def test_validate_incorrect_edge(edge):
"""
Test basic validation of an edge, where the edge is invalid.
"""
t = Transformer()
s = Source(t)
assert not s.validate_edge(edge)
assert len(t.get_errors()) > 0
t.write_report()
def test_validate_correct_edge(edge):
"""
Test basic validation of an edge, where the edge is valid.
"""
t = Transformer()
s = Source(t)
e = s.validate_edge(edge)
assert e is not None
assert len(t.get_errors()) == 0
t.write_report()
def test_incorrect_edge_filters(edge):
"""
Test filtering of an edge
"""
t = Transformer()
s = Source(t)
filters = {"some_field": {"bad_edge_filter": 1}}
s.set_edge_filters(filters)
s.check_edge_filter(edge)
assert len(t.get_errors("Error")) > 0
t.write_report()
def test_validate_incorrect_node(node):
"""
Test basic validation of a node, where the node is invalid.
"""
t = Transformer()
s = Source(t)
result = s.validate_node(node)
if len(t.get_errors("Error")) > 0:
assert result is None
else:
assert result is not None
t.write_report()
def test_incorrect_nodes():
"""
Test basic validation of a node, where the node is invalid.
"""
t = Transformer()
s = TsvSource(t)
g = s.parse(filename=os.path.join(RESOURCE_DIR, "incomplete_nodes.tsv"),
format="tsv")
nodes = []
for rec in g:
if rec:
nodes.append(rec)
t.write_report()
def test_validate_correct_node(node):
"""
Test basic validation of a node, where the node is valid.
"""
t = Transformer()
s = Source(t)
n = s.validate_node(node)
assert n is not None
assert "category" in n
assert n["category"][0] == DEFAULT_NODE_CATEGORY
if len(t.get_errors()) > 0:
assert len(t.get_errors("Error")) == 0
assert len(t.get_errors("Warning")) > 0
t.write_report(None, "Warning")
def test_error_detection():
t = Transformer()
s = ObographSource(t)
g = s.parse(
os.path.join(RESOURCE_DIR, "obo_error_detection.json"),
knowledge_source="Sample OBO",
)
nodes = {}
edges = {}
for rec in g:
if rec:
if len(rec) == 4:
edges[(rec[0], rec[1], rec[2])] = rec[3]
else:
nodes[rec[0]] = rec[1]
assert len(t.get_errors()) > 0
if len(t.get_errors("Error")) > 0:
t.write_report(None, "Error")
if len(t.get_errors("Warning")) > 0:
t.write_report(None, "Warning")
