def test_lexmap_multi():
"""
Text lexical mapping
"""
factory = OntologyFactory()
print("Creating ont")
files = ['x', 'm', 'h', 'bto']
onts = [
factory.create('tests/resources/autopod-{}.json'.format(f))
for f in files
]
lexmap = LexicalMapEngine()
lexmap.index_ontologies(onts)
#print(lexmap.lmap)
#print(ont.all_synonyms())
g = lexmap.get_xref_graph()
for x in g.nodes():
print("{} --> {}".format(x, lexmap.grouped_mappings(x)))
for x, y, d in g.edges_iter(data=True):
cl = nx.ancestors(g, x)
print("{} '{}' <-> {} '{}' :: {} CLOSURE={}".format(
x, lexmap.label(x), y, lexmap.label(y), d, len(cl)))
cpr = d[lexmap.CONDITIONAL_PR]
assert cpr > 0 and cpr <= 1.0
unmapped = lexmap.unmapped_nodes(g)
print('U: {}'.format(len(unmapped)))
unmapped = lexmap.unmapped_nodes(g, rs_threshold=4)
print('U4: {}'.format(len(unmapped)))
cliques = lexmap.cliques(g)
maxc = max(cliques, key=len)
print('CLIQUES: {}'.format(cliques))
print('MAX CLIQUES: {}'.format(maxc))
df = lexmap.as_dataframe(g)
print(df.to_csv(sep="\t"))
def test_align():
"""
Text lexical mapping
"""
factory = OntologyFactory()
print("Creating ont")
ont1 = factory.create('ma')
ont2 = factory.create('zfa')
lexmap = LexicalMapEngine()
lexmap.index_ontology(ont1)
lexmap.index_ontology(ont2)
print(lexmap.lmap)
print(ont1.all_synonyms())
print(ont2.all_synonyms())
g = lexmap.get_xref_graph()
for x, y, d in g.edges_iter(data=True):
print("{}<->{} :: {}".format(x, y, d))
for x in g.nodes():
print("{} --> {}".format(x, lexmap.grouped_mappings(x)))
def test_lexmap_basic():
"""
Text lexical mapping
"""
factory = OntologyFactory()
print("Creating ont")
ont = factory.create('tests/resources/lexmap_test.json')
lexmap = LexicalMapEngine()
lexmap.index_ontology(ont)
print(lexmap.lmap)
print(ont.all_synonyms())
g = lexmap.get_xref_graph()
for x, y, d in g.edges_iter(data=True):
print("{}<->{} :: {}".format(x, y, d))
for x in g.nodes():
print("{} --> {}".format(x, lexmap.grouped_mappings(x)))
assert g.has_edge('Z:2', 'ZZ:2') # roman numerals
assert g.has_edge('Z:2', 'Y:2') # case insensitivity
assert g.has_edge('A:1', 'B:1') # synonyms
assert g.has_edge('B:1', 'A:1') # bidirectional
for x, y, d in g.edges_iter(data=True):
print("{}<->{} :: {}".format(x, y, d))
cpr = d[lexmap.CONDITIONAL_PR]
assert cpr > 0 and cpr <= 1.0
df = lexmap.as_dataframe(g)
print(df.to_csv(sep="\t"))
lexmap = LexicalMapEngine(
config=dict(synsets=[dict(word="", synonym="ignoreme", weight=-2.0)],
normalized_form_confidence=0.25,
abbreviation_confidence=0.5,
meaningful_ids=True,
ontology_configurations=[
dict(prefix='AA', normalized_form_confidence=-1000)
]))
assert len(lexmap._get_config_val('NULL', 'synsets')) == 1
assert lexmap._normalize_label('ignoreme foo', {'ignoreme': ''}) == 'foo'
assert lexmap._normalize_label('replaceme foo',
{'replaceme': 'zz'}) == 'foo zz'
ont.add_node('TEST:1', 'foo bar')
ont.add_node('TEST:2', 'bar foo')
ont.add_node('TEST:3', 'foo bar')
ont.add_node('TEST:4', 'wiz')
syn = Synonym('TEST:4', val='bar foo', pred='hasRelatedSynonym')
ont.add_synonym(syn)
ont.add_node('http://x.org/wiz#FooBar')
ont.add_node('TEST:6', '123')
ont.add_node('TEST:7', '123')
ont.add_node('TEST:8', 'bar ignoreme foo')
ont.add_node('AA:1', 'foo bar')
ont.add_node('AA:2', 'bar foo')
ont.add_node('ABBREV:1', 'ABCD')
ont.add_node('ABBREV:2', 'ABCD')
for s in ont.synonyms('TEST:4'):
print('S={}'.format(s))
lexmap.index_ontology(ont)
g = lexmap.get_xref_graph()
for x, d in g['TEST:1'].items():
print('XREF: {} = {}'.format(x, d))
assert g.has_edge('TEST:1', 'TEST:2') # normalized
logging.info('E 1-2 = {}'.format(g['TEST:1']['TEST:2']))
assert int(g['TEST:1']['TEST:2']['score']) == 25
assert int(g['TEST:1']['TEST:3']['score']) == 100
assert int(g['TEST:1']['TEST:4']['score']) < 25
assert g.has_edge('TEST:3', 'http://x.org/wiz#FooBar') # IDs and CamelCase
assert not g.has_edge('TEST:6',
'TEST:7') # should omit syns with no alphanumeric
# test exclude normalized form
assert not g.has_edge('AA:1', 'AA:2')
# test custom synsets are used
assert g.has_edge('TEST:8', 'TEST:2')
assert g.has_edge('TEST:8', 'AA:2')
assert not g.has_edge('TEST:8', 'AA:1') # do not normalize AAs
assert lexmap.smap['ABBREV:1'][0].is_abbreviation()
assert lexmap.smap['ABBREV:2'][0].is_abbreviation()
assert g.has_edge('ABBREV:1', 'ABBREV:2')
assert int(g['ABBREV:1']['ABBREV:2']['score']) == 25
df = lexmap.unmapped_dataframe(g)
print(df.to_csv())