Sepsis Prediction API

.dockerignore

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+venv/
+__pycache__/
+*.venv
+*.venv.*
+venv.*
+*.pyc
+.git
+.vscode
+.gitattributes
+.gitkeep

Dockerfile

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+# Specifying the base image
+FROM python:3.11
+
+# Set the working directory to /Sepsis
+WORKDIR /Sepsis
+ 
+# Copy the current directory contents into the container at /Sepsis
+COPY ./requirements.txt /Sepsis/requirements.txt
+ 
+# Install requirements.txt 
+RUN pip install --no-cache-dir --upgrade -r /Sepsis/requirements.txt
+ 
+# Set up a new user named "user" with user ID 1000
+RUN useradd -m -u 1000 user
+# Switch to the "user" user
+USER user
+# Set home to the user's home directory
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+ 
+# Set the working directory to the user's home directory
+WORKDIR $HOME/app
+ 
+# Copy the current directory contents into the container at $HOME/app setting the owner to the user
+COPY --chown=user . $HOME/app
+ 
+# Start the FastAPI app on port 7860, the default port expected by Spaces
+CMD ["uvicorn", "src.main:app", "--host", "0.0.0.0", "--port", "7860"]

commands.txt

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+ python -m venv venv; # To create a venv environment
+ venv\Scripts\activate; # To activate the environment
+ python -m pip install -q --upgrade pip;# To upgrade the pip 
+ python -m pip install -qr requirements.txt # To install the requirements
+
+ # THe model of the input is useful to structure the input of the data (class)
+ #The variable for a function will be an object of the class defined
+
+ #   View a summary of image vulnerabilities and recommendations 
+ docker scout quickview

main.py

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+
+
+# Setup Section
+  
+ # Create FastAPI instance
+app = FastAPI(title="Sepsis Prediction API",description="API for Predicting Sespsis ")
+## A function to load machine Learning components to re-use
+def Ml_loading_components(fp):
+    with open(fp, "rb") as f:
+        object=pickle.load(f)
+        return(object)
+                                                                                                              # Loading the machine learning components
+DIRPATH = os.path.dirname(os.path.realpath(__file__))
+ml_core_fp = os.path.join(DIRPATH,"ML","ML_Model.pkl")
+ml_components_dict = Ml_loading_components(fp=ml_core_fp)
+
+
+
+# Defining the variables for each component
+label_encoder = ml_components_dict['label_encoder'] # The label encoder
+# Loaded scaler component
+scaler = ml_components_dict['scaler']
+#Loaded model 
+model = ml_components_dict['model']
+# Defining our input variables
+
+
+class InputData(BaseModel):
+    PRG:int
+    PL: int
+    BP: int
+    SK: int
+    TS: int
+    BMI: float
+    BD2: float
+    Age: int
+
+"""
+* PRG: Plasma glucose
+
+* PL: Blood Work Result-1 (mu U/ml)
+
+* PR: Blood Pressure (mmHg)
+
+* SK: Blood Work Result-2(mm)
+
+* TS: Blood Work Result-3 (muU/ml)
+
+* M11: Body mass index (weight in kg/(height in m)^2
+
+* BD2: Blood Work Result-4 (mu U/ml)
+
+* Age: patients age(years)
+
+"""  
+# Index route
+@app.get("/")
+def index():
+    return{'message':'Hello, Welcome to My Sepsis Prediction FastAPI'}
+
+ 
+# Create prediction endpoint
+@app.post("/predict")
+def predict (df:InputData):
+
+ 
+    # Prepare the feature and structure them like in the notebook
+    df = pd.DataFrame([df.dict().values()],columns=df.dict().keys())
+
+
+    print(f"[Info] The inputed dataframe is : {df.to_markdown()}")
+    age = df['Age']
+    print(age)
+    # Scaling the inputs
+    df_scaled = scaler.transform(df)
+
+
+    # Prediction
+    raw_prediction = model.predict(df_scaled)
+
+    if raw_prediction == 0:
+        raise HTTPException(status_code=status.HTTP_200_OK, detail="The patient will Not Develop Sepsis")
+    elif raw_prediction == 1:
+        raise HTTPException(status_code=status.HTTP_200_OK, detail="The patient Will Develop Sepsis")
+    else:
+        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="Prediction Error")
+
+
+if __name__ == "__main__":
+    uvicorn.run("main:app",reload=True)
+
+
+
+

requirements.txt

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+annotated-types==0.6.0
+anyio==3.7.1
+black==23.9.1
+certifi==2023.7.22
+click==8.1.7
+colorama==0.4.6
+dnspython==2.4.2
+email-validator==2.0.0.post2
+fastapi==0.103.2
+h11==0.14.0
+httpcore==0.18.0
+httptools==0.6.0
+httpx==0.25.0
+idna==3.4
+imbalanced-learn==0.11.0
+imblearn==0.0
+itsdangerous==2.1.2
+Jinja2==3.1.2
+joblib==1.3.2
+MarkupSafe==2.1.3
+mypy-extensions==1.0.0
+numpy==1.26.0
+orjson==3.9.7
+packaging==23.2
+pandas==2.1.1
+pathspec==0.11.2
+platformdirs==3.11.0
+pydantic==2.4.2
+pydantic-extra-types==2.1.0
+pydantic-settings==2.0.3
+pydantic_core==2.10.1
+python-dateutil==2.8.2
+python-dotenv==1.0.0
+python-multipart==0.0.6
+pytz==2023.3.post1
+PyYAML==6.0.1
+scikit-learn==1.2.2
+scipy==1.11.3
+six==1.16.0
+sniffio==1.3.0
+starlette==0.27.0
+threadpoolctl==3.2.0
+typing_extensions==4.8.0
+tzdata==2023.3
+ujson==5.8.0
+uvicorn==0.23.2
+watchfiles==0.20.0
+websockets==11.0.3
+uvicorn
+tabulate