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Commit Graph
241 Commits
Author SHA1 Message Date
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
Matej Trojak df7d1aa602 Reformatted files using black 2022-08-04 10:33:04 +02:00
Matej Trojak 5241c609a1 Add tests for introduced datatypes 2022-07-22 11:11:12 -05:00
John Davis def882932d Add verify_db_is_initialized function; tests 2022-07-13 16:10:58 -04:00
John Davis 1e75d85fd4 Prevent accessing LegacyScripts.database before processing script args 2022-07-13 15:40:42 -04:00
Nicola Soranzo d8f123f647 Code cleanups from pyupgrade 
Found by running:

```
ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus
```
 2022-07-12 13:40:36 +01:00
John Davis 1f3849bd1f Rename test 2022-07-08 13:41:40 -04:00
Nicola Soranzo cdaa23cea6 Merge branch 'release_22.05' into dev 2022-07-06 11:47:54 +01:00
Evan Bolyen 184f0d8eaf TST: fix qiime2.tabular auto-upload test 2022-07-05 09:43:30 -07:00
Evan Bolyen 9c06e232e1 lint: make format is neat 2022-07-05 09:43:30 -07:00
Evan Bolyen 88fed0ffff TST: added more tests 2022-07-05 09:43:30 -07:00
Oddant1 38b1bfc417 QIIME 2: Strip properties from semantic types (#2) 2022-07-05 09:43:30 -07:00
Nicola Soranzo 14b1730eb2 Combine "as" imports with other "from" imports 2022-06-20 20:06:30 +01:00
Nate Coraor a9047f848d Fix overlapping method/var name in domain validation 2022-06-16 21:09:59 -04:00
Sergey Golitsynskiy bf91dc5b75 Remove column update_time from model, tests 2022-06-01 18:30:30 -04:00