Migration to Pydantic v2: Enable compatibility with later FastAPI versions

[ChrisChapman-gh]

This PR migrates the Azure TRE codebase from Pydantic v1.10.19 to v2.13.4 to enable compatibility with later versions of FastAPI that require Pydantic v2.

Overview

Later versions of FastAPI require Pydantic v2, and this migration ensures Azure TRE can upgrade FastAPI without being blocked by Pydantic version constraints.

Key Changes

🔧 Core Infrastructure Updates

• Requirements updated: Both api_app/requirements.txt and airlock_processor/requirements.txt now specify Pydantic v2.13.4
• Backward compatibility: backwards compatibility for data written/read from cosmos or from templates in v1 must be maintained.

🏗️ Model Architecture Migration

• Base model modernized: AzureTREModel now uses Pydantic v2 ConfigDict with v1 fallback
• Configuration migration: allow_population_by_field_name → populate_by_name
• Validator updates: Migrated from @validator to @field_validator with compatibility layer

📦 Component Updates

• API App: 21 files updated including domain models and schemas
• Airlock Processor: Added compatibility layer for parse_obj_as → TypeAdapter pattern
• Schema modernization: Applied automated updates using bump-pydantic tool

Example Migration Pattern

Before (Pydantic v1):

from pydantic import BaseConfig, BaseModel, validator

class AzureTREModel(BaseModel):
    class Config(BaseConfig):
        allow_population_by_field_name = True
        arbitrary_types_allowed = True

    @validator("etag", pre=True)
    def parse_etag(cls, value):
        return value.replace('"', '')

After (Pydantic v2 with v1 compatibility):

try:
    # Pydantic v2
    from pydantic import BaseModel, ConfigDict, field_validator
    
    class AzureTREModel(BaseModel):
        model_config = ConfigDict(
            populate_by_name=True,
            arbitrary_types_allowed=True
        )
        
    @field_validator("etag", mode="before")
    @classmethod
    def parse_etag(cls, value):
        return value.replace('"', '')
        
except ImportError:
    # Pydantic v1 fallback
    from pydantic import BaseConfig, BaseModel, validator
    # ... v1 implementation

Testing & Validation

✅ Comprehensive test suite: All existing functionality preserved
✅ FastAPI compatibility: Confirmed working with FastAPI 0.115.3
✅ Component isolation: API app and airlock processor independently validated
✅ Migration tools: Used official bump-pydantic tool for schema updates

Impact

• Files changed: 23 files total (410 additions, 442 deletions)
• Net code reduction: Cleaner, more modern Pydantic v2 patterns
• Zero breaking changes: Maintains all existing API contracts
• Future-ready: Enables FastAPI upgrades requiring Pydantic v2

Migration Benefits

1. Unblocks FastAPI upgrades - Later FastAPI versions require Pydantic v2
2. Performance improvements - Pydantic v2 offers significant performance gains
3. Better type safety - Enhanced validation and serialization capabilities
4. Modern patterns - Cleaner configuration and validation syntax

Fixes #4637.

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[Copilot]

Pull request overview

Copilot reviewed 118 out of 118 changed files in this pull request and generated no new comments.

Suppressed comments (3)

api_app/models/schemas/airlock_request_url.py:16

• The OpenAPI example uses the key "container_url", but the response model field is "containerUrl" (camelCase). This makes the generated docs misleading for clients.
  api_app/models/schemas/workspace_service.py:29
• The OpenAPI example uses "workspace_service", but the response model field is "workspaceService". This mismatch can confuse API consumers reading the docs.
  api_app/models/schemas/user_resource.py:34
• The OpenAPI example uses "user_resource", but the response model field is "userResource". Align the example key with the actual response shape.

