chore: expand fhir2omop docstrings and clarify dropped field semantics

.fern/metadata.json

@@ -1,5 +1,5 @@
 {
-  "cliVersion": "5.49.1",
+  "cliVersion": "5.50.1",
   "generatorName": "fernapi/fern-python-sdk",
   "generatorVersion": "5.14.13",
   "generatorConfig": {
@@ -8,10 +8,10 @@
       "enabled": true
     }
   },
-  "originGitCommit": "64f369254225bd6c2d4c58d87f59165d7e8e8dc9",
+  "originGitCommit": "fff9ecb3e3ee9847a86bfb09de6df7e477ecd13e",
   "originGitCommitIsDirty": true,
   "invokedBy": "ci",
   "requestedVersion": "AUTO",
   "ciProvider": "unknown",
-  "sdkVersion": "16.2.0"
+  "sdkVersion": "16.2.1"
 }

code-examples.json

@@ -2,8 +2,8 @@
   "metadata": {
     "language": "python",
     "packageName": "phenoml",
-    "sdkVersion": "16.2.0",
-    "specCommit": "64f369254225bd6c2d4c58d87f59165d7e8e8dc9",
+    "sdkVersion": "16.2.1",
+    "specCommit": "fff9ecb3e3ee9847a86bfb09de6df7e477ecd13e",
     "generatorName": "fernapi/fern-python-sdk"
   },
   "renderRules": {

pyproject.toml

@@ -4,7 +4,7 @@ dynamic = ["version"]
 
 [tool.poetry]
 name = "phenoml"
-version = "16.2.0"
+version = "16.2.1"
 description = ""
 readme = "README.md"
 authors = []

reference.md

@@ -3526,6 +3526,32 @@ Maps a FHIR R4 resource or Bundle into OMOP Common Data Model v5.4 rows
 (person, visit_occurrence, condition_occurrence, drug_exposure,
 procedure_occurrence, measurement, observation).
 
+Resource support is intentionally limited to the OMOP tables returned by
+this endpoint:
+- `Patient` -> `person`
+- `Encounter` -> `visit_occurrence`
+- `Condition` -> `condition_occurrence`
+- `Procedure` -> `procedure_occurrence`
+- `MedicationRequest`, `MedicationStatement`, and
+  `MedicationAdministration` -> `drug_exposure`
+- `Immunization` -> `drug_exposure`
+- `Observation` with a numeric `valueQuantity`, `valueInteger`, or
+  numeric-looking `valueString` (for example `"<2"`) -> `measurement`
+- non-numeric `Observation` -> `observation`
+- `AllergyIntolerance` -> `observation`
+
+`Medication` is supported only as reference data for medication
+resources; it is not emitted as its own row because OMOP CDM has no
+Medication table. Other reference/admin resources such as `Practitioner`,
+`Organization`, `Location`, `Coverage`, and `Claim`, and clinical
+workflow/document resources such as `DiagnosticReport`, `ServiceRequest`,
+`CarePlan`, `DocumentReference`, `Composition`, `Specimen`, and
+`DeviceUseStatement`, are currently accepted in a Bundle but are not
+shaped into OMOP rows. Unsupported resource types are ignored rather than
+listed under `dropped`; `dropped` is reserved for supported resource types
+that were missing the subject/patient, code, or medication reference data
+needed to produce a valid row.
+
 Each resource's primary clinical coding is resolved to a standard OMOP
 `concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
 response carries `mappings` (how each source coding resolved, linked back
@@ -3599,9 +3625,12 @@ client.fhir2omop.create(
 **fhir_resources:** `typing.Dict[str, typing.Any]` 
 
 FHIR resources (single resource or Bundle). Must contain at least one
-Patient resource. Resources are mapped to OMOP rows; standalone
-Medication resources are consumed by medication references rather than
-mapped to their own table.
+Patient resource. Supported row-producing resources are Patient,
+Encounter, Condition, Procedure, MedicationRequest,
+MedicationStatement, MedicationAdministration, Immunization,
+Observation, and AllergyIntolerance. Standalone Medication resources
+are consumed by medication references rather than mapped to their own
+table. Other resource types are accepted but ignored.
 
