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from collections import OrderedDict
from contextlib import closing
from functools import lru_cache
import json
from pathlib import Path
import sqlite3
import threading
import time
import zlib
from huggingface_hub import HfApi, HfFileSystem, get_token
from huggingface_hub.hf_file_system import HfFileSystemFile
import pyarrow.parquet as pq
from catalog import Catalog, ROOT, PROBS, normalize, unversioned, segment_metadata
BUCKET = "HuggingFaceBio/genbank-annotations"
def source_info(api, bucket, path):
return next((e for e in api.list_bucket_tree(bucket, path, recursive=False)
if e.path == path and e.type == "file"), None)
class MeasuredFile(HfFileSystemFile):
"""Count returned range bytes, excluding HTTP headers and retries."""
def __init__(self, fs, path):
self.bytes_read = 0
self.range_reads = 0
super().__init__(fs, path, mode="rb", block_size=1024 * 1024, cache_type="none")
def _fetch_range(self, start, end):
data = super()._fetch_range(start, end)
self.bytes_read += len(data)
self.range_reads += 1
return data
class RemoteReadError(ValueError):
pass
class Records:
def __init__(self, catalog):
self.catalog = catalog
def __len__(self):
return self.catalog.manifest["rows"]
def __getitem__(self, index):
return self.catalog.record(int(index))
class RemoteCatalog(Catalog):
def __init__(self, path=None, cache_bytes=512 * 1024**2,
max_group_bytes=512 * 1024**2, api=None, fs=None):
if path is None:
from catalog_snapshot import catalog_path
path = catalog_path()
self.path = Path(path)
self.cache_limit = cache_bytes
self.max_group_bytes = max_group_bytes
self.api = api or HfApi(token=get_token())
self.fs = fs or HfFileSystem(token=get_token())
self.cache = OrderedDict()
self.cache_bytes = 0
self.lock = threading.Lock()
with closing(self.connect()) as conn:
self.manifest = json.loads(conn.execute("SELECT value FROM metadata WHERE key='manifest'").fetchone()[0])
self.records = Records(self)
def connect(self):
conn = sqlite3.connect(self.path.resolve().as_uri() + "?mode=ro&immutable=1", uri=True)
conn.row_factory = sqlite3.Row
return conn
@lru_cache(maxsize=512)
def entry(self, index):
with closing(self.connect()) as conn:
row = conn.execute("SELECT * FROM segments WHERE id=?", (int(index),)).fetchone()
if row is None:
raise RemoteReadError("Choose a segment from the current index.")
return dict(row)
def record(self, index):
entry = self.entry(index)
if self.manifest.get("schema_version", 1) >= 3:
result = json.loads(entry["context_json"])
for key in ("record_name", "aligned_bp_length", "segment_start_bp", "segment_end_bp", "segment_index", "segment_count"):
result[key] = entry[key]
result["segment_bp_length"] = entry["segment_end_bp"] - entry["segment_start_bp"]
result["source_key"] = entry["source_key"] or result["assembly_accession"] + "|" + result["record_name"]
return result
value = entry["metadata_json"]
return json.loads(zlib.decompress(value) if isinstance(value, bytes) else value)
def browse_ids(self, limit=200):
with closing(self.connect()) as conn:
return [r[0] for r in conn.execute("SELECT id FROM segments ORDER BY id LIMIT ?", (limit,))]
def find(self, accession, limit=200):
key = normalize(accession)
if not key:
return [], 0
if self.manifest.get("schema_version", 1) >= 3:
return self.find_compact(key, limit)
# Aliases include exact versions and versionless IDs; never strip a query's version.
with closing(self.connect()) as conn:
count = conn.execute("SELECT count(*) FROM aliases WHERE alias=?", (key,)).fetchone()[0]
ids = [r[0] for r in conn.execute(
"SELECT s.id FROM aliases a JOIN segments s ON s.id=a.segment_id "
"WHERE a.alias=? ORDER BY s.assembly_accession,s.record_name,s.segment_start_bp,s.id LIMIT ?",
(key, limit))]
return ids, count
def find_compact(self, key, limit):