[github-actions]

🤖 pr-bot 🤖

🏃 Running extended tests: https://github.com/microsoft/AzureTRE/actions/runs/30644447349 (with refid f090555c)

(in response to this comment from @ChrisChapman-gh)

[JC-wk]

I can't see the v1 compatibility code that is described in the PR ? @ChrisChapman-gh @marrobi
commit ebc7766 ("Remove Pydantic v1 backward compatibility") removed all try/except fallback blocks.

[JC-wk]

LGTM
I would suggest a future update to display a warning that a templates has failed v2 validation saying v1/legacy template support will be removed in version x and that they should upgrade their templates. And then tighten up and areas that were done for v1 compatibility reasons.

[marrobi]

@JC-wk @ChrisChapman-gh should this be in this PR? Is it not in a different PR?

[marrobi]

Some issues flagged by an AI review.

[marrobi]

ResourceTemplate.properties went from Dict[str, Property] to Dict[str, Any]. This means registered template properties are now completely unvalidated. Was this deliberate, or a workaround for a validation failure? Given it lands alongside remove_legacy_null_property_fields, it feels like the latter. If it's intentional it needs a comment explaining why; if it's a workaround, I'd like to know what was actually breaking.

[ChrisChapman-gh]

fixed - see commit: 61a28d4

[marrobi]

The default doesn't satisfy the annotation. v2 won't complain (defaults aren't validated unless validate_default=True), but this should be Optional[Union[dict, str]] = Field(default=None, ...) — otherwise the declared type is a lie for any step that omits value.

[ChrisChapman-gh]

fixed in 9059b0a5ff7f240d9161c2bcd1c2c832c8ea05dd

[marrobi]

"" is not a float. Passes silently in v2, but any Operation constructed without these gets a str where downstream code expects a number. Since almost every other field in this file was touched, worth fixing to 0.0 in the same pass. Line 49 (resourceTemplateName: Optional[str] = Field("")) and line 90 (status: Status = Field(None)) have the same smell.

[ChrisChapman-gh]

fixed in 9059b0a5ff7f240d9161c2bcd1c2c832c8ea05dd

[marrobi]

More feedback:

In AirlockRequestInCreate, remove the empty-string default from type so callers must provide a valid AirlockRequestType (import or export).

In AirlockReviewInCreate, remove the empty-string default from approval so callers must provide a boolean. Update the OpenAPI example from the string "True" to the boolean true.

Preserve intentional const: null and default: null values. Update the legacy schema cleanup so it does not remove const or default when their value is null; both are valid JSON Schema and can carry intentional semantics. Add tests proving that const: null continues to reject non-null values and that default: null remains present after template enrichment. Retain coverage for removing only the legacy null fields that are genuinely invalid or generated accidentally.

Correct invalid typed defaults across all models touched by this migration. Audit every changed Pydantic model for defaults that do not satisfy the annotated type, including empty strings assigned to enums, booleans, floats, or integers, and None assigned to non-optional fields. For required fields, remove the default; for genuinely optional fields, use Optional[...] with None; otherwise use a valid value of the declared type. Pay particular attention to AirlockRequestInCreate.type, AirlockReviewInCreate.approval, PipelineStepProperty.value, Operation.status, Operation.createdWhen, Operation.updatedWhen, and similar fields. Add tests that instantiate models with omitted fields and verify they either fail validation when required or produce values matching their declared types.

[Copilot]

Pull request overview

Copilot reviewed 118 out of 118 changed files in this pull request and generated no new comments.

Suppressed comments (2)

api_app/models/domain/resource_template.py:13

• This recursive cleanup removes every None value, including valid JSON Schema annotations and constraints such as "default": null and "const": null. Checked-in schemas already use null defaults (for example templates/workspace_services/ohdsi/template_schema.json:59), and a user-supplied const: null would be silently deleted, broadening validation. Restrict cleanup to keywords for which null is structurally invalid rather than deleting arbitrary null-valued schema entries.
  airlock_processor/StatusChangedQueueTrigger/init.py:13
• Under Pydantic v2, Optional[str] without a default is still required. RequestProperties.previous_status was optional under v1 but now rejects status events that omit it, even though the API's corresponding StatusChangedData.previous_status defaults to None. Preserve the existing queue contract by giving this field a None default.

from pydantic import BaseModel, TypeAdapter

[ChrisChapman-gh]

More feedback:

In AirlockRequestInCreate, remove the empty-string default from type so callers must provide a valid AirlockRequestType (import or export).

