py: minor fixes

Author: MikhailArtemyev

examples/python/client.py

@@ -103,4 +103,4 @@ def search(
         url = f"{self.base_url}/{resource_type}"
         response = self.session.get(url, params=params)
         response.raise_for_status()
-        return Bundle[resource_class].model_validate(response.json())  # type: ignore[valid-type]
+        return Bundle.model_validate(response.json())

examples/python/test_bundle.py

@@ -1,3 +1,6 @@
+import pytest
+from pydantic import ValidationError
+
 from fhir_types.hl7_fhir_r4_core.base import CodeableConcept
 from fhir_types.hl7_fhir_r4_core.bundle import Bundle, BundleEntry
 from fhir_types.hl7_fhir_r4_core.observation import Observation
@@ -37,4 +40,20 @@ def test_bundle_without_type_param_is_backwards_compatible() -> None:
         type="collection",
         entry=[BundleEntry(resource=patient)],
     )
-    assert len(bundle.entry) == 1
+    assert len(bundle.entry) == 1
+
+
+def test_bundle_from_json_raises_on_invalid_resource() -> None:
+    # Observation requires `status` and `code` — omitting them causes a runtime ValidationError
+    bundle_json = """{
+        "resourceType": "Bundle",
+        "type": "searchset",
+        "entry": [{
+            "resource": {
+                "resourceType": "Observation",
+                "id": "obs-1"
+            }
+        }]
+    }"""
+    with pytest.raises(ValidationError):
+        Bundle.from_json(bundle_json)

examples/python/test_sdk.py

@@ -237,8 +237,7 @@ def test_bundle_from_json() -> None:
     resource = bundle.entry[0].resource
     assert resource is not None
     assert resource.id == "p-1"
-    from fhir_types.hl7_fhir_r4_core.patient import Patient as PatientClass
-    assert type(resource) is PatientClass
+    assert type(resource) is Patient
 
 
 def test_to_json_shape() -> None:

src/api/writer-generator/python.ts

@@ -732,10 +732,6 @@ export class Python extends Writer<PythonGeneratorOptions> {
 
         for (const dep of resourceDeps) {
             this.pyImportType(dep);
-
-            // const familyName = `${pascalCase(dep.name)}Family`;
-            // const familyPackage = `${this.pyFhirPackage(dep)}.resource_families`;
-            // this.pyImportFrom(familyPackage, familyName);
         }
     }
 

