Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f9ba8d3823854e00e321b7776056d381132b0346
https://github.com/galaxyproject/galaxy/commit/f9ba8d3823854e00e321b7776056…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/parameters/output_collect.py
M test/api/test_dataset_collections.py
M test/api/test_tools_upload.py
Log Message:
-----------
Allow setting tags on targets & contents in data fetch API.
Rebased with default argument handling improvements suggested by Marius.
Commit: 31d331379188e11fe95cdbfe5d8f1035dd511b63
https://github.com/galaxyproject/galaxy/commit/31d331379188e11fe95cdbfe5d8f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M lib/galaxy/managers/collections.py
Log Message:
-----------
Minor typo in new text (or -> of), and two bonus old typo fixes.
Commit: 4719c4a3f1296d179e5e1dc107156ec5fae305ed
https://github.com/galaxyproject/galaxy/commit/4719c4a3f1296d179e5e1dc10715…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/parameters/output_collect.py
M test/api/test_dataset_collections.py
M test/api/test_tools_upload.py
Log Message:
-----------
Merge pull request #6499 from jmchilton/upload_tags_api
Allow setting tags on targets & contents in data fetch API.
Compare: https://github.com/galaxyproject/galaxy/compare/3c4eb54a9a87...4719c4a3f129
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 66af9ce96111685e8fe22c48aa7d0e6471027c64
https://github.com/galaxyproject/galaxy/commit/66af9ce96111685e8fe22c48aa7d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/web/framework/base.py
M tools/data_source/upload.py
Log Message:
-----------
Make upload tool python3 compatible
Commit: 8ce663addbb9f8cde2bd411ab45f097cffa017e8
https://github.com/galaxyproject/galaxy/commit/8ce663addbb9f8cde2bd411ab45f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Consistently use webob.compat.cgi_FieldStorage
This works around bugs in python3 cgi.FieldStorage.
Commit: a729faab8ba5e82e33baa837e804afd747532a9d
https://github.com/galaxyproject/galaxy/commit/a729faab8ba5e82e33baa837e804…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/web/framework/middleware/batch.py
Log Message:
-----------
Fix batch api middleware
Commit: 28cca49747d29bacbb0751df34475a47cd045cd9
https://github.com/galaxyproject/galaxy/commit/28cca49747d29bacbb0751df3447…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
Log Message:
-----------
Remove WebOb pin in Pipfile
Commit: ca8547ce1d729249f8ff07962e8e96d4f017a556
https://github.com/galaxyproject/galaxy/commit/ca8547ce1d729249f8ff07962e8e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
Log Message:
-----------
Inject `self` and `obj` into global scope
The list comprehension code in `transform_lines` gets its own local
scope, so just copying the local scope into the eval functions local
scope doesn't work.
Commit: c5fa023c26fafa53ea9da477243b13b3e6b85278
https://github.com/galaxyproject/galaxy/commit/c5fa023c26fafa53ea9da477243b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
Log Message:
-----------
Use webob.compat's FieldStorage in the remaining codebase
Commit: a65cd29c366035fb8b26e2274046e8c96e3cab33
https://github.com/galaxyproject/galaxy/commit/a65cd29c366035fb8b26e2274046…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/web/framework/base.py
Log Message:
-----------
Patch webob.compat.cgi_FieldStorage instead of overwrite it
Commit: c6c34beb812a966c224c30c17e675d6dfd278248
https://github.com/galaxyproject/galaxy/commit/c6c34beb812a966c224c30c17e67…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M tox.ini
Log Message:
-----------
Add py34-unit to default tox tests
Commit: 9d886c866da5a04e51e5ff6887867393a009257d
https://github.com/galaxyproject/galaxy/commit/9d886c866da5a04e51e5ff688786…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M lib/galaxy/tools/actions/upload_common.py
Log Message:
-----------
Use six.moves for urlparse import
Commit: 347e3124f4628cde3ad9f6ba169ecf1d2a0a0e4e
https://github.com/galaxyproject/galaxy/commit/347e3124f4628cde3ad9f6ba169e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M tools/data_source/upload.py
M tox.ini
Log Message:
-----------
Merge pull request #6467 from mvdbeek/fix_upload_tool_py3
Make upload tool python3 compatible
Compare: https://github.com/galaxyproject/galaxy/compare/051bc9507313...347e3124f462
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8a85270629b80b4c4b306a9130293f25dc7a2da6
https://github.com/galaxyproject/galaxy/commit/8a85270629b80b4c4b306a913029…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Fix and docs for advanced container options in job_conf.xml.
These options were added in #2790 but you know how @jmchilton is about documentation. The bug fix is to fix selecting the first valid option if multiple ones are present instead of just the first option which may be invalid given the other configured destination parameters.
Commit: 051bc950731365b580d3569be8c0481f8bcecf86
https://github.com/galaxyproject/galaxy/commit/051bc950731365b580d3569be8c0…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Merge pull request #6503 from jmchilton/destination_container_target_fixes
Fix and docs for advanced container options in job_conf.xml.
Compare: https://github.com/galaxyproject/galaxy/compare/9f352f77c0c7...051bc9507313
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 62482dd9fda547ba22391cd210518316a0bbbf76
https://github.com/galaxyproject/galaxy/commit/62482dd9fda547ba22391cd21051…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/WorkflowImport.vue
Log Message:
-----------
Use bootstrap vue classes for workflow import form
Commit: f8210d89ace977ec8857ef7205a778b5af0b680a
https://github.com/galaxyproject/galaxy/commit/f8210d89ace977ec8857ef7205a7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/WorkflowImport.vue
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Fix workflow import Selenium tests for #6489.
Commit: 86922d65572ee32b1498ccf422f3f52eb2405386
https://github.com/galaxyproject/galaxy/commit/86922d65572ee32b1498ccf422f3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/WorkflowImport.vue
Log Message:
-----------
Explicitly specify bootstrapvue (works currently either way, due to bundling and the way these are included, but it might not forever -- best to be explicit)
Commit: 9f352f77c0c7a747295ab9aa8e96afee9b13304a
https://github.com/galaxyproject/galaxy/commit/9f352f77c0c7a747295ab9aa8e96…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-16 (Mon, 16 Jul 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/WorkflowImport.vue
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge pull request #6489 from guerler/workflow_import
Use bootstrap vue classes for workflow import form
Compare: https://github.com/galaxyproject/galaxy/compare/d661d99b12ed...9f352f77c0c7
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.