Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2aa8ed4efbcf1224d335593e9d64966b8b173bac https://github.com/galaxyproject/galaxy/commit/2aa8ed4efbcf1224d335593e9d649... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2019-01-11 (Fri, 11 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py

Log Message: ----------- fix tag_using_filenames not converted to bool

Commit: 3fa43dfecea37a5f56e3675afad0bd65d3196f56 https://github.com/galaxyproject/galaxy/commit/3fa43dfecea37a5f56e3675afad0b... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Swap to normal event bindings for multipanel drop. get(0) isn't great, but we'll overhaul this more in the future.

Commit: 7c13cdf006733182b4bfb07ced24df729600e670 https://github.com/galaxyproject/galaxy/commit/7c13cdf006733182b4bfb07ced24d... Author: John Chilton jmchilton@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Merge pull request #7218 from dannon/fix_multipanel_drop

[19.01] Swap to normal event bindings for multipanel drag/drop.

Commit: 54aecb3f31812c86d370034cf557537780efbcdf https://github.com/galaxyproject/galaxy/commit/54aecb3f31812c86d370034cf5575... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Properly deal with missing tools in subworkflows

If a subworkflow is missing tools the entire parent workflow couldn't be loaded into the editor, because we raised an exception. This is now only logged as an error. On the user side we now prevent running and saving such workflows by actually implementing the `get_errors` method for the SubWorkflowModule class.

This should fix https://github.com/galaxyproject/galaxy/issues/7140.

Commit: 6ff84684bd577ea4610d63213cc090b86d983aa8 https://github.com/galaxyproject/galaxy/commit/6ff84684bd577ea4610d63213cc09... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py

Log Message: ----------- Fix displaying tool help images on python 3

Commit: ab8ea1ee40c2a7de3a7cc6e6aaafba95f451a6c6 https://github.com/galaxyproject/galaxy/commit/ab8ea1ee40c2a7de3a7cc6e6aaafb... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Add error listener for input elements, utilize to highlight numeric value range adjustments

Commit: 48c2807e2ebecf7fd01bd56e102ccaaa25947a29 https://github.com/galaxyproject/galaxy/commit/48c2807e2ebecf7fd01bd56e102cc... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js

Log Message: ----------- Fix name of error handler helper function

Commit: d20c6f6d8c1cfdd677afa04ad70c10e11c7228f4 https://github.com/galaxyproject/galaxy/commit/d20c6f6d8c1cfdd677afa04ad70c1... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-section.js

Log Message: ----------- Remove unused default error message

Commit: ef02c60f792a8aeadcaa58d8e0a4ac71d65aa42b https://github.com/galaxyproject/galaxy/commit/ef02c60f792a8aeadcaa58d8e0a4a... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Move local slider helper variables into score/statement

Commit: 8534ef5d5cef95bad2dbb882b8285a44deb0dca6 https://github.com/galaxyproject/galaxy/commit/8534ef5d5cef95bad2dbb882b8285... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Move field error binding to input element wrapper

Commit: 48811d4c0c79b5dfdba2e51471f71d9d9fa0b34e https://github.com/galaxyproject/galaxy/commit/48811d4c0c79b5dfdba2e51471f71... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js

Log Message: ----------- Use listento caller to bind input element error listener

Commit: 97651462212b2a08a18b67b9fe2d731732b3d1c3 https://github.com/galaxyproject/galaxy/commit/97651462212b2a08a18b67b9fe2d7... Author: guerler aysam.guerler@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Add additional validation to slider out-of-range error detection

Commit: b1b1d848d35816cfa344aeb687c78c7a0c93e66f https://github.com/galaxyproject/galaxy/commit/b1b1d848d35816cfa344aeb687c78... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/workflow/modules.py

Log Message: ----------- Fix loading subworkflows

Commit: 24f97f6917da606f8b9c1fc1fb4faef5c54f1933 https://github.com/galaxyproject/galaxy/commit/24f97f6917da606f8b9c1fc1fb4fa... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py

Log Message: ----------- Open files in binary mode when sending data

Commit: 7a9422600c76ad49515844d582bf6d5f507076e8 https://github.com/galaxyproject/galaxy/commit/7a9422600c76ad49515844d582bf6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M test/api/test_galaxy_interactor.py

Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test

Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 .