test/api/write-generator/__snapshots__/python.test.ts.snap

@@ -1,83 +1,5 @@
 // Bun Snapshot v1, https://bun.sh/docs/test/snapshots
 
-exports[`Python Writer Generator generates Patient resource in inMemoryOnly mode with snapshot 1`] = `
-"# WARNING: This file is autogenerated by @atomic-ehr/codegen.
-# GitHub: https://github.com/atomic-ehr/codegen
-# Any manual changes made to this file may be overwritten.
-
-from __future__ import annotations
-from pydantic import BaseModel, ConfigDict, Field, PositiveInt
-from typing import Any, List as PyList, Literal
-from typing_extensions import Self
-
-from fhir_types.hl7_fhir_r4_core.base import (\\
-    Address, Attachment, BackboneElement, CodeableConcept, ContactPoint, HumanName, Identifier, Period, Reference
-)
-from fhir_types.hl7_fhir_r4_core.domain_resource import DomainResource
-
-
-class PatientCommunication(BackboneElement):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    language: CodeableConcept[Literal["ar", "bn", "cs", "da", "de", "de-AT", "de-CH", "de-DE", "el", "en", "en-AU", "en-CA", "en-GB", "en-IN", "en-NZ", "en-SG", "en-US", "es", "es-AR", "es-ES", "es-UY", "fi", "fr", "fr-BE", "fr-CH", "fr-FR", "fy", "fy-NL", "hi", "hr", "it", "it-CH", "it-IT", "ja", "ko", "nl", "nl-BE", "nl-NL", "no", "no-NO", "pa", "pl", "pt", "pt-BR", "ru", "ru-RU", "sr", "sr-RS", "sv", "sv-SE", "te", "zh", "zh-CN", "zh-HK", "zh-SG", "zh-TW"] | str] = Field(alias="language", serialization_alias="language")
-    preferred: bool | None = Field(None, alias="preferred", serialization_alias="preferred")
-
-class PatientContact(BackboneElement):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    address: Address | None = Field(None, alias="address", serialization_alias="address")
-    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
-    name: HumanName | None = Field(None, alias="name", serialization_alias="name")
-    organization: Reference | None = Field(None, alias="organization", serialization_alias="organization")
-    period: Period | None = Field(None, alias="period", serialization_alias="period")
-    relationship: PyList[CodeableConcept] | None = Field(None, alias="relationship", serialization_alias="relationship")
-    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
-
-class PatientLink(BackboneElement):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    other: Reference = Field(alias="other", serialization_alias="other")
-    type: Literal["replaced-by", "replaces", "refer", "seealso"] = Field(alias="type", serialization_alias="type")
-
-
-class Patient(DomainResource):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    resource_type: Literal['Patient'] = Field(
-        default='Patient',
-        alias='resourceType',
-        serialization_alias='resourceType',
-        frozen=True,
-        pattern='Patient'
-    )
-    active: bool | None = Field(None, alias="active", serialization_alias="active")
-    address: PyList[Address] | None = Field(None, alias="address", serialization_alias="address")
-    birth_date: str | None = Field(None, alias="birthDate", serialization_alias="birthDate")
-    communication: PyList[PatientCommunication] | None = Field(None, alias="communication", serialization_alias="communication")
-    contact: PyList[PatientContact] | None = Field(None, alias="contact", serialization_alias="contact")
-    deceased_boolean: bool | None = Field(None, alias="deceasedBoolean", serialization_alias="deceasedBoolean")
-    deceased_date_time: str | None = Field(None, alias="deceasedDateTime", serialization_alias="deceasedDateTime")
-    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
-    general_practitioner: PyList[Reference] | None = Field(None, alias="generalPractitioner", serialization_alias="generalPractitioner")
-    identifier: PyList[Identifier] | None = Field(None, alias="identifier", serialization_alias="identifier")
-    link: PyList[PatientLink] | None = Field(None, alias="link", serialization_alias="link")
-    managing_organization: Reference | None = Field(None, alias="managingOrganization", serialization_alias="managingOrganization")
-    marital_status: CodeableConcept[Literal["A", "D", "I", "L", "M", "P", "S", "T", "U", "W", "UNK"] | str] | None = Field(None, alias="maritalStatus", serialization_alias="maritalStatus")
-    multiple_birth_boolean: bool | None = Field(None, alias="multipleBirthBoolean", serialization_alias="multipleBirthBoolean")
-    multiple_birth_integer: int | None = Field(None, alias="multipleBirthInteger", serialization_alias="multipleBirthInteger")
-    name: PyList[HumanName] | None = Field(None, alias="name", serialization_alias="name")
-    photo: PyList[Attachment] | None = Field(None, alias="photo", serialization_alias="photo")
-    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
-
-    def model_post_init(self, __context: Any) -> None:
-        self.__pydantic_fields_set__.add("resource_type")
-
-    def to_json(self, indent: int | None = None) -> str:
-        return self.model_dump_json(exclude_unset=True, exclude_none=True, indent=indent)
-
-    @classmethod
-    def from_json(cls, json: str) -> Self:
-        return cls.model_validate_json(json)
-
-"
-`;
-
 exports[`Python Writer Generator static files 1`] = `
 "fhirpy>=2.0.0,<3.0.0
 mypy>=1.9.0,<2.0.0
@@ -89,7 +11,7 @@ types-requests>=2.32.0,<3.0.0
 "
 `;
 
-exports[`Python Writer Generator generates BundleEntry with generic type-family parameters 1`] = `
+exports[`Python Writer Generator bundle.py matches snapshot 1`] = `
 "# WARNING: This file is autogenerated by @atomic-ehr/codegen.
 # GitHub: https://github.com/atomic-ehr/codegen
 # Any manual changes made to this file may be overwritten.
@@ -196,92 +118,70 @@ class Bundle(Resource, Generic[T1, T2]):
 "
 `;
 
-exports[`Python Writer Generator generates Bundle with inherited generic params from BundleEntry 1`] = `
+exports[`Python Writer Generator patient.py matches snapshot 1`] = `
 "# WARNING: This file is autogenerated by @atomic-ehr/codegen.
 # GitHub: https://github.com/atomic-ehr/codegen
 # Any manual changes made to this file may be overwritten.
 
