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import csv
import json
import os
import hashlib
import datetime
import lmdb
import pickle
from pathlib import Path
from gn2.base.data_set import query_table_timestamp
from gn2.base.webqtlConfig import TEXTDIR
from gn2.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"""
file_name = generate_filename(dataset_name, suffix="metadata")
file_path = Path(TMPDIR, file_name)
try:
with open(file_path, "r+") as file_handler:
dataset_metadata = json.load(file_handler)
return (file_path, dataset_metadata)
except FileNotFoundError:
pass
except JSONDecodeError:
file_path.unlink()
file_path.touch(exist_ok=True)
return (file_path, {})
def cache_new_traits_metadata(dataset_metadata: dict, new_traits_metadata, file_path: str):
"""function to cache the new traits metadata"""
if (dataset_metadata == {} and new_traits_metadata == {}):
return
dataset_metadata.update(new_traits_metadata)
with open(file_path, "w+") as file_handler:
json.dump(dataset_metadata, file_handler)
def generate_filename(*args, suffix="", file_ext="json"):
"""given a list of args generate a unique filename"""
string_unicode = f"{*args,}".encode()
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"""
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)
with conn.cursor() as cursor:
cursor.execute(
'SELECT Id, FullName FROM ProbeSetFreeze WHERE Name = %s', (dataset_name,))
results = cursor.fetchone()
if results:
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])
except Exception:
pass
def read_text_file(sample_dict, file_path):
def __fetch_id_positions__(all_ids, target_ids):
_vals = []
_posit = [0] # alternative for parsing
for (idx, strain) in enumerate(all_ids, 1):
if strain in target_ids:
_vals.append(target_ids[strain])
_posit.append(idx)
return (_posit, _vals)
with open(file_path) as csv_file:
csv_reader = csv.reader(csv_file, delimiter=',')
_posit, sample_vals = __fetch_id_positions__(
next(csv_reader)[1:], sample_dict)
return (sample_vals, [[line[i] for i in _posit] for line in csv_reader])
def write_db_to_textfile(db_name, conn, text_dir=TMPDIR):
def __sanitise_filename__(filename):
ttable = str.maketrans({" ": "_", "/": "_", "\\": "_"})
return str.translate(filename, ttable)
def __generate_file_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 __parse_to_dict__(results):
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]
return (data, ids)
def __write_to_file__(file_path, data, col_names):
with open(file_path, 'w+', encoding='UTF8') as file_handler:
writer = csv.writer(file_handler)
writer.writerow(col_names)
writer.writerows(data.values())
with conn.cursor() as cursor:
cursor.execute(
"SELECT ProbeSet.Name, Strain.Name, ProbeSetData.value "
"FROM Strain LEFT JOIN ProbeSetData "
"ON Strain.Id = ProbeSetData.StrainId "
"LEFT JOIN ProbeSetXRef ON ProbeSetData.Id = ProbeSetXRef.DataId "
"LEFT JOIN ProbeSet ON ProbeSetXRef.ProbeSetId = ProbeSet.Id "
"WHERE ProbeSetXRef.ProbeSetFreezeId IN "
"(SELECT Id FROM ProbeSetFreeze WHERE Name = %s) "
"ORDER BY Strain.Name",
(db_name,))
results = cursor.fetchall()
file_name = __generate_file_name__(db_name)
if (results and file_name):
__write_to_file__(os.path.join(text_dir, file_name),
*__parse_to_dict__(results))
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