[ENH] Set up federation prototype and CI workflows

.github/dependabot.yaml

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+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      interval: 'weekly'
+    labels:
+      - "_bot"
+      - "maint:dependency"
+      - "type:maintenance"

.github/workflows/build_docker.yaml

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+name: build docker
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/federation_api:latest

.github/workflows/codespell.yaml

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+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/lint.yaml

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+name: lint
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --per-file-ignores=./app/api/models.py:F722
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

Dockerfile

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+FROM python:3.10
+
+WORKDIR /usr/src/
+
+COPY ./requirements.txt /usr/src/app/requirements.txt
+
+RUN pip install --no-cache-dir --upgrade -r /usr/src/app/requirements.txt
+
+COPY ./app /usr/src/app
+
+# NB_API_PORT, representing the port on which the API will be exposed, 
+# is an environment variable that will always have a default value of 8000 when building the image
+# but can be overridden when running the container.
+ENTRYPOINT uvicorn app.main:app --proxy-headers --host 0.0.0.0 --port ${NB_API_PORT:-8000}

app/api/crud.py

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+"""CRUD functions called by path operations."""
+
+import httpx
+from fastapi import HTTPException
+
+from . import utility as util
+
+async def get(
+    min_age: float,
+    max_age: float,
+    sex: str,
+    diagnosis: str,
+    is_control: bool,
+    min_num_sessions: int,
+    assessment: str,
+    image_modal: str,
+):
+    """
+    Makes GET requests to one or more Neurobagel node APIs using httpx where the parameters are Neurobagel query parameters.
+
+    Parameters
+    ----------
+    min_age : float
+        Minimum age of subject.
+    max_age : float
+        Maximum age of subject.
+    sex : str
+        Sex of subject.
+    diagnosis : str
+        Subject diagnosis.
+    is_control : bool
+        Whether or not subject is a control.
+    min_num_sessions : int
+        Subject minimum number of imaging sessions.
+    assessment : str
+        Non-imaging assessment completed by subjects.
+    image_modal : str
+        Imaging modality of subject scans.
+
+    Returns
+    -------
+    httpx.response
+        Response of the POST request.
+
+    """
+    cross_node_results = []
+    params = {}
+    if min_age:
+        params["min_age"] = min_age
+    if max_age:
+        params["max_age"] = max_age
+    if sex:
+        params["sex"] = sex
+    if diagnosis:
+        params["diagnosis"] = diagnosis
+    if is_control:
+        params["is_control"] = is_control
+    if min_num_sessions:
+        params["min_num_sessions"] = min_num_sessions
+    if assessment:
+        params["assessment"] = assessment
+    if image_modal:
+        params["image_modal"] = image_modal
+
+    for node_url in util.NEUROBAGEL_NODES:
+        response = httpx.get(
+            url=node_url,
+            params=params,
+            # TODO: Revisit timeout value when query performance is improved
+            timeout=30.0,
+        )
+
+        if not response.is_success:
+            raise HTTPException(
+                status_code=response.status_code,
+                detail=f"{response.reason_phrase}: {response.text}",
+            )
+
+        cross_node_results += response.json()
+
+    return cross_node_results

app/api/models.py

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+"""Data models."""
+from pydantic import BaseModel
+
+
+class QueryModel(BaseModel):
+    """Data model and dependency for API that stores the query parameters to be accepted and validated."""
+
+    min_age: float = None
+    max_age: float = None
+    sex: str = None
+    diagnosis: str = None
+    is_control: bool = None
+    min_num_sessions: int = None
+    assessment: str = None
+    image_modal: str = None

app/api/routers/query.py

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+"""Router for query path operations."""
+
+from fastapi import APIRouter, Depends
+
+from .. import crud
+from ..models import QueryModel
+
+router = APIRouter(prefix="/query", tags=["query"])
+
+
+@router.get("/")
+async def get_query(query: QueryModel = Depends(QueryModel)):
+    """When a GET request is sent, return list of dicts corresponding to subject-level metadata aggregated by dataset."""
+    response = await crud.get(
+        query.min_age,
+        query.max_age,
+        query.sex,
+        query.diagnosis,
+        query.is_control,
+        query.min_num_sessions,
+        query.assessment,
+        query.image_modal,
+    )
+
+    return response

app/api/utility.py

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+"""Constants for federation."""
+
+import os
+
+#  Neurobagel nodes
+NEUROBAGEL_NODES = os.environ.get("NB_NODES", ["http://206.12.99.17:8000/query/"])

app/main.py

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+"""Main app."""
+
+import uvicorn
+from fastapi import FastAPI
+from fastapi.responses import ORJSONResponse
+from fastapi.middleware.cors import CORSMiddleware
+
+from .api.routers import query
+
+app = FastAPI(default_response_class=ORJSONResponse)
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["*"],
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+app.include_router(query.router)
+
+# Automatically start uvicorn server on execution of main.py
+if __name__ == "__main__":
+    uvicorn.run("app.main:app", port=8000, reload=True)