 from __future__ import annotations
-from pydantic import BaseModel, ConfigDict, Field, PositiveInt, model_validator
-from typing import Any, Generic, List as PyList, Literal
-from typing_extensions import Self, TypeVar
-
-from fhir_types.hl7_fhir_r4_core.base import BackboneElement, Identifier, Signature
-from fhir_types.hl7_fhir_r4_core.resource import Resource
-from fhir_types.hl7_fhir_r4_core.resource_preprocessor import preprocess_resource_fields
-
-T = TypeVar('T', bound=Resource, default=Resource)
-T1 = TypeVar('T1', bound=Resource, default=Resource)
-T2 = TypeVar('T2', bound=Resource, default=Resource)
-
-
-class BundleEntry(BackboneElement, Generic[T1, T2]):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    full_url: str | None = Field(None, alias="fullUrl", serialization_alias="fullUrl")
-    link: PyList[BundleLink] | None = Field(None, alias="link", serialization_alias="link")
-    request: BundleEntryRequest | None = Field(None, alias="request", serialization_alias="request")
-    resource: T1 | None = Field(None, alias="resource", serialization_alias="resource")
-    response: BundleEntryResponse[T2] | None = Field(None, alias="response", serialization_alias="response")
-    search: BundleEntrySearch | None = Field(None, alias="search", serialization_alias="search")
+from pydantic import BaseModel, ConfigDict, Field, PositiveInt
+from typing import Any, List as PyList, Literal
+from typing_extensions import Self
 
-    @model_validator(mode='before')
-    @classmethod
-    def _preprocess_resources(cls, data: Any) -> Any:
-        if isinstance(data, dict):
-            return preprocess_resource_fields(data, "fhir_types.hl7_fhir_r4_core")
-        return data
+from fhir_types.hl7_fhir_r4_core.base import (\\
+    Address, Attachment, BackboneElement, CodeableConcept, ContactPoint, HumanName, Identifier, Period, Reference
+)
+from fhir_types.hl7_fhir_r4_core.domain_resource import DomainResource
 
-class BundleEntryRequest(BackboneElement):
-    model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    if_match: str | None = Field(None, alias="ifMatch", serialization_alias="ifMatch")
-    if_modified_since: str | None = Field(None, alias="ifModifiedSince", serialization_alias="ifModifiedSince")
-    if_none_exist: str | None = Field(None, alias="ifNoneExist", serialization_alias="ifNoneExist")
-    if_none_match: str | None = Field(None, alias="ifNoneMatch", serialization_alias="ifNoneMatch")
-    method: Literal["GET", "HEAD", "POST", "PUT", "DELETE", "PATCH"] = Field(alias="method", serialization_alias="method")
-    url: str = Field(alias="url", serialization_alias="url")
 
-class BundleEntryResponse(BackboneElement, Generic[T]):
+class PatientCommunication(BackboneElement):
     model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    etag: str | None = Field(None, alias="etag", serialization_alias="etag")
-    last_modified: str | None = Field(None, alias="lastModified", serialization_alias="lastModified")
-    location: str | None = Field(None, alias="location", serialization_alias="location")
-    outcome: T | None = Field(None, alias="outcome", serialization_alias="outcome")
-    status: str = Field(alias="status", serialization_alias="status")
-
-    @model_validator(mode='before')
-    @classmethod
-    def _preprocess_resources(cls, data: Any) -> Any:
-        if isinstance(data, dict):
-            return preprocess_resource_fields(data, "fhir_types.hl7_fhir_r4_core")
-        return data
+    language: CodeableConcept[Literal["ar", "bn", "cs", "da", "de", "de-AT", "de-CH", "de-DE", "el", "en", "en-AU", "en-CA", "en-GB", "en-IN", "en-NZ", "en-SG", "en-US", "es", "es-AR", "es-ES", "es-UY", "fi", "fr", "fr-BE", "fr-CH", "fr-FR", "fy", "fy-NL", "hi", "hr", "it", "it-CH", "it-IT", "ja", "ko", "nl", "nl-BE", "nl-NL", "no", "no-NO", "pa", "pl", "pt", "pt-BR", "ru", "ru-RU", "sr", "sr-RS", "sv", "sv-SE", "te", "zh", "zh-CN", "zh-HK", "zh-SG", "zh-TW"] | str] = Field(alias="language", serialization_alias="language")
+    preferred: bool | None = Field(None, alias="preferred", serialization_alias="preferred")
 
-class BundleEntrySearch(BackboneElement):
+class PatientContact(BackboneElement):
     model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    mode: Literal["match", "include", "outcome"] | None = Field(None, alias="mode", serialization_alias="mode")
-    score: float | None = Field(None, alias="score", serialization_alias="score")
+    address: Address | None = Field(None, alias="address", serialization_alias="address")
+    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
+    name: HumanName | None = Field(None, alias="name", serialization_alias="name")
+    organization: Reference | None = Field(None, alias="organization", serialization_alias="organization")
+    period: Period | None = Field(None, alias="period", serialization_alias="period")
+    relationship: PyList[CodeableConcept] | None = Field(None, alias="relationship", serialization_alias="relationship")
+    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
 
