Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776dd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd87... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a20... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb030... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d08... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a2848... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b2068860... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb3... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.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/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01 Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed371... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e570... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5688 from martenson/security-rn [18.01] backport add security announcement to the release notes Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754 https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc6... Author: Jelle Scholtalbers <j.scholtalbers@gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999 https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type [18.01] Fix/default role type on auto created roles Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55 https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Clarfify that nginx-extras needs to be install for the upload_store directive to work Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c3... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #5717 from mvdbeek/nginx_doc_update [18.01] Clarify that nginx-extras needs to be install for the upload_store d… Commit: 3b87dac78028846a803e33ae13199535c70f567d https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae13199... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Add Galaxy `lib` directory to Python path for 2 scripts Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e . Fix https://github.com/galaxyproject/galaxy/issues/5722 . Commit: ef45ae3752a4ea4da73719e2917a064c8e239ab3 https://github.com/galaxyproject/galaxy/commit/ef45ae3752a4ea4da73719e2917a0... Author: pvanheus <pvh@webbedfeet.co.za> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Upgrade clone failure logging to error When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'. Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009 https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bfb... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts [17.09] Add Galaxy `lib` directory to Python path for 2 scripts Commit: 50035b184e0ceba61f21f223e5f701710dd86d19 https://github.com/galaxyproject/galaxy/commit/50035b184e0ceba61f21f223e5f70... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- improve update commands in RN, clarify uwsgi config changes Commit: 74d0bcb353b4824d4d4af9ffe6bd909924feca62 https://github.com/galaxyproject/galaxy/commit/74d0bcb353b4824d4d4af9ffe6bd9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 924eecc67a3155578aea6a484d9bfd86d0cc5aba https://github.com/galaxyproject/galaxy/commit/924eecc67a3155578aea6a484d9bf... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Add missing `.` Commit: 3699e9e4919dcb727af3ff0e7457794642973dfa https://github.com/galaxyproject/galaxy/commit/3699e9e4919dcb727af3ff0e74577... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- re-add the motivation for uwsgi switch Commit: 240f14d62fb6bdbf02f51ff1af19602494560880 https://github.com/galaxyproject/galaxy/commit/240f14d62fb6bdbf02f51ff1af196... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5730 from martenson/bootstrap [18.01] improve update commands in RN, clarify uwsgi config changes Commit: a73a1d6250373cd1e6bb1255052ee7cb541e4569 https://github.com/galaxyproject/galaxy/commit/a73a1d6250373cd1e6bb1255052ee... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5728 from mvdbeek/backport_logging_level_change [18.01] Backport 5724: upgrade clone failure logging to error Commit: 7c962975750c9747b12413309ac0c546fe8a9046 https://github.com/galaxyproject/galaxy/commit/7c962975750c9747b12413309ac0c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M doc/source/admin/nginx.md M doc/source/releases/18.01_announce.rst M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/version.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/hg_util.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.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/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/e12e773eddca...7c962975750c