Merge pull request #299 from Steinbeck-Lab/development

Development

.github/workflows/dev-build.yml

@@ -39,7 +39,7 @@ jobs:
         pip install flake8 pytest
     - name: Analysing the code with pylint
       run: |
-        flake8 --ignore E402,E501,W503 $(git ls-files '*.py')
+        flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files '*.py') .
     # - name: Run test
     #   run: |
     #     pytest -p no:warnings

.github/workflows/release-please.yml

@@ -42,7 +42,7 @@ jobs:
         pip install flake8 pytest
     - name: Analysing the code with pylint
       run: |
-        flake8 --ignore E402,E501,W503 $(git ls-files '*.py')
+        flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files '*.py') .
     - name: Run test
       run: |
         python3 -m pytest -p no:warnings

Dockerfile

@@ -4,15 +4,13 @@ ENV PYTHON_VERSION=3.10
 ENV RDKIT_VERSION=2023.03.1
 ENV OPENBABEL_VERSION=v3.1
 
-ARG RELEASE_VERSION
-ENV RELEASE_VERSION=${RELEASE_VERSION}
-
 # Install runtime dependencies
 RUN apt-get update && \
     apt-get install -y software-properties-common && \
     apt-get update -y && \
     apt-get install -y openjdk-11-jre && \
-    apt-get install -y curl
+    apt-get install -y curl && \
+    conda update -n base -c defaults conda
 
 RUN wget -O surge "https://github.com/StructureGenerator/surge/releases/download/v1.0/surge-linux-v1.0"
 RUN chmod +x surge

app/main.py

@@ -1,15 +1,16 @@
 import os
-from fastapi import FastAPI
+from fastapi import FastAPI, status
 from fastapi.responses import RedirectResponse
 from fastapi_versioning import VersionedFastAPI
 
 from .routers import chem, converters, depict, tools, ocsr
 from fastapi.middleware.cors import CORSMiddleware
 
 from prometheus_fastapi_instrumentator import Instrumentator
+from app.schemas import HealthCheck
 
 app = FastAPI(
-    title="Cheminformatics Python Microservice",
+    title="Cheminformatics Microservice",
     description="This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of STOUT and another instance of DECIMER (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).",
     terms_of_service="https://steinbeck-lab.github.io/cheminformatics-python-microservice",
     contact={
@@ -23,16 +24,6 @@
     },
 )
 
-origins = ["*"]
-
-app.add_middleware(
-    CORSMiddleware,
-    allow_origins=origins,
-    allow_credentials=True,
-    allow_methods=["*"],
-    allow_headers=["*"],
-)
-
 app.include_router(chem.router)
 app.include_router(converters.router)
 app.include_router(depict.router)
@@ -54,14 +45,54 @@
         "name": "CC BY 4.0",
         "url": "https://creativecommons.org/licenses/by/4.0/",
     },
-    version=os.getenv('RELEASE_VERSION', '1.0')
+    version=os.getenv("RELEASE_VERSION", "1.0"),
 )
 
 Instrumentator().instrument(app).expose(app)
 
+origins = ["*"]
+
+
+@app.middleware("http")
+async def add_cors_headers(request, call_next):
+    response = await call_next(request)
+    response.headers["Access-Control-Allow-Origin"] = "*"
+    response.headers["Access-Control-Allow-Credentials"] = "true"
+    response.headers["Access-Control-Allow-Methods"] = "GET, POST, PUT, DELETE, OPTIONS"
+    response.headers["Access-Control-Allow-Headers"] = "Content-Type, Authorization"
+    return response
+
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
 
 @app.get("/", include_in_schema=False)
 async def root():
-    return RedirectResponse(
-        url="https://steinbeck-lab.github.io/cheminformatics-python-microservice"
-    )
+    return RedirectResponse(url=os.getenv("HOMEPAGE_URL", "/latest/docs"))
+
+
+@app.get(
+    "/health",
+    tags=["healthcheck"],
+    summary="Perform a Health Check",
+    response_description="Return HTTP Status Code 200 (OK)",
+    status_code=status.HTTP_200_OK,
+    response_model=HealthCheck,
+)
+def get_health() -> HealthCheck:
+    """
+    ## Perform a Health Check
+    Endpoint to perform a healthcheck on. This endpoint can primarily be used Docker
+    to ensure a robust container orchestration and management is in place. Other
+    services which rely on proper functioning of the API service will not deploy if this
+    endpoint returns any other HTTP status code except 200 (OK).
+    Returns:
+        HealthCheck: Returns a JSON response with the health status
+    """
+    return HealthCheck(status="OK")