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Automation User Guide

This guide explains how to use Monitors, Webhooks, and Cron Jobs in the BioCortex Web UI and API.

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Overview

FeaturePurpose
MonitorsScheduled literature or genomics checks (PubMed, Google Scholar, ClinVar, UCSC) with results saved to the workspace.
WebhooksTrigger analysis from external systems (e.g. lab equipment, CI/CD) via HTTP POST.
Cron JobsArbitrary scheduled tasks (custom task template + cron expression).
All are available in the Web UI under Automation (tabs: Monitors, Webhooks, Cron Jobs).

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Monitors

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What they do

  • PubMed — Search for recent articles; get titles, authors, PMIDs, summaries.
  • Google Scholar — Recent papers by query; citation counts, years.
  • ClinVar — Pathogenic/likely-pathogenic variants for a gene (e.g. UCSC, hg38).

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How to add (Web UI)

  1. Go to Automation → Monitors.
  2. Click Add Monitor (or equivalent).
  3. Choose type (PubMed / Google Scholar / ClinVar).
  4. Enter search query (e.g. gene name or topic).
  5. Set schedule (e.g. “Daily at 8 AM” or cron expression).
  6. Save. The cron scheduler will run the task and store results.

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Backend

Monitors are implemented as cron jobs with metadata (e.g. monitor_type: pubmed, google_scholar, clinvar). The Automation UI filters cron jobs by this metadata to show the “Monitors” list. Creation uses the same cron API with a task template tailored to the monitor type.

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Webhooks

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What they do

Allow external systems to trigger a BioCortex analysis with a predefined task template (and optional payload).

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How to configure (Web UI)

  1. Go to Automation → Webhooks.
  2. View or add webhook endpoints (e.g. experiment_done).
  3. Configure: task template (natural language prompt), description.
  4. Use the shown URL and (if required) secret for POST requests from your system.

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API

  • Trigger: POST /api/v1/webhooks/{name} — body can include payload (e.g. file paths, experiment id). Backend runs the configured task with the agent.
  • List: GET /api/v1/webhooks
  • Configure: POST /api/v1/webhooks/{name}/configure — set task template, description.
  • Calls: GET /api/v1/webhooks/{name}/calls — list recent invocations (for debugging).

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Cron Jobs

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What they do

Run any BioCortex task on a schedule (cron expression). Use for custom recurring analyses (e.g. weekly QC, daily literature digest).

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How to add (Web UI)

  1. Go to Automation → Cron Jobs.
  2. Add job: name, task description (natural language), cron expression (e.g. 0 8 * * * for daily at 8 AM), optional enable/disable.
  3. Save. The global cron scheduler must be running (start from UI or API).

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API

  • List: GET /api/v1/cron/jobs
  • Create: POST /api/v1/cron/jobs — body: name, task, cron, enabled.
  • Get/Delete/Enable/Disable: GET/DELETE /api/v1/cron/jobs/{id}, POST .../enable, POST .../disable
  • Scheduler: POST /api/v1/cron/start, POST /api/v1/cron/stop

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Dependencies

  • Browser tools (for PubMed, Scholar, ClinVar): playwright, playwright install chromium.
  • Cron: Backend uses a persistent scheduler (e.g. APScheduler); state is stored so jobs survive restarts.

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Next Steps