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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This is a Clojure application that transforms ClinGen Variant Pathogenicity Interpretation messages (in JSON-LD format) into ClinVar submission records. The primary purpose is to improve consistency and reduce time to draft ClinVar Submission Variant sheets.

Architecture

The application is structured as both a command-line tool and a REST web service:

Core Modules

  • core.clj - Main entry point and orchestration
  • web_service.clj - REST API web service handlers using Ring/Jetty
  • ld.clj - Linked-data utility providing XPath-like queries against JSON-LD files
  • form.clj - ClinVar submission-specific form parsing functions
  • report.clj - Output generation and run report functions
  • variant.clj - Operations on submitted variants
  • env.clj - Environment configuration

Google Cloud Integration

  • gcp/function-source/main.py - BigQuery-based SCV lookup service
  • gcp/function-source/requirements.txt - Python dependencies for cloud function

Common Development Commands

Building and Running

# Run the web service
lein run

# Build executable JAR
lein uberjar

# Run tests
lein test

# Start development server with auto-reload
lein ring server-auto

Environment Variables

  • CLINVAR_SUBMITTER_PORT - Service port (defaults to 3000)
  • SCV_SERVICE_URL - Required URL for SCV cloud function

Batch Processing

Use generateSubmission.sh for processing archived ClinGen interpretation files:

./generateSubmission.sh -d YYYY-MM-DD -g GROUP_NAME [-s SCV_FILE] [-o]

Input File Combination

Use combineall.sh to combine multiple JSON interpretation files into a single input file (combines dmwg*.json files into allinput.json).

Project Structure

  • src/clinvar_submitter/ - Main Clojure source code
  • test/clinvar_submitter/ - Unit tests
  • data/ - Example JSON files, ClinVar template, and Postman collections
  • doc/ - Developer documentation and API specs
  • gcp/ - Google Cloud Platform artifacts (BigQuery, Cloud Functions)
  • deploy/ - Deployment configuration files

Key Dependencies

  • Clojure 1.9.0
  • Ring (web server)
  • Cheshire (JSON handling)
  • jsonld-java (JSON-LD processing)
  • clj-http (HTTP client)

Output Formats

The application generates:

  1. CSV submission file - Ready for ClinVar submission template
  2. Run report CSV - Processing summary and validation results
  3. JSON output - Intermediate processing results

Testing

Tests are located in test/clinvar_submitter/ and can be run with standard Leiningen commands. See test/repl-test-tips.txt for REPL testing guidance.