- galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] e4fbb8: Replace: pip_virtualenv_command > galaxy_virtualen...
by Enis Afgan 22 Feb '19

22 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: e4fbb80576d44b22c69eda13b8d3909e9c7b1fbb https://github.com/galaxyproject/ansible-galaxy/commit/e4fbb80576d44b22c69e… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M README.md M tasks/dependencies.yml M tasks/virtualenv.yml Log Message: ----------- Replace: pip_virtualenv_command > galaxy_virtualenv_command Keep backword compatible. Commit: badffb979b9ab537b7ce542cb3d5d8219606ae39 https://github.com/galaxyproject/ansible-galaxy/commit/badffb979b9ab537b7ce… Author: Enis Afgan <afgane(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M README.md M tasks/dependencies.yml M tasks/virtualenv.yml Log Message: ----------- Merge pull request #62 from ic4f/master Replace: pip_virtualenv_command > galaxy_virtualenv_command Compare: https://github.com/galaxyproject/ansible-galaxy/compare/3e9ff5520254...badf…

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[galaxyproject/galaxy] f00fb3: Place oidc login button under regular login form
by Dannon 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f00fb3e4add155268aaf7e17228699734b0bfeab https://github.com/galaxyproject/galaxy/commit/f00fb3e4add155268aaf7e172286… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Place oidc login button under regular login form Commit: 87261f625368f55b2d7ba7aa1711fd462e2afcb6 https://github.com/galaxyproject/galaxy/commit/87261f625368f55b2d7ba7aa1711… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Hide oidc options based on config setting Commit: 61a5c3b14f7e606b7d0513b2ae1cec3acf6b75b0 https://github.com/galaxyproject/galaxy/commit/61a5c3b14f7e606b7d0513b2ae1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Use lower-case galaxy local variable name Commit: 66b01d2b32181b6ae526f90e0c4cbde85f19c4c3 https://github.com/galaxyproject/galaxy/commit/66b01d2b32181b6ae526f90e0c4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Avoid computing oidc setting Commit: 2a05323daa84db46479f5ee9ca756dba51da45e7 https://github.com/galaxyproject/galaxy/commit/2a05323daa84db46479f5ee9ca75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js Log Message: ----------- Client formatting. Commit: 830c21d6f5ef34e4ddce498b2c02c9c4ae7ff027 https://github.com/galaxyproject/galaxy/commit/830c21d6f5ef34e4ddce498b2c02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/entry/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js Log Message: ----------- Merge branch 'move_google_login_button' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c53fb623d8cf...830c21d6f5ef

