refactored map to phen; refactored to standard directories for phenotypes that...

refactored map to phen; refactored to standard directories for phenotypes that user can set with subdirectory codes, config.json, phen_output.csv; defaults to build/phen if not specified as makes cli much simpler

.gitignore

@@ -14,12 +14,7 @@ __pycache__
 
 # Build
 build/*
-output/
-concepts-output/
-archive/
-maps/*
-concepts-new/
-codes/
+*output*
 
 # temporary 
 script

acmc.py

@@ -2,61 +2,36 @@ import argparse
 
 import trud
 import omop
-import map
+import phen
 
 from pathlib import Path
 
 def trud_install(args):
     """Handle the `trud install` command."""
-    print(f"Installing TRUD")
     trud.install(args.api_key)
-    print(f"TRUD installation completed")
 
 def omop_install(args):
     """Handle the `omop install` command."""
-    print(f"Installing OMOP database")
     omop.install(omop.OMOP_DB_PATH, args.omop_folder)
-    print(f"OMOP installation completed")    
 
 def omop_clear(args):
     """Handle the `omop clear` command."""
-    print(f"Clearing OMOP data from database")
     omop.clear(omop.OMOP_DB_PATH)   
-    print(f"OMOP database cleared")        
 
 def omop_delete(args):
     """Handle the `omop delete` command."""
-    print(f"Deleting OMOP database")
     omop.delete(omop.OMOP_DB_PATH)
-    print(f"OMOP database deleted")    
-
-def map_process(args):
-	"""Handle the `map process` command."""    
-	print(f"Processing map with phenotype config file: {args.config_file}")
-	print(f"Output directory: {args.output_file}")
-	print(f"Target coding format: {args.target_coding}")	
-	if args.translate:
-		print("Translating code types.")
-	else:
-		print("Not translating codes")
-	if args.verify:
-		print("Verifying codes.")
-	else:
-		print("Not verifying codes.")
-	if args.error_log:
-		print(f"Saving errors to: {args.error_log}")
-	else:
-		args.error_log = 'errors.csv'
-		
-	map.process(args.config_file,
-				args.source_codes_dir,
+
+def phen_init(args):
+	"""Handle the `phen init` command."""  
+	phen.init(args.phen_dir)
+
+def phen_map(args):
+	"""Handle the `phen map` command."""    
+	phen.map(args.phen_dir,
 			 args.target_coding,
 			 args.translate,
-				args.verify,
-				error_path=Path(args.error_log),
-				output_path=Path(args.output_file))
-
-	print(f"Phenotype processing completed")
+			 args.verify)
 
 def main():
 	parser = argparse.ArgumentParser(description="ACMC command-line tool")
@@ -85,30 +60,31 @@ def main():
 	# omop clear
 	omop_clear_parser = omop_subparsers.add_parser("clear", help="Clear OMOP data from database")
 	omop_clear_parser.set_defaults(func=omop_clear)
+	
 	# omop delete
 	omop_delete_parser = omop_subparsers.add_parser("delete", help="Delete OMOP database")
 	omop_delete_parser.set_defaults(func=omop_delete)
 	
-	### MAP Command ###
-	map_parser = subparsers.add_parser("map", help="Map commands")
-	map_subparsers = map_parser.add_subparsers(dest="subcommand", required=True, help="Map subcommands")
+	### PHEN Command ###
+	phen_parser = subparsers.add_parser("phen", help="Phen commands")
+	phen_subparsers = phen_parser.add_subparsers(dest="subcommand", required=True, help="Phen subcommands")
 
-	# map process
-	map_process_parser = map_subparsers.add_parser("process", help="Process map configuration file")
-	map_process_parser.add_argument("-c", "--config-file", required=True, help="Phenotype configuration file")
-	map_process_parser.add_argument("-s", "--source-codes-dir", required=True, help="Source codes root directory")
-	map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
-	map_process_parser.add_argument("-o", "--output-file", type=str, default=str(map.OUTPUT_PATH.resolve()), help="Output directory for CSV or OMOP database")	
+	# phen init
+	phen_init_parser = phen_subparsers.add_parser("init", help="Initiatise phenotype configuration")
+	phen_init_parser.add_argument("-d", "--phen-dir", type=str, default=phen.DEFAULT_PHEN_PATH.resolve, help="Phenotype directory")
+	phen_init_parser.set_defaults(func=phen_init)
 	
-	# Flags
-	map_process_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Do not translate code types")
-	map_process_parser.add_argument("-v", "--verify", action="store_true", default=False, help="Do not verify codes")
+	# phen map
+	phen_map_parser = phen_subparsers.add_parser("map", help="Process phen configuration file")
+	phen_map_parser.add_argument("-d", "--phen-dir", type=str, default=phen.DEFAULT_PHEN_PATH.resolve, help="Phenotype directory")
+	phen_map_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
 	
-	# Error log file
-	map_process_parser.add_argument("-l", "--error-log", type=str, default=str(map.ERROR_PATH.resolve()), help="Filepath to save error log to")
+	# Flags
+	phen_map_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Do not translate code types")
+	phen_map_parser.add_argument("-v", "--verify", action="store_true", default=False, help="Do not verify codes")
 
 	# Set the function to call when 'process' subcommand is used
-	map_process_parser.set_defaults(func=map_process)    
+	phen_map_parser.set_defaults(func=phen_map)    
 
 	# Parse arguments
 	args = parser.parse_args()