- galaxy-commits - lists.galaxyproject.org

[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 02 Mar '16

02 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 02 Mar '16

02 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 02 Mar '16

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

01 Mar '16

Branch: refs/heads/release_16.01 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 Compare: https://github.com/galaxyproject/galaxy/compare/50bc127a3b55...cf91ab451189

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[galaxyproject/galaxy] ae6548: Add license and repository information to package....
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae654873e211b4263430cce6419817fe3f1c59b9 https://github.com/galaxyproject/galaxy/commit/ae654873e211b4263430cce64198… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/package.json Log Message: ----------- Add license and repository information to package.json. This fixes a couple warnings for recent npm versions. Commit: 6b800a291dcfc4347b76f3b960e05e4a223777eb https://github.com/galaxyproject/galaxy/commit/6b800a291dcfc4347b76f3b960e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/package.json Log Message: ----------- Merge pull request #1829 from dannon/packagejson_license_repo Add license and repository information to package.json. Compare: https://github.com/galaxyproject/galaxy/compare/9f590b8a0ec7...6b800a291dcf

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[galaxyproject/galaxy] 1aa1d6: Fix workflow parameters not rendered when tool par...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Commit: 865f2d49bd04b636552002cd0e4830f2dbad5c75 https://github.com/galaxyproject/galaxy/commit/865f2d49bd04b636552002cd0e48… 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: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.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/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Commit: 50bc127a3b55432884ed6350bee3e0ea67beb95f https://github.com/galaxyproject/galaxy/commit/50bc127a3b55432884ed6350bee3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Merge pull request #1820 from jmchilton/db_script_fixes [16.01] Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 9f590b8a0ec755403f84f0fff1978530ee306ef8 https://github.com/galaxyproject/galaxy/commit/9f590b8a0ec755403f84f0fff197… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M manage_db.sh M templates/webapps/galaxy/workflow/run.mako M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/19a58f745089...9f590b8a0ec7

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[galaxyproject/galaxy] 6dbdc4: Loading a Job object eagerloads a lot of mappings ...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6dbdc430bd9d9281407e73988511f5e355d7f537 https://github.com/galaxyproject/galaxy/commit/6dbdc430bd9d9281407e73988511… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Loading a Job object eagerloads a lot of mappings down to the dataset level. For Jobs with many outputs with large metadata, this can consume many GB of memory. Attempt to lazy load instead such that only one row should be returned for querying jobs (but this could negatively impact performance in other places). Commit: 19a58f745089eea730674158153bf77adbf2bbbc https://github.com/galaxyproject/galaxy/commit/19a58f745089eea730674158153b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #1809 from natefoo/lazyload-job Change many job mapped properties to lazy loads Compare: https://github.com/galaxyproject/galaxy/compare/a01ff73c7b0d...19a58f745089

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