Refactor OpenAPI fetcher for improved clarity and robustness

Reorganized and enhanced the OpenAPI fetch logic for better maintainability and error handling. Key updates include improved environment variable validation, more detailed error messages, streamlined configuration loading, and additional safety checks for file paths and directories. Added proper logging and ensured the process flow is easy to trace.

backend/app/routers/sample.py

@@ -1,7 +1,13 @@
 from fastapi import APIRouter, HTTPException, Depends
 from sqlalchemy.orm import Session
 from typing import List
-from app.schemas import Puck as PuckSchema, Sample as SampleSchema
+from datetime import datetime
+from app.schemas import (
+    Puck as PuckSchema,
+    Sample as SampleSchema,
+    SampleEventResponse,
+    SampleEventCreate,
+)
 from app.models import (
     Puck as PuckModel,
     Sample as SampleModel,
@@ -45,3 +51,50 @@ async def get_all_pucks_with_samples_and_events(db: Session = Depends(get_db)):
             status_code=404, detail="No pucks found in the database"
         )  # More descriptive
     return pucks
+
+
+# Route to post a new sample event
+@router.post("/samples/{sample_id}/events", response_model=SampleEventResponse)
+async def create_sample_event(
+    sample_id: int, event: SampleEventCreate, db: Session = Depends(get_db)
+):
+    # Ensure the sample exists
+    sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
+    if not sample:
+        raise HTTPException(status_code=404, detail="Sample not found")
+
+    # Create the event
+    sample_event = SampleEventModel(
+        sample_id=sample_id,
+        event_type=event.event_type,
+        timestamp=datetime.now(),  # Use the current timestamp
+    )
+    db.add(sample_event)
+    db.commit()
+    db.refresh(sample_event)
+
+    return (
+        sample_event  # Response will automatically use the SampleEventResponse schema
+    )
+
+
+# Route to fetch the last (most recent) sample event
+@router.get("/samples/{sample_id}/events/last", response_model=SampleEventResponse)
+async def get_last_sample_event(sample_id: int, db: Session = Depends(get_db)):
+    # Ensure the sample exists
+    sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
+    if not sample:
+        raise HTTPException(status_code=404, detail="Sample not found")
+
+    # Get the most recent event for the sample
+    last_event = (
+        db.query(SampleEventModel)
+        .filter(SampleEventModel.sample_id == sample_id)
+        .order_by(SampleEventModel.timestamp.desc())
+        .first()
+    )
+
+    if not last_event:
+        raise HTTPException(status_code=404, detail="No events found for the sample")
+
+    return last_event  # Response will automatically use the SampleEventResponse schema

backend/app/schemas.py

@@ -83,6 +83,16 @@ class SampleEventCreate(BaseModel):
     event_type: str
 
 
+class SampleEventResponse(BaseModel):
+    id: int
+    sample_id: int
+    event_type: str
+    timestamp: datetime
+
+    class Config:
+        from_attributes = True
+
+
 class Results(BaseModel):
     # Define attributes for Results here
     pass

backend/main.py

@@ -36,6 +36,28 @@ def get_project_metadata():
     )
 
 
+def run_server():
+    import uvicorn
+
+    print(f"[INFO] Starting server in {environment} environment...")
+    print(f"[INFO] SSL Certificate Path: {cert_path}")
+    print(f"[INFO] SSL Key Path: {key_path}")
+    port = config.get("PORT", os.getenv("PORT"))
+    if not port:
+        print("[ERROR] No port defined in config or environment variables. Aborting!")
+        sys.exit(1)  # Exit if no port is defined
+    port = int(port)
+    print(f"[INFO] Running on port {port}")
+    uvicorn.run(
+        app,
+        host="127.0.0.1" if environment in ["dev", "test"] else "0.0.0.0",
+        port=port,
+        log_level="debug",
+        ssl_keyfile=key_path,
+        ssl_certfile=cert_path,
+    )
+
+
 # Get project metadata from pyproject.toml
 project_name, project_version = get_project_metadata()
 app = FastAPI(
@@ -145,7 +167,6 @@ app.include_router(sample.router, prefix="/samples", tags=["samples"])
 
 if __name__ == "__main__":
     import sys
-    import uvicorn
     from dotenv import load_dotenv
     from multiprocessing import Process
     from time import sleep
@@ -169,52 +190,28 @@ if __name__ == "__main__":
         print("openapi.json generated successfully.")
         sys.exit(0)  # Exit after generating the file
 
-    # Default behavior: Run the server
+    # Default behavior: Run the server based on the environment
     environment = os.getenv("ENVIRONMENT", "dev")
     port = int(os.getenv("PORT", 8000))
     is_ci = os.getenv("CI", "false").lower() == "true"
 
-    def run_server():
-        print(f"[INFO] Starting server in {environment} environment...")
-        print(f"[INFO] SSL Certificate Path: {cert_path}")
-        print(f"[INFO] SSL Key Path: {key_path}")
-        port = config.get("PORT", os.getenv("PORT"))
-        if not port:
-            print(
-                "[ERROR] No port defined in config or environment variables. Aborting!"
-            )
-            sys.exit(1)  # Exit if no port is defined
-        port = int(port)
-        print(f"[INFO] Running on port {port}")
-        uvicorn.run(
-            app,
-            host="127.0.0.1" if environment in ["dev", "test"] else "0.0.0.0",
-            port=port,
-            log_level="debug",
-            ssl_keyfile=key_path,
-            ssl_certfile=cert_path,
-        )
-
-    # Run in CI mode
-    # Generate or use SSL Key and Certificate
-    if environment in ["test", "dev", "ci"]:
-        ssl_dir = Path(
-            cert_path
-        ).parent  # Ensure we work with the parent directory of the cert path
-        ssl_dir.mkdir(
-            parents=True, exist_ok=True
-        )  # Create the directory structure if it doesn't exist
+    if is_ci or environment == "test":
+        # Test or CI Mode: Run server process temporarily for test validation
+        ssl_dir = Path(cert_path).parent
+        ssl_dir.mkdir(parents=True, exist_ok=True)
 
         # Generate self-signed certs if missing
         if not Path(cert_path).exists() or not Path(key_path).exists():
             print(f"[INFO] Generating self-signed SSL certificates at {ssl_dir}")
             ssl_heidi.generate_self_signed_cert(cert_path, key_path)
 
+        # Start the server as a subprocess, wait, then terminate
         server_process = Process(target=run_server)
         server_process.start()
-        sleep(5)  # Wait 5 seconds to ensure the server starts without errors
-        server_process.terminate()  # Terminate the server (test purposes)
+        sleep(5)  # Wait for 5 seconds to verify the server is running
+        server_process.terminate()  # Terminate the server process (for CI)
         server_process.join()  # Ensure proper cleanup
         print("CI: Server started and terminated successfully for test validation.")
     else:
+        # Dev or Prod: Start the server as usual
         run_server()

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aareDB"
-version = "0.1.0a5"
+version = "0.1.0a6"
 description = "Backend for next gen sample management system"
 authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
 license = {text = "MIT"}