 </dd>
 </dl>

src/phenoml/core/client_wrapper.py

@@ -29,12 +29,12 @@ def get_headers(self) -> typing.Dict[str, str]:
         import platform
 
         headers: typing.Dict[str, str] = {
-            "User-Agent": "phenoml/16.2.0",
+            "User-Agent": "phenoml/16.2.1",
             "X-Fern-Language": "Python",
             "X-Fern-Runtime": f"python/{platform.python_version()}",
             "X-Fern-Platform": f"{platform.system().lower()}/{platform.release()}",
             "X-Fern-SDK-Name": "phenoml",
-            "X-Fern-SDK-Version": "16.2.0",
+            "X-Fern-SDK-Version": "16.2.1",
             **(self.get_custom_headers() or {}),
         }
         token = self._get_token()

src/phenoml/fhir2omop/client.py

@@ -34,6 +34,32 @@ def create(
         (person, visit_occurrence, condition_occurrence, drug_exposure,
         procedure_occurrence, measurement, observation).
 
+        Resource support is intentionally limited to the OMOP tables returned by
+        this endpoint:
+        - `Patient` -> `person`
+        - `Encounter` -> `visit_occurrence`
+        - `Condition` -> `condition_occurrence`
+        - `Procedure` -> `procedure_occurrence`
+        - `MedicationRequest`, `MedicationStatement`, and
+          `MedicationAdministration` -> `drug_exposure`
+        - `Immunization` -> `drug_exposure`
+        - `Observation` with a numeric `valueQuantity`, `valueInteger`, or
+          numeric-looking `valueString` (for example `"<2"`) -> `measurement`
+        - non-numeric `Observation` -> `observation`
+        - `AllergyIntolerance` -> `observation`
+
+        `Medication` is supported only as reference data for medication
+        resources; it is not emitted as its own row because OMOP CDM has no
+        Medication table. Other reference/admin resources such as `Practitioner`,
+        `Organization`, `Location`, `Coverage`, and `Claim`, and clinical
+        workflow/document resources such as `DiagnosticReport`, `ServiceRequest`,
+        `CarePlan`, `DocumentReference`, `Composition`, `Specimen`, and
+        `DeviceUseStatement`, are currently accepted in a Bundle but are not
+        shaped into OMOP rows. Unsupported resource types are ignored rather than
+        listed under `dropped`; `dropped` is reserved for supported resource types
+        that were missing the subject/patient, code, or medication reference data
+        needed to produce a valid row.
+
         Each resource's primary clinical coding is resolved to a standard OMOP
         `concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
         response carries `mappings` (how each source coding resolved, linked back
@@ -64,9 +90,12 @@ def create(
         ----------
         fhir_resources : typing.Dict[str, typing.Any]
             FHIR resources (single resource or Bundle). Must contain at least one
-            Patient resource. Resources are mapped to OMOP rows; standalone
-            Medication resources are consumed by medication references rather than
-            mapped to their own table.
+            Patient resource. Supported row-producing resources are Patient,
+            Encounter, Condition, Procedure, MedicationRequest,
+            MedicationStatement, MedicationAdministration, Immunization,
+            Observation, and AllergyIntolerance. Standalone Medication resources
+            are consumed by medication references rather than mapped to their own
+            table. Other resource types are accepted but ignored.
 
         request_options : typing.Optional[RequestOptions]
             Request-specific configuration.
@@ -170,6 +199,32 @@ async def create(
         (person, visit_occurrence, condition_occurrence, drug_exposure,
         procedure_occurrence, measurement, observation).
 