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[galaxyproject/galaxy] eca238: Make pykube a conditional requirement
by John Chilton 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eca238d7837928c7ee962f10435fd667d61ccc4c https://github.com/galaxyproject/galaxy/commit/eca238d7837928c7ee962f10435f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Make pykube a conditional requirement Commit: c82cd04ca820d65c9279872c029d712358e4c65f https://github.com/galaxyproject/galaxy/commit/c82cd04ca820d65c9279872c029d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Use standard os.environ Commit: 879d7c22b63733dfd5f9e1c6cbe368c97e06495d https://github.com/galaxyproject/galaxy/commit/879d7c22b63733dfd5f9e1c6cbe3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/base/integration_util.py A test/integration/test_kubernetes_runner.py Log Message: ----------- Add basic kubernetes integration test Currently times out becasue jobs aren't monitored succesfully. Commit: 4eed32dc4c86da17a525419ba985d4d06d7a768b https://github.com/galaxyproject/galaxy/commit/4eed32dc4c86da17a525419ba985… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Propagate selected shell to job_script Commit: 912fc61592a92fbed329501b38b35a591e556b2d https://github.com/galaxyproject/galaxy/commit/912fc61592a92fbed329501b38b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Allow skipping pod_retrial Commit: e7b89122489083f80b0c183ff0a958a58d823118 https://github.com/galaxyproject/galaxy/commit/e7b89122489083f80b0c183ff0a9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Use galaxy's exisiting job_file abstraction This allows setting environment variables, job instrumentation, exit code checking and so on. Commit: 3498f87d8734ce5bc3341e546842dabe29b93d40 https://github.com/galaxyproject/galaxy/commit/3498f87d8734ce5bc3341e546842… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Use sh as job shell for kubernetes test, bash is not available in default container Commit: 5dd10c4f86b07d9483b76c59511148bdce8949d3 https://github.com/galaxyproject/galaxy/commit/5dd10c4f86b07d9483b76c595111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/tools/deps/dependencies.py Log Message: ----------- Drop mutable defaults Commit: 1a007682737af1b466a6a8545922e17c7f42fb19 https://github.com/galaxyproject/galaxy/commit/1a007682737af1b466a6a8545922… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Skip broken string encoding logic Commit: d2ed543ecd39fee1876fcbad063c1aa4c4c3ce33 https://github.com/galaxyproject/galaxy/commit/d2ed543ecd39fee1876fcbad063c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove return statements from queue_job, this is never consumed anywhere Commit: 1103ce1dccd0ac3dda0dca715da4cb0feafde4ee https://github.com/galaxyproject/galaxy/commit/1103ce1dccd0ac3dda0dca715da4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove commented out non-functional code in kubernetes runner. Commit: a23063b2dc3fdf82c645383fd36c3b6439b68f52 https://github.com/galaxyproject/galaxy/commit/a23063b2dc3fdf82c645383fd36c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Cleanup of kubernetes exception logging Commit: 4e39c0fc8488a4794870752f8895f61dc8d704cf https://github.com/galaxyproject/galaxy/commit/4e39c0fc8488a4794870752f8895… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Test cancelling jobs, running mulled containers on kubernetes Commit: 9019916ae2180afe6f35b6ead45f1ae294c2bfe9 https://github.com/galaxyproject/galaxy/commit/9019916ae2180afe6f35b6ead45f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Fix test skipping Commit: 34c0a2940b69c59b20bbdd8df0944332cb59e64c https://github.com/galaxyproject/galaxy/commit/34c0a2940b69c59b20bbdd8df094… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Don't write fake stderr file Commit: 5c5f199f812ff68e7d061c047956aeaa3627632f https://github.com/galaxyproject/galaxy/commit/5c5f199f812ff68e7d061c047956… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Add job properties test Commit: b43f1985d71fadf3f907feeab2b529408dc05588 https://github.com/galaxyproject/galaxy/commit/b43f1985d71fadf3f907feeab2b5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Capture stdout and stderr for kubernetes runner There is currently no way to discriminate stdout and stderr from kubernetes logs (https://github.com/kubernetes/kubernetes/issues/28167) but Galaxy really needs to know about the stderr. To work around this we capture the stdout and stderr into files using the approach outined in https://stackoverflow.com/a/692407. Commit: d0e749375a2e703f9f59e8794825867760ee7b44 