[ENH] FastAPI integration added

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: flake8
         language_version: python3
         args:
-          - --extend-ignore=E501
+          - --extend-ignore=E501,E402
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0

README.md

@@ -4,56 +4,142 @@
 
 Currently, the researcher or the data user has to answer a number of queries to get the desired results and it often requires iteration. 
 
-The aim of query-tol-ai would be to make this search process more user-friendly by adding an LLM style chatbot interface. This is to be done by utilizing large language models that will be able to interpret the user prompts and initiate the API calls accurately giving the user the desired results.
+The aim of query-tool-ai would be to make this search process more user-friendly by adding an LLM style chatbot interface. This is to be done by utilizing large language models that will be able to interpret the user prompts and initiate the API calls accurately giving the user the desired results.
 
-## Local installation
-- Clone the repository:
-  ```
+## Local installation - 
+  ### Clone the repository :
+  ```bash
   git clone https://github.com/neurobagel/query-tool-ai.git
   cd query-tool-ai
   ```
-- Create and activate a virtual environment:
-   ```
+
+  Before proceeding with either you need to set the environment variables.
+  ### Set the environment variables - 
+   | Environment Variable   | Type    | Required                                 | Default Value if Not Set | Example                                                   |
+   | ---------------------- | ------- | ---------------------------------------- | ------------------------ | --------------------------------------------------------- |
+   | `HOST`                 | string  | No                                       | `0.0.0.0`                | `127.0.0.1`                                               |
+   | `PORT`                 | integer | No                                       | `8000`                   | `8080`                                                    |
+
+
+  After cloning the repository, you can choose to either use the Dockerized version or run the application locally using Python. 
+  #### Follow the instructions for the option that suits you best:
+
+  ### Option 1 : Docker :
+  - #### First, [install Docker](https://docs.docker.com/get-docker/).
+  - #### Build the image using the Dockerfile
+    After cloning the current repository, build the Docker image locally:
+    ```bash
+    docker build -t neurobagel-query-tool-ai .
+    ```
+  - #### Run the container from the built image:
+    Start the container from the built image. Ensure you map the necessary volumes and set the container name.
+    ```bash
+    docker run -d \
+    -p 8000:8000 \
+    -v ollama:/root/.ollama \
+    -v /home/user/data:/app/output/ \
+    --name query-tool-ai-container neurobagel-query-tool-ai
+    ```
+
+    Then you can access the query tool ai at http://localhost:8000
+
+    **Note:** the query tool ai is listening on port 8000 inside the docker container, replace port 8000 by the port you would like to expose to the host. For example if you'd like to run the tool on port 8080 of your machine you can run the following command:
+    ```bash
+    docker run -d \
+    -p 8080:8000 \
+    -v ollama:/root/.ollama \
+    -v /home/user/data:/app/output/ \
+    --name query-tool-ai-container neurobagel-query-tool-ai
+    ```
+
+
+  - #### Verify Host and Port
+    To ensure the server is running on localhost, you can check the logs or try accessing the server in your browser or with `curl`(assuming the the query tool ai is listening on port 8000):
+    ```bash
+    curl -X GET "http://localhost:8000/"
+    ```
+    You should see the response:
+    ```json
+    {"message": "Welcome to the Neurobagel Query Tool AI API"}
+    ``` 
+
+### Option 2 : Python
+- #### Create and activate a virtual environment:
+   ```bash
    python3 -m venv venv
    source venv/bin/activate
    ```
-- Install the required packages and pull the Ollama model:
-   ```
+- #### Install the required packages and pull the Ollama model:
+   ```bash
    pip install -r requirements.txt
    ollama pull mistral
    ```
-- Run the python script:
+
+- #### Run the FastAPI Server:
+  ```bash
+  python app/main.py
   ```
-  python3 app/api/url_generator.py
+  This command starts the FastAPI server on `http://localhost:8000`. (assuming PORT=8000)
+
+- #### Verify Host and Port
+  To ensure the server is running on localhost, you can check the logs or try accessing the server in your browser or with `curl`:
+  ```bash
+  curl -X GET "http://localhost:8000/" 
   ```
-- You should see the following prompt:
+  You should see the response:
+  ```json
+  {"message": "Welcome to the Neurobagel Query Tool AI API"}
   ```
-  Enter user query (or 'exit' to quit): 
+
+## Interacting with the Query Tool AI 
+After the local installation is complete, you can ask your query in the following 2 ways.
+
+### API Interaction - 
+  You can interact with the FastAPI application by sending a POST request to the generate_url endpoint. Here’s how you can do it using curl (assuming the the query tool ai is listening on port 8000):
+  ```bash
+    curl -X POST "http://localhost:8000/generate_url/" -H "Content-Type: application/json" -d '{"query": "your query here"}'
   ```
-  Enter your query to get the desired API URL.
+  Replace "your query here" with the actual query you want to test.
 
-## Dockerized version
-- First, [install Docker](https://docs.docker.com/get-docker/).
+### Python Script Interaction (Optional) -
+  - If you have completed the local installation using **`docker`**, write the following command in the terminal.
+    ```bash
+    docker exec -it query-tool-ai-container python3 /  app/api/url_generator.py
+    ```
 
-- After cloning the current repository, build the Docker image locally:
-  ```
-  docker build -t query-tool-ai .
-  ```
-- Run the container from the built image:
-  ```
-  docker run -d \
-  -v ollama:/root/.ollama \
-  -v /home/user/data:/app/output/ \
-  --name query-tool-ai-container query-tool-ai
-  ```
-- Execute the python script:
-  ```
-  docker exec -it query-tool-ai-container python3 /app/api/url_generator.py
-  ```
-- You should see the following prompt:
-  ```
+  - If you have completed the local installation using **`python`**, write the following command in the terminal.
+    ```bash
+    python3 app/api/url_generator.py
+    ```
+
+  You should see the following prompt - 
+
+  ```bash
   Enter user query (or 'exit' to quit): 
   ```
+
   Enter your query to get the desired API URL.
 