+        Resource support is intentionally limited to the OMOP tables returned by
+        this endpoint:
+        - `Patient` -> `person`
+        - `Encounter` -> `visit_occurrence`
+        - `Condition` -> `condition_occurrence`
+        - `Procedure` -> `procedure_occurrence`
+        - `MedicationRequest`, `MedicationStatement`, and
+          `MedicationAdministration` -> `drug_exposure`
+        - `Immunization` -> `drug_exposure`
+        - `Observation` with a numeric `valueQuantity`, `valueInteger`, or
+          numeric-looking `valueString` (for example `"<2"`) -> `measurement`
+        - non-numeric `Observation` -> `observation`
+        - `AllergyIntolerance` -> `observation`
+
+        `Medication` is supported only as reference data for medication
+        resources; it is not emitted as its own row because OMOP CDM has no
+        Medication table. Other reference/admin resources such as `Practitioner`,
+        `Organization`, `Location`, `Coverage`, and `Claim`, and clinical
+        workflow/document resources such as `DiagnosticReport`, `ServiceRequest`,
+        `CarePlan`, `DocumentReference`, `Composition`, `Specimen`, and
+        `DeviceUseStatement`, are currently accepted in a Bundle but are not
+        shaped into OMOP rows. Unsupported resource types are ignored rather than
+        listed under `dropped`; `dropped` is reserved for supported resource types
+        that were missing the subject/patient, code, or medication reference data
+        needed to produce a valid row.
+
         Each resource's primary clinical coding is resolved to a standard OMOP
         `concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
         response carries `mappings` (how each source coding resolved, linked back
@@ -200,9 +255,12 @@ async def create(
         ----------
         fhir_resources : typing.Dict[str, typing.Any]
             FHIR resources (single resource or Bundle). Must contain at least one
-            Patient resource. Resources are mapped to OMOP rows; standalone
-            Medication resources are consumed by medication references rather than
-            mapped to their own table.
+            Patient resource. Supported row-producing resources are Patient,
+            Encounter, Condition, Procedure, MedicationRequest,
+            MedicationStatement, MedicationAdministration, Immunization,
+            Observation, and AllergyIntolerance. Standalone Medication resources
+            are consumed by medication references rather than mapped to their own
+            table. Other resource types are accepted but ignored.
 
         request_options : typing.Optional[RequestOptions]
             Request-specific configuration.

src/phenoml/fhir2omop/raw_client.py

@@ -32,6 +32,32 @@ def create(
         (person, visit_occurrence, condition_occurrence, drug_exposure,
         procedure_occurrence, measurement, observation).
 
+        Resource support is intentionally limited to the OMOP tables returned by
+        this endpoint:
+        - `Patient` -> `person`
+        - `Encounter` -> `visit_occurrence`
+        - `Condition` -> `condition_occurrence`
+        - `Procedure` -> `procedure_occurrence`
+        - `MedicationRequest`, `MedicationStatement`, and
+          `MedicationAdministration` -> `drug_exposure`
+        - `Immunization` -> `drug_exposure`
+        - `Observation` with a numeric `valueQuantity`, `valueInteger`, or
+          numeric-looking `valueString` (for example `"<2"`) -> `measurement`
+        - non-numeric `Observation` -> `observation`
+        - `AllergyIntolerance` -> `observation`
+
+        `Medication` is supported only as reference data for medication
+        resources; it is not emitted as its own row because OMOP CDM has no
+        Medication table. Other reference/admin resources such as `Practitioner`,
+        `Organization`, `Location`, `Coverage`, and `Claim`, and clinical
+        workflow/document resources such as `DiagnosticReport`, `ServiceRequest`,
+        `CarePlan`, `DocumentReference`, `Composition`, `Specimen`, and
+        `DeviceUseStatement`, are currently accepted in a Bundle but are not
+        shaped into OMOP rows. Unsupported resource types are ignored rather than
+        listed under `dropped`; `dropped` is reserved for supported resource types
+        that were missing the subject/patient, code, or medication reference data
+        needed to produce a valid row.
+
         Each resource's primary clinical coding is resolved to a standard OMOP
         `concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
         response carries `mappings` (how each source coding resolved, linked back
@@ -62,9 +88,12 @@ def create(
         ----------
         fhir_resources : typing.Dict[str, typing.Any]
             FHIR resources (single resource or Bundle). Must contain at least one
-            Patient resource. Resources are mapped to OMOP rows; standalone
-            Medication resources are consumed by medication references rather than
-            mapped to their own table.
+            Patient resource. Supported row-producing resources are Patient,
+            Encounter, Condition, Procedure, MedicationRequest,
+            MedicationStatement, MedicationAdministration, Immunization,
+            Observation, and AllergyIntolerance. Standalone Medication resources
+            are consumed by medication references rather than mapped to their own
+            table. Other resource types are accepted but ignored.
 