-class BundleLink(BackboneElement):
+class PatientLink(BackboneElement):
     model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    relation: str = Field(alias="relation", serialization_alias="relation")
-    url: str = Field(alias="url", serialization_alias="url")
+    other: Reference = Field(alias="other", serialization_alias="other")
+    type: Literal["replaced-by", "replaces", "refer", "seealso"] = Field(alias="type", serialization_alias="type")
 
 
-class Bundle(Resource, Generic[T1, T2]):
+class Patient(DomainResource):
     model_config = ConfigDict(validate_by_name=True, serialize_by_alias=True, extra="forbid")
-    resource_type: Literal['Bundle'] = Field(
-        default='Bundle',
+    resource_type: Literal['Patient'] = Field(
+        default='Patient',
         alias='resourceType',
         serialization_alias='resourceType',
         frozen=True,
-        pattern='Bundle'
+        pattern='Patient'
     )
-    entry: PyList[BundleEntry[T1, T2]] | None = Field(None, alias="entry", serialization_alias="entry")
-    identifier: Identifier | None = Field(None, alias="identifier", serialization_alias="identifier")
-    link: PyList[BundleLink] | None = Field(None, alias="link", serialization_alias="link")
-    signature: Signature | None = Field(None, alias="signature", serialization_alias="signature")
-    timestamp: str | None = Field(None, alias="timestamp", serialization_alias="timestamp")
-    total: int | None = Field(None, alias="total", serialization_alias="total")
-    type: Literal["document", "message", "transaction", "transaction-response", "batch", "batch-response", "history", "searchset", "collection"] = Field(alias="type", serialization_alias="type")
+    active: bool | None = Field(None, alias="active", serialization_alias="active")
+    address: PyList[Address] | None = Field(None, alias="address", serialization_alias="address")
+    birth_date: str | None = Field(None, alias="birthDate", serialization_alias="birthDate")
+    communication: PyList[PatientCommunication] | None = Field(None, alias="communication", serialization_alias="communication")
+    contact: PyList[PatientContact] | None = Field(None, alias="contact", serialization_alias="contact")
+    deceased_boolean: bool | None = Field(None, alias="deceasedBoolean", serialization_alias="deceasedBoolean")
+    deceased_date_time: str | None = Field(None, alias="deceasedDateTime", serialization_alias="deceasedDateTime")
+    gender: Literal["male", "female", "other", "unknown"] | None = Field(None, alias="gender", serialization_alias="gender")
+    general_practitioner: PyList[Reference] | None = Field(None, alias="generalPractitioner", serialization_alias="generalPractitioner")
+    identifier: PyList[Identifier] | None = Field(None, alias="identifier", serialization_alias="identifier")
+    link: PyList[PatientLink] | None = Field(None, alias="link", serialization_alias="link")
+    managing_organization: Reference | None = Field(None, alias="managingOrganization", serialization_alias="managingOrganization")
+    marital_status: CodeableConcept[Literal["A", "D", "I", "L", "M", "P", "S", "T", "U", "W", "UNK"] | str] | None = Field(None, alias="maritalStatus", serialization_alias="maritalStatus")
+    multiple_birth_boolean: bool | None = Field(None, alias="multipleBirthBoolean", serialization_alias="multipleBirthBoolean")
+    multiple_birth_integer: int | None = Field(None, alias="multipleBirthInteger", serialization_alias="multipleBirthInteger")
+    name: PyList[HumanName] | None = Field(None, alias="name", serialization_alias="name")
+    photo: PyList[Attachment] | None = Field(None, alias="photo", serialization_alias="photo")
+    telecom: PyList[ContactPoint] | None = Field(None, alias="telecom", serialization_alias="telecom")
 
     def model_post_init(self, __context: Any) -> None:
         self.__pydantic_fields_set__.add("resource_type")
@@ -293,12 +193,5 @@ class Bundle(Resource, Generic[T1, T2]):
     def from_json(cls, json: str) -> Self:
         return cls.model_validate_json(json)
 
-    @model_validator(mode='before')
-    @classmethod
-    def _preprocess_resources(cls, data: Any) -> Any:
-        if isinstance(data, dict):
-            return preprocess_resource_fields(data, "fhir_types.hl7_fhir_r4_core")
-        return data
-
 "
 `;