load edam data into MariaDB edam_etl table

apps/openchallenges/edam-etl/src/main.py

@@ -3,6 +3,10 @@
 import requests
 from os import getenv
 from typing import Optional
+import mariadb
+import sys
+import mysql.connector
+from sqlalchemy import create_engine
 
 # Get config from the environment variables
 
@@ -11,6 +15,66 @@
 print(f"EDAM Version: {VERSION}")
 print(f"OC DB URL: {OC_DB_URL}")
 
+# Intialize required connection variables from environment variables
+
+USERNAME = getenv("USERNAME")
+PASSWORD = getenv("PASSWORD")
+PORT = getenv("PORT")
+DB = getenv("DB")
+HOST = getenv("HOST")
+
+
+def connect_to_mariadb(
+    username: str, password: str, port: str, host: str, database: str, df: pd.DataFrame
+) -> None:
+    """Connect to the MariaDB database"""
+    try:
+        conn = mariadb.connect(
+            user=username,
+            password=password,
+            host=host,
+            port=int(port),
+            database=database,
+        )
+        print("Establishing a connection to the MariaDB Platform.")
+        # Get the cursor
+        cur = conn.cursor()
+        print("Connection has been established to MariaDB Platform!")
+
+        # Commit the transaction
+        conn.commit()
+        print("The table edam_etl has been added to the edam database!")
+
+        # Create a SQLAlchemy engine from the MySQL Connector connection
+        engine = create_engine(
+            f"mysql+mysqlconnector://{username}:{password}@{host}/{database}"
+        )
+
+        # Drop the table if it exists
+        cur.execute("DROP TABLE IF EXISTS edam_etl")
+
+        # Create the table with columns
+        cur.execute(
+            """
+            CREATE TABLE edam_etl (
+                id INT PRIMARY KEY,
+                class_id VARCHAR(255),
+                preferred_label VARCHAR(255)
+            )
+        """
+        )
+
+        # Load the concepts
+        df.to_sql(name="edam_etl", con=engine, if_exists="append", index=False)
+
+        print("The table edam_etl has been populated with the EDAM concepts!")
+
+        # Close the connection
+        conn.close()
+    except mariadb.Error as e:
+        print(f"Error connecting to MariaDB Platform: {e}")
+        sys.exit(1)
+
 
 def download_edam_csv(url: str, version: str) -> Optional[bool]:
     """Download EDAM concepts from GitHub or S3 bucket (CSV file)"""
@@ -101,6 +165,7 @@ def main() -> None:
     if download_edam_csv(url, VERSION):
         df: pd.DataFrame = transform_to_dataframe(VERSION)
         print_info_statistics(df)
+    connect_to_mariadb(USERNAME, PASSWORD, PORT, HOST, DB, df)
 
 
 if __name__ == "__main__":