March 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 5aea44: mutable confs for Main; add labels
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5aea4451d1e354f1d0783d24cffe4a70bcf5ba91 https://github.com/galaxyproject/usegalaxy-playbook/commit/5aea4451d1e354f1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- mutable confs for Main; add labels

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[galaxyproject/galaxy] 499268: Hide tools that have been replaced.
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Compare: https://github.com/galaxyproject/galaxy/compare/dfef64db75c4...de70306407c0

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[galaxyproject/infrastructure-playbook] 66421a: Change access list on leeroy
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 66421a2b51af676da937f5608b8200fdfd0bf8b1 https://github.com/galaxyproject/infrastructure-playbook/commit/66421a2b51a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Change access list on leeroy

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[galaxyproject/galaxy] a49401: Improve dataset error log message
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf4814… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Compare: https://github.com/galaxyproject/galaxy/compare/0051cab4f352...dfef64db75c4

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[galaxyproject/galaxy] 9aefb9: Fix workflow saving broken in dev.
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aefb989e660e1e6e48e28338471e5642bb65236 https://github.com/galaxyproject/galaxy/commit/9aefb989e660e1e6e48e28338471… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow saving broken in dev. Broken with PR #1735 (kind of accross two non-atomic commits I think - 92d978dd9d9b15bab7b3852787c2ce094880f97d and 0dac0c207757cf160901df387214dcfc56016469). Testing: Try to save a workflow. \#minor Commit: 158732edb6ceb1ed073d058b3a71c4c26e4887d2 https://github.com/galaxyproject/galaxy/commit/158732edb6ceb1ed073d058b3a71… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1835 from jmchilton/from_editor_fix Fix workflow saving broken in dev. Compare: https://github.com/galaxyproject/galaxy/compare/45bd65f85e22...158732edb6ce

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[galaxyproject/galaxy] 78b1f9: Dockerfile testing improvements.
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78b1f9af3741889a542d881cf242a12acc932a7e https://github.com/galaxyproject/galaxy/commit/78b1f9af3741889a542d881cf242… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Dockerfile testing improvements. - Use wheel from inside container. - Update to the latest pre-release phantom and casper dependencies (they seem more stable). Commit: dc897cf86a25a834455db4c16c6d99f7d0c6e7cd https://github.com/galaxyproject/galaxy/commit/dc897cf86a25a834455db4c16c6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 6135d7ea5634255242e13bea87075fb7422a2656 https://github.com/galaxyproject/galaxy/commit/6135d7ea5634255242e13bea8707… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Update to phantomjs 2.1 and official sources. Commit: 45bd65f85e22e5abe3ea77249e45730cff71ef02 https://github.com/galaxyproject/galaxy/commit/45bd65f85e22e5abe3ea77249e45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1449 from jmchilton/updated_client_test_deps Docker Testing - Newer versions of phantomjs and casperjs, in container wheels. Compare: https://github.com/galaxyproject/galaxy/compare/97c2fa3c0f97...45bd65f85e22

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[galaxyproject/galaxy] f67cbe: revert escaping added in a24e206ff7762d5b86d3dc724...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f67cbe72d571f87a87e868161650e5965e681881 https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e868161650… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly Commit: 0051cab4f35240ff8b85f010b1ae0d66de7273c0 https://github.com/galaxyproject/galaxy/commit/0051cab4f35240ff8b85f010b1ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1830 from martenson/revert-ts-repo-rendering [16.01] revert ts repo long desc escaping Compare: https://github.com/galaxyproject/galaxy/compare/cf91ab451189...0051cab4f352

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[galaxyproject/galaxy] 9d4722: Improved logging during tool executions.
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d4722c7e99b669da09a014f994c011e2f8552be https://github.com/galaxyproject/galaxy/commit/9d4722c7e99b669da09a014f994c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Improved logging during tool executions. Haven't a hard time untangling what messages belong to what job/tool during workflow executions. Commit: 97c2fa3c0f9735167e5cf2446b5c5e7bde72999e https://github.com/galaxyproject/galaxy/commit/97c2fa3c0f9735167e5cf2446b5c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #1832 from jmchilton/job_log_1 Improved logging during tool executions. Compare: https://github.com/galaxyproject/galaxy/compare/eb2005e7a224...97c2fa3c0f97

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[galaxyproject/galaxy] d3b343: Use visit_inputs for check_and_update_param_values
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3b343acab7567ce80f9a427f0e61afc55ba4005 https://github.com/galaxyproject/galaxy/commit/d3b343acab7567ce80f9a427f0e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M test/api/test_workflows.py Log Message: ----------- Use visit_inputs for check_and_update_param_values Commit: d32c6b90210a6481d829eb1f7a050e1a48ee1405 https://github.com/galaxyproject/galaxy/commit/d32c6b90210a6481d829eb1f7a05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move job resource parameter xml to job config Commit: 0b5651a5ed6553c1ddb3d9c25dd3b0019fc97ad7 https://github.com/galaxyproject/galaxy/commit/0b5651a5ed6553c1ddb3d9c25dd3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Do not rely on __current_case__ Commit: 02187afb57a3b212c4e9a05b153e117bc8778866 https://github.com/galaxyproject/galaxy/commit/02187afb57a3b212c4e9a05b153e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-27 (Sat, 27 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Handle missing parameters Commit: eb2005e7a2245e2e3e09ccbf7489081da393e57e https://github.com/galaxyproject/galaxy/commit/eb2005e7a2245e2e3e09ccbf7489… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Merge pull request #1764 from guerler/fix_check_and_update_000 Use visit inputs for check_and_update_param_values Compare: https://github.com/galaxyproject/galaxy/compare/18128fa97d07...eb2005e7a224

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[galaxyproject/galaxy] 93494a: This silences logging when display whitelist isn't...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93494a833ee390811bdc1d13c1ef54b52ed005f2 https://github.com/galaxyproject/galaxy/commit/93494a833ee390811bdc1d13c1ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 16280c63236621082ce4c3b3d93eb679294cd515 https://github.com/galaxyproject/galaxy/commit/16280c63236621082ce4c3b3d93e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: 7534182d7afd8c997df7d919d0633345ee5c4dfa https://github.com/galaxyproject/galaxy/commit/7534182d7afd8c997df7d919d063… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. Commit: cf91ab4511897ef5ac4beb8d56219119073073c4 https://github.com/galaxyproject/galaxy/commit/cf91ab4511897ef5ac4beb8d5621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1828 from dannon/cherrypick_logging [16.01] Fix startup logging Commit: 18128fa97d076bd42959435a004a0ee70ea63a04 https://github.com/galaxyproject/galaxy/commit/18128fa97d076bd42959435a004a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Manually merge to resolve conflict, 16.01->dev Compare: https://github.com/galaxyproject/galaxy/compare/6b800a291dcf...18128fa97d07

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