 
+## Testing
+
+Neurobagel API utilizes [Pytest](https://docs.pytest.org/en/7.2.x/) framework for testing.
+
+To run the tests first make sure you're in repository's main directory.
+
+You can then run the tests by executing the following command in your terminal:
+
+```bash
+pytest tests
+```
+
+### License
+
+Neurobagel API is released under the terms of the [MIT License](LICENSE)
+
+
+
+
+
+
+

app/__init__.py

@@ -0,0 +1,6 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.dirname(os.path.realpath(__file__))
+)  # Fixes relative import error.

app/api/url_generator.py

@@ -1,6 +1,9 @@
 import sys
 import os
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))  # Fixes import errors
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+)  # Fixes import errors
 
 import json
 from llm_processing.extractions import extract_information

app/main.py

@@ -0,0 +1,25 @@
+import os
+from fastapi import FastAPI
+from dotenv import load_dotenv
+from router import routes
+
+# Load environment variables from .env file
+load_dotenv()
+
+app = FastAPI()
+
+app.include_router(routes.router)
+
+
+@app.get("/")
+async def root():
+    return {"message": "Welcome to the Neurobagel Query Tool AI API"}
+
+
+if __name__ == "__main__":
+    import uvicorn
+
+    host = os.getenv("HOST", "0.0.0.0")
+    port = int(os.getenv("PORT", 8000))
+
+    uvicorn.run(app, host=host, port=port)

