Revise text on reference taxonomy; test for the phylogeny reference (#11

) * Revise text on reference taxonomy * Test for the phylogeny file
biocore · Feb 15, 2023 · 139e365 · 139e365
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diff --git a/q2_gg2/_methods.py b/q2_gg2/_methods.py
@@ -548,6 +548,13 @@ def _load_tree_and_cache(data, features):
         if node.parent.is_root():
             node.ancestor_cache = []
         else:
+            if node.parent.name is None:
+                raise ValueError("The provided reference seems malformed. "
+                                 "This error would happen if the "
+                                 "<version>.phylogeny.*.nwk.qza file was "
+                                 "provided. Please try rerunning using the "
+                                 "<version>.taxonomy.*.nwk.qza file as the "
+                                 "reference")
             parent_cache = node.parent.ancestor_cache
             node.ancestor_cache = [node.parent.name] + parent_cache
     return tree

diff --git a/q2_gg2/plugin_setup.py b/q2_gg2/plugin_setup.py
@@ -214,7 +214,9 @@
     parameters={},
     outputs=[('classification', FeatureData[Taxonomy])],
     input_descriptions={
-        'reference_taxonomy': 'The reference taxonomy to derive from',
+        'reference_taxonomy': ('The reference taxonomy to derive from. Note '
+                               'that this input corresponds to the .nwk '
+                               'reference artifact'),
         'table': 'The feature table to classify'
     },
     parameter_descriptions={},