# Exact and versionless IDs use separate B-tree indexes. Assembly and
# contig lookups never require a full scan of the segment table.
with closing(self.connect()) as conn:
if "|" in key:
assembly, record = key.split("|", 1)
query = ("SELECT s.id FROM segment_data s JOIN contexts c ON c.id=s.context_id "
"WHERE c.assembly_accession=? AND s.record_name=? COLLATE NOCASE "
"AND s.source_key IS NULL UNION SELECT id FROM segment_data "
"WHERE source_key=? COLLATE NOCASE")
params = (assembly, record, key)
elif key.startswith(("GCA_", "GCF_")):
column = "assembly_accession" if unversioned(key) != key else "assembly_base"
query = (f"SELECT s.id FROM contexts c JOIN segment_data s ON s.context_id=c.id WHERE c.{column}=?")
params = (key,)
else:
column = "record_name" if unversioned(key) != key else "record_base"
query = f"SELECT id FROM segment_data WHERE {column}=? COLLATE NOCASE"
# record_base is normalized; its index uses binary collation.
if column == "record_base": query = "SELECT id FROM segment_data WHERE record_base=?"
params = (key,)
if "|" not in key:
query += " UNION SELECT id FROM segment_data WHERE source_key=? COLLATE NOCASE"
params += (key,)
count = conn.execute(f"SELECT count(*) FROM ({query})", params).fetchone()[0]
ordered = (f"SELECT s.id FROM ({query}) hits JOIN segment_data s ON s.id=hits.id "
"JOIN contexts c ON c.id=s.context_id "
"ORDER BY c.assembly_accession,s.record_name,s.segment_start_bp,s.id LIMIT ?")
ids = [r[0] for r in conn.execute(ordered, params + (limit,))]
return ids, count
def lookup(self, accession):
return self.find(accession)[0]
def check_source(self, entry):
source = source_info(self.api, self.manifest["bucket_id"], entry["object_path"])
if source is None or source.xet_hash != entry["object_hash"]:
raise RemoteReadError("The bucket object has changed since indexing. Rebuild the index before retrieving this segment.")
def fetch(self, index):
began = time.perf_counter()
entry = self.entry(int(index))
key = (entry["object_path"], entry["object_hash"], entry["row_group"])
stats = {"cache_hit": False, "bytes_read": 0, "range_reads": 0}
# Serialize cache fills to bound memory and avoid duplicate remote downloads.
with self.lock:
if key in self.cache:
table = self.cache.pop(key)
self.cache[key] = table
stats["cache_hit"] = True
else:
try:
self.check_source(entry)
path = f"buckets/{self.manifest['bucket_id']}/{entry['object_path']}"
self.fs.invalidate_cache(path)
with MeasuredFile(self.fs, path) as remote:
parquet = pq.ParquetFile(remote)
group = parquet.metadata.row_group(entry["row_group"])
if group.total_byte_size > self.max_group_bytes:
raise RemoteReadError("This row group exceeds the 512 MiB read limit. It needs a smaller storage chunk.")
table = parquet.read_row_group(entry["row_group"], use_threads=False)
stats.update(bytes_read=remote.bytes_read, range_reads=remote.range_reads)
self.check_source(entry)
except RemoteReadError:
raise
except Exception as exc:
raise RemoteReadError("Could not retrieve annotations from the bucket. Check bucket access and try again; this is not an accession-not-found result.") from exc
if table.nbytes <= self.cache_limit:
while self.cache and self.cache_bytes + table.nbytes > self.cache_limit:
_, old = self.cache.popitem(last=False)
self.cache_bytes -= old.nbytes
self.cache[key] = table
self.cache_bytes += table.nbytes
result = table.slice(entry["row_in_group"], 1)
if result.num_rows != 1:
raise RemoteReadError("The retrieved segment does not match the index. Rebuild the index.")
actual = segment_metadata(result.select([c for c in result.column_names if c not in PROBS and c != "sequence"]).to_pylist()[0])
if any(actual[k] != entry[k] for k in ("record_name", "assembly_accession", "segment_start_bp", "segment_end_bp")):
raise RemoteReadError("The retrieved segment does not match the index. Rebuild the index.")
stats["seconds"] = time.perf_counter() - began
return result, stats
def segment_table(self, index):
return self.fetch(index)[0]
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