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# -*- coding: utf-8 -*-
import re
import unittest
from pybel.constants import DIRTY
from pybel.exceptions import MissingNamespaceRegexWarning, NakedNameWarning
from pybel.parser import ConceptParser
class _ParserMixin(unittest.TestCase):
def setUp(self):
self.namespace_to_term = {
"A": {
(None, "1"): "P",
(None, "2"): "P",
(None, "3"): "P",
},
"B": {
(None, "4"): "P",
(None, "5"): "P",
(None, "6"): "P",
},
}
class TestConceptEnumerated(_ParserMixin):
def setUp(self):
super().setUp()
self.parser = ConceptParser(namespace_to_term_to_encoding=self.namespace_to_term)
def test_valid_1(self):
s = "A:3"
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertEqual("A", result["namespace"])
self.assertEqual("3", result["name"])
def test_valid_2(self):
s = 'A:"3"'
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertEqual("A", result["namespace"])
self.assertEqual("3", result["name"])
def test_invalid_1(self):
s = "C:4"
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_2(self):
s = "A:4"
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_3(self):
s = "bare"
with self.assertRaises(NakedNameWarning):
self.parser.parseString(s)
def test_invalid_4(self):
s = '"quoted"'
with self.assertRaises(NakedNameWarning):
self.parser.parseString(s)
class TestConceptParserDefault(_ParserMixin):
"""Tests where the concept parser allows an enumerated list of unqualified entities."""
def setUp(self):
super().setUp()
default_namespace = {"X", "Y", "W Z"}
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
default_namespace=default_namespace,
)
def test_valid_1(self):
s = "A:3"
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual("A", result["namespace"])
self.assertEqual("3", result["name"])
def test_valid_2(self):
s = "X"
result = self.parser.parseString(s)
self.assertIn("name", result)
self.assertEqual("X", result["name"])
def test_valid_3(self):
s = '"W Z"'
result = self.parser.parseString(s)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual("W Z", result["name"])
def test_not_in_defaultNs(self):
s = "D"
with self.assertRaises(Exception):
self.parser.parseString(s)
class TestConceptParserLenient(_ParserMixin):
"""Tests where naked names are allowed."""
def setUp(self):
super().setUp()
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
allow_naked_names=True,
)
def test_valid_1(self):
s = "A:3"
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual("A", result["namespace"])
self.assertEqual("3", result["name"])
def test_valid_2(self):
s = 'A:"3"'
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual("A", result["namespace"])
self.assertEqual("3", result["name"])
def test_invalid_1(self):
s = "C:4"
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_2(self):
s = "A:4"
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_not_invalid_3(self):
s = "bare"
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual(DIRTY, result["namespace"])
self.assertEqual("bare", result["name"])
def test_not_invalid_4(self):
s = '"quoted"'
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual(DIRTY, result["namespace"])
self.assertEqual("quoted", result["name"])
class TestConceptParserRegex(unittest.TestCase):
"""Tests for regular expression parsing"""
def setUp(self) -> None:
self.parser = ConceptParser(
namespace_to_pattern={
"hgnc": re.compile(r"\d+"),
"ec-code": re.compile(r".+"),
}
)
self.assertEqual({}, self.parser.namespace_to_identifier_to_encoding)
self.assertEqual({}, self.parser.namespace_to_name_to_encoding)
def test_valid(self):
for curie, namespace, name in [
("hgnc:391", "hgnc", "391"),
("ec-code:1.1.1.27", "ec-code", "1.1.1.27"),
]:
with self.subTest(curie=curie):
result = self.parser.parseString(curie)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertNotIn("identifier", result)
self.assertEqual(namespace, result["namespace"])
self.assertEqual(name, result["name"])
def test_invalid(self):
"""Test invalid BEL term."""
s = "hgnc:AKT1"
with self.assertRaises(MissingNamespaceRegexWarning):
result = self.parser.parseString(s)
print(result.asDict())
def test_valid_obo(self):
"""Test parsing an identifier that has a name."""
s = "hgnc:391 ! AKT1"
result = self.parser.parseString(s)
self.assertIn("namespace", result)
self.assertIn("name", result)
self.assertIn("identifier", result)
self.assertEqual("hgnc", result["namespace"])
self.assertEqual("AKT1", result["name"])
self.assertEqual("391", result["identifier"])
def test_invalid_obo(self):
"""Test parsing an OBO-style identifier where the identifier and name are switched."""
s = "hgnc:AKT1 ! 391"
with self.assertRaises(MissingNamespaceRegexWarning):
result = self.parser.parseString(s)
print(result.asDict())
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