mvdbeek
ec7929c742
Construct CTEs using sqlalchemy core
2025-08-11 17:17:15 +02:00
mvdbeek
c2ddea2217
Implement touch collection update time CTE
2025-08-11 17:17:10 +02:00
Nicola Soranzo
7f89e0eab9
Code cleanups from pyupgrade
...
Found by running:
```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```
The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases
Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
packages needed by Pulsar, including the new galaxy-tool-util-models
package.
2025-07-31 11:17:22 +01:00
John Chilton
d26605517e
Implement sample sheets.
2025-07-25 11:46:59 -04:00
John Chilton
cb2d5cc611
Implement nested collection test in test_model_discovery.
2025-05-14 12:57:29 -04:00
Eli Chadwick
70cd4511b0
avoid caching in python 3.9
2025-05-07 10:45:12 +01:00
Eli Chadwick
f9688c43a7
isort
2025-05-07 10:45:11 +01:00
Eli Chadwick
09458577b2
linting
2025-05-07 10:45:10 +01:00
Eli Chadwick
007541d1e3
add version check to xfail
2025-05-07 10:45:10 +01:00
Eli Chadwick
a4fbf706b4
fix version check
2025-05-07 10:45:09 +01:00
Eli Chadwick
bd4da7a339
fix problem with non-existent files failing validation
2025-05-07 10:45:08 +01:00
Eli Chadwick
d1906cbf54
work around dependency issues
2025-05-07 10:45:08 +01:00
Eli Chadwick
419930627b
work around dependency issues
2025-05-07 10:45:08 +01:00
Eli Chadwick
5cf1dde60c
checked tests
2025-05-07 10:45:07 +01:00
Eli Chadwick
ed36c907b7
add tests using roc_validator
2025-05-07 10:45:06 +01:00
mvdbeek
c03d179db0
Implement dataset collection support in workflow landing requests
...
and tweak request models to make them compatible with workflow test format
2025-04-22 14:18:47 +02:00
Nicola Soranzo
b7591a0872
Improve type annotations of `ModelPersistenceContext` and derived classes
2025-03-20 12:46:35 +00:00
Nicola Soranzo
05b9467c35
Merge branch 'release_24.2' into dev
2025-03-13 00:37:29 +00:00
John Davis
104a375ea4
Add get_private_role_user_emails_dict, test
...
Retrieves a mapping of private role ids to associated users' emails.
Used to lookup a user's email when generating a displayed_name for
private roles.
2025-03-11 00:34:22 -04:00
John Davis
c4c66078d8
Factor out get_displayable_roles, add test
2025-03-10 11:13:13 -04:00
John Davis
f2f55131b2
Fix unit tests
2025-03-10 11:13:13 -04:00
John Davis
dfe1536a5d
Update test fixture
...
Specify correct role name for private roles. See comment in make_role
definition for why this must be set.
2025-03-10 11:13:13 -04:00
Nicola Soranzo
9477c7773e
Use model classes from `galaxy.model instead of app.model` object
...
for proper type annotation of query results.
Also:
- Drop unused code from `lib/tool_shed/webapp/controllers/user.py`
- Drop Galaxy model code from
`lib/tool_shed/util/admin_util.py:Admin.purge_user()`
2025-02-26 12:41:40 +00:00
Nicola Soranzo
0f1bfb6839
Type annotation improvements
2025-02-21 15:46:14 +00:00
mjosse
c6267d690d
imrpove ro-crate with eli's review
2025-01-30 16:14:21 +01:00
Marius van den Beek
951044096c
Drop stray print statement
2025-01-30 16:14:21 +01:00
mjosse
6204702f1d
rm useless import
2025-01-30 16:14:17 +01:00
mjosse
5a2c9c3fe8
rm label
2025-01-30 16:14:17 +01:00
mjosse
89920ee828
try to fix conflicts
2025-01-30 16:14:16 +01:00
mjosse
29b9fbe860
add some tests
2025-01-30 16:14:15 +01:00
mjosse
7eee144b31
remove useless tests
2025-01-30 16:13:47 +01:00
mjosse
861174e44e
fix lint rm useless import
2025-01-30 16:13:46 +01:00
mjosse
81e055fa90
add some tests
2025-01-30 16:13:46 +01:00
John Davis
6f47682a39
Remove transaction helper from test.unit.data
2025-01-23 11:39:24 -05:00
Nicola Soranzo
aa49793ecf
Make CompressedFile a context manager
...
to ensure that the archive is closed.
