import hashlib, json, os, re, stat, sys, datetime
R="/ibex/project/c2041/hany0c/bench_h2h_20260915/real"
APPROVAL_TEXT="批准，先跑我们的模型，快速的先出一个结果我看看"
APPROVAL={"text": APPROVAL_TEXT, "by": "Larry", "date": "2026-09-15", "relayed_by": "orchestrator (real-data quick-look task prompt)"}
E="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections"
VCF=E+"/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz"
items=[
 ("ped", E+"/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt","ref",97483,"quick-look approval 2026-09-15"),
 ("gap","https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz","ref",12368,"T0 (previously approved)"),
 ("centromeres","https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz","ref",1549,"T0 (previously approved)"),
 ("pilot_mask",E+"/1000_genomes_project/working/20160622_genome_mask_GRCh38/PilotMask/20160622.allChr.pilot_mask.bed","ref",16728941,"T0 (previously approved)"),
 ("strict_mask",E+"/1000_genomes_project/working/20160622_genome_mask_GRCh38/StrictMask/20160622.allChr.mask.bed","ref",128218530,"T0 (previously approved)"),
 ("vcf_tbi",VCF+".tbi","raw",None,"quick-look approval 2026-09-15 (tbi named as part of the approval; size taken from HEAD)"),
 ("vcf",VCF,"raw",2506332497,"quick-look approval 2026-09-15"),
]
log=open(R+"/logs/download.log").read().splitlines()
def logtime(kind,name):
    for l in log:
        p=l.split()
        if len(p)>=3 and p[1]==kind and p[2]==name: return p[0]
def sha(path):
    h=hashlib.sha256()
    with open(path,"rb") as f:
        for b in iter(lambda: f.read(8<<20), b""): h.update(b)
    return h.hexdigest()
def hdrs(path):
    d={}
    for l in open(path, encoding="latin-1"):
        l=l.strip()
        if l.startswith("HTTP/"): d["status_line"]=l
        elif ":" in l:
            k,v=l.split(":",1); k=k.strip().lower()
            if k in ("content-length","last-modified","etag","content-type","accept-ranges","date","server"): d[k]=v.strip()
    return d
out={"schema":"bench_h2h real-data downloads v1","written_utc":datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ"),
 "actor":"download","approval":APPROVAL,
 "scope_rule":"ONLY these files may be downloaded for the real-data quick look (no other chromosomes, no Ensembl ancestor, no other maps)",
 "method":{"host":"login509-02-r (Ibex login node), single stream, sequential",
   "head":"curl -sS -I -L --retry 5 --retry-delay 10 URL > headers/<basename>.headers",
   "get":"curl -sS -L --fail --retry 20 --retry-delay 15 --retry-connrefused -C - -o <dest> URL",
   "checks":"HEAD Content-Length == approved bytes (refuse otherwise; tbi: HEAD only); bytes on disk == Content-Length; sha256sum of the on-disk file; chmod a-w",
   "script":"real/scripts/download_real.sh","script_sha256":sha(R+"/scripts/download_real.sh"),"log":"real/logs/download.log","log_sha256":sha(R+"/logs/download.log")},
 "files":[]}
for name,url,d,approved,basis in items:
    base=os.path.basename(url); f=f"{R}/{d}/{base}"; h=hdrs(f"{R}/headers/{base}.headers")
    size=os.stat(f).st_size; s=sha(f); side=open(f+".sha256").read().split()[0]
    cl=int(h["content-length"])
    assert size==cl and s==side and (approved is None or approved==cl), name
    assert not (os.stat(f).st_mode & (stat.S_IWUSR|stat.S_IWGRP|stat.S_IWOTH)), name
    out["files"].append({"name":name,"url":url,"path":f"real/{d}/{base}","approval_basis":basis,
      "approved_bytes":approved,"head":h,"headers_file":f"real/headers/{base}.headers","bytes":size,
      "content_length_match":size==cl,"sha256":s,"sha256_sidecar":f"real/{d}/{base}.sha256",
      "head_utc":logtime("HEAD",name),"done_utc":logtime("DONE",name),"mode":oct(os.stat(f).st_mode & 0o777)})
dec=f"{R}/ref/decode2019_avg_hg38.bed"
ds=sha(dec); assert ds==open(dec+".sha256").read().split()[0]
out["copies"]=[{"name":"decode2019_avg_hg38","source":"laptop:/Users/larryivanhan/Desktop/Projects/genomics/DLCoal/maps/recomb_map/output/decode2019_avg_hg38.bed",
  "source_sha256":sys.argv[1],"path":"real/ref/decode2019_avg_hg38.bed","bytes":os.stat(dec).st_size,"sha256":ds,
  "sha_match":ds==sys.argv[1],"mode":oct(os.stat(dec).st_mode & 0o777),"note":"local copy, not a download; built by maps/recomb_map/build_decode2019.py"}]
tmp=R+"/.DOWNLOADS.partial.json"
with open(tmp,"w") as fh: json.dump(out,fh,indent=1,ensure_ascii=False); fh.write("\n")
os.chmod(tmp,0o444); os.link(tmp,R+"/DOWNLOADS.json"); os.unlink(tmp)
print(sha(R+"/DOWNLOADS.json"))
for x in out["files"]+out["copies"]: print(x["name"],x["bytes"],x["sha256"],x.get("done_utc"))