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# -*- coding: utf-8 -*-
"""Tests for data structures in PyBEL."""
import os
import random
import tempfile
import unittest
from io import StringIO
import pybel
import pybel.examples
from pybel import BELGraph
from pybel.constants import CITATION_TYPE_PUBMED, IDENTIFIER, NAMESPACE
from pybel.dsl import hgvs, protein
from pybel.io.api import InvalidExtensionError
from pybel.language import Entity
from pybel.testing.utils import n
class TestGraphProperties(unittest.TestCase):
"""Test setting and access to graph properties."""
def setUp(self):
"""Make fake metadata for the graphs."""
(
self.name,
self.version,
self.description,
self.authors,
self.contact,
self.licenses,
self.copyrights,
self.disclaimer,
) = [n() for _ in range(8)]
def _help_test_metadata(self, graph: BELGraph) -> None:
"""Help test the right metadata got in the graph."""
self.assertEqual(self.name, graph.name)
self.assertEqual(self.version, graph.version)
self.assertEqual(self.description, graph.description)
self.assertEqual(self.authors, graph.authors)
self.assertEqual(self.contact, graph.contact)
self.assertEqual(self.licenses, graph.license)
self.assertEqual(self.copyrights, graph.copyright)
self.assertEqual(self.disclaimer, graph.disclaimer)
self.assertEqual("{name} v{version}".format(name=self.name, version=self.version), str(graph))
def test_str_kwargs(self):
"""Test setting of metadata through keyword arguments."""
graph = BELGraph(
name=self.name,
version=self.version,
description=self.description,
authors=self.authors,
contact=self.contact,
license=self.licenses,
copyright=self.copyrights,
disclaimer=self.disclaimer,
)
self._help_test_metadata(graph)
def test_name(self):
"""Test setting of metadata through attributes."""
graph = BELGraph()
graph.name = self.name
graph.version = self.version
graph.description = self.description
graph.authors = self.authors
graph.contact = self.contact
graph.license = self.licenses
graph.copyright = self.copyrights
graph.disclaimer = self.disclaimer
self._help_test_metadata(graph)
class TestStruct(unittest.TestCase):
"""Test the BEL graph data structure."""
def test_add_simple(self):
"""Test that a simple node can be added, but not duplicated."""
graph = BELGraph()
node = protein(namespace="TEST", name="YFG")
graph.add_node_from_data(node)
self.assertEqual(1, graph.number_of_nodes())
graph.add_node_from_data(node)
self.assertEqual(1, graph.number_of_nodes(), msg="should not add same node again")
def test_summarize(self):
"""Test summarizing a graph."""
self.maxDiff = None
sio = StringIO()
random.seed(5)
pybel.examples.sialic_acid_graph.version = "1.0.0"
pybel.examples.sialic_acid_graph.summarize(file=sio, examples=False)
test_str = """--------------------- -------------------
Name Sialic Acid Graph
Version 1.0.0
Authors Charles Tapley Hoyt
Number of Nodes 9
Number of Namespaces 3
Number of Edges 11
Number of Annotations 2
Number of Citations 1
Number of Authors 0
Number of Components 1
Number of Warnings 0
Network Density 1.53E-01
--------------------- -------------------
Type (3) Count
---------- -------
Protein 7
Complex 1
Abundance 1
Namespace (3) Count
--------------- -------
go 15
hgnc 8
chebi 2
Edge Type (7) Count
--------------------------------- -------
Protein increases Protein 3
Protein directlyIncreases Protein 2
Protein directlyDecreases Protein 2
Complex increases Protein 1
Abundance partOf Complex 1
Protein partOf Complex 1
Protein hasVariant Protein 1"""
self.assertEqual(test_str.strip(), sio.getvalue().strip())
def test_citation_type_error(self):
"""Test error handling on adding qualified edges."""
graph = BELGraph()
with self.assertRaises(TypeError):
graph.add_increases(
protein(namespace="TEST", name="YFG1"),
protein(namespace="TEST", name="YFG2"),
evidence=n(),
citation=5,
)
class TestGetGraphProperties(unittest.TestCase):
"""The tests in this class check the getting and setting of node properties."""
def setUp(self):
"""Set up the test case with a fresh BEL graph."""
self.graph = BELGraph()
self.graph.annotation_pattern["Species"] = r"\d+"
self.graph.annotation_list["Confidence"] = {
"Very Low",
"Low",
"Medium",
"High",
"Very High",
}
def test_get_qualified_edge(self):
"""Test adding an edge to a graph."""
test_source = protein(namespace="TEST", name="YFG")
test_target = protein(namespace="TEST", name="YFG2")
self.graph.add_node_from_data(test_source)
self.graph.add_node_from_data(test_target)
test_evidence = n()
test_pmid = n()
test_key = self.graph.add_increases(
test_source,
test_target,
citation=test_pmid,
evidence=test_evidence,
annotations={"Species": "9606", "Confidence": "Very High"},
)
citation = self.graph.get_edge_citation(test_source, test_target, test_key)
self.assertIsNotNone(citation)
self.assertIsInstance(citation, dict)
self.assertIn(NAMESPACE, citation)
self.assertEqual(CITATION_TYPE_PUBMED, citation[NAMESPACE])
self.assertIn(IDENTIFIER, citation)
self.assertEqual(test_pmid, citation[IDENTIFIER])
evidence = self.graph.get_edge_evidence(test_source, test_target, test_key)
self.assertIsNotNone(evidence)
self.assertIsInstance(evidence, str)
self.assertEqual(test_evidence, evidence)
annotations = self.graph.get_edge_annotations(test_source, test_target, test_key)
self.assertIsNotNone(annotations)
self.assertIsInstance(annotations, dict)
self.assertIn("Species", annotations)
self.assertIn(Entity(namespace="Species", identifier="9606"), annotations["Species"])
self.assertIn("Confidence", annotations)
self.assertIn(
Entity(namespace="Confidence", identifier="Very High"),
annotations["Confidence"],
)
def test_get_unqualified_edge(self):
"""Test adding an unqualified edge."""
test_source = protein(namespace="TEST", name="YFG")
test_target = protein(namespace="TEST", name="YFG2")
key = self.graph.add_part_of(test_source, test_target)
citation = self.graph.get_edge_citation(test_source, test_target, key)
self.assertIsNone(citation)
evidence = self.graph.get_edge_evidence(test_source, test_target, key)
self.assertIsNone(evidence)
annotations = self.graph.get_edge_annotations(test_source, test_target, key)
self.assertIsNone(annotations)
def test_add_node_with_variant(self):
"""Test that the identifier is carried through to the child."""
graph = BELGraph()
namespace, name, identifier, variant_name = n(), n(), n(), n()
node = protein(
namespace=namespace,
name=name,
identifier=identifier,
variants=hgvs(variant_name),
)
node.get_parent()
graph.add_node_from_data(node)
self.assertEqual(2, graph.number_of_nodes())
class TestExtensionIO(unittest.TestCase):
def test_io(self):
with tempfile.TemporaryDirectory() as directory:
path = os.path.join(directory, "ampk.bel.nodelink.json")
pybel.dump(pybel.examples.ampk_graph, path)
self.assertTrue(os.path.exists(path))
new_graph = pybel.load(path)
self.assertIsNotNone(new_graph)
def test_invalid_io(self):
with tempfile.TemporaryDirectory() as directory:
path = os.path.join(directory, "ampk.bel.invalid.json")
with self.assertRaises(InvalidExtensionError):
pybel.dump(pybel.examples.ampk_graph, path)
self.assertFalse(os.path.exists(path))
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