Commit Graph
2304 Commits
Author SHA1 Message Date
Martin Cech 81ecaca10f add urls to openapi redoc documents 2023-03-06 14:59:45 -08:00
Dannon Baker 6e527ca9ab Tours cleanup (this went with the swap to a custom tour driver) 2023-02-13 11:43:09 -05:00
Nate Coraor d94f1f644e Merge pull request #15550 from mvdbeek/use_sentry_fastapi_integration
[23.0] Use sentry-fastapi integration, expose sampling rate
2023-02-10 09:45:31 -05:00
mvdbeek a31eb0489c Use sentry-fastapi integration, expose sampling rate 2023-02-10 13:03:09 +01:00
mvdbeek 981c0f83f9 Drop SentryWSGIMiddleware
It appears that we can't combine the WSGI middleware with the ASGI
middleware in the same app. We're currently not sending events that
occur in the WSGI portion of the app. With this change they're logged
again, though we do lose the WSGI request context (which contains,
browser, route, etc.) It's usually pretty clear from the traceback what
went wrong though, so I think this is much better than what's happening
now.
2023-02-10 12:06:44 +01:00
John Davis 11ca95ba3c Add new release tags to db migration scripts
Note: we add release_23.1 to the TS script because that's the release
that will contain the base revision.
2023-02-09 14:52:32 -05:00
John Davis e6b9da9070 Factor out common code into migrations.base 2023-02-08 14:33:30 -05:00
John Davis df0c6b6292 Move migration exception classes into their own module 2023-02-08 12:12:21 -05:00
John Davis d4e7a0f3f8 Implement script handling for TS migrations; refactor core 2023-02-08 00:33:48 -05:00
John Davis e7726f04f1 Move up AlembicManager: must be available for type hints 2023-02-08 00:33:48 -05:00
John Davis e4948af546 Do not initialize db-dependent objects in constructor 2023-02-08 00:33:48 -05:00
John Davis 1046d958c3 Fix mypy for db_heads 2023-02-08 00:33:48 -05:00
John Davis f275638c25 Delete old migrate code 2023-02-08 00:33:48 -05:00
John Davis 4f4b994b60 Handle db verification of tool shed startup with Alembic 2023-02-08 00:33:48 -05:00
John Chilton e9832bfbfb Some typing for api/categories.py 2023-02-03 13:47:39 -05:00
John Chilton 1d99e14900 Remove unused function from twilltestcase. 2023-02-03 13:47:39 -05:00
John Chilton 6b3a2d3cd6 Enhance schema models. 2023-02-03 13:47:38 -05:00
John Chilton 18f73b5532 Some initial type checking for shed_util_common.py 2023-02-03 13:47:38 -05:00
John Chilton 5d49042db9 Remove unused code from shed_util_common.py 2023-02-03 13:47:38 -05:00
John Chilton 089d8abf2e Interface for tool shed trans... 2023-02-03 13:47:38 -05:00
John Chilton 8a74a550bc A little cleanup of suc. 2023-02-03 13:47:38 -05:00
John Chilton fd96765475 Remove test_0540... I'm not sure it is worth maintaince cost.
It is using legacy features and I don't see it really testing obsecure aspects of them.
2023-02-03 13:47:38 -05:00
John Chilton e0887dce68 Improved type signature for repository_util. 2023-02-03 13:47:38 -05:00
John Chilton 86d5ab6bb3 Typing for various tool shed utilities. 2023-02-03 13:47:38 -05:00
John Chilton 90c0f61747 Remove unused code in tool version manager. 2023-02-03 13:47:38 -05:00
John Chilton 786e8bec44 Remove unused method in twilltestcase. 2023-02-03 13:47:38 -05:00
John Chilton cc2be393b0 Remove unused helper in twilltestcase for tool shed. 2023-02-03 13:47:38 -05:00
John Chilton e87697bb9d Refactor tool_util only used by tool_shed code into tool_shed. 2023-02-03 13:47:38 -05:00
John Chilton 9b7897e728 Remove unused code from lib/tool_shed/webapp/templates/webapps/tool_shed/repository/common.mako 2023-02-03 13:47:38 -05:00
John Chilton 24c204915c Simplilfy relation_builder now that we don't export capsules... 2023-02-03 13:47:38 -05:00
Nicola Soranzo 30f60493c3 Format Python code with black 23.1.0
