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Commit Graph
18802 Commits
Author SHA1 Message Date
John Chilton 14978355ee Support for de-duplicated workflow import. 2018-10-12 13:41:06 -04:00
John Chilton 42c2580a46 Rev gxformat2 to fix non-data parameters and de-duplicating subworkflows. 2018-10-12 13:41:06 -04:00
John Chilton 00625839b3 Allow downloading Galaxy workflows as format 2 workflows. 2018-10-12 13:41:06 -04:00
John Chilton feddcfaa5a Allow upload format 2 workflows to Galaxy. 2018-10-12 13:41:06 -04:00
John Chilton 85d4706662 Merge pull request #6837 from natefoo/inactive-user-jobs 
Don't create jobs for inactive users
 2018-10-11 08:25:29 -04:00
Nicola Soranzo 483a23a5a4 Fix sorting of error codes 2018-10-11 10:55:56 +01:00
John Chilton 12929f9acb Merge pull request #6827 from pvanheus/patch-9 
Clarify code used in output <filter> tags
 2018-10-10 20:14:47 -04:00
John Chilton caec18236d Merge pull request #6838 from VJalili/authnz_trans 
Replace trans with session and request in psa Storage
 2018-10-10 12:19:33 -04:00
John Chilton fb52755601 Merge pull request #6811 from jmchilton/gxformat2_060 
Support for Enhancements to gxformat2 (part II)
 2018-10-10 08:42:37 -04:00
Nicola Soranzo afa7299705 Merge branch 'release_18.09' into dev 2018-10-10 10:11:13 +01:00
Nate Coraor c0961ec296 Remove some model objects added in #5013 but unused before the PR was 
merged. Also, fix the typo:

  WorkflowRequestInputStepParmeter -> WorkflowRequestInputStepParameter

Both found by @nsoranzo in #6757.
 2018-10-09 10:07:37 -04:00
John Chilton c5700431c4 check user activation with less duplication/imports 2018-10-09 09:04:58 -04:00
John Chilton fd251b16e8 Rev gxformat2 dependencies to get latest features. 2018-10-09 08:18:29 -04:00
Nicola Soranzo 2e6f96bcf6 Remove unneeded parentheses 2018-10-09 12:39:39 +01:00
vahid eda2f1a976 Add a missing z from authnz. 2018-10-08 20:38:20 -07:00
vahid 07d3aa9f79 Return path if request is none when building absolute auth backend URI. 2018-10-08 20:23:35 -07:00
vahid 0cdf629d89 Set request optional with default None in get_cloud_access_credentials. 2018-10-08 20:22:03 -07:00
Nate Coraor c4374f9a81 Fix tabs, wow 2018-10-08 16:40:10 -04:00
Nate Coraor d606996241 Don't create jobs for inactive users 2018-10-08 15:24:23 -04:00
vahid eb7653ee81 Remove trans.session dependency for getting cloudauthz tokens. 2018-10-08 12:07:27 -07:00
Nate Coraor aad1e3fd0a Convert user_is_admin and user_can_do_run_as to properties 2018-10-08 14:53:41 -04:00
vahid ea02d643fd Update get_cloud_access_credentials doc string. 2018-10-08 11:41:55 -07:00
vahid 74ce3c7611 Remove trans from get_cloud_access_credentials. 2018-10-08 11:12:27 -07:00
vahid d15263329e Remove trans from _extend_cloudauthz_config. 2018-10-08 11:08:19 -07:00
vahid 376be2ec9d In psa Strategy, check if request is given asserting for https redirect. 2018-10-08 10:58:07 -07:00
vahid bc7017664c Remove trans from authnz Strategy constructor signature. 2018-10-08 10:44:35 -07:00
vahid b420363436 Add session to authnz Strategy constructor signature. 2018-10-08 10:36:31 -07:00
vahid d5cd53ab8e Add request to authnz Strategy constructor signature. 2018-10-08 10:27:55 -07:00
Nicola Soranzo c83c5cb784 Change conda channel priority: conda-forge > bioconda 
xref. https://github.com/bioconda/bioconda-utils/issues/330
 2018-10-08 11:02:23 +01:00
Nicola Soranzo b99fedefa8 Update to latest galaxy-lib 
Includes:
- change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 )
- channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 )
 2018-10-08 10:08:02 +01:00
John Chilton 8ed5d8c941 Merge pull request #6826 from VJalili/authnz_trans 
Remove `trans` from OIDC-related types
 2018-10-07 15:48:55 -04:00
pvanheus 3b4ffc2565 Fix missing ] 2018-10-07 21:18:04 +02:00
pvanheus a46984991e Clarify code used in output <filter> tags 
Add extra detail to the explanation of how the Python code to ``<filter>`` tags works in outputs.
 2018-10-07 20:22:30 +02:00
vahid 69bd26e604 Remove app from on_the_fly_config signature. 2018-10-06 16:14:41 -07:00
vahid ebb37f8ff0 Replace trans with app & sa_session in on_the_fly_config function. 2018-10-06 14:17:09 -07:00
vahid 17eac4fe84 Replace trans.sa_session with sa_session in UserAuthnzToken. 2018-10-06 12:56:59 -07:00
vahid a4d03f0de0 Replace trans.sa_session with sa_session in PSAPartial. 2018-10-06 12:44:50 -07:00
vahid 49bb3a6666 Replace trans.sa_session with sa_session in PSANonce. 2018-10-06 12:21:32 -07:00
vahid 12a3f7b545 Replace trans.sa_session with sa_session in PSAAssociation. 2018-10-06 11:44:08 -07:00
vahid c61617fed6 Replace trans.sa_session with sa_session in PSACode. 2018-10-06 11:34:42 -07:00
John Chilton d010077830 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.
 2018-10-06 09:39:21 -04:00
John Chilton 18b4274e65 Import gxformat2 as an external dependency. 2018-10-06 09:39:20 -04:00
John Chilton 98a9c86bad Allow testing tags in input collections. 2018-10-06 09:36:41 -04:00
Marius van den Beek 10e984ce85 Merge pull request #6746 from jmchilton/workflow_state_touch_1 
Fill in needed state defaults when importing manually crafted workflows.
 2018-10-06 10:17:41 +02:00
pvanheus 5601d893a3 Fixes to workding as per nsoranzo 2018-10-05 15:24:41 +02:00
pvanheus 0a6de6b8d7 Add more detail about container tags 
Explain that singularity container tags are now supported and add some detail about how to use them.
 2018-10-05 14:37:14 +02:00
Nicola Soranzo 13d92c0070 Merge pull request #6709 from jmchilton/galaxy-lib-update-20180913 
Update to latest galaxy-lib.
 2018-10-05 12:59:26 +01:00
John Chilton 493816e245 Merge branch 'release_18.09' into dev 2018-10-04 11:46:35 -04:00
John Chilton 1c4a4ed8cb Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 2018-10-04 11:43:05 -04:00
John Chilton 4a345b99c3 Fix security problems when extracting untrusted tar files. 
Fixes GX-2018-0006.
 2018-10-04 11:32:52 -04:00