Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c61617fed6ae59f237cb22fa0f6103508484fc3b
https://github.com/galaxyproject/galaxy/commit/c61617fed6ae59f237cb22fa0f61…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Replace trans.sa_session with sa_session in PSACode.
Commit: 12a3f7b54531f667885d1187538c9b06f244744b
https://github.com/galaxyproject/galaxy/commit/12a3f7b54531f667885d1187538c…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Replace trans.sa_session with sa_session in PSAAssociation.
Commit: 49bb3a66668f94bed1534b007237f0b1db3b71d9
https://github.com/galaxyproject/galaxy/commit/49bb3a66668f94bed1534b007237…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Replace trans.sa_session with sa_session in PSANonce.
Commit: a4d03f0de07df762055210f0c3812cbe0c0bccaf
https://github.com/galaxyproject/galaxy/commit/a4d03f0de07df762055210f0c381…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Replace trans.sa_session with sa_session in PSAPartial.
Commit: 17eac4fe84465706f3b6b8290ae8872d6985afe7
https://github.com/galaxyproject/galaxy/commit/17eac4fe84465706f3b6b8290ae8…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Replace trans.sa_session with sa_session in UserAuthnzToken.
Commit: ebb37f8ff02f246344d73db7c3751b531c4fd38f
https://github.com/galaxyproject/galaxy/commit/ebb37f8ff02f246344d73db7c375…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
Log Message:
-----------
Replace trans with app & sa_session in on_the_fly_config function.
Commit: 69bd26e6046c0dd18eaae4cee433d34d26d87d80
https://github.com/galaxyproject/galaxy/commit/69bd26e6046c0dd18eaae4cee433…
Author: vahid <jalili.vahid(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
Log Message:
-----------
Remove `app` from `on_the_fly_config` signature.
Commit: 8ed5d8c9414f8b086852a2a347d79e530c231b0c
https://github.com/galaxyproject/galaxy/commit/8ed5d8c9414f8b086852a2a347d7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-07 (Sun, 07 Oct 2018)
Changed paths:
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #6826 from VJalili/authnz_trans
Remove `trans` from OIDC-related types
Compare: https://github.com/galaxyproject/galaxy/compare/7d9093d5ab30...8ed5d8c9414f
**NOTE:** This service has 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: 18b4274e651f85db2019faba0674613ef02921aa
https://github.com/galaxyproject/galaxy/commit/18b4274e651f85db2019faba0674…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M test/base/populators.py
R test/base/workflows_format_2/README.txt
R test/base/workflows_format_2/__init__.py
R test/base/workflows_format_2/converter.py
R test/base/workflows_format_2/interface.py
R test/base/workflows_format_2/main.py
Log Message:
-----------
Import gxformat2 as an external dependency.
Commit: 319c29937e30075d0dab45bca87577fd86bc7492
https://github.com/galaxyproject/galaxy/commit/319c29937e30075d0dab45bca875…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
Log Message:
-----------
gxformat2 - allow CWL style 'in' declarations for step connections.
Makes gxformat2 look a lot closer to CWL workflows with Galaxy tools and state.
Commit: c7fa2860d807229ebb29233d99c545534f3d7079
https://github.com/galaxyproject/galaxy/commit/c7fa2860d807229ebb29233d99c5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
Log Message:
-----------
Toward new format2 syntaxes in test workflows.
Commit: d010077830ccdf2c28e978bc65c9871db646f880
https://github.com/galaxyproject/galaxy/commit/d010077830ccdf2c28e978bc65c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/api/test_workflows_from_yaml.py
Log Message:
-----------
Allow workflow import of workflows with connections that don't have matching empty tool state entries.
There is a long conversation in the added doc string.
Commit: 7d9093d5ab308301e2ec9e464ce8e7cfbeba77ea
https://github.com/galaxyproject/galaxy/commit/7d9093d5ab308301e2ec9e464ce8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-10-07 (Sun, 07 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/populators.py
R test/base/workflows_format_2/README.txt
R test/base/workflows_format_2/__init__.py
R test/base/workflows_format_2/converter.py
R test/base/workflows_format_2/interface.py
R test/base/workflows_format_2/main.py
Log Message:
-----------
Merge pull request #6807 from jmchilton/gxformat2_030
Support for Enhancements to gxformat2.
Compare: https://github.com/galaxyproject/galaxy/compare/10e984ce85c2...7d9093d5ab30
**NOTE:** This service has 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: 50019e503adf811a54b54011d64ef92b8a610b13
https://github.com/galaxyproject/galaxy/commit/50019e503adf811a54b54011d64e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-24 (Mon, 24 Sep 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/populators.py
Log Message:
-----------
Refactor method for running format 2 workflows into populators.py for reuse.
Commit: 3e774713a902fb59b4164e4deac2688b9678f0ce
https://github.com/galaxyproject/galaxy/commit/3e774713a902fb59b4164e4deac2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-24 (Mon, 24 Sep 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows_from_yaml.py
M test/base/populators.py
M test/base/workflows_format_2/main.py
M test/functional/tools/disambiguate_cond.xml
Log Message:
-----------
Fill in needed state defaults when importing manually curated workflows.
Commit: 10e984ce85c2d02d95cb96a11d1738fb1d6ab951
https://github.com/galaxyproject/galaxy/commit/10e984ce85c2d02d95cb96a11d17…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-10-06 (Sat, 06 Oct 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/populators.py
M test/base/workflows_format_2/main.py
M test/functional/tools/disambiguate_cond.xml
Log Message:
-----------
Merge pull request #6746 from jmchilton/workflow_state_touch_1
Fill in needed state defaults when importing manually crafted workflows.
Compare: https://github.com/galaxyproject/galaxy/compare/56ca1cdef4d3...10e984ce85c2
**NOTE:** This service has 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.