app/router/routes.py

@@ -0,0 +1,26 @@
+import sys
+import os
+
+sys.path.insert(
+    0, os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+)  # Fixes import errors
+
+from fastapi import APIRouter, HTTPException, status
+from pydantic import BaseModel
+from api.url_generator import get_api_url
+
+
+router = APIRouter()
+
+
+class QueryRequest(BaseModel):
+    query: str
+
+
+@router.post("/generate_url/")
+async def generate_url(request: QueryRequest):
+    try:
+        api_url = get_api_url(request.query)
+        return {"response": api_url}
+    except Exception as e:
+        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e))

entrypoint.sh

@@ -1,4 +1,11 @@
 #!/bin/bash
 
-ollama serve &&
-ollama run mistral.
+# Start the Ollama services first
+ollama serve &
+ollama run mistral &
+
+# Start the FastAPI application
+uvicorn main:app --host 0.0.0.0 --port 8000
+
+# Wait for all background processes to complete
+wait

requirements.txt

@@ -7,9 +7,11 @@ attrs==23.2.0
 certifi==2024.6.2
 cfgv==3.4.0
 charset-normalizer==3.3.2
+click==8.1.7
 dataclasses-json==0.6.7
 distlib==0.3.8
 exceptiongroup==1.2.1
+fastapi==0.112.0
 filelock==3.14.0
 frozenlist==1.4.1
 fsspec==2024.6.0
@@ -48,12 +50,14 @@ PyYAML==6.0.1
 requests==2.32.3
 sniffio==1.3.1
 SQLAlchemy==2.0.30
+starlette==0.37.2
 tenacity==8.3.0
 tomli==2.0.1
 tqdm==4.66.4
 types-requests==2.32.0.20240622
 typing-inspect==0.9.0
 typing_extensions==4.12.2
 urllib3==2.2.1
+uvicorn==0.30.5
 virtualenv==20.26.2
 yarl==1.9.4

tests/test_app.py

@@ -0,0 +1,67 @@
+import pytest
+from fastapi.testclient import TestClient
+from app.main import app
+from unittest.mock import patch
+
+client = TestClient(app)
+
+
+def test_root():
+    response = client.get("/")
+    assert response.status_code == 200
+    assert response.json() == {
+        "message": "Welcome to the Neurobagel Query Tool AI API"
+    }
+
+
+@pytest.mark.parametrize(
+    "query, expected_status_code, expected_response",
+    [
+        (
+            "How many subjects between 20 and 80 yrs old who have at least 3 phenotypic sessions and 2 imaging sessions?",
+            200,
+            {
+                "response": "https://api.neurobagel.org/query/?min_age=20.0&max_age=80.0&min_num_imaging_sessions=2&min_num_phenotypic_sessions=3"
+            },
+        ),
+        (
+            "male healthy control subjects",
+            200,
+            {
+                "response": "https://api.neurobagel.org/query/?sex=snomed:248153007&is_control=true"
+            },
+        ),
+        (
+            "subjects diagnosed with traumatic brain injury assessed with balloon analogue risk task and T2 weighted image modality",
+            200,
+            {
+                "response": "https://api.neurobagel.org/query/?diagnosis=snomed:127295002&is_control=false&assessment=cogatlas:trm_4d559bcd67c18&image_modal=nidm:T2Weighted"
+            },
+        ),
+        (
+            "female healthy control subjects with parkinsons",
+            200,
+            {
+                "response": "Subjects cannot both be healthy controls and have a diagnosis."
+            },
+        ),
+        (
+            "Female subjects suffering from Arachnoiditis assessed by regulated heat stimulation",
+            200,
+            {
+                "response": "Unfortunately, Neurobagel does not yet support searches for the following terms: arachnoiditis diagnosis, regulated heat stimulation assessment"
+            },
+        ),
+    ],
+)
+@patch(
+    "app.router.routes.get_api_url",
+)
+def test_generate_url(
+    mock_get_api_url, query, expected_status_code, expected_response
+):
+    mock_get_api_url.return_value = expected_response
+    response = client.post("/generate_url/", json={"query": query})
+
+    assert response.status_code == expected_status_code
+    assert response.json() == expected_response