BioMCP

#!/usr/bin/env bash set -euo pipefail ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" BIN="${BIOMCP_BIN:-$ROOT/target/debug/biomcp}" if [[ ! -x "$BIN" ]]; then BIN="biomcp" fi echo "GeneAgent demo: variant, pathway, and protein pivots" variant_json="$("$BIN" --json get variant "BRAF V600E" clinvar)" pathway_json="$("$BIN" --json get pathway R-HSA-5673001 genes)" drug_json="$("$BIN" --json pathway drugs R-HSA-5673001 --limit 3)" protein_json="$("$BIN" --json protein structures P15056)" if ! grep -q '"id"' <<<"$variant_json" || ! grep -q '"gene"' <<<"$variant_json"; then echo "Variant lookup failed" >&2 exit 1 fi if ! grep -q '"genes"' <<<"$pathway_json"; then echo "Pathway lookup failed to include genes" >&2 exit 1 fi if ! grep -q '"structures"' <<<"$protein_json"; then echo "Protein helper failed to include structures" >&2 exit 1 fi drug_count="$(sed -n 's/.*"count":[[:space:]]*\([0-9][0-9]*\).*/\1/p' <<<"$drug_json" | head -n1)" drug_count="${drug_count:-0}" if [[ $drug_count -le 0 ]]; then echo "No pathway-linked drugs were returned for demo scoring" >&2 exit 1 fi echo "GeneAgent reproduction score: $drug_count" echo "GeneAgent demo complete"