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Copy pathflow_sample_data_pull.py
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389 lines (345 loc) · 13.8 KB
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#!/usr/bin/env python3
import argparse
import getpass
import json
import logging
import re
from typing import Any, Dict, List, Optional, Pattern, Set
import requests
API_BASE = "https://api.flow.bio"
APP_API_BASE = "https://app.flow.bio/api"
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(
description=(
"Log in to Flow.bio, fetch all samples in a project, load full sample details, "
"and collect sample-associated data metadata."
)
)
parser.add_argument(
"-p",
"--project",
required=True,
help="Flow project URL or project ID (e.g. https://app.flow.bio/projects/<id>/ or <id>)",
)
parser.add_argument("-u", "--username", default=None, help="Flow username (prompted if omitted)")
parser.add_argument("--password", default=None, help="Flow password (prompted if omitted)")
parser.add_argument("--page-size", type=int, default=100, help="Page size for project sample listing")
parser.add_argument(
"--data-page-size",
type=int,
default=100,
help="Page size for /samples/{id}/data listing (default: 100)",
)
parser.add_argument(
"--max-samples",
type=int,
default=None,
help="Optional cap on number of project samples to process",
)
parser.add_argument(
"--uploaded-only",
action="store_true",
help="Only emit samples that have at least one associated data record marked as Uploaded",
)
parser.add_argument(
"--data-source",
choices=("filesets", "sample_data", "both"),
default="filesets",
help=(
"Where to list sample-associated files: filesets (uploaded FASTQs), "
"sample_data (/samples/{id}/data, includes pipeline outputs), or both."
),
)
parser.add_argument(
"--filename-regex",
default=None,
help=(
"Only keep data files whose filename matches this regex. "
"Example for C34_2.markdup.sorted.bam: '\\.markdup\\.sorted\\.bam$' "
"(in shell: --filename-regex '\\.markdup\\.sorted\\.bam$')"
),
)
parser.add_argument(
"--output-json",
default=None,
help="Optional path to save collected sample/data metadata as JSON",
)
parser.add_argument("--debug", action="store_true", help="Enable debug logging")
return parser.parse_args()
def setup_logging(debug: bool = False) -> None:
level = logging.DEBUG if debug else logging.INFO
logging.basicConfig(level=level, format="%(asctime)s | %(levelname)-8s | %(message)s")
def extract_project_id(project_input: str) -> str:
candidate = project_input.strip()
if candidate.isdigit():
return candidate
match = re.search(r"/projects/(\d+)", candidate)
if match:
return match.group(1)
raise ValueError(f"Could not parse project id from input: {project_input}")
def raise_for_status(resp: requests.Response) -> None:
try:
resp.raise_for_status()
except requests.HTTPError as exc:
message = f"HTTP {resp.status_code} error for {resp.request.method} {resp.url}: {resp.text}"
raise requests.HTTPError(message) from exc
def rest_login(session: requests.Session, username: Optional[str], password: Optional[str]) -> str:
if not username:
username = input("Enter your username: ").strip()
if not password:
password = getpass.getpass("Enter your password: ")
resp = session.post(
f"{API_BASE}/login",
json={"username": username, "password": password},
timeout=30,
)
raise_for_status(resp)
payload = resp.json()
token = payload.get("token")
if not token:
raise RuntimeError("Login succeeded but no token returned in response body")
return token
def fetch_all_project_samples(
session: requests.Session, token: str, project_id: str, page_size: int = 100
) -> List[Dict[str, Any]]:
headers = {"Authorization": f"Bearer {token}"}
page = 1
collected: List[Dict[str, Any]] = []
while True:
resp = session.get(
f"{API_BASE}/projects/{project_id}/samples",
params={"page": page, "count": page_size},
headers=headers,
timeout=30,
