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Update FHIR converter API docs (#521)
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@emmastephenson
emmastephenson authored May 11, 2023
1 parent 05358b5 commit c149815
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73 changes: 65 additions & 8 deletions containers/fhir-converter/app/main.py
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import uuid
from enum import Enum
from fastapi import FastAPI, Response, status
from pydantic import BaseModel

# Instantiate FastAPI via PHDI's BaseService class
app = FastAPI()
from pydantic import BaseModel, Field

# Reading sample request & response files for docs
raw_sample_response = json.load(
open(
Path(__file__).parent.parent
/ "assets"
/ "sample_vxu_fhir_conversion_response.json"
)
)
sample_response = {200: raw_sample_response}

sample_request = open(
Path(__file__).parent.parent / "assets" / "sample_request.hl7"
).read()

description = (Path(__file__).parent.parent / "description.md").read_text(
encoding="utf-8"
)

app = FastAPI(
title="PHDI FHIR Converter Service",
version="0.0.1",
contact={
"name": "CDC Public Health Data Infrastructure",
"url": "https://cdcgov.github.io/phdi-site/",
"email": "dmibuildingblocks@cdc.gov",
},
license_info={
"name": "Creative Commons Zero v1.0 Universal",
"url": "https://creativecommons.org/publicdomain/zero/1.0/",
},
description=description,
)


class InputType(str, Enum):
Expand Down Expand Up @@ -92,18 +122,45 @@ class FhirConverterInput(BaseModel):
Input parameters for the FHIR Converter.
"""

input_data: str
input_type: InputType
root_template: RootTemplate
input_data: str = Field(
description="The message to be converted as a string.",
example=sample_request,
)
input_type: InputType = Field(
description="The type of message to be converted.", example="vxu"
)
root_template: RootTemplate = Field(
description="Name of the liquid template within to be used for conversion.",
example="VXU_V04",
)


@app.get("/")
async def health_check():
"""
Check service status. If an HTTP 200 status code is returned along with
'{"status": "OK"}' then the FHIR conversion service is available and running
properly.
"""
return {"status": "OK"}


