diff options
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 38 |
1 files changed, 33 insertions, 5 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index 961f5161..d5916673 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -2,6 +2,10 @@ import csv import json import os import hashlib +import datetime + +import lmdb +import pickle from pathlib import Path from base.data_set import query_table_timestamp @@ -10,6 +14,31 @@ from base.webqtlConfig import TMPDIR from json.decoder import JSONDecodeError +def cache_trait_metadata(dataset_name, data): + + + try: + with lmdb.open(os.path.join(TMPDIR,f"metadata_{dataset_name}"),map_size=20971520) as env: + with env.begin(write=True) as txn: + data_bytes = pickle.dumps(data) + txn.put(f"{dataset_name}".encode(), data_bytes) + current_date = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') + txn.put(b"creation_date", current_date.encode()) + return "success" + + except lmdb.Error as error: + pass + +def read_trait_metadata(dataset_name): + try: + with lmdb.open(os.path.join(TMPDIR,f"metadata_{dataset_name}"), + readonly=True, lock=False) as env: + with env.begin() as txn: + db_name = txn.get(dataset_name.encode()) + return (pickle.loads(db_name) if db_name else {}) + except lmdb.Error as error: + return {} + def fetch_all_cached_metadata(dataset_name): """in a gvein dataset fetch all the traits metadata""" @@ -174,11 +203,10 @@ def get_datasets_data(base_dataset, target_dataset_data): def fetch_text_file(dataset_name, conn, text_dir=TMPDIR): """fetch textfiles with strain vals if exists""" - - def __file_scanner__(text_dir,target_file): - for file in os.listdir(text_dir): + def __file_scanner__(text_dir, target_file): + for file in os.listdir(text_dir): if file.startswith(f"ProbeSetFreezeId_{target_file}_"): - return os.path.join(text_dir,file) + return os.path.join(text_dir, file) with conn.cursor() as cursor: cursor.execute( @@ -188,7 +216,7 @@ def fetch_text_file(dataset_name, conn, text_dir=TMPDIR): try: # checks first for recently generated textfiles if not use gn1 datamatrix - return __file_scanner__(text_dir,results[0]) or __file_scanner__(TEXTDIR,results[0]) + return __file_scanner__(text_dir, results[0]) or __file_scanner__(TEXTDIR, results[0]) except Exception: pass |