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48 changes: 27 additions & 21 deletions scripts/bootstrap_db.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
DEFAULT_DB_PATH = os.path.join(BASE_DIR, "database", "annotations.db")
DEFAULT_DB_DIR = os.path.dirname(DEFAULT_DB_PATH)
DEFAULT_GENOME_PATH = os.path.join(BASE_DIR, "database", "raw_data", "GRCh38.primary_assembly.genome.fa.gz")
DOWNLOAD_CHUNK_SIZE = 1024 * 1024

def _env(name, default=None):
value = os.getenv(name)
Expand All @@ -20,36 +21,41 @@ def _ensure_dir(path):
if path:
os.makedirs(path, exist_ok=True)

def _download_stream(resp, dest_path):
with open(dest_path, "wb") as out_file:
while True:
chunk = resp.read(DOWNLOAD_CHUNK_SIZE)
if not chunk:
break
out_file.write(chunk)

def _download_file(url, dest_path):
req = urllib.request.Request(url, headers={"User-Agent": "Mozilla/5.0"})
with urllib.request.urlopen(req) as resp, open(dest_path, "wb") as out_file:
out_file.write(resp.read())
with urllib.request.urlopen(req) as resp:
_download_stream(resp, dest_path)

def _download_google_drive(url, dest_path):
req = urllib.request.Request(url, headers={"User-Agent": "Mozilla/5.0"})
with urllib.request.urlopen(req) as resp:
data = resp.read()
cookies = resp.headers.get_all("Set-Cookie") or []
confirm_token = None
for cookie in cookies:
if "download_warning" in cookie:
parts = cookie.split(";")[0].split("=")
if len(parts) == 2:
confirm_token = parts[1]
break

confirm_token = None
for cookie in cookies:
if "download_warning" in cookie:
parts = cookie.split(";")[0].split("=")
if len(parts) == 2:
confirm_token = parts[1]
break

if confirm_token:
parsed = urllib.parse.urlparse(url)
query = urllib.parse.parse_qs(parsed.query)
query["confirm"] = [confirm_token]
new_query = urllib.parse.urlencode(query, doseq=True)
url = urllib.parse.urlunparse(parsed._replace(query=new_query))
_download_file(url, dest_path)
return
if not confirm_token:
_download_stream(resp, dest_path)
return

with open(dest_path, "wb") as out_file:
out_file.write(data)
parsed = urllib.parse.urlparse(url)
query = urllib.parse.parse_qs(parsed.query)
query["confirm"] = [confirm_token]
new_query = urllib.parse.urlencode(query, doseq=True)
url = urllib.parse.urlunparse(parsed._replace(query=new_query))
_download_file(url, dest_path)

def main():
db_url = _env("DB_URL")
Expand Down