In AirlockReviewInCreate, remove the empty-string default from approval so callers must provide a boolean. Update the OpenAPI example from the string "True" to the boolean true.

Preserve intentional const: null and default: null values. Update the legacy schema cleanup so it does not remove const or default when their value is null; both are valid JSON Schema and can carry intentional semantics. Add tests proving that const: null continues to reject non-null values and that default: null remains present after template enrichment. Retain coverage for removing only the legacy null fields that are genuinely invalid or generated accidentally.

Correct invalid typed defaults across all models touched by this migration. Audit every changed Pydantic model for defaults that do not satisfy the annotated type, including empty strings assigned to enums, booleans, floats, or integers, and None assigned to non-optional fields. For required fields, remove the default; for genuinely optional fields, use Optional[...] with None; otherwise use a valid value of the declared type. Pay particular attention to AirlockRequestInCreate.type, AirlockReviewInCreate.approval, PipelineStepProperty.value, Operation.status, Operation.createdWhen, Operation.updatedWhen, and similar fields. Add tests that instantiate models with omitted fields and verify they either fail validation when required or produce values matching their declared types.

Fixed the first two in 9059b0a5ff7f240d9161c2bcd1c2c832c8ea05dd

[Copilot]

Pull request overview

Copilot reviewed 121 out of 121 changed files in this pull request and generated no new comments.

Suppressed comments (3)

api_app/models/domain/resource_template.py:42

• Pydantic v2 no longer coerces numeric or boolean values to strings by default, so keeping enum as List[str] makes registration reject valid JSON Schemas such as {"enum": [1, 2]}. JSON Schema enum values may be heterogeneous; preserve them as Any values instead.
  airlock_processor/StatusChangedQueueTrigger/init.py:13
• Under Pydantic v2, Optional[str] without a default is still a required field. The previous v1 parser accepted status-change messages that omitted previous_status, but this new TypeAdapter path rejects them before processing; give the field a None default to preserve that input contract.

from pydantic import BaseModel, TypeAdapter

api_app/requirements.txt:25

• The PR description promises a Pydantic v1/v2 compatibility fallback, but this hard pin and the direct use of v2-only APIs (ConfigDict, field_validator, and TypeAdapter) make the application v2-only. Either implement the documented fallback or update the migration/rollback expectations to describe a hard cutover.

[Copilot]

Pull request overview

Copilot reviewed 122 out of 122 changed files in this pull request and generated 1 comment.

Suppressed comments (1)

api_app/requirements.txt:25

• The PR description promises a Pydantic v1/v2 compatibility layer, but this hard pin and the unconditional use of v2-only APIs (ConfigDict, field_validator, TypeAdapter, and model_dump) make the application unable to import under Pydantic v1. Either implement and test the documented fallback across both components or update the PR description to state that this is a v2-only migration.

[Copilot]

Pull request overview

Copilot reviewed 122 out of 122 changed files in this pull request and generated no new comments.

Suppressed comments (2)

api_app/models/domain/resource.py:113

• value still has a default of None, so Output(name=..., type=...) is accepted. This directly contradicts the new test_output_requires_value test and allows malformed deployment outputs through validation. Make the field required while retaining Optional only if an explicit JSON null is valid.
  api_app/requirements.txt:25
• The PR description explicitly promises a Pydantic v1 fallback, but this hard pin (along with unconditional use of v2-only APIs such as TypeAdapter, field_validator, and model_dump) makes both components v2-only. Either implement the documented compatibility path or update the PR description and migration claims so operators do not expect a rolling v1/v2 transition.