IMP: AlphaDiversityFormat to Metadata transformer supports multi-colu…

…mn (#193)

q2_types/sample_data/_transformer.py

@@ -7,6 +7,7 @@
 # ----------------------------------------------------------------------------
 
 import pandas as pd
+import numpy as np
 
 import qiime2
 
@@ -20,7 +21,11 @@ def _read_alpha_diversity(fh):
     df = pd.read_csv(fh, sep='\t', header=0, dtype=object)
     df.set_index(df.columns[0], drop=True, append=False, inplace=True)
     df.index.name = None
-    return pd.to_numeric(df.iloc[:, 0], errors='raise')
+    # casting of columns adapted from SO post:
+    # https://stackoverflow.com/a/36814203/3424666
+    cols = df.columns
+    df[cols] = df[cols].apply(pd.to_numeric, errors='ignore')
+    return df
 
 
 @plugin.register_transformer
@@ -34,12 +39,17 @@ def _1(data: pd.Series) -> AlphaDiversityFormat:
 @plugin.register_transformer
 def _2(ff: AlphaDiversityFormat) -> pd.Series:
     with ff.open() as fh:
-        return _read_alpha_diversity(fh)
+        df = _read_alpha_diversity(fh)
+        series = df.iloc[:, 0]
+        if not np.issubdtype(series, np.number):
+            raise ValueError('Non-numeric values detected in alpha diversity '
+                             'estimates.')
+        return series
 
 
 @plugin.register_transformer
 def _3(ff: AlphaDiversityFormat) -> qiime2.Metadata:
     with ff.open() as fh:
-        series = _read_alpha_diversity(fh)
-        series.index.name = 'Sample ID'
-        return qiime2.Metadata(series.to_frame())
+        df = _read_alpha_diversity(fh)
+        df.index.name = 'Sample ID'
+        return qiime2.Metadata(df)

q2_types/sample_data/tests/test_transformer.py

@@ -72,7 +72,7 @@ def test_alpha_diversity_format_to_metadata(self):
 
     def test_non_alpha_diversity(self):
         filename = 'also-not-alpha-diversity.tsv'
-        with self.assertRaisesRegex(ValueError, 'Unable to parse string'):
+        with self.assertRaisesRegex(ValueError, 'Non-numeric values '):
             self.transform_format(AlphaDiversityFormat, pd.Series, filename)