with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
2023-02-01 23:51:03 +00:00
John Davis 38afccd780 Fix linting 2023-01-21 11:13:36 -05:00
John Davis fe7bf27658 Join/load: replace strings with attrs (toolshed-related) 2023-01-21 10:59:59 -05:00
guerler 93a1df097f Avoid renaming masthead identifier 2023-01-12 16:30:21 -05:00
guerler 94f09e8275 Move styles to toolshed scss, allow simple variables 2023-01-12 16:15:33 -05:00
guerler 66fc8ddd99 Fix fixed-top class identifier, properly close title tag 2023-01-12 16:15:33 -05:00
guerler 0ae2f6bacd Properly close masthead nav tag in toolshed masthead template 2023-01-12 16:15:33 -05:00
guerler 0dabed6464 Properly indent toolshed masthead template details 2023-01-12 16:15:33 -05:00
guerler abb4298746 Remove duplicate masthead id and class specification 2023-01-12 16:15:33 -05:00
guerler c163b88b06 Add static css to toolshed legacy makos to restore previous default appearance 2023-01-12 16:15:33 -05:00
Dannon Baker 485fa57ba8 Python formatting w/black -- make format 2023-01-10 09:25:35 -05:00
jhl667 5b961965fb add set_random_password to tool_shed User
Fixes #15278
```
Traceback (most recent call last):
  File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__
    app_iter = self.application(environ, sr_checker)
  File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__
    return self.app(environ, start_response)
  File "/galaxy/.venv/lib/python3.6/site-packages/paste/translogger.py", line 69, in __call__
    return self.application(environ, replacement_start_response)
  File "/galaxy/.venv/lib/python3.6/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "/galaxy/.venv/lib/python3.6/site-packages/routes/middleware.py", line 153, in __call__
    response = self.app(environ, start_response)
  File "/galaxy/.venv/lib/python3.6/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "lib/galaxy/web/framework/base.py", line 138, in __call__
    return self.handle_request(environ, start_response)
  File "lib/galaxy/web/framework/base.py", line 217, in handle_request
    body = method(trans, **kwargs)
  File "lib/tool_shed/webapp/controllers/user.py", line 68, in login
    response = self.__validate_login(trans, **kwd)
  File "lib/galaxy/webapps/galaxy/controllers/user.py", line 139, in __validate_login
    message, user = self.__autoregistration(trans, login, password)
  File "lib/galaxy/webapps/galaxy/controllers/user.py", line 97, in __autoregistration
    user = self.user_manager.create(email=email, username=username, password="")
  File "lib/galaxy/managers/users.py", line 116, in create
    user.set_random_password()
AttributeError: 'User' object has no attribute 'set_random_password'
```
2023-01-06 11:25:14 -08:00
Martin Cech 063405a1cd replace the png favicon with svg version
goes down from 16kb to 9kb and preserves all details

add padding to masthead logo

it now has no padding in the image itself

Add margin to svg

drop padding

since we decided to include it in logos

Slightly increase margin further
2022-12-20 15:44:07 -08:00
Michael R. Crusoe 75ba9cfd13 Even more typing 2022-11-28 04:50:00 +00:00
Michael R. CrusoeandNicola Soranzo c500fa1347 minimal changes for MyPy 0.991
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
2022-11-27 18:23:35 +01:00
mvdbeek 7f0754eef7 Upgrade FastAPI to 0.87.0, drop old workarounds 2022-11-16 14:31:49 +01:00
John Chilton 92a885e280 Remove old WSGI middleware that is no longer useful. 2022-11-10 05:28:24 -05:00
Nicola Soranzo c8dc648119 Merge branch 'release_22.05' into dev 2022-11-07 23:12:32 +00:00
John Davis dc528e7283 Update migration instructions 2022-11-04 10:26:02 -04:00
Nicola Soranzo 8b461d2639 Merge branch 'release_22.05' into dev 2022-11-04 09:37:23 +00:00