feat: add custom openBIS type #299
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Panaetius
requested changes
Jul 11, 2024
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Failing due to not passing style checks. If you install https://pre-commit.com/ it'd check this before every commit. Alternatively, run make style_checks to run the checks locally.
In this case, a simple ruff check --fix should fix it.
Pull Request Test Coverage Report for Build 10897839042Details
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olloz26
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Panaetius
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Aug 30, 2024
README.md
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| @@ -27,12 +27,14 @@ details. | |||
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| 1. Write code | |||
| 2. Run tests: `make tests` | |||
| * Run a specific test e.g.: `poetry run pytest test/bases/renku_data_services/data_api/test_storage_v2.py::test_storage_v2_create_openbis_secret` | |||
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| * Run a specific test e.g.: `poetry run pytest test/bases/renku_data_services/data_api/test_storage_v2.py::test_storage_v2_create_openbis_secret` | |
| * Run a specific test e.g.: `poetry run pytest -k test_storage_v2_create_openbis_secret` |
also works :)
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| provider = validator.providers[storage.storage_type] | ||
| sensitive_lookup = [o.name for o in provider.options if o.sensitive] | ||
| for secret in secrets: | ||
| if len(secret.value) > 0 and secret.name in sensitive_lookup: | ||
| continue | ||
| raise errors.ValidationError( | ||
| message=f"The '{secret.name}' property is not marked sensitive and can not be saved in the secret " | ||
| f"storage." | ||
| ) | ||
| expiration_timestamp = None | ||
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| if storage.storage_type == "openbis": | ||
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| async def openbis_transform_session_token_to_pat() -> tuple[str, datetime]: | ||
| if len(secrets) == 1 and secrets[0].name == "session_token": | ||
| try: | ||
| return await get_openbis_pat(storage.configuration["host"], secrets[0].value) | ||
| except Exception as e: | ||
| raise errors.ProgrammingError(message=str(e)) | ||
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| raise errors.ValidationError(message="The openBIS storage has only one secret: session_token") | ||
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| ( | ||
| secrets[0].value, | ||
| expiration_timestamp, | ||
| ) = await openbis_transform_session_token_to_pat() | ||
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| result = await self.storage_v2_repo.upsert_storage_secrets( | ||
| storage_id=storage_id, user=user, secrets=secrets | ||
| storage_id=storage_id, | ||
| user=user, | ||
| secrets=secrets, | ||
| expiration_timestamp=expiration_timestamp, | ||
| ) |
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suggestion: I'd put this in a storage/core.py file as this is business logic that shouldn't be in the presentation layer (blueprints.py file).
I'd also do the openbis check as a plain function, not a nested one with closures.
Comment on lines
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| provider = validator.providers[storage.storage_type] | ||
| sensitive_lookup = [o.name for o in provider.options if o.sensitive] |
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issue: I think you can use validator.get_provider here and you should definitely use provider.sensitive_options instead of the list comprehension
| try: | ||
| return await get_openbis_pat(storage.configuration["host"], secrets[0].value) | ||
| except Exception as e: | ||
| raise errors.ProgrammingError(message=str(e)) |
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Suggested change
| raise errors.ProgrammingError(message=str(e)) | |
| raise errors.ProgrammingError(message=str(e)) from e |
this way the inner stack trace does not get lost in e.g. sentry
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Panaetius
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Sep 10, 2024
Panaetius
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Panaetius
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/deploy renku-ui=olloz26/connect-renkulab-and-openbis-datasets