5_systematic_review.py

"""Run a systematic review: search, screen, extract, and generate a report."""

import os
import time
import requests

api_key = os.environ["ELICIT_API_KEY"]

# Create
response = requests.post(
    "https://elicit.com/api/v2/sessions/systematic-reviews",
    headers={"Authorization": f"Bearer {api_key}"},
    json={
        "researchQuestion": "Do GLP-1 receptor agonists reduce major adverse cardiovascular events in adults with type 2 diabetes?",
        "searches": [
            {"query": "GLP-1 receptor agonist cardiovascular outcomes", "maxResults": 100},
            {"query": "GLP-1 agonist MACE type 2 diabetes", "corpus": "pubmed", "maxResults": 100},
        ],
        "abstractScreening": {
            "criteria": [
                {
                    "name": "Human RCT",
                    "instructions": "The study must be a randomized controlled trial in human adults.",
                }
            ]
        },
        "extraction": {
            "questions": [
                {
                    "name": "MACE hazard ratio",
                    "instructions": "Extract the hazard ratio and 95% confidence interval for major adverse cardiovascular events.",
                }
            ]
        },
        "generateReport": True,
    },
)
response.raise_for_status()
review = response.json()

session_id = review["sessionId"]
print(f"Review created: {review['url']}")

# Poll — reviews run through several stages and can take a while
while True:
    time.sleep(60)
    review = requests.get(
        f"https://elicit.com/api/v2/sessions/systematic-reviews/{session_id}",
        headers={"Authorization": f"Bearer {api_key}"},
    ).json()
    print(f"Status: {review['status']} ({review['executionStage']})")
    if review["status"] != "processing":
        break

if review["status"] == "completed":
    # export URLs are presigned, valid for 7 days
    data = review["data"]
    for stage in ("search", "screen", "fulltext", "extract"):
        if stage in data:
            print(f"  {stage} export: {data[stage]['csv']}")
    if "report" in data:
        print(f"\n{data['report']['result']['title']}")
        print(data["report"]["result"]["summary"])
        print(f"  PDF: {data['report']['pdf']}")
elif review["status"] == "failed":
    print(f"Review failed: {review.get('error')}")