https://github.com/galaxyproject/galaxy/commit/d0e749375a2e703f9f59e8794825… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Drop custom fail_job and stderr logging methods We now log stdout and stderr to files, so this isn't needed. Commit: 98b571e19aec1b182dbb636d23ab8a3ff290f30d https://github.com/galaxyproject/galaxy/commit/98b571e19aec1b182dbb636d23ab… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Remove user-cancelled jobs from monitor queue Commit: dc184567376ec25eba3d317c9a70d2a27d4aefed https://github.com/galaxyproject/galaxy/commit/dc184567376ec25eba3d317c9a70… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: A lib/galaxy/util/bytesize.py Log Message: ----------- Add utility class for manipulating byte sizes Commit: c61c790fccc84f06991d48dcbea70ef8181fe452 https://github.com/galaxyproject/galaxy/commit/c61c790fccc84f06991d48dcbea7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M test/functional/tools/samples_tool_conf.xml M test/integration/test_kubernetes_runner.py Log Message: ----------- Make kubernetes pass GALAXY_SLOTS and GALAXY_MEMORY_MB Also drops __transform_cpu_value, incoming values are always strings, so this wasn't functional in any case. Commit: fe02dbbf8107b8ded12cb9c76fd1686515a47dd4 https://github.com/galaxyproject/galaxy/commit/fe02dbbf8107b8ded12cb9c76fd1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix typo in config/job_conf.xml.sample_advanced Commit: 54c964011a29eca1c72360f17f5114022ad626bf https://github.com/galaxyproject/galaxy/commit/54c964011a29eca1c72360f17f51… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Take ceiling of kubernetes cpu value Commit: 936679ea817151438ff76d2e14ac2557c4caa3a0 https://github.com/galaxyproject/galaxy/commit/936679ea817151438ff76d2e14ac… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Inject env vars for k8s job to avoid changing tool environment inside container. Commit: e52bb5daa78eb040304919299dc624491573c53f https://github.com/galaxyproject/galaxy/commit/e52bb5daa78eb040304919299dc6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Import from correct module Commit: 626657e3c2b8dc3325a4c2dee35777ac45ac8f0c https://github.com/galaxyproject/galaxy/commit/626657e3c2b8dc3325a4c2dee357… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Revert "job script returns tool exit code in any case" This breaks exit code reporting and leads to pod re-scheduling. This reverts commit 6beeec836f6c6ab479700e6a1e1accbe5069dacf. Commit: 7cf161ba0155abf02582cbbf4636d1ca8681efbe https://github.com/galaxyproject/galaxy/commit/7cf161ba0155abf02582cbbf4636… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py M test/integration/test_kubernetes_runner.py Log Message: ----------- Allow adding multiple volume claims Commit: e293a74e66002a28adc1045fda0e3415c6f2e08b https://github.com/galaxyproject/galaxy/commit/e293a74e66002a28adc1045fda0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/integration/test_kubernetes_runner.py Log Message: ----------- Add test for tool using python dependencies Commit: 32cad5977b102c33088111abe80887ab1a567a19 https://github.com/galaxyproject/galaxy/commit/32cad5977b102c33088111abe808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Set galaxy_virtual_env to None for kubernetes runner This prevents attempts of activating Galaxy's virtualenv inside the container. Commit: b931576ed1ebcdfc0f9e0d5cbab74d199e8bbb2a https://github.com/galaxyproject/galaxy/commit/b931576ed1ebcdfc0f9e0d5cbab7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Drop GALAXY_VIRTUAL_ENV env hack GALAXY_VIRTUAL_ENV is injected through job_wrapper.galaxy_virtual_env, which does `os.environ.get(VIRTUAL_ENV, None)`, so this didn't work. The previous commit addresses that. Commit: db387ab898cf47076279ac9d97407ba0fdc45e49 https://github.com/galaxyproject/galaxy/commit/db387ab898cf47076279ac9d9740… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-19 (Tue, 19 Feb 2019) Changed paths: M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix typo fixed by reverted commit 6beeec8 Commit: c53fb623d8cf3af99732a3fe9d1f513f9b538c2b https://github.com/galaxyproject/galaxy/commit/c53fb623d8cf3af99732a3fe9d1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/dependencies.py A lib/galaxy/util/bytesize.py M test/base/integration_util.py M test/functional/tools/samples_tool_conf.xml M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py A test/integration/test_kubernetes_runner.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #6958 from mvdbeek/kubernetes_integration_test Kubernetes job runner integration test and enhancements Compare: https://github.com/galaxyproject/galaxy/compare/65f0c2ac8da8...c53fb623d8cf

