(docs) updated module descriptions

acmc/logging_config.py

+"""
+logging_config.py
+
+This module defines functions to setup logging for acmc across all module. 
+
+Constants
+- DEFAULT_LOG_FILE: The default acmc application log filename.
+
+"""
+
 import pandas as pd
 import logging
 
-DEFAULT_LOG_FILE = "acmc.log"
-
+DEFAULT_LOG_FILE = "acmc.log" # default log filename
 
 def setup_logger(log_level: int = logging.INFO):
-    """Sets up logger as a singleton outputing to file and sysout syserr"""
+    """Sets up acmc logger as a singleton outputing to file and sysout syserr."""
+    
     # Create a logger
     logger = logging.getLogger("acmc_logger")
     logger.setLevel(logging.INFO)
@@ -20,7 +30,6 @@ def setup_logger(log_level: int = logging.INFO):
         stream_handler.setLevel(logging.INFO)
 
         # Create a formatter for how the log messages should look
-
         # Add the formatter to both handlers
         file_formatter = logging.Formatter(
             "%(asctime)s - - %(levelname)s - %(message)s"
@@ -37,9 +46,9 @@ def setup_logger(log_level: int = logging.INFO):
 
 
 def set_log_level(log_level: int):
-    """Sets the log level for the acmc logger"""
+    """Sets the log level for the acmc logger."""
     logger = logging.getLogger("acmc_logger")
-    logger.setLevel(log_level)  # Set logger level
+    logger.setLevel(log_level)
 
     # Also update handlers to match the new level
     for handler in logger.handlers:

acmc/omop.py

 """
-OMOP Module
+omop module
 ================
 This module provides functionality to manage OMOP vocabularies.
 """
@@ -62,9 +62,18 @@ omop_vocab_types = {
 }
 
 
-# Populate SQLite3 Database with default OMOP CONCEPTS
 def install(omop_zip_file: str, version: str):
-    """Installs the OMOP release csv files in a file-based sql database"""
+    """"Installs the OMOP release csv files in a file-based sql database
+
+    Args:
+        omop_zip_file (str): vocabularies zip file distributed by OHDSI Athena
+        version (str): version of the vocabularies distributed by OHDSI Athena
+
+    Raises:
+        ValueError: if the zip file does not exist
+        ValueError: if the file is not a zip file
+        Exception: if error reading omop csv files
+    """
     logger.info(f"Installing OMOP from zip file: {omop_zip_file}")
     omop_zip_path = Path(omop_zip_file)
 
@@ -73,6 +82,7 @@ def install(omop_zip_file: str, version: str):
         msg = f"{omop_zip_path} does not exist."
         logger.error(msg)
         raise ValueError(msg)
+    
     if not zipfile.is_zipfile(omop_zip_path):
         msg = f"Error: {omop_zip_path} is not a valid ZIP file."
         logger.error(msg)
@@ -127,7 +137,11 @@ def install(omop_zip_file: str, version: str):
 
 
 def write_version_file(version: str):
-    """Writes the OMOP vocaburaries and version to a file"""
+    """Writes the OMOP vocaburaries and version to a file
+
+    Args:
+        version (str): version of the vocabularies distributed by OHDSI Athena
+    """
     vocabularies["version"] = version
     with open(VERSION_PATH, "w") as file:
         yaml.dump(
@@ -141,7 +155,14 @@ def write_version_file(version: str):
 
 
 def clear(db_path: Path):
-    """Clears the OMOP sql database"""
+    """Clears the OMOP sql database
+
+    Args:
+        db_path (Path): the path to the omop sqllite database
+
+    Raises:
+        FileNotFoundError: if the omop sqllite database does not exist
+    """
     logger.info(f"Clearing OMOP data from database")
     if not db_path.is_file():
         raise FileNotFoundError(f"Error: OMOP DB file '{db_path}' does not exist.")
@@ -161,7 +182,15 @@ def clear(db_path: Path):
 
 
 def delete(db_path: Path):
-    """Deletes the OMOP sql database"""
+    """Deletes the OMOP sql database
+
+    Args:
+        db_path (Path): the path to the omop sqllite database
+
+    Raises:
+        FileNotFoundError: if the omop sqllite database does not exist
+    """
+    
     logger.info(f"Deleting OMOP database")
     if not db_path.is_file():
         raise FileNotFoundError(f"Error: OMOP DB file '{db_path}' does not exist.")
@@ -171,7 +200,16 @@ def delete(db_path: Path):
 
 
 def table_exists(cursor: sqlite3.Cursor, table_name: str) -> bool:
-    # Query to check if the table exists
+    """Query to check if the table exists
+
+    Args:
+        cursor (sqlite3.Cursor): a sqllite database cursor
+        table_name (str): the table name to check
+
+    Returns:
+        bool: true if table exists
+    """    
+        
     cursor.execute(
         """
 		SELECT name
@@ -188,7 +226,16 @@ def table_exists(cursor: sqlite3.Cursor, table_name: str) -> bool:
 
 
 def vocab_exists(cursor: sqlite3.Cursor, vocab_id: str) -> bool:
-    # Query to check if the table exists
+    """Query to check if the vocabulary exists
+
+    Args:
+        cursor (sqlite3.Cursor): a sqllite database cursor
+        vocab_id (str): the vocabulary id to check
+
+    Returns:
+        bool: true if vocabulary id exists
+    """    
+    
     cursor.execute(
         """
 		SELECT vocabulary_id 
@@ -205,6 +252,16 @@ def vocab_exists(cursor: sqlite3.Cursor, vocab_id: str) -> bool:
 
 
 def concept_set_exist(cursor: sqlite3.Cursor, concept_set_name: str) -> bool:
+    """Query to check if the concept set exists
+
+    Args:
+        cursor (sqlite3.Cursor): a sqllite database cursor
+        concept_set_name (str): the concept set name to check
+
+    Returns:
+        bool: true if concept set exists
+    """
+    
     query = f"SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)"
     cursor.execute(query, (concept_set_name,))
 
@@ -212,7 +269,20 @@ def concept_set_exist(cursor: sqlite3.Cursor, concept_set_name: str) -> bool:
     return cursor.fetchone()[0] == 1
 
 
-def export(map_path: Path, export_path: Path, version: str, omop_metadata) -> Path:
+def export(map_path: Path, export_path: Path, version: str, omop_metadata: dict) -> Path:
+    """Export concept sets to omop database in csv format
+
+    Args:
+        map_path (Path): path to the acmc map directory containing concept sets in csv format
+        export_path (Path): path to the directory where the omop database csv files are to be written
+        version (str): phenotype version for omop vocabulary version
+        omop_metadata (dict): phenotype omop metadata for omop vocabulary metadata 
+                
+    Returns:
+        Path: path to the exported sqllite database
+    """
+    
+    
     logger.debug(f"exporting with metadata {omop_metadata} at version {version}")
 
     # copy the baseline omop database