John Davis
bd56131ebd
Split script into admin and dev
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TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
2022-09-28 15:45:00 -04:00
John Davis
e43552fdc5
Rename db.sh > manage_db.sh, following code review feedback
2022-09-28 15:45:00 -04:00
John Davis
0c348a5759
Update test comments
2022-09-28 15:32:10 -04:00
John Davis
dfd32a2ee8
Add type hints
2022-09-28 15:32:01 -04:00
John Davis
6fcc58a85c
Drop LegacyScripts: no longer used
2022-09-28 15:31:25 -04:00
John Davis
d8e8a8efb6
Add --raiseerr option; hide error traceback by default
2022-09-28 15:25:14 -04:00
John Davis
b4b76c91a2
Add missing tests
2022-09-28 15:25:06 -04:00
John Davis
bf83b4347a
Fix mypy by asserting object before accessing its attributes
2022-09-28 15:24:40 -04:00
John Davis
e0e30a5744
Fix packages tests: script is one level up
2022-09-28 15:24:26 -04:00
John Davis
3be7c53eb9
Fix linting
2022-09-28 15:24:16 -04:00
John Davis
ab1854f3a7
Test against 1 or 2 databases
2022-09-28 15:23:50 -04:00
John Davis
887b882ff0
Add inline testing documentation
2022-09-28 15:23:42 -04:00
John Davis
b64fda7478
Add initial draft
2022-09-28 15:23:21 -04:00
John Davis
4cd3291598
Refactor get_alembic_cfg: make available to other code
2022-09-28 15:23:09 -04:00
mvdbeek
aceaa698fc
Ensure guid is hexadecimal value
2022-09-08 14:04:35 +02:00
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
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
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
Nate Coraor
1f299a5cbf
Test with quoted @ in local part of email (technically valid but we're
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not allowing it)
2022-05-26 15:05:30 -04:00
Nate Coraor
d1e79e0441
Test split without @
2022-05-26 15:05:30 -04:00
Nate Coraor
37edbaf74c
Trim spaces from around email addresses and usernames when registering.
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Additionally, include a stricter email address validation.
2022-05-26 14:55:27 -04:00
John Chilton
c5bf63bc91
Add DEFERRED datasets to Galaxy
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- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
2022-05-23 19:48:47 -04:00
Sergey Golitsynskiy
34e8b182d4
Map Dataset declaratively
2022-04-29 13:37:32 -04:00
Sergey Golitsynskiy
cc1c2e4b94
Enable postgresql testing for new annotations module
2022-04-20 22:16:40 -04:00
Sergey Golitsynskiy
e9eb6c1500
Proof of concept: replace annotation mapping tests
2022-04-20 18:14:43 -04:00
Sergey Golitsynskiy
254830a33b
Add fixture for WorkflowStepAnnotationAssociation
2022-04-20 17:48:37 -04:00
Sergey Golitsynskiy
ed2798e044
Fix module path for remote unit tests
2022-04-20 17:03:03 -04:00
Sergey Golitsynskiy
52bb6c90e6
Fix linting
2022-04-20 16:23:05 -04:00
Sergey Golitsynskiy
95a4fd5667
Use plugins instead of importing fixtures directly
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Also handle setting the fully qualified module name depending on wht's
the cwd from which the test is executed.
2022-04-20 15:50:52 -04:00
Sergey Golitsynskiy
c9e3d340f6
Move tmp_dir fixture one level up
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Otherwise url_factory is not usable outside of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
1228bfa769
Refactor code for dropping postgres
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
495dd6daaf
Move last context managers out of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
c3059de4a5
Move disposing_engine out of migrations
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
eec0a87028
Move url_factory out of migrations
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Make available for use in other testing contexts.
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
476da34b7a
Move test revisions into testing_utils
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
f5c962d8d7
Move common.py to testing_utils
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
d2ecb7ee68
Fix linting (unused import)
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
0a7d2113bd
Factor out helper function (kill more dups)
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
9ae2d4e08f
Simplify (no need for scoped_session), consolidate redundant fixtures
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
1a95857271
Rename test modules for testing_utils
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
9e4cb1176c
Fix linting errors
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
7278126dd6
Move model testing utils into designated dir
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
de4498c3c3
Factor out model fixtures, adjust tests
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
a037b22f6e
Move mapping testing utils into designated dir
2022-04-20 10:28:03 -04:00
Sergey Golitsynskiy
90288acaf0
Distribute tests following prev. commit, fix imports
2022-04-20 10:28:03 -04:00
John Davis