(refactor) Changed codes to concepts directory for alignment with OMOP. Closes #52

acmc/phen.py

@@ -29,12 +29,12 @@ pd.set_option("mode.chained_assignment", None)
 PHEN_DIR = "phen"
 DEFAULT_PHEN_PATH = Path("./workspace") / PHEN_DIR
 
-CODES_DIR = "codes"
+CONCEPTS_DIR = "concepts"
 MAP_DIR = "map"
 CONCEPT_SET_DIR = "concept-set"
 CSV_PATH = Path(CONCEPT_SET_DIR) / "csv"
 OMOP_PATH = Path(CONCEPT_SET_DIR) / "omop"
-DEFAULT_PHEN_DIR_LIST = [CODES_DIR, MAP_DIR, CONCEPT_SET_DIR]
+DEFAULT_PHEN_DIR_LIST = [CONCEPTS_DIR, MAP_DIR, CONCEPT_SET_DIR]
 CONFIG_FILE = "config.yaml"
 VOCAB_VERSION_FILE = "vocab_version.yaml"
 
@@ -327,10 +327,10 @@ def validate(phen_dir):
             f"Error: phen configuration file '{config_path}' does not exist."
         )
 
-    codes_path = phen_path / CODES_DIR
-    if not codes_path.is_dir():
+    concepts_path = phen_path / CONCEPTS_DIR
+    if not concepts_path.is_dir():
         raise FileNotFoundError(
-            f"Error: source codes directory {source_codes_dir} does not exist."
+            f"Error: source concepts directory {concepts_path} does not exist."
         )
 
     # Calidate the directory is a git repo
@@ -384,7 +384,7 @@ def validate(phen_dir):
     # check codes definition
     for item in phenotype["concept_sets"]:
         # check concepte code file exists
-        concept_code_file_path = codes_path / item["file"]["path"]
+        concept_code_file_path = concepts_path / item["file"]["path"]
         if not concept_code_file_path.exists():
             validation_errors.append(
                 f"Coding file {str(concept_code_file_path.resolve())} does not exist"
@@ -683,7 +683,7 @@ def map(phen_dir, target_code_type):
 
 def map_target_code_type(phen_path, phenotype, target_code_type):
     logger.debug(f"Target coding format: {target_code_type}")
-    codes_path = phen_path / CODES_DIR
+    concepts_path = phen_path / CONCEPTS_DIR
     # Create output dataframe
     out = pd.DataFrame([])
     code_errors = []
@@ -693,7 +693,7 @@ def map_target_code_type(phen_path, phenotype, target_code_type):
         logger.debug(f"--- {concept_set['file']} ---")
 
         # Load code file
-        codes_file_path = Path(codes_path / concept_set["file"]["path"])
+        codes_file_path = Path(concepts_path / concept_set["file"]["path"])
         df = read_table_file(codes_file_path)
 
         # process structural actions