updated readme and counts for omop table messages

README.md

@@ -136,6 +136,22 @@ Please execute the following process:
 	```bash
 	acmc omop install -f <path to downloaded OMOP zip file> -v <release version from email>
 	```
+Expected output:
+
+```bash
+[INFO] - Installing OMOP from zip file: ../data/acmc-omop.zip
+[INFO] - Extracted OMOP zip file ../data/acmc-omop.zip to vocab/omop/
+[INFO] - Processing 1 of 9 tables: vocab/omop/CONCEPT.csv
+[INFO] - Processing 2 of 9 tables: vocab/omop/DOMAIN.csv
+[INFO] - Processing 3 of 9 tables: vocab/omop/CONCEPT_CLASS.csv
+[INFO] - Processing 4 of 9 tables: vocab/omop/RELATIONSHIP.csv
+[INFO] - Processing 5 of 9 tables: vocab/omop/DRUG_STRENGTH.csv
+[INFO] - Processing 6 of 9 tables: vocab/omop/VOCABULARY.csv
+[INFO] - Processing 7 of 9 tables: vocab/omop/CONCEPT_SYNONYM.csv
+[INFO] - Processing 8 of 9 tables: vocab/omop/CONCEPT_ANCESTOR.csv
+[INFO] - Processing 9 of 9 tables: vocab/omop/CONCEPT_RELATIONSHIP.csv
+[INFO] - OMOP installation completed
+```
 
 ---
 
@@ -451,7 +467,7 @@ The `phen` command is used phenotype-related operations.
 
 ## License
 
-MIT License
+This project is licensed under the terms of the **Apache License 2.0**. For more details, please see the full license [here](http://www.apache.org/licenses/LICENSE-2.0).
 
 ## Support
 

acmc/omop.py

@@ -42,7 +42,7 @@ vocabularies = {
 #Populate SQLite3 Database with default OMOP CONCEPTS 
 def install (omop_zip_file, version):
 	"""Installs the OMOP release csv files in a file-based sql database"""
-	logger.info(f"Installing OMOP downloads {omop_zip_file}")
+	logger.info(f"Installing OMOP from zip file: {omop_zip_file}")
 	omop_zip_path = Path(omop_zip_file)
 	
 	# Check if the file exists and is a ZIP file
@@ -74,22 +74,24 @@ def install (omop_zip_file, version):
 	# connect to database, if it does not exist it will be created
 	conn = sqlite3.connect(DB_PATH)    
 	# Iterate through files in the folder
-	for filename in os.listdir(VOCAB_PATH):
-		if filename.endswith(".csv"):  # Check if the file is a CSV
-			file_path = os.path.join(VOCAB_PATH, filename)
-			try:
-				logger.info(f"Reading table: {file_path}")
-				# read the CSV file with the specified delimiter
-				df = pd.read_csv(file_path, delimiter="\t", low_memory=False)
-				table_name = os.path.splitext(os.path.basename(file_path))[0] #Get name of file
+	csv_files = list(VOCAB_PATH.glob("*.csv"))
+	total_tables_count = len(csv_files)
+	table_count = 1
+	for filename in csv_files:
+		try:
+			logger.info(f"Processing {table_count} of {total_tables_count} tables: {filename}")
+			# read the CSV file with the specified delimiter
+			df = pd.read_csv(filename, delimiter="\t", low_memory=False)
+		
+			# export Table to sqlite db
+			df.to_sql(filename.stem, conn, if_exists='replace', index=False)
 			
-				# export Table to sqlite db
-				df.to_sql(table_name, conn, if_exists='replace', index=False)
+			# add to the metadata
+			vocabularies["tables"].append(filename.stem)
+			table_count = table_count + 1
+		except Exception as e:
+			raise Exception(f"Error reading file {filename}: {e}")
 				
-				# add to the metadata
-				vocabularies["tables"].append(filename)
-			except Exception as e:
-				raise Exception(f"Error reading file {file_path}: {e}")
 	conn.close()
 
 	# write version file