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[galaxyproject/galaxy] 4484eb: Use bootstrapped controller helper for admin app
by Dannon 22 Feb '19

22 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4484eb4b205e865a8bec1874d64e945a562ec30d https://github.com/galaxyproject/galaxy/commit/4484eb4b205e865a8bec1874d64e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Use bootstrapped controller helper for admin app Commit: ca44e2413a47a843d9b42e266b462d3c5712ec57 https://github.com/galaxyproject/galaxy/commit/ca44e2413a47a843d9b42e266b46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix the server-side route resolution for admin app, ship same bootstrapped client with additional config. Commit: 420e92917ee33672cf65f7406c285bb48968d255 https://github.com/galaxyproject/galaxy/commit/420e92917ee33672cf65f7406c28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Filter kwds for admin client bootstrapping. Commit: 65f0c2ac8da8693a6b111b9fbff544aa98cc8b3a https://github.com/galaxyproject/galaxy/commit/65f0c2ac8da8693a6b111b9fbff5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #7394 from guerler/fix_admin_router Restore admin client router handling Compare: https://github.com/galaxyproject/galaxy/compare/75ac7d8d82ac...65f0c2ac8da8

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[galaxyproject/galaxy] bfcee3: Refactor dataset fetching in get/set dataset metho...
by Nate Coraor 21 Feb '19

21 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bfcee382c7cdabdaeee8acc5c6b066bb10ec3d34 https://github.com/galaxyproject/galaxy/commit/bfcee382c7cdabdaeee8acc5c6b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller. Commit: 844dbf39b6a99858c96b5bf6e9794a037248c1aa https://github.com/galaxyproject/galaxy/commit/844dbf39b6a99858c96b5bf6e979… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M test/api/test_history_contents.py M test/api/test_jobs.py Log Message: ----------- testing edit controller. Commit: 75ac7d8d82ac0bb9be0c7c09cf649523770e77f6 https://github.com/galaxyproject/galaxy/commit/75ac7d8d82ac0bb9be0c7c09cf64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M test/api/test_history_contents.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #7322 from jmchilton/edit_dataset_refactor Refactor dataset controller to reuse input validation checks between get/set Compare: https://github.com/galaxyproject/galaxy/compare/4bb57e5ffcdf...75ac7d8d82ac

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[galaxyproject/galaxy] 726ad9: Bump yarn's network timeout from 2 minutes to 5 mi...
by Martin Cech 21 Feb '19

21 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 726ad9a0f68d134d7bc2ffa37ad3f369787d19da https://github.com/galaxyproject/galaxy/commit/726ad9a0f68d134d7bc2ffa37ad3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M Makefile M scripts/common_startup.sh Log Message: ----------- Bump yarn's network timeout from 2 minutes to 5 minutes. Commit: 4ad4fe59be7bbcc1917d3a1e039fa3f3a8367709 https://github.com/galaxyproject/galaxy/commit/4ad4fe59be7bbcc1917d3a1e039f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M Makefile M scripts/common_startup.sh Log Message: ----------- Merge pull request #7399 from dannon/bump_yarn_network_tolerance [19.01] Bump yarn network tolerance Compare: https://github.com/galaxyproject/galaxy/compare/648d01685bf2...4ad4fe59be7b

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[galaxyproject/galaxy] e9c6c1: Remove openid related legacy check
by Dannon 21 Feb '19

21 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9c6c12e29e2920a25a08bc3f86c4f8bd8ee8e78 https://github.com/galaxyproject/galaxy/commit/e9c6c12e29e2920a25a08bc3f86c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M templates/display_common.mako Log Message: ----------- Remove openid related legacy check Commit: 4bb57e5ffcdfcc7e58b2663683d19f03e9d19d4f https://github.com/galaxyproject/galaxy/commit/4bb57e5ffcdfcc7e58b2663683d1… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M templates/display_common.mako Log Message: ----------- Merge pull request #7395 from guerler/remove_openid_legacy_check Remove openid related legacy check Compare: https://github.com/galaxyproject/galaxy/compare/3c3d36c62b44...4bb57e5ffcdf

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[galaxyproject/galaxy] b4fc7c: Report line number mismatch in sort collection tool
by Martin Cech 20 Feb '19

