lint and comments

rescript/bv_brc.py

@@ -10,7 +10,8 @@
 import qiime2
 import pandas as pd
 import requests
-from q2_types.feature_data import MixedCaseDNAFASTAFormat, ProteinFASTAFormat, TSVTaxonomyDirectoryFormat
+from q2_types.feature_data import (MixedCaseDNAFASTAFormat, ProteinFASTAFormat,
+                                   TSVTaxonomyDirectoryFormat)
 from q2_types.genome_data import GenomeSequencesDirectoryFormat
 
 from rescript.ncbi import _allowed_ranks, _default_ranks
@@ -46,17 +47,19 @@ def fetch_genomes_bv_brc(
 
 def fetch_metadata_bv_brc(data_type: str, rql_query: str) -> qiime2.Metadata:
 
-    # Get requests response
+    # Download data
     response = download_data(
         url=f"https://www.bv-brc.org/api/{data_type}/?{rql_query}&http_accept=text/tsv",
         data_type=data_type
     )
 
+    # Convert data to data frame
     tsv_data = StringIO(response.text)
     metadata = pd.read_csv(tsv_data, sep='\t')
     metadata.index.name = "id"
     metadata.index = metadata.index.astype(str)
 
+    # Return as qiime2 metadata
     return qiime2.Metadata(metadata)
 
 
@@ -249,11 +252,13 @@ def error_handling(response, data_type):
                 f"Allowed fields for data type {data_type}: \n{data_fields[data_type]}"
             )
 
+        # Handling any other errors that start with "A Database Error Occured:"
         else:
             raise ValueError(
                 f"Error code {response_dict['code']}: {response_dict['msg']}."
             )
 
+    # Handling any other error codes
     else:
         raise ValueError(response.text)
 
@@ -269,7 +274,7 @@ def id_list_handling(rql_query: str, ids: list, parameter_name: str, data_field:
         raise ValueError("At least one of the parameters rql_query and "
                          f"{parameter_name} has to be given.")
 
-    # construct the RQL queries
+    # Construct the RQL queries
     elif ids:
         rql_query = f"in({data_field},({','.join(map(str, ids))}))"
 

rescript/tests/test_bv_brc.py

@@ -6,7 +6,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 import unittest
-from typing import Any
 from unittest.mock import Mock, patch, mock_open, MagicMock
 
 import pandas as pd
@@ -324,7 +323,8 @@ class TestFetchMetadataBVBR(TestPluginBase):
     @patch('rescript.bv_brc.qiime2.Metadata')
     @patch('rescript.bv_brc.pd.read_csv')
     @patch('rescript.bv_brc.download_data')
-    def test_fetch_metadata_bv_brc(self, mock_download_data, mock_read_csv, mock_metadata):
+    def test_fetch_metadata_bv_brc(self, mock_download_data,
+                                   mock_read_csv, mock_metadata):
         # Mock the download_data response
         mock_response = MagicMock()
         mock_response.text = "id\tcolumn1\tcolumn2\n1\tdata1\tdata2\n2\tdata3\tdata4"
@@ -349,15 +349,17 @@ def test_fetch_metadata_bv_brc(self, mock_download_data, mock_read_csv, mock_met
 
         # Assertions
         mock_download_data.assert_called_once_with(
-            url="https://www.bv-brc.org/api/genome/?genome_id=in(1,2)&http_accept=text/tsv",
+            url="https://www.bv-brc.org/api/genome/"
+                "?genome_id=in(1,2)&http_accept=text/tsv",
             data_type="genome"
         )
 
         mock_read_csv.assert_called_once()
         args, kwargs = mock_read_csv.call_args
         self.assertEqual(kwargs['sep'], '\t')
 
-        self.assertEqual(args[0].getvalue(), "id\tcolumn1\tcolumn2\n1\tdata1\tdata2\n2\tdata3\tdata4")
+        self.assertEqual(args[0].getvalue(),
+                         "id\tcolumn1\tcolumn2\n1\tdata1\tdata2\n2\tdata3\tdata4")
 
         mock_metadata.assert_called_once_with(mock_df)
         self.assertEqual(result, mock_metadata_instance)
@@ -372,7 +374,8 @@ class TestFetchTaxonomyBVBR(TestPluginBase):
     @patch('rescript.bv_brc.pd.read_csv')
     @patch('rescript.bv_brc.id_list_handling')
     def test_fetch_taxonomy_bv_brc(
-        self, mock_id_list_handling, mock_read_csv, mock_download_data, mock_transform_taxonomy_df, mock_to_csv
+        self, mock_id_list_handling, mock_read_csv, mock_download_data,
+            mock_transform_taxonomy_df, mock_to_csv
     ):
         # Mock the id_list_handling function
         mock_id_list_handling.return_value = "taxon_id=in(taxon1,taxon2)"
@@ -382,7 +385,6 @@ def test_fetch_taxonomy_bv_brc(
         mock_response.text = "id\trank1\trank2\n1\tdata1\tdata2\n2\tdata3\tdata4"
         mock_download_data.return_value = mock_response
 
-
         # Prepare mocks for file output
         with patch('builtins.open', unittest.mock.mock_open()) as mock_file:
             directory = fetch_taxonomy_bv_brc(
@@ -400,7 +402,8 @@ def test_fetch_taxonomy_bv_brc(
             )
 
             mock_download_data.assert_called_once_with(
-                url="https://www.bv-brc.org/api/taxonomy/?taxon_id=in(taxon1,taxon2)&http_accept=text/tsv",
+                url="https://www.bv-brc.org/api/taxonomy/?taxon_id=in(taxon1,taxon2)"
+                    "&http_accept=text/tsv",
                 data_type="taxonomy"
             )