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-rw-r--r--wqflask/base/data_set/utils.py77
1 files changed, 77 insertions, 0 deletions
diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
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+++ b/wqflask/base/data_set/utils.py
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+"data_set package utilities"
+
+import os
+import json
+import hashlib
+from typing import List
+
+
+from utility.tools import SQL_URI
+from base.webqtlConfig import TMPDIR
+from wqflask.database import parse_db_url, database_connection
+
+def geno_mrna_confidentiality(ob):
+ with database_connection() as conn, conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT confidentiality, "
+ f"AuthorisedUsers FROM {ob.type}Freeze WHERE Name = %s",
+ (ob.name,)
+ )
+ result = cursor.fetchall()
+ if len(result) > 0 and result[0]:
+ return True
+
+def query_table_timestamp(dataset_type: str):
+ """function to query the update timestamp of a given dataset_type"""
+
+ # computation data and actions
+ with database_connection() as conn, conn.cursor() as cursor:
+ fetch_db_name = parse_db_url(SQL_URI)
+ cursor.execute(
+ "SELECT UPDATE_TIME FROM "
+ "information_schema.tables "
+ f"WHERE TABLE_SCHEMA = '{fetch_db_name[3]}' "
+ f"AND TABLE_NAME = '{dataset_type}Data'")
+ date_time_obj = cursor.fetchone()[0]
+ return date_time_obj.strftime("%Y-%m-%d %H:%M:%S")
+
+
+def generate_hash_file(dataset_name: str, dataset_type: str, dataset_timestamp: str, samplelist: str):
+ """given the trait_name generate a unique name for this"""
+ string_unicode = f"{dataset_name}{dataset_timestamp}{samplelist}".encode()
+ md5hash = hashlib.md5(string_unicode)
+ return md5hash.hexdigest()
+
+
+def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List, query_results: List):
+ """function to cache dataset query results to file
+ input dataset_name and type query_results(already processed in default dict format)
+ """
+ # data computations actions
+ # store the file path on redis
+
+ table_timestamp = query_table_timestamp(dataset_type)
+ samplelist_as_str = ",".join(samplelist)
+
+ file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
+ file_path = os.path.join(TMPDIR, f"{file_name}.json")
+
+ with open(file_path, "w") as file_handler:
+ json.dump(query_results, file_handler)
+
+
+def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List):
+ """function to fetch the cached results"""
+
+ table_timestamp = query_table_timestamp(dataset_type)
+ samplelist_as_str = ",".join(samplelist)
+
+ file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
+ file_path = os.path.join(TMPDIR, f"{file_name}.json")
+ try:
+ with open(file_path, "r") as file_handler:
+
+ return json.load(file_handler)
+
+ except Exception:
+ pass