Merge pull request #159 from monarch-initiative/lint_quick_fix

Lint/Format fixes

src/koza/cli_utils.py

@@ -127,14 +127,16 @@ def _check_row_count(type: Literal["node", "edge"]):
         _check_row_count("edge")
 
 
-def split_file(file: str,
-               fields: str,
-               format: OutputFormat = OutputFormat.tsv,
-               remove_prefixes: bool = False,
-               output_dir: str = "./output"):
+def split_file(
+    file: str,
+    fields: str,
+    format: OutputFormat = OutputFormat.tsv,
+    remove_prefixes: bool = False,
+    output_dir: str = "./output",
+):
     db = duckdb.connect(":memory:")
 
-    #todo: validate that each of the fields is actually a column in the file
+    # todo: validate that each of the fields is actually a column in the file
     if format == OutputFormat.tsv:
         read_file = f"read_csv('{file}')"
     elif format == OutputFormat.json:
@@ -179,14 +181,18 @@ def get_filename_suffix(name):
     for row in list_of_value_dicts:
         # export to a tsv file named with the values of the pivot fields
         where_clause = ' AND '.join([f"{k} = '{row[k]}'" for k in keys])
-        file_name = output_dir + "/" + get_filename_prefix(file) +  generate_filename_from_row(row) + get_filename_suffix(file)
+        file_name = (
+            output_dir + "/" + get_filename_prefix(file) + generate_filename_from_row(row) + get_filename_suffix(file)
+        )
         print(f"writing {file_name}")
-        db.execute(f"""
+        db.execute(
+            f"""
         COPY (
             SELECT * FROM {read_file}
             WHERE {where_clause}
         ) TO '{file_name}' (HEADER, DELIMITER '\t');
-        """)
+        """
+        )
 
 
 def validate_file(

src/koza/main.py

@@ -65,15 +65,20 @@ def validate(
     """Validate a source file"""
     validate_file(file, format, delimiter, header_delimiter, skip_blank_lines)
 
+
 @typer_app.command()
 def split(
     file: str = typer.Argument(..., help="Path to the source kgx file to be split"),
     fields: str = typer.Argument(..., help="Comma separated list of fields to split on"),
-    remove_prefixes: bool = typer.Option(False, help="Remove prefixes from the file names for values from the specified fields. (e.g, NCBIGene:9606 becomes 9606"),
+    remove_prefixes: bool = typer.Option(
+        False,
+        help="Remove prefixes from the file names for values from the specified fields. (e.g, NCBIGene:9606 becomes 9606",
+    ),
     output_dir: str = typer.Option(default="output", help="Path to output directory"),
 ):
     """Split a file by fields"""
-    split_file(file, fields,remove_prefixes=remove_prefixes, output_dir=output_dir)
+    split_file(file, fields, remove_prefixes=remove_prefixes, output_dir=output_dir)
+
 
 if __name__ == "__main__":
     typer_app()

src/koza/model/source.py

@@ -87,13 +87,13 @@ def __next__(self) -> Dict[str, Any]:
         return row
 
     def _get_row(self):
-        #If we built a filter for this source, run extra code to validate each row for inclusion in the final output.
+        # If we built a filter for this source, run extra code to validate each row for inclusion in the final output.
         if self._filter:
             row = next(self._reader)
             reject_current_row = not self._filter.include_row(row)
-            #If the filter says we shouldn't include the current row; we filter it out and move onto the next row.
-            #We'll only break out of the following loop if "reject_current_row" is false (i.e. include_row is True/we
-            #have a valid row to return) or we hit a StopIteration exception from self._reader.
+            # If the filter says we shouldn't include the current row; we filter it out and move onto the next row.
+            # We'll only break out of the following loop if "reject_current_row" is false (i.e. include_row is True/we
+            # have a valid row to return) or we hit a StopIteration exception from self._reader.
             while reject_current_row:
                 row = next(self._reader)
                 reject_current_row = not self._filter.include_row(row)

src/koza/utils/row_filter.py

@@ -54,22 +54,22 @@ def include_row(self, row) -> bool:
         return include_row
 
     def inlist(self, column_value, filter_values):
-        #Check if the passed in column is exactly matched against
-        #For a filter_list of ['abc','def','ghi']; this will be true
-        #for column_value 'abc' but not 'abcde.'
+        # Check if the passed in column is exactly matched against
+        # For a filter_list of ['abc','def','ghi']; this will be true
+        # for column_value 'abc' but not 'abcde.'
         col_exact_match = column_value in filter_values
-        #The following iterates through all filters and will return true if
-        #the text of the  filter is found within the column_value.
-        #So for the above example this boolean will return True, because :'abc' in 'abcde': returns True. 
-        if(type(column_value)==str):
+        # The following iterates through all filters and will return true if
+        # the text of the  filter is found within the column_value.
+        # So for the above example this boolean will return True, because :'abc' in 'abcde': returns True.
+        if type(column_value) == str:
             col_inexact_match = any([filter_value in column_value for filter_value in filter_values])
         else:
             col_inexact_match = False
         return col_exact_match or col_inexact_match
-    
+
     def inlist_exact(self, column_value, filter_values):
-        #Check if the passed in column is exactly matched against
-        #For a filter_list of ['abc','def','ghi']; this will be true
-        #for column_value 'abc' but not 'abcde.'
+        # Check if the passed in column is exactly matched against
+        # For a filter_list of ['abc','def','ghi']; this will be true
+        # for column_value 'abc' but not 'abcde.'
         col_exact_match = column_value in filter_values
         return col_exact_match