Read from database ini

app/routes/pride.py

@@ -23,6 +23,7 @@
 from app.models.spectrumidentificationprotocol import SpectrumIdentificationProtocol
 from index import get_session
 from process_dataset import convert_pxd_accession_from_pride
+from db_config_parser import security_API_key
 
 import logging
 import logging.config
@@ -35,18 +36,7 @@
 
 
 def get_api_key(key: str = Security(api_key_header)) -> str:
-    # Get the path to the mounted config directory from the environment variable, if not get default
-    database_ini_path = os.environ.get('DATABASE_INI_PATH', 'database.ini')
-    logger.info("database_ini_path: " + database_ini_path)
-    API_KEY = ""
-    if database_ini_path:
-        config.read(database_ini_path)
-        API_KEY = config.get('security', 'apikey')
-        logger.info(API_KEY)
-    else:
-        print("Error: DATABASE_INI_PATH environment variable not set.")
-
-    if key == API_KEY:
+    if key == security_API_key():
         return key
     raise HTTPException(
         status_code=status.HTTP_401_UNAUTHORIZED,

db_config_parser.py

@@ -2,30 +2,37 @@
 import os
 
 
-def parse_database_info(filename, section='postgresql'):
+def parse_info(filename, section='postgresql'):
     # create a parser
     parser = ConfigParser()
     # read config file
     parser.read(filename)
 
     # get section, default to postgresql
-    db = {}
+    section_info = {}
     if parser.has_section(section):
         params = parser.items(section)
         for param in params:
-            db[param[0]] = param[1]
+            section_info[param[0]] = param[1]
     else:
         raise Exception('Section {0} not found in the {1} file'.format(section, filename))
-    return db
+    return section_info
 
 
 def get_conn_str():
     config = os.environ.get('DB_CONFIG', 'database.ini')
-    db_info = parse_database_info(config)
+    db_info = parse_info(config, 'postgresql')
     hostname = db_info.get("host")
     database = db_info.get("database")
     username = db_info.get("user")
     password = db_info.get("password")
     port = db_info.get("port")
     conn_str = f"postgresql://{username}:{password}@{hostname}:{port}/{database}"
     return conn_str
+
+
+def security_API_key():
+    config = os.environ.get('DB_CONFIG', 'database.ini')
+    security_info = parse_info(config, 'security')
+    apikey = security_info.get("apikey")
+    return apikey