Commit: d460d218ad898242046c2422aa211fe6a4830462 https://github.com/galaxyproject/galaxy/commit/d460d218ad898242046c2422aa211... Author: Dannon dannon.baker@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/ui/ui-slider.js

Log Message: ----------- Merge pull request #7229 from mvdbeek/backport_sliding_validator

[19.01] Backport #7183 input element listener

Commit: ed6011755cf7cf5c7232bd43365dd01ab0b12af5 https://github.com/galaxyproject/galaxy/commit/ed6011755cf7cf5c7232bd43365dd... Author: John Chilton jmchilton@gmail.com Date: 2019-01-17 (Thu, 17 Jan 2019)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/api/test_galaxy_interactor.py

Log Message: ----------- Merge pull request #7228 from mvdbeek/fix_image_display_py3

[19.01] Fix displaying tool help images on python 3

Commit: 06aa30ffdca0fe092fa2d094aa23da34b10a1667 https://github.com/galaxyproject/galaxy/commit/06aa30ffdca0fe092fa2d094aa23d... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/actions/library.py

Log Message: ----------- disable tag_using_filenames by default (consistent with #5115)

Commit: 8d99791afb6a699e987bd1e25aaea8582f7f7065 https://github.com/galaxyproject/galaxy/commit/8d99791afb6a699e987bd1e25aaea... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- Fix data_source tools on python 3

Commit: b0b5fb44d282b52391becdac1b190ebbd075168d https://github.com/galaxyproject/galaxy/commit/b0b5fb44d282b52391becdac1b190... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py

Log Message: ----------- Merge pull request #7204 from abretaud/tag_fn

[19.01] Data library: fix tag_using_filenames not properly converted to bool

Commit: 7b14c3099876d5991ebdea85ff18c027de434be8 https://github.com/galaxyproject/galaxy/commit/7b14c3099876d5991ebdea85ff18c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Reduce duplicated code

Commit: e92e978ca179870d586e08f16a0542b9dd499a2a https://github.com/galaxyproject/galaxy/commit/e92e978ca179870d586e08f16a054... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/interval.py

Log Message: ----------- Drop use of col1_startswith

Contigs may start with whatever sequence you like. Luckily this isn't essential to the datatypes.

Leaving data.col1_startswith in case toolshed datatypes import this.

Commit: 6f861dec7e897bbc06b2cffbb33b2fdd9e6ac11a https://github.com/galaxyproject/galaxy/commit/6f861dec7e897bbc06b2cffbb33b2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/exceptions/__init__.py

Log Message: ----------- Overridde __init__ for ToolMissingException

Commit: d2d87625f0a5989c40c40a8d50857efb5dc21c36 https://github.com/galaxyproject/galaxy/commit/d2d87625f0a5989c40c40a8d50857... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Merge pull request #7237 from mvdbeek/datatype_fixes

[19.01] Interval datatype fixes

Commit: 9467d0261cab5712d15dfcfa7ca5d7cdb765f631 https://github.com/galaxyproject/galaxy/commit/9467d0261cab5712d15dfcfa7ca5d... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M tools/data_source/data_source.py

Log Message: ----------- Merge pull request #7236 from mvdbeek/data_source_fix

[19.01] Fix data_source tools on python 3

Commit: 889c1026c0893636b4fc6375443408c0ec2b4a8a https://github.com/galaxyproject/galaxy/commit/889c1026c0893636b4fc637544340... Author: John Chilton jmchilton@gmail.com Date: 2019-01-18 (Fri, 18 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving

[18.09] Properly deal with missing tools in workflows

Commit: 5c90e02d3665caec50369baf0918e58f043af6e4 https://github.com/galaxyproject/galaxy/commit/5c90e02d3665caec50369baf0918e... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Fix workflow save_as functionality

Fixes https://github.com/galaxyproject/galaxy/issues/7240, broken in https://github.com/galaxyproject/galaxy/pull/7019, where it was renamed from `build_workflow_from_dict` to `build_workflow_from_raw_description`.

Commit: 8862b9311b000b83a733ed216130f0a7cfe7d4ba https://github.com/galaxyproject/galaxy/commit/8862b9311b000b83a733ed216130f... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Use update_workflow_from_raw_description method

not build_workflow_from_raw_description

Co-Authored-By: mvdbeek m.vandenbeek@gmail.com

Commit: b4e450cff021b68831337a8e0bf12c892f54eb8c https://github.com/galaxyproject/galaxy/commit/b4e450cff021b68831337a8e0bf12... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge branch 'release_18.09' into release_19.01

Commit: f24176d95060288a0973ef78dab43bf552efb3ba https://github.com/galaxyproject/galaxy/commit/f24176d95060288a0973ef78dab43... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py

Log Message: ----------- Merge pull request #7245 from nsoranzo/release_19.01

Merge branch 'release_18.09' into release_19.01

Commit: bdd340cf1c2e31a5a8c82995bad26d07c7ed5adb https://github.com/galaxyproject/galaxy/commit/bdd340cf1c2e31a5a8c82995bad26... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Merge pull request #7241 from mvdbeek/fix_workflow_save_as

[19.01] Fix workflow save_as functionality

Commit: c58f9acf7fe2cf515ab7440c835257c24b0440cd https://github.com/galaxyproject/galaxy/commit/c58f9acf7fe2cf515ab7440c83525... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-01-21 (Mon, 21 Jan 2019)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/actions/library.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M tools/data_source/data_source.py

Log Message: ----------- Merge branch 'release_19.01' into dev

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