#!/usr/bin/env bash
# Download the public PGx sources for `simurg pgx db build` (spec PGX-001) into a dated folder.
#   bash scripts/pgx/fetch_sources.sh [OUT_DIR]       (default data/pgx/sources)
# CPIC (CC0): tables from the CPIC API (https://api.cpicpgx.org, PostgREST) as JSON; the newest change-log date is
# recorded as the data version. PharmVar (https://www.pharmvar.org; cite Gaedigk et al. 2018 CPT 103:399): per-gene
# zips (haplotype VCFs, GRCh37/GRCh38) for the star-allele genes CPIC does not define. Never committed (data/ is
# ignored); the DB records each source's version and file hashes.
set -euo pipefail
OUT=${1:-data/pgx/sources}
DATE=$(date -u +%Y%m%d)
D="$OUT/cpic-$DATE"
mkdir -p "$D"
API=https://api.cpicpgx.org/v1
for t in gene allele allele_definition allele_location_value sequence_location gene_result gene_result_lookup \
         gene_result_diplotype population change_log; do
  curl -sSf --retry 3 -H "Accept: application/json" "$API/$t" -o "$D/$t.json"
  python3 -c "import json,sys; print(sys.argv[1], len(json.load(open(sys.argv[2]))))" "$t" "$D/$t.json"
done
python3 - "$D" <<'PY'
import hashlib, json, pathlib, sys
d = pathlib.Path(sys.argv[1])
log = json.loads((d / "change_log.json").read_text())
ver = max(e["date"] for e in log if e.get("date"))
files = {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in sorted(d.glob("*.json")) if p.name != "source.json"}
(d / "source.json").write_text(json.dumps({"name": "CPIC", "version": ver, "retrieved": d.name.split("-")[1],
                                          "url": "https://api.cpicpgx.org/v1", "license": "CC0-1.0",
                                          "files": files}, indent=1))
print("CPIC data version", ver)
PY

# ---- PharmVar: star-allele genes without CPIC definitions
PV="$OUT/pharmvar-$DATE"
mkdir -p "$PV"
PV_GENES=${PV_GENES:-"CYP1A2 CYP2A6 CYP2A13 CYP2C8 CYP3A4"}  # the PharmVar genes CPIC does not define (2026-09)
for g in $PV_GENES; do
  if curl -sSf --retry 3 -o "$PV/$g.zip" \
       "https://www.pharmvar.org/get-download-file?name=$g&refSeq=ALL&fileType=zip&version=current"; then
    echo "PharmVar $g $(unzip -l "$PV/$g.zip" | awk 'NR==4{print $4}' | cut -d/ -f1)"
  else
    echo "PharmVar $g: not available"; rm -f "$PV/$g.zip"
  fi
done
python3 - "$PV" <<'PY'
import hashlib, json, pathlib, re, sys, zipfile
d = pathlib.Path(sys.argv[1])
vers = set()
for z in sorted(d.glob("*.zip")):
    top = zipfile.ZipFile(z).namelist()[0].split("/")[0]
    m = re.search(r"-(\d+\.\d+\.\d+)$", top)
    if m:
        vers.add(m.group(1))
files = {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in sorted(d.glob("*.zip"))}
(d / "source.json").write_text(json.dumps({"name": "PharmVar", "version": ",".join(sorted(vers)),
                                          "retrieved": d.name.split("-")[1], "url": "https://www.pharmvar.org",
                                          "license": "PharmVar terms of use (cite Gaedigk et al. 2018)",
                                          "files": files}, indent=1))
print("PharmVar version", ",".join(sorted(vers)))
PY

# ---- ClinPGx (formerly PharmGKB; CC BY-SA 4.0): clinical-annotation variants (variant-based genes, genotype only)
CP="$OUT/clinpgx-$DATE"
mkdir -p "$CP"
curl -sSfL --retry 3 -o "$CP/clinicalVariants.zip" "https://api.clinpgx.org/v1/download/file/data/clinicalVariants.zip"
python3 - "$CP" <<'PY'
import hashlib, json, pathlib, sys, zipfile
d = pathlib.Path(sys.argv[1])
z = zipfile.ZipFile(d / "clinicalVariants.zip")
created = next((n.split("_", 1)[1].rsplit(".", 1)[0] for n in z.namelist() if n.startswith("CREATED_")), "")
(d / "source.json").write_text(json.dumps({"name": "ClinPGx clinical variants", "version": created,
                                          "retrieved": d.name.split("-")[1], "url": "https://www.clinpgx.org",
                                          "license": "CC BY-SA 4.0",
                                          "files": {"clinicalVariants.zip": hashlib.sha256(
                                              (d / "clinicalVariants.zip").read_bytes()).hexdigest()}}, indent=1))
print("ClinPGx clinical variants", created)
PY