browser-automation

Browser Automation for Scientific Data Collection

Access scientific databases that have no REST API by controlling a real browser programmatically. Uses the browser-use framework (vision-based LLM browser automation).

When to Use

• Target database has no REST API (e.g., GEPIA2, some COSMIC pages)
• curl returns 403/captcha/login required and the data is publicly viewable in a browser
• Need to navigate multi-step web forms (e.g., TIMER2.0 correlation analysis)
• Need to download files from web interfaces (e.g., GEO supplementary data)
• API exists but is severely rate-limited and web access is faster

When NOT to use:

• REST API is available and working → use curl
• Data requires paid subscription → do not circumvent paywalls
• Data can be obtained from an alternative open API → prefer the API

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Installation Check

Before using browser automation, verify the environment:

bash: python3 -c "
try:
    import browser_use
    print('✅ browser-use installed')
except ImportError:
    print('❌ browser-use not installed')
    print('   Install: pip install browser-use')

import shutil
if shutil.which('chromium') or shutil.which('chromium-browser') or shutil.which('google-chrome'):
    print('✅ Chromium/Chrome found')
else:
    print('⚠️  No Chromium/Chrome found')
    print('   Install: apt-get install chromium-browser (Linux)')
    print('   Or: brew install --cask chromium (macOS)')

try:
    import playwright
    print('✅ Playwright installed')
except ImportError:
    print('❌ Playwright not installed')
    print('   Install: pip install playwright && python -m playwright install chromium')
"

If not installed:

pip install -q browser-use playwright && python -m playwright install chromium

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Usage Pattern

Basic: Extract data from a web page

from browser_use import Agent, Browser, BrowserConfig
from langchain_openai import ChatOpenAI
import asyncio

async def extract_gepia2_data(gene: str, cancer: str):
    """Extract gene expression data from GEPIA2 (no API available)."""
    browser = Browser(config=BrowserConfig(headless=True))
    llm = ChatOpenAI(model="gpt-4o", api_key=os.environ["OPENAI_API_KEY"])

    agent = Agent(
        task=f"""Go to http://gepia2.cancer-pku.cn/#analysis
        1. Click on 'Expression DIY' in the left menu
        2. In the gene input box, type '{gene}'
        3. Select '{cancer}' from the cancer type dropdown
        4. Click 'Plot' button
        5. Wait for the plot to load
        6. Extract the median expression values for Tumor and Normal from the plot
        7. Return the values as JSON: {{"gene": "{gene}", "cancer": "{cancer}", "tumor_median": X, "normal_median": Y}}
        """,
        llm=llm,
        browser=browser,
    )

    result = await agent.run()
    await browser.close()
    return result

result = asyncio.run(extract_gepia2_data("THBS2", "PAAD"))
print(result)