e44d4f668 https://github.com/galaxyproject/galaxy/commit/b71a163a8ce84403cec829e12265… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Merge pull request #5906 from VJalili/patch-6 Add OIDC and OAuth2.0 config to authentication docs Compare: https://github.com/galaxyproject/galaxy/compare/60b5a9a52ab8...b71a163a8ce8

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[galaxyproject/galaxy] b24a1b: Small fix for workflow editor Selenium testing.
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b24a1b723dd0d378b5f5c181f74f3340409839d8 https://github.com/galaxyproject/galaxy/commit/b24a1b723dd0d378b5f5c181f74f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small fix for workflow editor Selenium testing. Commit: 54721122e7439eeea2d2c6840ed668f827eed577 https://github.com/galaxyproject/galaxy/commit/54721122e7439eeea2d2c6840ed6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Small fixes, enhancements for workflow run Selenium tests. Commit: 8f529d177ada3ef179a982d05dd4f04ba82e8abe https://github.com/galaxyproject/galaxy/commit/8f529d177ada3ef179a982d05dd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Improve a few workflow run API test cases. Use the more abstract test_data specification that will translate to GUI testing. Commit: aafd9de76ba61e2e3b2467188bb53e93c8b6fb2b https://github.com/galaxyproject/galaxy/commit/aafd9de76ba61e2e3b2467188bb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Add more complicated workflow run test case. Re-use test_data specification used by many of the API workflow tests and a workflow used by another test. Add abstractions and DOM element for mapping labeled test data to tool form inputs. Commit: 60b5a9a52ab853bf9ff3adf09bbcc6ae0c4d7992 https://github.com/galaxyproject/galaxy/commit/60b5a9a52ab853bf9ff3adf09bbc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #5886 from jmchilton/selenium_workflow_run More, better workflow run Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/3922065d8a29...60b5a9a52ab8

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[galaxyproject/infrastructure-playbook] 654ae0: Create slurm log directory and rotate logs
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 654ae08ccf30844b0f5b7332e32f20703d66c0ed https://github.com/galaxyproject/infrastructure-playbook/commit/654ae08ccf3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A roles/slurm/files/logrotate-slurm M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmd.yml Log Message: ----------- Create slurm log directory and rotate logs

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