update test to use qiime2.Metadata

biocore · Feb 22, 2022 · ab9e616 · ab9e616
1 parent 85521c4
commit ab9e616
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Showing 2 changed files with 6 additions and 14 deletions.
diff --git a/q2_katharoseq/tests/support_files/input_estimating_biomass.tsv b/q2_katharoseq/tests/support_files/input_estimating_biomass.tsv
@@ -1,4 +1,5 @@
 sample_name	total_reads	control_cell_into_extraction	extraction_mass_g	positive_control
+#q2:types	numeric	numeric	categorical	categorical
 13414.plate1.h9	4			False
 13414.plate1.b10	6			False
 13414.plate1.e12	6			False

diff --git a/q2_katharoseq/tests/test_method.py b/q2_katharoseq/tests/test_method.py
@@ -166,26 +166,17 @@ def test_threshold(self):
 
     def test_estimating_biomass(self):
         fp = join(dirname(abspath(getfile(currentframe()))), 'support_files')
-        data = pd.read_csv(
-            f'{fp}/input_estimating_biomass.tsv', sep='\t', dtype={
-                'sample_name': str, 'total_reads': float,
-                'control_cell_into_extraction': float,
-                'extraction_mass_g': float,
-                'positive_control': str})
-        data.set_index('sample_name', inplace=True)
+        data = qiime2.Metadata.load(f'{fp}/input_estimating_biomass.tsv')
 
         obs = estimating_biomass(
-            total_reads=qiime2.NumericMetadataColumn(data['total_reads']),
-            control_cell_extraction=qiime2.NumericMetadataColumn(
-                data['control_cell_into_extraction']),
+            total_reads=data.get_column('total_reads'),
+            control_cell_extraction=data.get_column('control_cell_into_extraction'),  # noqa
             min_total_reads=1150,
             positive_control_value='True',
-            positive_control_column=qiime2.CategoricalMetadataColumn(
-                data['positive_control']),
+            positive_control_column=data.get_column('positive_control'),
             pcr_template_vol=5,
             dna_extract_vol=60,
-            extraction_mass_g=qiime2.NumericMetadataColumn(
-                data['extraction_mass_g'])
+            extraction_mass_g=data.get_column('extraction_mass_g')
         )
         exp = pd.read_csv(
             f'{fp}/output_estimating_biomass.tsv', sep='\t', index_col=0)