removed create append df

bokulich-lab · Oct 9, 2024 · f3865cf · f3865cf
1 parent 2aab907
commit f3865cf
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 44 deletions.
diff --git a/q2_amrfinderplus/types/_transformer.py b/q2_amrfinderplus/types/_transformer.py
@@ -37,11 +37,11 @@ def _transfomer_helper(data):
                 else:
                     id_value = file_dir_name + "/" + file_name[:-18]
 
-                create_append_df(
-                    file_path=file,
-                    df_list=df_list,
-                    id_value=id_value,
-                )
+                # Create df and append it to df_list
+                df = pd.read_csv(file, sep="\t")
+                df.insert(0, "Sample/MAG_ID", id_value)
+                df_list.append(df)
+
         else:
             # Annotations file from feature data mags or sample data contigs
             if file_dir_name.endswith("_amr_annotations.tsv"):
@@ -50,26 +50,14 @@ def _transfomer_helper(data):
             else:
                 id_value = file_dir_name[:-22]
 
-            create_append_df(
-                file_path=os.path.join(str(data), file_dir_name),
-                df_list=df_list,
-                id_value=id_value,
-            )
+            # Create df and append it to df_list
+            df = pd.read_csv(os.path.join(str(data), file_dir_name), sep="\t")
+            df.insert(0, "Sample/MAG_ID", id_value)
+            df_list.append(df)
 
     return combine_dataframes(df_list)
 
 
-def create_append_df(file_path, df_list, id_value):
-    # Read in df
-    df = pd.read_csv(file_path, sep="\t")
-
-    # Insert column with sample or mag IDs
-    df.insert(0, "Sample/MAG_ID", id_value)
-
-    # Append df to df list
-    df_list.append(df)
-
-
 def combine_dataframes(df_list):
     # Concat all dfs
     df_combined = pd.concat(df_list, axis=0)

diff --git a/q2_amrfinderplus/types/tests/test_types_formats_transformers.py b/q2_amrfinderplus/types/tests/test_types_formats_transformers.py
@@ -7,7 +7,6 @@
 # ----------------------------------------------------------------------------
 import os
 import tempfile
-from io import StringIO
 
 import pandas as pd
 import qiime2
@@ -20,11 +19,7 @@
     AMRFinderPlusAnnotationsDirFmt,
     AMRFinderPlusDatabaseDirFmt,
 )
-from q2_amrfinderplus.types._transformer import (
-    _transfomer_helper,
-    combine_dataframes,
-    create_append_df,
-)
+from q2_amrfinderplus.types._transformer import _transfomer_helper, combine_dataframes
 
 
 class TestAMRFinderPlusTypesAndFormats(TestPluginBase):
@@ -125,20 +120,12 @@ def test_amrfinderplus_annotations_dir_fmt_path_maker(self):
         self.assertEqual(str(path), os.path.join(str(fmt), "id_amr_annotations.tsv"))
 
 
-class MetadataUtilsTest(TestPluginBase):
+class MetadataTransformerUtilsTest(TestPluginBase):
     package = "q2_amrfinderplus.types.tests"
 
     def setUp(self):
         super().setUp()
         # Setup test data
-        self.file_data_1 = "col1\tcol2\nval1\tval2\nval3\tval4"
-        self.file_data_2 = "col1\tcol2\nval5\tval6\nval7\tval8"
-
-        self.df1 = pd.read_csv(StringIO(self.file_data_1), sep="\t")
-        self.df2 = pd.read_csv(StringIO(self.file_data_2), sep="\t")
-
-        self.df_list = []
-
         self.df1 = pd.DataFrame(
             {
                 "Sample/MAG_ID": ["id_value_1", "id_value_1"],
@@ -171,14 +158,6 @@ def setUp(self):
         self.expected_combined_df.index = self.expected_combined_df.index.astype(str)
         self.expected_combined_df.index.name = "id"
 
-    def test_create_append_df(self):
-        # Test create_append_df function
-        create_append_df(StringIO(self.file_data_1), self.df_list, "id_value_1")
-        create_append_df(StringIO(self.file_data_2), self.df_list, "id_value_2")
-
-        pd.testing.assert_frame_equal(self.df_list[0], self.df1)
-        pd.testing.assert_frame_equal(self.df_list[1], self.df2)
-
     def test_combine_dataframes(self):
         # Test combine_dataframes function
         df_list = [self.df1, self.df2]