diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_file_generator.py | 62 |
1 files changed, 35 insertions, 27 deletions
diff --git a/wqflask/wqflask/correlation/correlation_file_generator.py b/wqflask/wqflask/correlation/correlation_file_generator.py index 3b6a0984..4d8a2f23 100644 --- a/wqflask/wqflask/correlation/correlation_file_generator.py +++ b/wqflask/wqflask/correlation/correlation_file_generator.py @@ -2,12 +2,13 @@ from urllib.parse import urlparse import pymysql as mdb import os import csv -import lmdb +import lmdb import os -import tempfile -import numpy as np -from io import BytesIO +import functools +import tempfile +import numpy as np +from io import BytesIO def parse_db_url(): @@ -16,7 +17,6 @@ def parse_db_url(): always expected""" parsed_db = urlparse(SQL_URI) - return ( parsed_db.hostname, parsed_db.username, parsed_db.password, parsed_db.path[1:], 3306) @@ -26,7 +26,7 @@ def parse_db_url(): def database_connector(): """function to create db connector""" host, user, passwd, db_name, db_port = parse_db_url() - return mdb.connect(host=host,user=user,password=passwd,database=db_name) + return mdb.connect(host=host, user=user, password=passwd, database=db_name) def get_probesetfreezes(conn, inbredsetid=1): @@ -88,8 +88,8 @@ def get_probesetfreeze(conn, probes): def query_for_last_modification(): - pass - """ + pass + """ SELECT database_name,table_name,last_update FROM mysql.innodb_table_stats a, @@ -111,18 +111,18 @@ WHERE a.database_name = b.db_last_update_name def parse_dataset(results): - ids = ["ID"] - data = {} - for (trait, strain,val) in results: - if strain not in ids: - ids.append(strain) + ids = ["ID"] + data = {} + for (trait, strain,val) in results: + if strain not in ids: + ids.append(strain) - if trait in data: - data[trait].append(val) - else: - data[trait] = [trait,val] + if trait in data: + data[trait].append(val) + else: + data[trait] = [trait,val] - return (data,ids) + return (data,ids) # above refactor the code @@ -164,27 +164,35 @@ def bytes_to_array(b: bytes) -> np.ndarray: def lmdb_file_generator(file_name,data:np.ndarray): - #create unique filename + # create unique filename # pass + +def lmdb_error_handler(func): + @functools.wraps(func) + def inner_function(*args, **kwargs): + try: + return func(*args, **kwargs) + except lmdb.Error as error: + print(f"{func.__name__} >>>> error . {str(error)}") + return None + return inner_function + + def create_dataset(file_name, db_name, dataset: np.ndarray): # map size int(ie12) - with lmdb.open(file_name, map_size=(dataset.nbytes*10)) as env: + with lmdb.open(file_name, map_size=dataset.nbytes*10) as env: with env.begin(write=True) as txn: txn.put(db_name.encode(), array_to_bytes(dataset)) - return (file_name, db_name) +@lmdb_error_handler def read_dataset(file_name, db_name): with lmdb.open(file_name, readonly=True, create=False) as env: with env.begin() as txn: - ndaray_bytes = txn.get(db_name.encode()) - # error handling - return bytes_to_array(ndaray_bytes) - - -#simple lmdb file
\ No newline at end of file + results = txn.get(db_name.encode()) + return bytes_to_array(results) if results else None
\ No newline at end of file |