Bump Pydantic to v2+ #1285
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Bump Pydantic to v2+ #1285
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BenjaminCharmes
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1285 +/- ##
==========================================
- Coverage 78.49% 77.95% -0.55%
==========================================
Files 67 69 +2
Lines 4645 4885 +240
==========================================
+ Hits 3646 3808 +162
- Misses 999 1077 +78
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ml-evs
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Jul 29, 2025
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Hi @BenjaminCharmes, here's some partial initial comments/suggestions. I'll try to deploy a system based on this PR from scratch (and also investigate some of the new incantations that you've had to use for pydantic 2 compat).
pydatalab/src/pydatalab/login.py
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| if "_id" in user: | ||
| user["immutable_id"] = str(user.pop("_id")) | ||
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| if "managers" not in user: | ||
| user["managers"] = None | ||
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Note to self that I want to come back and verify this wrt. model aliases
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| Sample.model_rebuild() | ||
| StartingMaterial.model_rebuild() | ||
| Cell.model_rebuild() | ||
| Equipment.model_rebuild() | ||
| Collection.model_rebuild() |
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Suggested change
| Sample.model_rebuild() | |
| StartingMaterial.model_rebuild() | |
| Cell.model_rebuild() | |
| Equipment.model_rebuild() | |
| Collection.model_rebuild() | |
| {model.model_rebuild() for model in ITEM_MODELS.values()} |
Might be neater, though not sure why we need this now and not before (will play around with it later)
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Doesn't work with pre-commit for me, need to find out why.
It seems that this is necessary because Pydantic v2 is stricter with forward reference and circular dependencies
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Also need to keep Collection since it's not in ITEM_MODELS
pydatalab now start, but not working well pydatalab now start, but not working well pydatalab now start, but not working well pydatalab now start, but not working well pydatalab now start, but not working well Fix login with Pydantic v2+ Fix sample creation Fix sample creation Fix edit page
Fix pytest Fix pytest Fix pytest Fix pytest Fix pytest Fix pytest Fix pytest
Try fix .env PYDATALAB_TESTING Try fix .env PYDATALAB_TESTING Add temp. debug Add temp. debug Add temp. debug Add temp. debug Add temp. debug Add temp. debug Add temp. debug
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ml-evs
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| @model_validator(mode="before") | ||
| @classmethod | ||
| def add_missing_synthesis_relationships(cls, values): | ||
| """Add any missing sample synthesis constituents to parent relationships""" |
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I've moved this whole module, but want to check this validator as it seems a bit excessive
ml-evs
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| @model_validator(mode="before") | ||
| @classmethod | ||
| def add_missing_collection_relationships(cls, values): | ||
| if values.get("collections") is not None: |
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| except Exception as e: | ||
| LOGGER.exception(f"Error in get_item_data: {e}") | ||
| return jsonify({"status": "error", "message": str(e), "error_type": type(e).__name__}), 500 |
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Better to avoid this -- there are app-level error handlers that will produce better error messages for all routes + it makes PRs hard to review
ml-evs
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| if contact_email or contact_email in (None, ""): | ||
| if contact_email in ("", None): | ||
| update["contact_email"] = None | ||
| else: | ||
| update["contact_email"] = EmailStr(contact_email) | ||
| if "@" not in contact_email or len(contact_email) > 1000: |
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Things like this really need to be handled at the validator level
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Update Pydantic from v1.10 to v2+
Also closes #1282