March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f21f96: Change API path in docstrings to correct /api/depe...
by GitHub 14 Mar '17

14 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f21f963a23427e2b5aa1f58a7d9b0fb85aed7607 https://github.com/galaxyproject/galaxy/commit/f21f963a23427e2b5aa1f58a7d9b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Change API path in docstrings to correct /api/dependency_resolvers/* Commit: 65e7ee0c78e5c61a6ef9d9eaa8ccd6d8666014ad https://github.com/galaxyproject/galaxy/commit/65e7ee0c78e5c61a6ef9d9eaa8cc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Merge pull request #3749 from mvdbeek/docstring_fix_api Change API path in docstrings to correct /api/dependency_resolvers/* Compare: https://github.com/galaxyproject/galaxy/compare/7d08f8f2fecf...65e7ee0c78e5

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[galaxyproject/galaxy] 90b300: Return empty list if resolve_all() has failed
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90b300cbd731df2e6005ca1dcd2f5c1c59a34e0e https://github.com/galaxyproject/galaxy/commit/90b300cbd731df2e6005ca1dcd2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return empty list if resolve_all() has failed This should solve the problems pointed out by :eyes: @nsoranzo introduced in https://github.com/galaxyproject/galaxy/pull/3725. This commit also clarifies this behaviour in the docstrings. Commit: 8192d3562937d07410aa5d7dd73727efc5832634 https://github.com/galaxyproject/galaxy/commit/8192d3562937d07410aa5d7dd737… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Add `:returns: list of resolved dependencies` to docstring of `resolve_all` method Commit: 7d08f8f2fecf08743a58f71c431e1d71f84f0d76 https://github.com/galaxyproject/galaxy/commit/7d08f8f2fecf08743a58f71c431e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3746 from mvdbeek/resolve_all_fix_3725 BUG: Return empty list if resolve_all() has failed Compare: https://github.com/galaxyproject/galaxy/compare/7e1c04cc6df8...7d08f8f2fecf

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[galaxyproject/galaxy] f94174: update xsd codefile doc with info from moin
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f94174912a09a56eebe2e14e63238c3f3f172327 https://github.com/galaxyproject/galaxy/commit/f94174912a09a56eebe2e14e6323… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- update xsd codefile doc with info from moin Commit: 7e1c04cc6df810ca3a4e726a85cc9566d9d1ff61 https://github.com/galaxyproject/galaxy/commit/7e1c04cc6df810ca3a4e726a85cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3739 from martenson/update-codefile-schema update xsd codefile doc with info from moin Compare: https://github.com/galaxyproject/galaxy/compare/fc1df7bad17e...7e1c04cc6df8

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[galaxyproject/galaxy] 46e452: Fix typo in install_dependencies docstring
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46e452bfe820ddbb329e694d0eb2b7b755594910 https://github.com/galaxyproject/galaxy/commit/46e452bfe820ddbb329e694d0eb2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix typo in install_dependencies docstring Commit: 8b5d408e438c346f04088374d70eaca65e06c292 https://github.com/galaxyproject/galaxy/commit/8b5d408e438c346f04088374d70e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Add API to remove requirements installed by Conda This is currently limited to the Conda dependency resolver, but other resolver would only need to implement the resolver.uninstall method and set can_uninstall_dependencies to True. To use this endpoint, POST to <galaxy_url>/tools/<tool_id>/uninstall_dependencies'. Commit: 3b067ef62a4dfa8af54bc4c75c6260f98d660aeb https://github.com/galaxyproject/galaxy/commit/3b067ef62a4dfa8af54bc4c75c62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return last non-zero returncode Commit: d5b5d29137ee1e5577530ed2c56579b9394520b3 https://github.com/galaxyproject/galaxy/commit/d5b5d29137ee1e5577530ed2c565… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Change endpoint to `api/tools/<tool_id>/dependencies` A POST will trigger installation and DELETE will trigger uninstalling the dependencies (Thx for the suggestion @jmchilton). Commit: 6902e62d38e3c5741a238736f640b5b847c5e8c2 https://github.com/galaxyproject/galaxy/commit/6902e62d38e3c5741a238736f640… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix uninstall when not all dependencies are resolved by all-in-one resolver Commit: 95106ea3c9ad875ce35b16c6b9bb8556f3d82076 https://github.com/galaxyproject/galaxy/commit/95106ea3c9ad875ce35b16c6b9bb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add UI for Conda dependency uninstall Commit: fc1df7bad17e53c54bd57602b82bbec22cc0e074 https://github.com/galaxyproject/galaxy/commit/fc1df7bad17e53c54bd57602b82b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3725 from mvdbeek/remove_env_conda Add API and UI to remove requirements installed by Conda Compare: https://github.com/galaxyproject/galaxy/compare/33ff2754cc75...fc1df7bad17e

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[galaxyproject/infrastructure-playbook] 53c6ff: Ansible 2.0+ updates
by GitHub 13 Mar '17

13 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 53c6ff16eedab22e0abe472f7096de56da94f2cc https://github.com/galaxyproject/infrastructure-playbook/commit/53c6ff16eed… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- Ansible 2.0+ updates

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[galaxyproject/galaxy] 5818bb: Prefer versioned Conda dependencies to unversioned...
by GitHub 10 Mar '17