20 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: b4fc7c19a80c38b595cb08f05fd6765a07f95920 https://github.com/galaxyproject/galaxy/commit/b4fc7c19a80c38b595cb08f05fd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Report line number mismatch in sort collection tool Otherwise this would just fail because sorted_elements is undefined. I don't think there can be a HDA without metadata, so I've dropped that check. Commit: 648d01685bf26c9dcb5231cc61755d95a4696928 https://github.com/galaxyproject/galaxy/commit/648d01685bf26c9dcb5231cc6175… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #7390 from mvdbeek/more_useful_error_message [19.01] Report line number mismatch in sort collection tool Compare: https://github.com/galaxyproject/galaxy/compare/015ce5cedc21...648d01685bf2

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[galaxyproject/galaxy] ae8bf6: Release notes raw.
by Martin Cech 20 Feb '19

20 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: ae8bf6f793edda9211b59c68d6c029b9fa74154a https://github.com/galaxyproject/galaxy/commit/ae8bf6f793edda9211b59c68d6c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst Log Message: ----------- Release notes raw. Commit: b5713ca170cfeb574063a2ec9dca8adbee1f7d74 https://github.com/galaxyproject/galaxy/commit/b5713ca170cfeb574063a2ec9dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Progress on 19.01 release notes... Commit: 16af73423f2c5a1181b016dcc01955c1c2ab037a https://github.com/galaxyproject/galaxy/commit/16af73423f2c5a1181b016dcc019… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 072b8d73eca68201bcf691c7dc9fa22272433ac3 https://github.com/galaxyproject/galaxy/commit/072b8d73eca68201bcf691c7dc9f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Update doc/source/releases/19.01.rst Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 2a3555d9d73e4a9f72b003a319698f7e8fb01d3c https://github.com/galaxyproject/galaxy/commit/2a3555d9d73e4a9f72b003a31969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst Log Message: ----------- Better Singularity summary thanks to @mvdbeek. Commit: 94bcb8d00f3fc8817cdca5ef3ab383e705b950d6 https://github.com/galaxyproject/galaxy/commit/94bcb8d00f3fc8817cdca5ef3ab3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- More fixes to 19.01 release notes. Commit: ca4acf78df6cfc89f76b0f09143d0301aac234b4 https://github.com/galaxyproject/galaxy/commit/ca4acf78df6cfc89f76b0f09143d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01_announce.rst Log Message: ----------- Sort PR numbers Small fixes. Commit: 37a93972d59459ffd50d340d53c5f278b3e15dae https://github.com/galaxyproject/galaxy/commit/37a93972d59459ffd50d340d53c5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M doc/source/releases/19.01.rst Log Message: ----------- Fix PR link Commit: 015ce5cedc21c1a318d6455534f52f8acc3d36ca https://github.com/galaxyproject/galaxy/commit/015ce5cedc21c1a318d6455534f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #7308 from jmchilton/19.01_release_notes [19.01] Release notes for 19.01. Compare: https://github.com/galaxyproject/galaxy/compare/ac9b300df66b...015ce5cedc21

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[galaxyproject/galaxy] 57af07: Update application documentation
by Martin Cech 20 Feb '19

20 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57af0738139db28939d83f1ae76b981eeb77b530 https://github.com/galaxyproject/galaxy/commit/57af0738139db28939d83f1ae76b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M doc/source/api/guidelines.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.managers.rst A doc/source/lib/galaxy.metadata.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.verify.asserts.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Update application documentation with: ``` make -C doc/ updaterst ``` Also fix 2 links in `doc/source/api/guidelines.rst` . Commit: 3c3d36c62b445daaa30ea6448b45184583c0b89f https://github.com/galaxyproject/galaxy/commit/3c3d36c62b445daaa30ea6448b45… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-20 (Wed, 20 Feb 2019) Changed paths: M doc/source/api/guidelines.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.managers.rst A doc/source/lib/galaxy.metadata.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.verify.asserts.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Merge pull request #7391 from nsoranzo/api_doc_update Update application documentation Compare: https://github.com/galaxyproject/galaxy/compare/394ce04c37ba...3c3d36c62b44

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