class MetadataTableTests(TestCase):
def setUp(self):
"""Initialize data used in the tests."""
self.md_table = MetadataTable(METADATA_1.split('\n'))
self.vocabs_1 = VocabularySet({
'vocab_1': VOCAB_1.split('\n'),
'vocab_2': VOCAB_2.split('\n')
})
self.vocabs_2 = VocabularySet({
'vocab_1': VOCAB_1.split('\n'),
'vocab_3': VOCAB_2.split('\n')
})
def test_candidate_controlled_fields(self):
"""Test finding fields that look like they use controlled vocabs."""
obs = self.md_table.candidate_controlled_fields()
self.assertEqual(obs, {'Baz': {'vocab_1', 'vocab_3'}})
obs = self.md_table.candidate_controlled_fields(self.vocabs_1)
self.assertEqual(obs, {'Baz': {'vocab_1'}})
def test_validate_controlled_fields(self):
"""Test validating fields that look like they use controlled vocabs."""
obs = self.md_table.validate_controlled_fields(self.vocabs_1)
self.assertEqual(obs, {'Baz': {'na', 'vocab_3:baz', 'vocab_1:foobar'}})
with self.assertRaises(MultipleVocabulariesError):
_ = self.md_table.validate_controlled_fields(self.vocabs_2)
def test_find_discrepancies(self):
"""Test finding discrepancies in fields."""
exp = {
'Foo': {
'hanging whitespace': [{'NO ', ' NO'}],
'capitalization': [{'Yes', 'yes'}],
'whitespace': [{'NO ', ' NO'}]
},
'Bar': {
'whitespace': [{'foo bar', 'foobar', ' foo bar '}]
}
}
obs = self.md_table.find_discrepancies()
self.assertEqual(obs, exp)
def test_field_values(self):
"""Test collecting all values in each field."""
exp = {
'#ID': {'A', 'B', 'C', 'D', 'E'},
'Foo': {'Yes', 'yes', 'NO ', ' NO'},
'Bar': {'foobar', 'foo bar', 'baz', ' foo bar '},
'Baz': {'vocab_1:foobar', 'vocab_1:BAr', 'vocab_3:baz', 'na'}
}
obs = self.md_table.field_values()
self.assertEqual(obs, exp)
def test_extract_vocab_id(self):
"""Test extracting vocabulary ID from a cell value."""
obs = self.md_table._extract_vocab_id('ENVO:foo')
self.assertEqual(obs, ('ENVO', 'foo'))
obs = self.md_table._extract_vocab_id('foo')
self.assertEqual(obs, (None, 'foo'))
class MetadataTableTests(TestCase):
def setUp(self):
"""Initialize data used in the tests."""
self.md_table = MetadataTable(METADATA_1.split('\n'))
self.vocabs_1 = VocabularySet({
'vocab_1': VOCAB_1.split('\n'),
'vocab_2': VOCAB_2.split('\n')
})
self.vocabs_2 = VocabularySet({
'vocab_1': VOCAB_1.split('\n'),
'vocab_3': VOCAB_2.split('\n')
})
def test_candidate_controlled_fields(self):
"""Test finding fields that look like they use controlled vocabs."""
obs = self.md_table.candidate_controlled_fields()
self.assertEqual(obs, {'Baz': {'vocab_1', 'vocab_3'}})
obs = self.md_table.candidate_controlled_fields(self.vocabs_1)
self.assertEqual(obs, {'Baz': {'vocab_1'}})
def test_validate_controlled_fields(self):
"""Test validating fields that look like they use controlled vocabs."""
obs = self.md_table.validate_controlled_fields(self.vocabs_1)
self.assertEqual(obs, {'Baz': {'na', 'vocab_3:baz', 'vocab_1:foobar'}})
with self.assertRaises(MultipleVocabulariesError):
_ = self.md_table.validate_controlled_fields(self.vocabs_2)
def test_find_discrepancies(self):
"""Test finding discrepancies in fields."""
exp = {
'Foo': {
'hanging whitespace': [{'NO ', ' NO'}],
'capitalization': [{'Yes', 'yes'}],
'whitespace': [{'NO ', ' NO'}]
},
'Bar': {
'whitespace': [{'foo bar', 'foobar', ' foo bar '}]
}
}
obs = self.md_table.find_discrepancies()
self.assertEqual(obs, exp)
def test_field_values(self):
"""Test collecting all values in each field."""
exp = {
'#ID': {'A', 'B', 'C', 'D', 'E'},
'Foo': {'Yes', 'yes', 'NO ', ' NO'},
'Bar': {'foobar', 'foo bar', 'baz', ' foo bar '},
'Baz': {'vocab_1:foobar', 'vocab_1:BAr', 'vocab_3:baz', 'na'}
}
obs = self.md_table.field_values()
self.assertEqual(obs, exp)
def test_extract_vocab_id(self):
"""Test extracting vocabulary ID from a cell value."""
obs = self.md_table._extract_vocab_id('ENVO:foo')
self.assertEqual(obs, ('ENVO', 'foo'))
obs = self.md_table._extract_vocab_id('foo')
self.assertEqual(obs, (None, 'foo'))
