simplifies type handling, removes invalid filepath testing

q2_diversity_lib/_util.py

@@ -7,7 +7,6 @@
 # ----------------------------------------------------------------------------
 
 from inspect import signature
-import os
 
 import numpy as np
 from decorator import decorator
@@ -40,13 +39,8 @@ def _disallow_empty_tables(some_function, *args, **kwargs):
     if table is None:
         raise TypeError("The wrapped function has no parameter 'table'")
 
-# TODO: It is not possible for a string passed to the framework to make it here
-# TODO: if table is an instance of BIOM, is it possible for it to have an
-# invalid filepath?
     if isinstance(table, BIOMV210Format):
         table = str(table)
-        # if not os.path.exists(table):
-        #     raise ValueError(f'Invalid file path: {table} does not exist')
         table_obj = load_table(table)
     elif isinstance(table, bTable):
         table_obj = table

q2_diversity_lib/beta.py

@@ -58,17 +58,7 @@ def unweighted_unifrac(table: BIOMV210Format,
                        bypass_tips: bool = False) -> skbio.DistanceMatrix:
     f = unifrac.unweighted
 
-    # TODO: is there ever a scenario in which an str will actually reach
-    # this function? If not, torch this logic, and remove str handling from
-    # _disallow_empty_tables
-    if type(table) == str:
-        table_fp = table
-    elif type(table) == BIOMV210Format:
-        table_fp = table.open().filename
-    else:
-        raise TypeError("Invalid table: must be BIOMV210Format or str.")
-
-    return f(table_fp, str(phylogeny), threads=n_jobs,
+    return f(str(table), str(phylogeny), threads=n_jobs,
              variance_adjusted=False, bypass_tips=bypass_tips)
 
 
@@ -80,15 +70,5 @@ def weighted_unifrac(table: BIOMV210Format,
                      bypass_tips: bool = False) -> skbio.DistanceMatrix:
     f = unifrac.weighted_unnormalized
 
-    # TODO: is there ever a scenario in which an str will actually reach
-    # this function? If not, torch this logic, and remove str handling from
-    # _disallow_empty_tables, and revert return from table_fp to table.open...
-    if type(table) == str:
-        table_fp = table
-    elif type(table) == BIOMV210Format:
-        table_fp = table.open().filename
-    else:
-        raise TypeError("Invalid table: must be BIOMV210Format or str.")
-
-    return f(table_fp, str(phylogeny), threads=n_jobs,
+    return f(str(table), str(phylogeny), threads=n_jobs,
              variance_adjusted=False, bypass_tips=bypass_tips)

q2_diversity_lib/tests/test_util.py

@@ -33,8 +33,6 @@ def setUp(self):
         self.valid_table_fp = self.get_data_path('crawford.biom')
         self.valid_table_as_BIOMV210Format = \
             BIOMV210Format(self.valid_table_fp, mode='r')
-        # TODO: remove?
-        # self.invalid_table_fp = 'invalid_path_name.baaad'
         self.not_a_table_fp = self.get_data_path('crawford.nwk')
         self.invalid_view_type = NewickFormat(self.not_a_table_fp, mode='r')
 
@@ -66,12 +64,6 @@ def test_wrapped_function_has_no_table_param(self):
         with self.assertRaisesRegex(TypeError, "no parameter.*table"):
             self.function_without_table_param()
 
-# TODO: remove?
-    # def test_passed_invalid_file_path(self):
-    #     with self.assertRaisesRegex(
-    #                 ValueError, "file path.*invalid_path_name.baaad"):
-    #         self.function_with_table_param(table=self.invalid_table_fp)
-
     def test_passed_invalid_view_type(self):
         with self.assertRaisesRegex(
                     ValueError, "Invalid view type.*Newick"):