galaxy-commits March 2016

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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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[galaxyproject/galaxy] bc33f9: Fix upload tool routing
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc33f9b182df89f78679d15e71269000d6d35c5f https://github.com/galaxyproject/galaxy/commit/bc33f9b182df89f78679d15e7126… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js 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 Log Message: ----------- Fix upload tool routing Commit: a01ff73c7b0d5d15f34929de3f0e48366c34a79f https://github.com/galaxyproject/galaxy/commit/a01ff73c7b0d5d15f34929de3f0e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js 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 Log Message: ----------- Merge pull request #1827 from guerler/fix_upload_link_000 Fix upload tool routing Compare: https://github.com/galaxyproject/galaxy/compare/763fb112904f...a01ff73c7b0d

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[galaxyproject/galaxy] e122bb: Annotate make targets
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e122bb8f5dd8120f155fcd0b3be87e836663d4a0 https://github.com/galaxyproject/galaxy/commit/e122bb8f5dd8120f155fcd0b3be8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Annotate make targets Saw this cute trick http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html and figured it wouldn't be too hard to do here as well. Produces a nice help text for commands Commit: a034238c8cb75db1ce165366e87498f48a4a38f6 https://github.com/galaxyproject/galaxy/commit/a034238c8cb75db1ce165366e874… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Silence expr warning Commit: b9c8d5beb48dbd71f1cfedd39afb75eb5ceb569e https://github.com/galaxyproject/galaxy/commit/b9c8d5beb48dbd71f1cfedd39afb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Duplicate @jxtx's fix Commit: 763fb112904f51a0a646c0e951d5b759083832db https://github.com/galaxyproject/galaxy/commit/763fb112904f51a0a646c0e951d5… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1824 from erasche/makefile-help Makefile help target + formatting Compare: https://github.com/galaxyproject/galaxy/compare/e730af5a27bc...763fb112904f

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[galaxyproject/galaxy] 340024: 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: 34002458f432ea83ba510bcc25100753f80d4430 https://github.com/galaxyproject/galaxy/commit/34002458f432ea83ba510bcc2510… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-19 (Fri, 19 Feb 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: 9dc1d56dabf5630d1dbd8b2eacb3c2cf62d5b773 https://github.com/galaxyproject/galaxy/commit/9dc1d56dabf5630d1dbd8b2eacb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 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: e730af5a27bc1fd41231986d8a35e9581b34988b https://github.com/galaxyproject/galaxy/commit/e730af5a27bc1fd41231986d8a35… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> 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 #1819 from dannon/whitelist_reloading_logging Whitelist logging tweaks Compare: https://github.com/galaxyproject/galaxy/compare/e43c2ef5dea0...e730af5a27bc

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[galaxyproject/galaxy] 865f2d: Fix create/manage db scripts to respect GALAXY_VIR...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/fa8beb225004...50bc127a3b55

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galaxy-commits March 2016