Allow multiple files per concept set - validation passed

acmc/phen.py

@@ -514,46 +514,47 @@ def validate(phen_dir: str):
     # create a list of all the concept set names defined in the concept set configuration
     concept_set_names = []
     for item in phenotype["concept_sets"]:
-        # if item["name"] in concept_set_names:
-        #     validation_errors.append(
-        #         f"Duplicate concept set defined in concept sets {item['name'] }"
-        #     )
-        # else:
-        concept_set_names.append(item["name"])
-
-    # check codes definition
-    for item in phenotype["concept_sets"]:
-        # check concepte code file exists
-        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"
-            )
-
-        # check concepte code file is not empty
-        if concept_code_file_path.stat().st_size == 0:
+        if item["name"] in concept_set_names:
             validation_errors.append(
-                f"Coding file {str(concept_code_file_path.resolve())} is an empty file"
+                f"Duplicate concept set defined in concept sets {item['name'] }"
             )
+        else:
+            concept_set_names.append(item["name"])
 
-        # check code file type is supported
-        if concept_code_file_path.suffix not in CODE_FILE_TYPES:
-            raise ValueError(
-                f"Unsupported filetype {concept_code_file_path.suffix}, only support csv, xlsx, xls code file types"
-            )
+    # check codes definition
+    for files in phenotype["concept_sets"]: 
+        for item in files["files"]:
+            # check concepte code file exists
+            concept_code_file_path = concepts_path / item["path"]
+            if not concept_code_file_path.exists():
+                validation_errors.append(
+                    f"Coding file {str(concept_code_file_path.resolve())} does not exist"
+                )
 
-        # check columns specified are a supported medical coding type
-        for column in item["file"]["columns"]:
-            if column not in code_types:
+            # check concepte code file is not empty
+            if concept_code_file_path.stat().st_size == 0:
                 validation_errors.append(
-                    f"Column type {column} for file {concept_code_file_path} is not supported"
+                    f"Coding file {str(concept_code_file_path.resolve())} is an empty file"
                 )
 
-        # check the actions are supported
-        if "actions" in item["file"]:
-            for action in item["file"]["actions"]:
-                if action not in COL_ACTIONS:
-                    validation_errors.append(f"Action {action} is not supported")
+            # check code file type is supported
+            if concept_code_file_path.suffix not in CODE_FILE_TYPES:
+                raise ValueError(
+                    f"Unsupported filetype {concept_code_file_path.suffix}, only support csv, xlsx, xls code file types"
+                )
+
+            # check columns specified are a supported medical coding type
+            for column in item["columns"]:
+                if column not in code_types:
+                    validation_errors.append(
+                        f"Column type {column} for file {concept_code_file_path} is not supported"
+                    )
+
+            # check the actions are supported
+            if "actions" in item:
+                for action in item["actions"]:
+                    if action not in COL_ACTIONS:
+                        validation_errors.append(f"Action {action} is not supported")
 
     if len(validation_errors) > 0:
         _logger.error(validation_errors)