Replace FastAPI class with PHDI BaseService for container apps

containers/alerts/Dockerfile

@@ -2,11 +2,15 @@ FROM python:3.10-slim
 
 WORKDIR /code
 
+RUN apt-get update && \
+  apt-get upgrade -y && \
+  apt-get install -y git 
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 
 COPY ./app /code/app
 COPY ./description.md /code/description.md
 
 EXPOSE 8080
-CMD uvicorn app.main:api --host 0.0.0.0 --port 8080
+CMD uvicorn app.main:api --host 0.0.0.0 --port 8080

containers/alerts/app/main.py

@@ -1,3 +1,4 @@
+from phdi.containers.base_service import BaseService
 from azure.communication.identity import CommunicationIdentityClient
 from azure.communication.phonenumbers import (
     PhoneNumbersClient,
@@ -8,7 +9,7 @@
 )
 from azure.communication.sms import SmsClient
 from azure.identity import DefaultAzureCredential
-from fastapi import FastAPI, Response, status
+from fastapi import Response, status
 from pydantic import BaseModel, BaseSettings, Field
 import pymsteams
 from functools import lru_cache
@@ -17,24 +18,10 @@
 from slack_sdk.errors import SlackApiError
 from typing import Optional
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-api = FastAPI(
-    title="PHDI Alerts 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,
-)
+# Instantiate FastAPI via PHDI's BaseService class
+api = BaseService(
+    "PHDI Alerts Service", Path(__file__).parent.parent / "description.md"
+).start()
 
 
 class Settings(BaseSettings):
@@ -73,15 +60,6 @@ class TeamsAlertInput(BaseModel):
     message: str = Field(description="The message to send to the Teams channel.")
 
 
-@api.get("/")
-async def health_check():
-    """
-    Check service status. If an HTTP 200 status code is returned along with
-    '{"status": "OK"}' then the alerts service is available and running properly.
-    """
-    return {"status": "OK"}
-
-
 @api.post("/sms-alert", status_code=200)
 async def sms_alert(input: SmsAlertInput, response: Response):
     """

containers/alerts/requirements.txt

@@ -7,4 +7,5 @@ uvicorn
 httpx
 slack_sdk
 pymsteams
-pytest
+pytest
+phdi @ git+https://github.com/CDCgov/phdi.git@main

containers/fhir-converter/requirements.txt

@@ -36,4 +36,4 @@ uvicorn==0.17.6
 uvloop==0.16.0
 watchgod==0.8.2
 websockets==10.3
-uuid
+uuid

containers/ingestion/app/main.py

@@ -1,4 +1,4 @@
-from fastapi import FastAPI
+from phdi.containers.base_service import BaseService
 from app.routers import (
     fhir_harmonization_standardization,
     fhir_geospatial,
@@ -12,32 +12,14 @@
 # Read settings immediately to fail fast in case there are invalid values.
 get_settings()
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-app = FastAPI(
-    title="PHDI Ingestion 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,
-)
+# Instantiate FastAPI via PHDI's BaseService class
+app = BaseService(
+    service_name="PHDI Ingestion Service",
+    description_path=Path(__file__).parent.parent / "description.md",
+).start()
 
 app.include_router(fhir_harmonization_standardization.router)
 app.include_router(fhir_geospatial.router)
 app.include_router(fhir_linkage_link.router)
 app.include_router(fhir_transport_http.router)
 app.include_router(cloud_storage.router)
-
-
-@app.get("/")
-async def health_check():
-    return {"status": "OK"}

containers/message-parser/app/main.py

@@ -1,4 +1,5 @@
-from fastapi import FastAPI, Response, status
+from phdi.containers.base_service import BaseService
+from fastapi import Response, status
 from pydantic import BaseModel, Field, root_validator
 from typing import Literal, Optional, Union
 from pathlib import Path
@@ -16,35 +17,11 @@
 # Read settings immediately to fail fast in case there are invalid values.
 get_settings()
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-app = FastAPI(
-    title="PHDI Message Parser",
-    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,
-)
-
-
-# /health_check endpoint #
-@app.get("/")
-async def health_check():
-    """
-    Check service status. If an HTTP 200 status code is returned along with
-    '{"status": "OK"}' then the extraction service is available and running properly.
-    """
-    return {"status": "OK"}
-
+# Instantiate FastAPI via PHDI's BaseService class
+app = BaseService(
+    service_name="PHDI Message Parser",
+    description_path=Path(__file__).parent.parent / "description.md",
+).start()
 
