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Commit Graph
255 Commits
Author SHA1 Message Date
Nicola Soranzo 95ccefacb8 Improve type annotations for model store 
and related files.

Follow-up on https://github.com/galaxyproject/galaxy/pull/14971 .
 2022-11-30 01:45:56 +00:00
John Davis d11eab88aa Merge pull request #15010 from jdavcs/dev_galaxy_root_func 
Use galaxy_directory() util function to check if code is running from root or from packages
 2022-11-22 10:25:38 -05:00
John Davis 29053fa9e4 Move test_dbscript into app 
JUSTIFICATION:
As per @jmchilton:
The package tests should pretend they don't have galaxy_directory()
available because they're meant to be installed into a Python env.
This test is fundamentally not testing anything about the Galaxy data
package - it is testing scripts placed in Galaxy root directory and that
would not be available in an installed Galaxy environment.
 2022-11-21 18:12:04 -05:00
John Davis 4e5a94a2b2 Use resource_path for test_dbscript 2022-11-21 18:12:04 -05:00
John Davis faf8efafd0 Use resource_path for test_migrations 2022-11-21 18:12:04 -05:00
John Davis dd267e2d3e Refactor test, use galaxy_directory() 2022-11-21 18:12:04 -05:00
John Davis 821b60f30a Use galaxy_directory() instead of hacking the path 2022-11-21 18:12:04 -05:00
John Davis 44e7c97b6d Fix get_chunk(), add test 2022-11-18 18:24:54 -05:00
John Chilton dac9f39266 Move model/mapping utils into packaged code for reuse by the tool shed. 2022-10-29 12:07:46 -04:00
Nicola Soranzo 5c43d2961f Use dnspython to check specifically for an "MX" DNS record 
when validating the domain name of the email address for a new user.

Fix https://github.com/galaxyproject/galaxy/issues/14829 .
 2022-10-27 11:17:14 +01:00
John Davis d5295de026 Merge pull request #14817 from jdavcs/dev_datatypes_misc2 
Misc. fixes to datatypes modules
 2022-10-22 17:36:41 -04:00
John Davis bd88031366 Fix linting 2022-10-22 01:17:26 -04:00
davelopez 881c57eb64 Fix export history RO-Crate without workflows 
The workflows_directory may not exists if no workflow was invoked in the history.

Includes unit test + small tests refactor
 2022-10-21 10:25:32 +02:00
John Davis 51eadc3663 Read 5 lines instead of file 2022-10-19 13:54:01 -04:00
Marius van den Beek 934369aa3a Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options 
Make connect_args for SQLAlchemy's engine configurable
 2022-10-17 10:30:44 +02:00
Björn Grüning 93e47e485d Merge pull request #14489 from itisAliRH/api-key-Enhancement 
API key enhancements
 2022-10-14 22:05:23 +02:00
John Davis d957e143ea Engine options are never null 2022-10-14 15:27:20 -04:00
John Davis 7578edbd00 Fix mypy error 2022-10-14 13:31:54 -04:00
John Davis da87ca9209 Allow to set connect_args for SQLAlchemy's engine in config 2022-10-14 13:17:42 -04:00
davelopez 8aebe9079e Fix some BCO fields 
- Pass the workflow url for the execution_domain instead of a fixed galaxy url
- Fix step annotations in PipelineStep description
- Use API url for downloading collections in InputSubdomainItem
 2022-10-14 12:20:24 +02:00
John Chilton 61b9e57c7f Implement Workflow Invocation -> BCO export. 2022-10-14 12:20:24 +02:00
davelopez 0356c2e01f Add unit test for api_keys.deleted column 2022-09-30 16:39:12 +02:00
Nicola Soranzo c35d8f2a06 Replace `unittest.TestCase` with pytest-based partial re-implementation 
Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
  by pytest only because they were `unittest.TestCase` derived, but normally
  pytest collects only test classes whose name starts with `Test`, see
  https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
 2022-09-27 03:34:58 +01:00
Nicola Soranzo 3091737ab9 Misc test fixes 2022-09-27 03:34:55 +01:00
John Chilton ba9df94510 Merge pull request #14674 from nsoranzo/replace_self.assert_methods 
Replace ``self.assert*()`` method calls with plain asserts
 2022-09-22 11:20:29 -04:00
Nicola Soranzo a5c41adb96 Remove unused `get_suite()` functions 2022-09-22 02:21:12 +01:00
Nicola Soranzo 853c8f913a Use `self.assertRaises*()` as a context manager 2022-09-21 23:50:06 +01:00
Nicola Soranzo f3b04b8f26 Remove `unittest.main()` calls 2022-09-21 23:50:05 +01:00
Nicola Soranzo b5c7e2c86a Replace `self.assert* method calls with plain asserts in test/` 
using https://github.com/pytest-dev/unittest2pytest with the following command:

```
unittest2pytest -f self_assert -w -n test/
```

(excluding ``self.assertRaises*`` method calls).
 2022-09-21 23:50:05 +01:00
John Davis 1eb4d15f38 Split script into admin and dev 
TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
 2022-09-16 00:39:44 -04:00
John Davis b6a5286487 Rename db.sh > manage_db.sh, following code review feedback 2022-09-16 00:39:44 -04:00
John Davis 3c094790a1 Update test comments 2022-09-16 00:39:03 -04:00
John Davis 372d4af0b8 Add type hints 2022-09-16 00:39:03 -04:00
John Davis 1f5b0e6bba Drop LegacyScripts: no longer used 2022-09-16 00:39:03 -04:00
John Davis 7e238bf591 Add --raiseerr option; hide error traceback by default 2022-09-16 00:39:03 -04:00
John Davis 959bc49e66 Add missing tests 2022-09-16 00:39:03 -04:00
John Davis 0745e2e05c Fix mypy by asserting object before accessing its attributes 2022-09-16 00:39:03 -04:00
John Davis 89f753767b Fix packages tests: script is one level up 2022-09-16 00:39:03 -04:00
John Davis ac6b0ceee0 Fix linting 2022-09-16 00:39:03 -04:00
John Davis 0a798ea536 Test against 1 or 2 databases 2022-09-16 00:39:03 -04:00
John Davis b30e4e14ae Add inline testing documentation 2022-09-16 00:39:03 -04:00
John Davis a69ab407a6 Add initial draft 2022-09-16 00:39:03 -04:00
John Davis 6abc9dc1c5 Refactor get_alembic_cfg: make available to other code 2022-09-16 00:39:03 -04:00
John Chilton 3dbe2891e7 Implement RO Crate export of Galaxy histories and invocations. 2022-09-13 19:20:48 -04:00
Nicola Soranzo cb012c7fb2 Merge branch 'release_22.05' into dev 2022-09-09 17:14:20 +01:00
mvdbeek aceaa698fc Ensure guid is hexadecimal value 2022-09-08 14:04:35 +02:00
Matej Troják 7d1807fc1e Merge branch 'dev' into sybila-tools-datatypes 2022-08-31 12:07:18 +01:00
mvdbeek a351bd1ce9 Merge branch 'release_22.05' into dev 2022-08-09 15:12:15 +02:00
Matej Trojak bbf8eea34f Remove storm.regions datatype (obsolete) 2022-08-08 15:36:04 +02:00
Matej Trojak 63352c0155 Reformatted import according to isort 2022-08-04 10:56:24 +02:00