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Author SHA1 Message Date
Martin Cech e080babaad Merge pull request #6727 from VJalili/oidc_consent 
Updates to OIDC backends default config
 2018-09-17 14:04:11 -04:00
vjalili 5a784890de Update a comment in the default config of OIDC backends. 2018-09-17 10:56:38 -07:00
vjalili 56fb283d9b Add a comment on why user does not see a consent screen with Google. 2018-09-17 10:43:49 -07:00
vjalili 04a75bd33b Change default prompt option for Google OIDC IdP. 2018-09-17 09:41:29 -07:00
John Chilton 4ebfad7526 Merge pull request #6722 from nsoranzo/fix_warnings 
Small mixed fixes
 2018-09-17 12:40:45 -04:00
Nicola Soranzo 0c931235af Change all remaining old-style classes to new style 2018-09-17 12:26:07 +01:00
Nicola Soranzo 721a4656d9 pytest: disable test collection of classes starting with Test 
Fix warnings like:

```
/home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor
  class TestDataResolver(object):
```

appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 .

See pytest documentation:
https://docs.pytest.org/en/latest/reference.html#confval-python_classes
 2018-09-17 12:01:14 +01:00
Nicola Soranzo 19bd8e0dff Fix typos 2018-09-17 11:45:01 +01:00
Nicola Soranzo e950579bf2 Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter() 2018-09-17 11:00:08 +01:00
Nicola Soranzo 7d71d98675 async is a reserved keyword in Python 3.7 
- Remove unused `async` parameter of `stage_data_async()` method.
- Rename `async` parameter of `quick_load()` method.

Fix https://github.com/galaxyproject/galaxy/issues/6717 .

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-09-17 10:32:35 +01:00
Nicola Soranzo 9b4d955853 Remove deprecated decode_param_names parameter 
It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 .
 2018-09-17 09:39:04 +01:00
Martin Cech 33cac64546 Merge pull request #6710 from mvdbeek/change_version_parameter_to_tool_version 
Use tool_version instead of version parameter
 2018-09-13 22:07:36 -04:00
mvdbeek 17d148eb8f Use tool_version instead of version parameter 
To be consistent with other routes that accept this parameter.
 2018-09-13 20:30:52 +02:00
Nicola Soranzo d1352c4b27 Merge pull request #6702 from mvdbeek/fix_latest_version 
Fix wrong version being returned if requested version doesn't exist
 2018-09-13 15:29:54 +01:00
mvdbeek 56ed50400f Sort rval so that newest tool appears last in rval 2018-09-13 14:51:03 +02:00
mvdbeek f8430b110d Sort by tool version when picking a tool with an unavailable version 2018-09-13 13:25:09 +02:00
mvdbeek 5de1c2c980 Unit test that fails if we don't return the latest version upon version mismatch 2018-09-13 13:25:09 +02:00
mvdbeek 943e67e4e5 Test that newest version will be returned if tool id or version don't match 2018-09-13 13:25:09 +02:00
Nicola Soranzo 5286a1e757 Merge pull request #6694 from VJalili/patch-5 
Patch update.sh to address dependency update issues on a macOS.
 2018-09-12 11:37:19 +01:00
Vahid c871a03e5b Patch update.sh 
to address dependency update issues on a macOS.
 2018-09-11 15:10:04 -07:00
Dannon 0c9d02f962 Merge pull request #6688 from dannon/version-19.01.dev 
Version 19.01.dev
 2018-09-10 18:55:05 -04:00
Dannon Baker 88c2130ed1 Merge branch 'version-18.09' into version-19.01.dev 2018-09-10 18:52:45 -04:00
Dannon Baker c06464a78c Update version to 19.01.dev 2018-09-10 18:52:44 -04:00
Dannon Baker be04959cf3 Update version to 18.09.rc1 2018-09-10 18:52:44 -04:00
Dannon ebc5858f02 Merge pull request #6660 from VJalili/upgrade_cloudbridge 
Upgrade CloudBridge to v1.0.1
 2018-09-10 17:32:30 -04:00
Dannon Baker b8fe2fe294 Merge branch 'release_18.05' into dev 2018-09-10 17:31:24 -04:00
Dannon 3e4bbfbbc2 Merge pull request #6683 from mvdbeek/expose_workflow_versions 
Expose workflow versions
 2018-09-10 16:46:24 -04:00
Nate Coraor 9217680ab6 Merge pull request #6647 from dannon/page_fixes 
[18.05] Pages - fixes for encoded ids in the database
 2018-09-10 16:21:46 -04:00
Dannon d349d4763d Merge pull request #6678 from jmchilton/subworkflow_parameters 
Workflow replacement parameters polish.
 2018-09-10 15:28:05 -04:00
Dannon d42fb41cb0 Merge pull request #6681 from mvdbeek/continue_reloading_if_tool_is_broken 
Keep newly broken tool in toolbox
 2018-09-10 14:56:25 -04:00
mvdbeek efec721676 Move version selection out of editor.mako 
Also adds an API that lists workflow versions for a workflow id.
 2018-09-10 20:06:44 +02:00
vjalili 240074224f Rename bucket_obj to bucket. 2018-09-10 10:50:33 -07:00
vjalili 11274995ca Rename bucket to bucket_name in cloud API and manager. 2018-09-10 10:37:52 -07:00
Nicola Soranzo c95d995e9d Fix pyinotify environment marker 
Remove outdated pin on boto.
 2018-09-10 18:13:38 +01:00
Nicola Soranzo ae41b22113 Update dependencies 
using `make update-dependencies`.
 2018-09-10 12:40:48 +01:00
vjalili 94fe62803b Update cloudbridge version in conditional requirements. 2018-09-10 12:27:30 +01:00
vjalili 0956604e55 Update cloud manager to adhere with v1 cloudbridge interface. 2018-09-10 12:27:06 +01:00
vjalili a52b8a4365 Catch a cloudbridge exception if a given bucket does not exist. 2018-09-10 12:25:53 +01:00
vjalili d0e2820b4f Log exception message failing to create bucket in cloud objectstore. 2018-09-10 12:25:53 +01:00
vjalili ec320d2bad Update cloud objectstore to adhere with cloudbridge v1 interface. 2018-09-10 12:25:53 +01:00
mvdbeek d377b00388 Indicate which version is currently on display 2018-09-10 10:18:07 +02:00
mvdbeek 85adb0a371 Move version selection to right-hand most location 2018-09-10 09:57:58 +02:00
mvdbeek 85d80ec20b Always pass in a version when loading the wf-editor 2018-09-09 19:24:53 +02:00
mvdbeek 98a2526cec Show current version in version selection 2018-09-09 19:24:53 +02:00
charesredhat f1e94f8473 Added Workflow version change control to the top bar 2018-09-09 19:24:53 +02:00
mvdbeek 56411c3c11 Hack around routes returning 'None' for parameter 2018-09-09 19:24:53 +02:00
mvdbeek 3d8db3a91f Inform user that workflow loading has failed 
This sends the user back to the worflow index page.
 2018-09-09 19:24:53 +02:00
mvdbeek c652cf4b07 Allow loading non-latest workflows into editor 
There is no UI-element so far, but you can append &version=<N>
to the editor URL to load any arbitrary version of a workflow.
 2018-09-09 19:24:53 +02:00
mvdbeek e18433127f Order list of workflows related to a StoredWorkflow 
This will put the newest workflows first.
 2018-09-09 19:24:53 +02:00
mvdbeek f49da14e45 Move recovery functionality for getting perticular workflow versions into StoredWorkflow 2018-09-09 19:24:53 +02:00