         request_options : typing.Optional[RequestOptions]
             Request-specific configuration.
@@ -162,6 +191,32 @@ async def create(
         (person, visit_occurrence, condition_occurrence, drug_exposure,
         procedure_occurrence, measurement, observation).
 
+        Resource support is intentionally limited to the OMOP tables returned by
+        this endpoint:
+        - `Patient` -> `person`
+        - `Encounter` -> `visit_occurrence`
+        - `Condition` -> `condition_occurrence`
+        - `Procedure` -> `procedure_occurrence`
+        - `MedicationRequest`, `MedicationStatement`, and
+          `MedicationAdministration` -> `drug_exposure`
+        - `Immunization` -> `drug_exposure`
+        - `Observation` with a numeric `valueQuantity`, `valueInteger`, or
+          numeric-looking `valueString` (for example `"<2"`) -> `measurement`
+        - non-numeric `Observation` -> `observation`
+        - `AllergyIntolerance` -> `observation`
+
+        `Medication` is supported only as reference data for medication
+        resources; it is not emitted as its own row because OMOP CDM has no
+        Medication table. Other reference/admin resources such as `Practitioner`,
+        `Organization`, `Location`, `Coverage`, and `Claim`, and clinical
+        workflow/document resources such as `DiagnosticReport`, `ServiceRequest`,
+        `CarePlan`, `DocumentReference`, `Composition`, `Specimen`, and
+        `DeviceUseStatement`, are currently accepted in a Bundle but are not
+        shaped into OMOP rows. Unsupported resource types are ignored rather than
+        listed under `dropped`; `dropped` is reserved for supported resource types
+        that were missing the subject/patient, code, or medication reference data
+        needed to produce a valid row.
+
         Each resource's primary clinical coding is resolved to a standard OMOP
         `concept_id`. Alongside the OMOP rows grouped by table (`tables`), the
         response carries `mappings` (how each source coding resolved, linked back
@@ -192,9 +247,12 @@ async def create(
         ----------
         fhir_resources : typing.Dict[str, typing.Any]
             FHIR resources (single resource or Bundle). Must contain at least one
-            Patient resource. Resources are mapped to OMOP rows; standalone
-            Medication resources are consumed by medication references rather than
-            mapped to their own table.
+            Patient resource. Supported row-producing resources are Patient,
+            Encounter, Condition, Procedure, MedicationRequest,
+            MedicationStatement, MedicationAdministration, Immunization,
+            Observation, and AllergyIntolerance. Standalone Medication resources
+            are consumed by medication references rather than mapped to their own
+            table. Other resource types are accepted but ignored.
 
         request_options : typing.Optional[RequestOptions]
             Request-specific configuration.

src/phenoml/fhir2omop/types/create_omop_response.py

@@ -21,7 +21,10 @@ class CreateOmopResponse(UniversalBaseModel):
 
     dropped: typing.Optional[typing.List[DroppedResource]] = pydantic.Field(default=None)
     """
-    Resources that could not be shaped into an OMOP row (rather than emitted as blank rows).
+    Supported resource instances that could not be shaped into an OMOP
+    row because required subject/patient, code, or medication reference
+    data was missing. Unsupported resource types are ignored and do not
+    appear here.
     """
 
     vocab_version: typing.Optional[str] = pydantic.Field(default=None)