fix: Use Path rather than str for file path

Author: karatugo

README.md

@@ -4,8 +4,8 @@ A command-line tool for genomic-wide association studies (GWAS) data validation
 
 ## Features
 
-- Validate: 
-  - Input: GWAS Submission template that contains top associations
+- Validate:
+  - Input: File path of GWAS Submission template that contains top associations
   - Output: Validation report of top associations
 
 ## Installation
@@ -102,4 +102,3 @@ poetry run pre-commit run --all-files
 ## License
 
 [License](LICENSE)
-

src/gwas_assoc/cli.py

@@ -33,10 +33,10 @@ def cli() -> None:
 
 
 @cli.command()
-@click.argument("file", type=click.Path(exists=True))
-def validate(file: str) -> None:
+@click.argument("_file", type=click.Path(exists=True))
+def validate(_file: str) -> None:
     """Validate SNPs in an Excel file."""
-    file_path = Path(file)
+    file_path = Path(_file)
 
     console.print(f"Starting validation of [bold]{file_path}[/]")
 
@@ -50,7 +50,7 @@ def validate(file: str) -> None:
 
         try:
             validator = SnpValidator()
-            result = validator.validate_snps(file)
+            result = validator.validate_snps(file_path)
             progress.update(task, completed=True)
         except Exception as e:
             progress.update(

src/gwas_assoc/commands/validate.py

@@ -29,7 +29,7 @@ def __init__(self) -> None:
         """
         self.ensembl_api_url = "https://rest.ensembl.org/variation/human/"
 
-    def _get_study_tags(self, file_path: str) -> Set:
+    def _get_study_tags(self, file_path: Path) -> Set:
         # Read study sheet to get study tags
         console.print("[info]Reading study tags...[/]")
         try:
@@ -44,7 +44,7 @@ def _get_study_tags(self, file_path: str) -> Set:
             print_error(f"Error reading study sheet: {str(e)}")
             return set()
 
-    def _get_schema_version(self, file_path: str) -> str:
+    def _get_schema_version(self, file_path: Path) -> str:
         """Get the schema version from the meta sheet of the Excel file"""
         console.print("[info]Reading schema version...[/]")
         meta_df = pd.read_excel(file_path, sheet_name="meta")
@@ -224,7 +224,7 @@ def _validate_associations_against_template(
             pd.DataFrame(invalid_rows) if invalid_rows else pd.DataFrame()
         )
 
-    def validate_snps(self, file_path: str) -> bool:
+    def validate_snps(self, file_path: Path) -> bool:
         """
         Validate SNPs from an Excel file