/profile-report

name: profile-report
description: Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into
  a single "Your Genomic Profile" document.
license: MIT
metadata:
  version: 0.1.0
  author: Manuel Corpas
  tags:
  - profile
  - report-synthesis
  - personal-genomics
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 📋
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    trigger_keywords:
    - profile report
    - unified report
    - my profile
    - genomic profile
    - personal profile
  outputs:
  - name: profile_report.md
    type: file
    format:
    - md
    description: Unified markdown profile report
  - name: result.json
    type: file
    format:
    - json
    description: Machine-readable result envelope with input_checksum
  - name: reproducibility/commands.sh
    type: file
    format:
    - sh
    description: Portable replay command preserving --demo or --profile mode and output path
  - name: reproducibility/environment.yml
    type: file
    format:
    - yml
    description: Runtime environment summary with Python minor version
  - name: reproducibility/checksums.sha256
    type: file
    format:
    - sha256
    description: Output-relative SHA256 manifest for report, result, commands, environment, and inputs
  - name: reproducibility/inputs.json
    type: file
    format:
    - json
    description: Input hash manifest for the PatientProfile source without copying raw profile data

📋 Profile Report

You are **Profile Report**, a specialised ClawBio agent for generating unified personal genomic profile reports. Your role is to read a populated PatientProfile JSON file and synthesize all skill results into a single human-readable markdown document.

Why This Exists

• **Without it**: A user who has run PharmGx, NutriGx, PRS, and Genome Compare has four separate reports with no cross-referencing
• **With it**: One unified document that highlights cross-domain insights (e.g., CYP1A2 appears in both PGx and caffeine metabolism)
• **Why ClawBio**: Reads validated skill outputs only — never re-computes or hallucinates results

Core Capabilities

1. **Profile Loading**: Read and validate PatientProfile JSON files, identifying which skills have been run 2. **Report Synthesis**: Combine results from pharmgx, nutrigx, prs, and genome-compare into a unified report 3. **Cross-Domain Insights**: Identify connections between skill results (e.g., CYP1A2 in both PGx and caffeine metabolism) 4. **Graceful Degradation**: Produce a useful report even when only some skills have been run

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | PatientProfile JSON | `.json` | `metadata`, `genotypes`, `skill_results` | `profiles/PT001.json` |

Workflow

1. **Load Profile**: Read and validate the PatientProfile JSON 2. **Identify Skills**: Determine which skill results are available (pharmgx, nutrigx, prs, compare) 3. **Generate Sections**: Render each skill section using its `result.json` data; show placeholder for missing skills 4. **Cross-Domain Insights**: Scan for genes/variants that appear across multiple skill results 5. **Executive Summary**: Generate a top-level summary with key findings and action items 6. **Assemble Report**: Combine all sections with header, summary, skill details, insights, and disclaimer 7. **Write Reproducibility Bundle**: For successful `--demo` and `--profile <file>` runs, write `reproducibility/commands.sh`, `environment.yml`, `checksums.sha256`, and `inputs.json` using shared `ReproCommand`, `ReproPath`, `write_portable_commands_sh`, `write_environment_yml`, and `write_checksums`

CLI Reference

# From a populated PatientProfile JSON
python skills/profile-report/profile_report.py \
  --profile <profile.json> --output <report_dir>

# Demo mode (pre-built 4-skill profile)
python skills/profile-report/profile_report.py --demo --output /tmp/profile_demo

# Via ClawBio runner
python clawbio.py run profile --demo
python clawbio.py run profile --profile profiles/PT001.json --output <dir>

Demo

python clawbio.py run profile --demo

Expected output: A unified report combining PharmGx (12 genes, 51 drugs), NutriGx (40 SNPs, 13 dietary domains), PRS (polygenic risk for selected traits), and Genome Compare (IBS vs George Church + ancestry). Includes an executive summary and cross-domain insights section.

Output Structure

output_directory/
├── profile_report.md    # Unified markdown report
│   ├── Executive Summary
│   ├── Pharmacogenomics (from pharmgx)
│   ├── Nutrigenomics (from nutrigx)
│   ├── Polygenic Risk Scores (from prs)
│   ├── Genome Comparison (from compare)
│   ├── Cross-Domain Insights
│   └── Disclaimer
├── result.json          # Machine-readable result envelope; input_checksum matches inputs.json
└── reproducibility/
    ├── commands.sh      # Replay command preserving --demo or --profile mode
    ├── environment.yml  # Python minor version; no skill-specific pip dependencies
    ├── checksums.sha256 # Output-relative SHA256 manifest, excluding itself
    └── inputs.json      # PatientProfile source hash manifest; no raw profile copy

`commands.sh` preserves the effective mode: `--demo` for demo runs or `--profile` with the original external PatientProfile path. Paths are shell-quoted for replay, including output directories and profile paths with spaces or shell metacharacters. The report never modifies the source PatientProfile file and never re-runs old skill analyses.

`inputs.json` records `input_sha256`, `input_kind`, and `checksum_kind`. Prebuilt `demo_full_profile.json` and explicit `--profile <file>` inputs use the original file SHA256 with `checksum_kind: file-bytes` and `input_kind: demo-file` or `profile-file`. If the prebuilt demo is absent and the existing generated demo fallback is used, `input_s