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Quick Test Guide

Use this guide to quickly verify that core features and optional components work.

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Prerequisites

pip install -r requirements.txt
pip install -e .

# Optional: browser tools
pip install playwright
playwright install chromium

# Optional: cron/automation
# APScheduler is typically in requirements.txt

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1. Core

python -c "from biocortex.agent import BioCortexAgent; print('OK')"

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2. Browser Tools

python -c "from biocortex.tools.browser import BrowserTool; print('Browser OK')"
Chat test: Start the Web UI, open Chat, try:
  • “Search PubMed for CRISPR papers”
  • “Find information about gene BRCA1”
  • “Get ClinVar variants for TP53”
Expect structured results (tables, links, summaries).

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3. Cron / Automation

python -c "from biocortex.automation import CronScheduler; print('Cron OK')"
Web UI: Automation → Monitors / Cron Jobs — add a job or monitor, start the scheduler, check list and status.

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4. Resources API

With the backend running and a logged-in user: 
curl -b cookies.txt http://localhost:7860/api/v1/resources
Expect { "databases": [...], "tools": [...], "packages": [...] }. The Web UI Resources page uses this endpoint.

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5. Full Analysis (CLI)

biocortex "What does the gene BRCA1 do?"
Expect strategy selection (likely SimpleReAct), execution, and a short answer. For a longer pipeline (e.g. scRNA-seq), use a task that triggers DAG mode and check plan steps and final report.

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6. Web UI End-to-End

  1. Start backend: python -m biocortex.web.app
  2. Start frontend (if separate): cd frontend && npm run dev
  3. Log in, open Chat, run a task → plan and report.
  4. Open Resources → tabs and search.
  5. Open Automation → add a monitor or webhook, trigger or wait for schedule.

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Troubleshooting

  • Browser: Ensure playwright install chromium was run and no firewall blocks database access.
  • API keys: Set in .env or user settings; check /status and /me/settings.
  • Cron: Scheduler must be started (API or UI); check job list and enable state.
For more detail, see repo docs: QUICK_TEST_GUIDE.md, AUTOMATION_USER_GUIDE.md, BROWSER_WEBHOOK_CRON_GUIDE.md.