2025-01-18 14:40:30 +00:00
Nicola Soranzo
944450aa38
Uniform use of tmp_path in ro-crate tests
2025-01-10 15:12:17 +00:00
John Davis
16f7700ea4
Move method out of managers into model
...
To accommodate package unit testing
2024-11-20 16:52:23 -05:00
John Davis
b3e57cb9a2
Cleanup sharing roles on user purge, refactor, test
...
1. Update sharing role name removing purged user email
2. If sharing role has only one user association, delete it.
3. Factor out cleanup, add test.
Note: this will not work if user email has been udpated after the sharing
role was created.
2024-11-20 16:52:23 -05:00
John Davis
4be1eaf692
Update unit test w/new method name
2024-10-31 09:28:49 -04:00
John Davis and David López
4a7eb0a6ec
Fix typo
...
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2024-10-31 09:25:48 -04:00
John Davis
16f1d3f0e3
Fix error in select, add test
...
We must use a union because when we retrieve roles with a query, we
check against:
1) role name
2) email of associated user for private roles
We factor out this select into a helper method, which we then test
extensively.
2024-10-30 15:28:47 -04:00
John Davis
0e51a52272
Move test fixture to conftest
2024-10-30 15:28:47 -04:00
John Davis
e255a384cd
Modify make_role fixture to accommodate downgrading in migration tests
2024-10-30 15:28:47 -04:00
John Davis
f623ee851f
Adjust unit test: role name == user's current email
2024-10-30 15:28:47 -04:00
John Chilton
7f7710d392
Implement recovering normalized workflow request from invocation.
2024-10-15 09:12:05 -04:00
John Davis
00bebee7c7
Add test exposing bug
...
After user's email has been modified, we can't retrieve sharing roles
for that user
2024-10-04 14:44:41 -04:00
John Chilton
813ed02d53
Merge pull request #18886 from jdavcs/dev_db_test_update
...
Refactor migration testing setup code
2024-09-25 10:49:27 -04:00
Matthias Bernt
7dd606a6b2
Merge branch 'release_24.1' into dev
...
# Conflicts:
# lib/galaxy/version.py
# packages/app/HISTORY.rst
# packages/app/setup.cfg
# packages/auth/HISTORY.rst
# packages/auth/setup.cfg
# packages/config/HISTORY.rst
# packages/config/setup.cfg
# packages/data/HISTORY.rst
# packages/data/setup.cfg
# packages/files/HISTORY.rst
# packages/files/setup.cfg
# packages/job_execution/HISTORY.rst
# packages/job_execution/setup.cfg
# packages/job_metrics/HISTORY.rst
# packages/job_metrics/setup.cfg
# packages/navigation/HISTORY.rst
# packages/navigation/setup.cfg
# packages/objectstore/HISTORY.rst
# packages/objectstore/setup.cfg
# packages/schema/HISTORY.rst
# packages/schema/setup.cfg
# packages/selenium/HISTORY.rst
# packages/selenium/setup.cfg
# packages/test_api/HISTORY.rst
# packages/test_api/setup.cfg
# packages/test_base/HISTORY.rst
# packages/test_base/setup.cfg
# packages/test_driver/HISTORY.rst
# packages/test_driver/setup.cfg
# packages/tool_shed/HISTORY.rst
# packages/tool_shed/setup.cfg
# packages/tool_util/HISTORY.rst
# packages/tool_util/setup.cfg
# packages/tours/HISTORY.rst
# packages/tours/setup.cfg
# packages/util/HISTORY.rst
# packages/util/setup.cfg
# packages/web_apps/HISTORY.rst
# packages/web_apps/setup.cfg
# packages/web_framework/HISTORY.rst
# packages/web_framework/setup.cfg
# packages/web_stack/HISTORY.rst
# packages/web_stack/setup.cfg
2024-09-25 14:29:37 +02:00
John Davis
b57ec18991
Refactor migration testing setup code
...
- Do not explicitly import fixtures (a little duplication is safer/cleaner)
- Move dangerous fixture into module to prevent accidental usage from other modules
- Ensure only one database is used for all tests in module
2024-09-24 20:47:09 -04:00
John Davis
03641a98fa
Fix migration data fixes tests
...
When upgrading back to a valid revision, upgrade to head, not the
revision under test: we need the latest version of the model definition
in the database for the test to cleanup correctly.
2024-09-24 16:16:05 -04:00
mvdbeek