 # /parse_message endpoint #
 

containers/record-linkage/app/main.py

@@ -1,6 +1,7 @@
 from app.config import get_settings
-from fastapi import FastAPI, Response, status
+from fastapi import Response, status
 from pathlib import Path
+from phdi.containers.base_service import BaseService
 from phdi.linkage import (
     add_person_resource,
     link_record_against_mpi,
@@ -62,24 +63,12 @@ def run_migrations():
             print_psycopg2_exception(err)
 
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-app = FastAPI(
-    title="DIBBs Record Linkage 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,
-)
+# Instantiate FastAPI via PHDI's BaseService class
+app = BaseService(
+    service_name="DIBBs Record Linkage Service",
+    description_path=Path(__file__).parent.parent / "description.md",
+    include_health_check_endpoint=False,
+).start()
 
 
 # Request and and response models

containers/tabulation/app/main.py

@@ -1,10 +1,11 @@
-from fastapi import FastAPI, Response, status
+from fastapi import Response, status
 from pydantic import BaseModel, Field, validator
 from typing import Optional, Literal
 import urllib.parse
 import datetime
 import jsonschema
 from pathlib import Path
+from phdi.containers.base_service import BaseService
 from phdi.cloud.core import BaseCredentialManager
 from phdi.tabulation import validate_schema
 from phdi.tabulation.tables import write_data
@@ -23,24 +24,12 @@
 # Read settings from environmnent.
 get_settings()
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-app = FastAPI(
-    title="PHDI Tabulation 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,
-)
+
+# Instantiate FastAPI via PHDI's BaseService class
+app = BaseService(
+    service_name="PHDI Tabulation Service",
+    description_path=Path(__file__).parent.parent / "description.md",
+).start()
 
 
 class SchemaValidationInput(BaseModel):
@@ -79,15 +68,6 @@ class TabulateInput(BaseModel):
     )
 
 
-@app.get("/")
-async def health_check():
-    """
-    Check service status. If an HTTP 200 status code is returned along with
-    '{"status": "OK"}' then the tabulation service is available and running properly.
-    """
-    return {"status": "OK"}
-
-
 @app.post("/validate-schema", status_code=200)
 async def validate_schema_endpoint(input: SchemaValidationInput):
     try:

containers/validation/app/main.py

@@ -1,7 +1,7 @@
-from fastapi import FastAPI
 from pydantic import BaseModel, Field
 from typing import Literal
 from pathlib import Path
+from phdi.containers.base_service import BaseService
 from phdi.validation.validation import validate_ecr
 from .utils import load_ecr_config, validate_error_types
 
@@ -11,24 +11,11 @@
 ecr_config = load_ecr_config()
 
 
-# Instantiate FastAPI and set metadata.
-description = (Path(__file__).parent.parent / "description.md").read_text(
-    encoding="utf-8"
-)
-app = FastAPI(
-    title="PHDI Validation 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,
-)
+# Instantiate FastAPI via PHDI's BaseService class
+app = BaseService(
+    service_name="PHDI Validation Service",
+    description_path=Path(__file__).parent.parent / "description.md",
+).start()
 
 
 # Request and and response models
@@ -117,15 +104,6 @@ def validate_vxu_msg(message: str, include_error_types: list) -> ValidateRespons
 
 
 # Endpoints
-@app.get("/")
-async def health_check():
-    """
-    Check service status. If an HTTP 200 status code is returned along with
-    '{"status": "OK"}' then the tabulation service is available and running properly.
-    """
-    return {"status": "OK"}
-
-
 @app.post("/validate", status_code=200)
 async def validate_endpoint(input: ValidateInput) -> ValidateResponse:
     """