def test_read_tsv():
"""
Read a TSV using TsvSource.
"""
s = TsvSource()
g = s.parse(filename=os.path.join(RESOURCE_DIR, 'test_nodes.tsv'), format='tsv')
nodes = []
for rec in g:
if rec:
nodes.append(rec)
assert len(nodes) == 3
nodes.sort()
n1 = nodes.pop()[-1]
assert n1['id'] == 'CURIE:456'
assert n1['name'] == 'Disease 456'
assert 'biolink:Disease' in n1['category']
assert n1['description'] == '"Node of type Disease, CURIE:456"'
g = s.parse(filename=os.path.join(RESOURCE_DIR, 'test_edges.tsv'), format='tsv')
edges = []
for rec in g:
if rec:
edges.append(rec)
e1 = edges.pop()[-1]
assert 'id' in e1
assert e1['subject'] == 'CURIE:123'
assert e1['object'] == 'CURIE:456'
assert e1['predicate'] == 'biolink:related_to'
assert e1['relation'] == 'biolink:related_to'
assert 'PMID:1' in e1['publications']
def test_read_tsv_compressed():
"""
Read a compressed TSV archive using TsvSource.
"""
s = TsvSource()
g = s.parse(filename=os.path.join(RESOURCE_DIR, 'test.tar'), format='tsv', compression='tar')
nodes = []
edges = []
for rec in g:
if rec:
if len(rec) == 4:
edges.append(rec)
else:
nodes.append(nodes)
assert len(nodes) == 3
assert len(edges) == 1
g = s.parse(
filename=os.path.join(RESOURCE_DIR, 'test.tar.gz'), format='tsv', compression='tar.gz'
)
nodes = []
edges = []
for rec in g:
if rec:
if len(rec) == 4:
edges.append(rec)
else:
nodes.append(nodes)
assert len(nodes) == 3
assert len(edges) == 1
def test_read_tsv():
"""
Read a TSV using TsvSource.
"""
t = Transformer()
s = TsvSource(t)
g = s.parse(filename=os.path.join(RESOURCE_DIR, "test_nodes.tsv"),
format="tsv")
nodes = []
for rec in g:
if rec:
nodes.append(rec)
assert len(nodes) == 3
nodes.sort()
n1 = nodes.pop()[-1]
assert n1["id"] == "CURIE:456"
assert n1["name"] == "Disease 456"
assert "biolink:Disease" in n1["category"]
assert "biolink:NamedThing" in n1["category"]
assert n1["description"] == '"Node of type Disease, CURIE:456"'
g = s.parse(filename=os.path.join(RESOURCE_DIR, "test_edges.tsv"),
format="tsv")
edges = []
for rec in g:
if rec:
edges.append(rec)
e1 = edges.pop()[-1]
assert "id" in e1
assert e1["subject"] == "CURIE:123"
assert e1["object"] == "CURIE:456"
assert e1["predicate"] == "biolink:related_to"
assert e1["relation"] == "biolink:related_to"
assert "PMID:1" in e1["publications"]
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_read_tsv_tar_compressed():
"""
Read a compressed TSV TAR archive using TsvSource.
"""
t = Transformer()
s = TsvSource(t)
g = s.parse(filename=os.path.join(RESOURCE_DIR, "test.tar"),
format="tsv",
compression="tar")
nodes = []
edges = []
for rec in g:
if rec:
if len(rec) == 4:
edges.append(rec)
else:
nodes.append(nodes)
assert len(nodes) == 3
assert len(edges) == 1
def test_read_tsv_tar_gz_compressed_inverted_file_order():
"""
Read a compressed TSV TAR archive using TsvSource, where source tar archive has edge file first, node second.
"""
t = Transformer()
s = TsvSource(t)
g = s.parse(
filename=os.path.join(RESOURCE_DIR, "test-inverse.tar.gz"),
format="tsv",
compression="tar.gz",
)
nodes = []
edges = []
for rec in g:
if rec:
if len(rec) == 4:
edges.append(rec)
else:
nodes.append(nodes)
assert len(nodes) == 3
assert len(edges) == 1