tests

hdmf-dev · Mar 14, 2024 · 901cb56 · 901cb56
1 parent b806404
commit 901cb56
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Showing 2 changed files with 15 additions and 16 deletions.
diff --git a/src/hdmf/term_set.py b/src/hdmf/term_set.py
@@ -5,7 +5,6 @@
 import warnings
 import numpy as np
 from .data_utils import append_data, extend_data
-import yaml
 
 
 class TermSet:
@@ -163,6 +162,7 @@ def __schemasheets_convert(self):
         This method returns a path to the new schema to be viewed via SchemaView.
         """
         try:
+            import yaml
             from linkml_runtime.utils.schema_as_dict import schema_as_dict
             from schemasheets.schemamaker import SchemaMaker
         except ImportError:   # pragma: no cover
@@ -262,13 +262,6 @@ def __getitem__(self, val):
         """
         return self.__value[val]
 
-    # uncomment when DataChunkIterator objects can be wrapped by TermSet
-    # def __next__(self):
-    #     """
-    #     Return the next item of a wrapped iterator.
-    #     """
-    #     return self.__value.__next__()
-    #
     def __len__(self):
         return len(self.__value)
 
@@ -313,6 +306,11 @@ class TermSetConfigurator:
     """
     @docval({'name': 'path', 'type': str, 'doc': 'Path to the configuration file.', 'default': None})
     def __init__(self, **kwargs):
+        try:
+            import yaml
+        except ImportError:
+            msg = "Install yaml"
+            raise ValueError(msg)
         self.config = None
         if kwargs['path'] is None:
             self.path = []

diff --git a/tests/unit/common/test_table.py b/tests/unit/common/test_table.py
@@ -36,9 +36,10 @@
 
 try:
     import linkml_runtime  # noqa: F401
-    LINKML_INSTALLED = True
+    import yaml
+    REQUIREMENTS_INSTALLED = True
 except ImportError:
-    LINKML_INSTALLED = False
+    REQUIREMENTS_INSTALLED = False
 
 
 class TestDynamicTable(TestCase):
@@ -135,7 +136,7 @@ def test_constructor_all_columns_are_iterators(self):
         # now test that when we supply id's that the error goes away
         _ = DynamicTable(name="TestTable", description="", columns=[column], id=list(range(3)))
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_add_col_validate(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
@@ -154,7 +155,7 @@ def test_add_col_validate(self):
         expected_df.index.name = 'id'
         pd.testing.assert_frame_equal(species.to_dataframe(), expected_df)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_add_col_validate_bad_data(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
@@ -169,7 +170,7 @@ def test_add_col_validate_bad_data(self):
                                data=TermSetWrapper(value=['bad data'],
                                                    termset=terms))
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
@@ -191,7 +192,7 @@ def test_add_row_validate(self):
         expected_df.index.name = 'id'
         pd.testing.assert_frame_equal(species.to_dataframe(), expected_df)
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate_bad_data_one_col(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
@@ -208,7 +209,7 @@ def test_add_row_validate_bad_data_one_col(self):
         with self.assertRaises(ValueError):
             species.add_row(Species_1='bad', Species_2='Ursus arctos horribilis')
 
-    @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
+    @unittest.skipIf(not REQUIREMENTS_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate_bad_data_all_col(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
@@ -2786,7 +2787,7 @@ def __init__(self, **kwargs):
 
 class TestTermSetConfig(TestCase):
     def setUp(self):
-        if not LINKML_INSTALLED:
+        if not REQUIREMENTS_INSTALLED:
             self.skipTest("optional LinkML module is not installed")
 
         unload_termset_config()