10 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5818bbcbaaeca54a85bef9acaadd41d12386a6ad https://github.com/galaxyproject/galaxy/commit/5818bbcbaaeca54a85bef9acaadd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Prefer versioned Conda dependencies to unversioned Galaxy ones. Commit: 45971b29bd8b93825fe48134750bd866c82f7a9f https://github.com/galaxyproject/galaxy/commit/45971b29bd8b93825fe48134750b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Update dependency resolver docs for new default order Commit: 33ff2754cc75981796176b7e7ae75ce362db62a0 https://github.com/galaxyproject/galaxy/commit/33ff2754cc75981796176b7e7ae7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3708 from natefoo/dep-resolve-order Prefer versioned Conda dependencies to unversioned Galaxy ones Compare: https://github.com/galaxyproject/galaxy/compare/5a7eab0f06b4...33ff2754cc75

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[galaxyproject/galaxy] 90108e: tool-form needs to not be required at the top leve...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90108e450fd2d13d3010e05a2fcb1224a2549a2a https://github.com/galaxyproject/galaxy/commit/90108e450fd2d13d3010e05a2fcb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- tool-form needs to not be required at the top level of the Galaxy webapp Commit: 2134d6c3856edf8358c185178f9efe35a232c03b https://github.com/galaxyproject/galaxy/commit/2134d6c3856edf8358c185178f9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Use a redirect (which will get routed, soon) instead of instantiating a toolform within the overlay -- this is much lighter weight Commit: da9ee941afa604586cfc6dfdacb2594284b3e6f0 https://github.com/galaxyproject/galaxy/commit/da9ee941afa604586cfc6dfdacb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Standardize tabs/spaces in webhook overlay search Commit: 3d33586d4a5758e566dc5d1eceda91e97cd3d73a https://github.com/galaxyproject/galaxy/commit/3d33586d4a5758e566dc5d1eceda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Cleanup pass on formatting/unused vars in webhooks Commit: 5a7eab0f06b4eb9f877c8e582bb6e078622be1ad https://github.com/galaxyproject/galaxy/commit/5a7eab0f06b4eb9f877c8e582bb6… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/search/static/script.js M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #3731 from dannon/fix_webhook_search_overlay Fix webhook search overlay interfering with masthead load Compare: https://github.com/galaxyproject/galaxy/compare/8911e491a56c...5a7eab0f06b4

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[galaxyproject/infrastructure-playbook] 3111f6: Galaxy site moved to athena
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3111f6620693c4145f942fc916a9786140cd5314 https://github.com/galaxyproject/infrastructure-playbook/commit/3111f662069… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M common_env/secret_group_vars/sslwebservers.yml M galaxyenv/files/jenkins/jenkins_server_user_ssh_config M galaxyenv/files/jenkins/jenkins_slave_user_ssh_config A galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem M galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/host_vars/chouffe.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml M galaxyenv/secret_host_vars/chouffe.galaxyproject.org.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml A galaxyenv/templates/nginx/cloudlaunch.j2 A galaxyenv/templates/nginx/galaxyproject.j2 A galaxyenv/templates/nginx/moin.j2 M galaxyenv/templates/nginx/new.j2 M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Galaxy site moved to athena

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[galaxyproject/usegalaxy-playbook] 29479b: Move all athena stuff to infrastructure-playbook
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 29479b5ca735b13b5b5716c5858f1966e57125a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/29479b5ca735b13b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: R common/host_vars/athena.galaxyproject.org.yml M common/inventory M common/secret_vars/ssl.yml R files/ssl/athena.galaxyproject.org_cert.pem R templates/nginx/cloudlaunch.j2 R templates/nginx/galaxyproject.j2 Log Message: ----------- Move all athena stuff to infrastructure-playbook

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[galaxyproject/galaxy] 33abab: Move the user calculate_and_set_disk_usage functio...
by GitHub 09 Mar '17

09 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33ababaeb48e8ecfad487a54e96550ce7e43bc78 https://github.com/galaxyproject/galaxy/commit/33ababaeb48e8ecfad487a54e965… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py Log Message: ----------- Move the user calculate_and_set_disk_usage functionality to the model instead of the queue worker. Commit: c928f15b4d00bb798453d42a6f6a79042692edfc https://github.com/galaxyproject/galaxy/commit/c928f15b4d00bb798453d42a6f6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Robustify calculate_and_set_disk_usage for handling changes during the long calc Commit: cd6e7f73d8a54698aa63d670e8aba6e45f8eef1b https://github.com/galaxyproject/galaxy/commit/cd6e7f73d8a54698aa63d670e8ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Swap admin recalculate to use model-based recalc-and-set Commit: 751182640d1a76962cbac872ae31c0ce471872dd https://github.com/galaxyproject/galaxy/commit/751182640d1a76962cbac872ae31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove now-unused import of pgcalc Commit: 8002ef31ea6f4cb52d6e907dcdf1d002ced45eb6 https://github.com/galaxyproject/galaxy/commit/8002ef31ea6f4cb52d6e907dcdf1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Ensure there's a user before calling calculate_and_set_disk_usage Commit: e088a48323a06e80d55e85944a4c09cf368b8391 https://github.com/galaxyproject/galaxy/commit/e088a48323a06e80d55e85944a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add error logging to recalculate task. Commit: 2d964eb50c9f2f2246044a1d7b83e0f920046510 https://github.com/galaxyproject/galaxy/commit/2d964eb50c9f2f2246044a1d7b83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- I have no idea what I would be doing without Nicola. Commit: 8911e491a56cdc3b8fb327bc702b4843d7d22a4d https://github.com/galaxyproject/galaxy/commit/8911e491a56cdc3b8fb327bc702b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #3734 from dannon/queue_worker_trim Quota recalculation logic consolidation Compare: https://github.com/galaxyproject/galaxy/compare/bcc4e025c36c...8911e491a56c

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