diff options
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 56 |
1 files changed, 48 insertions, 8 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index 2831bd39..e82eb0ec 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -14,25 +14,26 @@ from base.webqtlConfig import TMPDIR from json.decoder import JSONDecodeError -def cache_trait_metadata(dataset_name, data): +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: + 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: + 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 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 {}) @@ -82,8 +83,6 @@ def generate_filename(*args, suffix="", file_ext="json"): return f"{hashlib.md5(string_unicode).hexdigest()}_{suffix}.{file_ext}" - - def fetch_text_file(dataset_name, conn, text_dir=TMPDIR): """fetch textfiles with strain vals if exists""" @@ -176,3 +175,44 @@ def write_db_to_textfile(db_name, conn, text_dir=TMPDIR): if (results and file_name): __write_to_file__(os.path.join(text_dir, file_name), *__parse_to_dict__(results)) + + +# check for file path +# I need the lmdb path # tmpdir +def __generate_target_name__(db_name): + # todo add expiry time and checker + with conn.cursor() as cursor: + cursor.execute( + 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Name = %s', (db_name,)) + results = cursor.fetchone() + if (results): + return __sanitise_filename__( + f"ProbeSetFreezeId_{results[0]}_{results[1]}") + + +def fetch_csv_info(textfile_path: str, db_target_name: str): + """ + alternative for processing csv textfiles with rust + !.currently expiremental + """ + raise ValueError + + +def fetch_lmdb_info(db_path: str, db_target_name: str): + """ + check for if lmdb db exist and also the target db + e.g ProbeSets: ProbestFreeze__112_ + """ + # open db_read if results return none write the file write the file target + with lmdb.open(target_file_path, readonly=True, lock=False) as env: + with env.begin() as txn: + target_key = __generate_file_name__(db_target_name) + dataset = txn.get(target_key.encode()) + if dataset: + return { + "lmdb_target_path": f"{db_path}data.mdb", + "lmdb_target_key": target_key, + "file_type": "lmdb", + } + + return {} |