@app.post("/convert-to-fhir", status_code=200)
@app.post(
"/convert-to-fhir",
status_code=200,
responses=sample_response,
)
async def convert(input: FhirConverterInput, response: Response):
"""
Converts an HL7v2 or C-CDA message to FHIR format using the Microsoft FHIR
Converter CLI tool. When conversion is successful, a dictionary containing the
response from the FHIR Converter is returned.
In order to successfully call this function, the Microsoft FHIR Converter tool
must be installed. For information on how to do this, please refer to the
description.md file. The source code for the converter can be found at
https://github.com/microsoft/FHIR-Converter.
"""
result = convert_to_fhir(**dict(input))
if "original_request" in result.get("response"):
response.status_code = status.HTTP_400_BAD_REQUEST
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6 changes: 6 additions & 0 deletions containers/fhir-converter/assets/sample_request.hl7
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MSH|^~\&|WIR11.3.2^^|WIR^^||WIRPH^^|20200514010000-0400||VXU^V04|2020051411020600|P^|2.4^^|||ER
PID|||3054790^^^^SR^~^^^^PI^||ZTEST^PEDIARIX^^^^^^|HEPB^DTAP^^^^^^|20180808|M|||||||||||||||||||||
PD1|||||||||||02^^^^^|Y||||A
NK1|1||BRO^BROTHER^HL70063^^^^^|^^NEW GLARUS^WI^^^^^^^|
PV1||R||||||||||||||||||
RXA|0|999|20180809|20180809|08^HepB pediatric^CVX^90744^HepB pediatric^CPT|1.0|||01^^^^^~38193939^WIR immunization id^IMM_ID^^^|||||||||||NA
273 changes: 273 additions & 0 deletions containers/fhir-converter/assets/sample_vxu_fhir_conversion_response.json
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{"description": "Success",
"content": {
"application/json": {
"examples": {
"elr": {
"value": {
"response": {
"Status": "OK",
"FhirResource": {
"resourceType": "Bundle",
"type": "batch",
"timestamp": "2020-05-14T01:00:00-04:00",
"identifier": {
"value": "2020051411020600"
},
"id": "945561fc-cf00-ebd7-5f1c-865ab4abfcb5",
"entry": [
{
"fullUrl": "urn:uuid:53d0ea89-a281-523f-f0fb-02e3ee1ef0a2",
"resource": {
"resourceType": "MessageHeader",
"id": "53d0ea89-a281-523f-f0fb-02e3ee1ef0a2",
"source": {
"name": "WIR11.3.2",
"_endpoint": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "unknown"
}
]
}
},
"destination": [
{
"_endpoint": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "unknown"
}
]
},
"receiver": {
"reference": "Organization/f51a22ef-628f-d014-5a33-da96b68ae53d"
}
}
],
"meta": {
"tag": [
{
"code": "P",
"system": "http://terminology.hl7.org/CodeSystem/v2-0103"
}
]
},
"eventCoding": {
"code": "V04",
"system": "http://terminology.hl7.org/CodeSystem/v2-0003",
"display": "VXU^V04"
},
"sender": {
"reference": "Organization/b727354b-9ca6-74fd-6b6b-ae0851c7998a"
}
},
"request": {
"method": "PUT",
"url": "MessageHeader/53d0ea89-a281-523f-f0fb-02e3ee1ef0a2"
}
},
{
"fullUrl": "urn:uuid:d24c7a73-ebcf-8f4f-51bc-e95f47452e80",
"resource": {
"resourceType": "Provenance",
"id": "d24c7a73-ebcf-8f4f-51bc-e95f47452e80",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><span>Resource bundle generated on 2023-05-03T19:07:14.523Z using Microsoft FHIR Converter.</span><span>Template Version: TEMPLATE_VERSION_PLACEHOLDER.</span><span>Template URL: https://github.com/microsoft/FHIR-Converter/releases/download/vTEMPLATE_VERSION_PLACEHOLDER/Hl7v2DefaultTemplates.tar.gz.</span><span>Root template: VXU_V04.</span></p></div>"
},
"occurredDateTime": "2020-05-14T01:00:00-04:00",
"recorded": "2020-05-14T01:00:00-04:00",
"agent": [
{
"type": {
"coding": [
{
"code": "author",
"system": "http://terminology.hl7.org/CodeSystem/provenance-participant-type"
}
]
},
"who": {
"reference": "Organization/b727354b-9ca6-74fd-6b6b-ae0851c7998a"
}
}
],
"activity": {
"coding": [
{
"display": "VXU^V04^"
}
]
},
"target": [
{
"reference": "Bundle/945561fc-cf00-ebd7-5f1c-865ab4abfcb5"
}
]
},
"request": {
"method": "PUT",
"url": "Provenance/d24c7a73-ebcf-8f4f-51bc-e95f47452e80"
}
},
{
"fullUrl": "urn:uuid:b727354b-9ca6-74fd-6b6b-ae0851c7998a",
"resource": {
"resourceType": "Organization",
"id": "b727354b-9ca6-74fd-6b6b-ae0851c7998a",
"identifier": [
{
"value": "WIR",
"system": "http://example.com/v2-to-fhir-converter/Identifier/WIR"
}
]
},
"request": {
"method": "PUT",
"url": "Organization/b727354b-9ca6-74fd-6b6b-ae0851c7998a"
}
},
{
"fullUrl": "urn:uuid:f51a22ef-628f-d014-5a33-da96b68ae53d",
"resource": {
"resourceType": "Organization",
"id": "f51a22ef-628f-d014-5a33-da96b68ae53d",
"identifier": [
{
"value": "WIRPH",
"system": "http://example.com/v2-to-fhir-converter/Identifier/WIRPH"
}
]
},
"request": {
"method": "PUT",
"url": "Organization/f51a22ef-628f-d014-5a33-da96b68ae53d"
}
},
{
"fullUrl": "urn:uuid:3f8fc2a0-1d50-42de-bfed-9c01a071c6b6",
"resource": {
"resourceType": "Patient",
"id": "3f8fc2a0-1d50-42de-bfed-9c01a071c6b6",
"identifier": [
{
"value": "3054790",
"type": {
"coding": [
{
"code": "SR",
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"display": "State registry ID"
}
]
}
},
{
"type": {
"coding": [
{
"code": "PI",
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"display": "Patient internal identifier"
}
]
}
}
],
"name": [
{
"family": "ZTEST",
"given": [
"PEDIARIX"
]
}
],
"birthDate": "2018-08-08",
"gender": "male",
"active": true,
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
"valueString": "HEPB--DTAP"
}
],
"contact": [
{
"address": {
"city": "NEW GLARUS",
"state": "WI"
}
}
]
},
"request": {
"method": "PUT",
"url": "Patient/3f8fc2a0-1d50-42de-bfed-9c01a071c6b6"
}
},
{
"fullUrl": "urn:uuid:caeb94a6-281c-4bd0-1dad-4998a2f80c35",
"resource": {
"resourceType": "Encounter",
"id": "caeb94a6-281c-4bd0-1dad-4998a2f80c35",
"class": {
"code": "R",
"display": "Recurring patient",
"system": "http://terminology.hl7.org/CodeSystem/v2-0004"
},
"status": "in-progress",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><span>Visit Description: </span></p></div>"
},
"subject": {
"reference": "Patient/3f8fc2a0-1d50-42de-bfed-9c01a071c6b6"
}
},
"request": {
"method": "PUT",
"url": "Encounter/caeb94a6-281c-4bd0-1dad-4998a2f80c35"
}
},
{
"fullUrl": "urn:uuid:1b3b6f92-c3c9-7440-d08b-3023cd94c569",
"resource": {
"resourceType": "RelatedPerson",
"id": "1b3b6f92-c3c9-7440-d08b-3023cd94c569",
"relationship": [
{
"coding": [
{
"code": "BRO",
"display": "brother",
"system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode"
}
]
}
],
"address": [
{
"city": "NEW GLARUS",
"state": "WI"
}
],
"patient": {
"reference": "Patient/3f8fc2a0-1d50-42de-bfed-9c01a071c6b6"
}
},
"request": {
"method": "PUT",
"url": "RelatedPerson/1b3b6f92-c3c9-7440-d08b-3023cd94c569"
}
}
]
}
}
}
}
}
}
}
}
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