changed phen/output directory to phen/map and added concept-sets directory

phen.py

@@ -22,8 +22,12 @@ pd.set_option("mode.chained_assignment", None)
 
 PHEN_DIR = 'phen'
 DEFAULT_PHEN_PATH = Path('build') / PHEN_DIR
+
 CODES_DIR = 'codes'
-OUTPUT_DIR = 'output'
+MAP_DIR = 'map'
+CONCEPT_SET_DIR = 'concept-set'
+DEFAULT_PHEN_DIR_LIST = [CODES_DIR, MAP_DIR, CONCEPT_SET_DIR]
+
 CONFIG_FILE = 'config.json'
 ERROR_FILE = 'errors.csv'
 REPORT_FILE = 'report.md'
@@ -64,6 +68,12 @@ def construct_git_url(remote_url):
 	new_netloc = f"{auth}@{parsed_url.netloc}"
 	return urlunparse((parsed_url.scheme, new_netloc, parsed_url.path, parsed_url.params, parsed_url.query, parsed_url.fragment))
 
+def create_empty_git_dir(path):
+	"""Creates a directory with a .gitkeep file so that it's tracked in git"""		
+	path.mkdir(exist_ok=True)
+	keep_path = path / '.gitkeep'
+	keep_path.touch(exist_ok=True)
+
 def init(phen_dir, remote_url):
 	"""Initial phenotype directory as git repo with standard structure"""	
 	print(f"Initialising Phenotype in directory: {phen_dir}")
@@ -138,17 +148,8 @@ def init(phen_dir, remote_url):
 		return
 		
 	print("Creating phen directory structure and config files")
-	# create codes directory
-	codes_path = phen_path / CODES_DIR
-	codes_path.mkdir(exist_ok=True)
-	keep_path = codes_path / '.gitkeep'
-	keep_path.touch(exist_ok=True)
-	
-	# create concept sets directory
-	output_path = phen_path / OUTPUT_DIR
-	output_path.mkdir(exist_ok=True)
-	keep_path = output_path / '.gitkeep'
-	keep_path.touch(exist_ok=True)
+	for d in DEFAULT_PHEN_DIR_LIST:
+		create_empty_git_dir(phen_path / d)
 	
 	# set initial version based on the number of commits in the repo, depending on how the repo was created
 	# e.g., with a README.md, then there will be some initial commits before the phen config is added
@@ -175,8 +176,8 @@ def init(phen_dir, remote_url):
 		json.dump(config, f, indent=4) 
 		
 	# add to git repo and commit
-	repo.git.add(codes_path)
-	repo.git.add(output_path)				
+	for d in DEFAULT_PHEN_DIR_LIST:
+		repo.git.add(phen_path / d)			
 	repo.git.add(all=True)		
 	repo.index.commit("initialised the phen git repo.")			
 		
@@ -529,10 +530,10 @@ def map(phen_dir,
 	else:
 		output_filename = target_code_type + '_no_translate.csv'
 	
-	output_path = phen_path / OUTPUT_DIR / output_filename
+	map_path = phen_path / MAP_DIR / output_filename
 		
-	out.to_csv(output_path, index=False)
-	print("Saved to", output_path)
+	out.to_csv(map_path, index=False)
+	print("Saved translations to", map_path)
 
 	# Save Error File
 	error_path = phen_path / ERROR_FILE
@@ -660,12 +661,12 @@ def diff(phen_dir, phen_old_dir):
 		raise ValueError(f"Unsupported filetype provided for report file {str(report_path.resolve())}")
 
 	# Get maps files from phenotype 
-	old_output_path = old_phen_path / OUTPUT_DIR
-	new_output_path = new_phen_path / OUTPUT_DIR
+	old_map_path = old_phen_path / MAP_DIR
+	new_map_path = new_phen_path / MAP_DIR
 
 	# List files from output directories
-	old_output_files = [file.name for file in old_output_path.iterdir() if file.is_file() and not file.name.startswith('.')]
-	new_output_files = [file.name for file in new_output_path.iterdir() if file.is_file() and not file.name.startswith('.')]
+	old_output_files = [file.name for file in old_map_path.iterdir() if file.is_file() and not file.name.startswith('.')]
+	new_output_files = [file.name for file in new_map_path.iterdir() if file.is_file() and not file.name.startswith('.')]
 
 	# Convert the lists to sets for easy comparison
 	old_output_set = set(old_output_files)
@@ -689,8 +690,8 @@ def diff(phen_dir, phen_old_dir):
 	report.write(f"\n\n## Compare concepts {str(old_phen_path.resolve())} to {str(new_phen_path.resolve())}\n\n")
 	# Compare common outputs between versions
 	for file in common_outputs:
-		old_output = old_output_path / file
-		new_output = new_output_path / file
+		old_output = old_map_path / file
+		new_output = new_map_path / file
 		
 		df1 = pd.read_csv(old_output)
 		df1 = df1[["CONCEPT","CONCEPT_SET"]].groupby("CONCEPT_SET").count()