)
raise_for_status(resp)
payload = resp.json()
samples = payload.get("samples", [])
if not samples:
break
collected.extend(samples)
logging.info("Fetched project sample page %s (%s samples)", page, len(samples))
if len(samples) < page_size:
break
page += 1
logging.info("Collected %s project sample records", len(collected))
return collected
def fetch_sample_detail(session: requests.Session, token: str, sample_id: str) -> Dict[str, Any]:
headers = {"Authorization": f"Bearer {token}"}
resp = session.get(f"{API_BASE}/samples/{sample_id}", headers=headers, timeout=30)
raise_for_status(resp)
return resp.json()
def fetch_data_detail(session: requests.Session, token: str, data_id: str) -> Dict[str, Any]:
headers = {"Authorization": f"Bearer {token}"}
resp = session.get(f"{API_BASE}/data/{data_id}", headers=headers, timeout=30)
raise_for_status(resp)
return resp.json()
def _collect_sample_data_entries(
session: requests.Session, token: str, sample_id: str, page_size: int = 100
) -> List[Dict[str, Any]]:
headers = {"Authorization": f"Bearer {token}"}
page = 1
collected: List[Dict[str, Any]] = []
seen_ids: Set[str] = set()
total_reported: Optional[int] = None
while True:
resp = session.get(
f"{APP_API_BASE}/samples/{sample_id}/data",
params={"page": page, "count": page_size},
headers=headers,
timeout=30,
)
raise_for_status(resp)
payload = resp.json()
if total_reported is None:
total_reported = payload.get("count")
entries = payload.get("data", [])
if not isinstance(entries, list) or not entries:
break
for entry in entries:
if not isinstance(entry, dict):
continue
data_id = entry.get("id")
if not data_id:
continue
sid = str(data_id)
if sid in seen_ids:
continue
seen_ids.add(sid)
collected.append(entry)
if len(entries) < page_size:
break
if total_reported is not None and len(collected) >= int(total_reported):
break
page += 1
logging.debug(
"Sample %s: paginated data entries=%s (reported total=%s, pages=%s)",
sample_id,
len(collected),
total_reported,
page,
)
return collected
def _collect_data_ids_from_filesets(sample_detail: Dict[str, Any]) -> List[str]:
data_ids: List[str] = []
filesets = sample_detail.get("filesets", [])
if not isinstance(filesets, list):
return data_ids
for fileset in filesets:
if not isinstance(fileset, dict):
continue
data_entries = fileset.get("data", [])
if not isinstance(data_entries, list):
continue
for entry in data_entries:
if not isinstance(entry, dict):
continue
data_id = entry.get("id")
if data_id:
data_ids.append(str(data_id))
return data_ids
def _is_uploaded_data_record(record: Dict[str, Any]) -> bool:
if record.get("execution") is None:
return True
possible_keys = ("source", "origin", "status", "data_origin", "upload_source", "type")
for key in possible_keys:
value = record.get(key)
if isinstance(value, str) and value.strip().lower() == "uploaded":
return True
provenance = record.get("provenance")
if isinstance(provenance, dict):
for key in ("source", "origin", "status"):
value = provenance.get(key)
if isinstance(value, str) and value.strip().lower() == "uploaded":
return True
return False
def _matches_filename(record: Dict[str, Any], pattern: Optional[Pattern[str]]) -> bool:
if pattern is None:
return True
filename = record.get("filename") or ""
return bool(pattern.search(str(filename)))
def collect_sample_and_data_metadata(
project_samples: List[Dict[str, Any]],
session: requests.Session,
token: str,
uploaded_only: bool = False,
data_source: str = "filesets",
filename_pattern: Optional[Pattern[str]] = None,
data_page_size: int = 100,
max_samples: Optional[int] = None,
) -> List[Dict[str, Any]]:
collected: List[Dict[str, Any]] = []
total = len(project_samples) if max_samples is None else min(len(project_samples), max_samples)
for idx, sample in enumerate(project_samples, start=1):
if max_samples is not None and idx > max_samples:
break
sample_id = str(sample.get("id", ""))
sample_name = sample.get("name", "")
if not sample_id:
continue
detail = fetch_sample_detail(session, token, sample_id)
sample_metadata = detail.get("metadata") if isinstance(detail.get("metadata"), dict) else {}
data_ids: List[str] = []
if data_source in ("filesets", "both"):
data_ids.extend(_collect_data_ids_from_filesets(detail))
list_entries: List[Dict[str, Any]] = []
if data_source in ("sample_data", "both"):
try:
list_entries = _collect_sample_data_entries(
session, token, sample_id, page_size=data_page_size
)
data_ids.extend(str(entry["id"]) for entry in list_entries if entry.get("id"))
except Exception as exc:
logging.warning("Failed to fetch /samples/%s/data: %s", sample_id, exc)
unique_ids: List[str] = []
seen = set()
for data_id in data_ids:
if data_id not in seen:
seen.add(data_id)
unique_ids.append(data_id)
ids_to_fetch: List[str] = []
if filename_pattern is not None and list_entries:
by_filename: Dict[str, Dict[str, Any]] = {}
for entry in list_entries:
if not _matches_filename(entry, filename_pattern):
continue
filename = str(entry.get("filename") or "")
if not filename:
continue
prev = by_filename.get(filename)
if prev is None or int(entry.get("size") or 0) >= int(prev.get("size") or 0):
by_filename[filename] = entry
ids_to_fetch = [str(entry["id"]) for entry in by_filename.values() if entry.get("id")]
else:
ids_to_fetch = unique_ids
data_candidates: List[Dict[str, Any]] = []
for data_id in ids_to_fetch:
try:
data_candidates.append(fetch_data_detail(session, token, data_id))
except Exception as exc:
logging.warning("Failed to fetch /data/%s: %s", data_id, exc)
if filename_pattern is not None and not list_entries:
data_candidates = [d for d in data_candidates if _matches_filename(d, filename_pattern)]
uploaded_data = [d for d in data_candidates if _is_uploaded_data_record(d)]
if uploaded_only and not uploaded_data:
logging.debug("Skipping sample %s with no Uploaded data records", sample_id)
continue
if filename_pattern is not None and not data_candidates:
logging.debug("Skipping sample %s with no filename matches", sample_id)
continue
record = {
"sample_id": sample_id,
"sample_name": sample_name or detail.get("name", ""),
"sample_metadata": sample_metadata,
"data_count": len(data_candidates),
"uploaded_data_count": len(uploaded_data),
"data": data_candidates,
"uploaded_data": uploaded_data,
}
collected.append(record)
logging.info(
"Processed sample %s/%s: id=%s, data=%s, uploaded=%s",
idx,
total,
sample_id,
len(data_candidates),
len(uploaded_data),
)
return collected
def main() -> None:
args = parse_args()
setup_logging(args.debug)
project_id = extract_project_id(args.project)
filename_pattern = re.compile(args.filename_regex) if args.filename_regex else None
session = requests.Session()
token = rest_login(session, args.username, args.password)
project_samples = fetch_all_project_samples(
session=session, token=token, project_id=project_id, page_size=args.page_size
)
collected = collect_sample_and_data_metadata(
project_samples=project_samples,
session=session,
token=token,
uploaded_only=args.uploaded_only,
data_source=args.data_source,
filename_pattern=filename_pattern,
data_page_size=args.data_page_size,
max_samples=args.max_samples,
)
print(f"\nProject {project_id}: collected {len(collected)} sample detail records")
if collected:
first = collected[0]
print(
"First sample preview: "
f"id={first['sample_id']} name={first['sample_name']} "
f"data_count={first['data_count']} uploaded_data_count={first['uploaded_data_count']}"
)
if first["uploaded_data_count"] > 0:
uploaded_ids = [x.get("id") for x in first["uploaded_data"][:3]]
print(f"First sample uploaded data IDs (up to 3): {uploaded_ids}")
if args.output_json:
with open(args.output_json, "w", encoding="utf-8") as handle:
json.dump(collected, handle, indent=2)
logging.info("Wrote JSON output to %s", args.output_json)
if __name__ == "__main__":
main()