def test_get_category(query):
"""
Test to guess the appropriate category for a sample OBO Graph JSON.
"""
node = query[0]
s = ObographSource()
c = s.get_category(node['id'], node)
assert c == query[1]
def test_get_category(query):
"""
Test to guess the appropriate category for a sample OBO Graph JSON.
"""
node = query[0]
t = Transformer()
s = ObographSource(t)
c = s.get_category(node["id"], node)
assert c == query[1]
def test_read_jsonl2():
"""
Read from an Obograph JSON using ObographSource.
This test also supplies the knowledge_source parameter.
"""
t = Transformer()
s = ObographSource(t)
g = s.parse(
os.path.join(RESOURCE_DIR, "goslim_generic.json"),
provided_by="GO slim generic",
knowledge_source="GO slim generic",
)
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(nodes) == 176
assert len(edges) == 206
n1 = nodes["GO:0003677"]
assert n1["id"] == "GO:0003677"
assert n1["name"] == "DNA binding"
assert (
n1["description"] ==
"Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)."
)
assert n1["category"] == ["biolink:MolecularActivity"]
assert "structure-specific DNA binding" in n1["synonym"]
assert "structure specific DNA binding" in n1["synonym"]
assert "microtubule/chromatin interaction" in n1["synonym"]
assert "plasmid binding" in n1["synonym"]
assert "GO slim generic" in n1["provided_by"]
n2 = nodes["GO:0005575"]
assert n2["id"] == "GO:0005575"
assert n2["name"] == "cellular_component"
assert (
n2["description"] ==
"A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)."
)
assert n2["category"] == ["biolink:CellularComponent"]
assert n2["xref"] == ["NIF_Subcellular:sao1337158144"]
assert "goslim_chembl" in n2["subsets"]
assert "goslim_generic" in n2["subsets"]
assert "GO slim generic" in n2["provided_by"]
def test_read_jsonl2():
"""
Read from an Obograph JSON using ObographSource.
This test also supplies the provided_by parameter.
"""
s = ObographSource()
g = s.parse(os.path.join(RESOURCE_DIR, 'goslim_generic.json'),
provided_by='GO slim generic')
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(nodes) == 176
assert len(edges) == 206
n1 = nodes['GO:0003677']
assert n1['id'] == 'GO:0003677'
assert n1['name'] == 'DNA binding'
assert (
n1['description'] ==
'Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).'
)
assert n1['category'] == ['biolink:MolecularActivity']
assert 'structure-specific DNA binding' in n1['synonym']
assert 'structure specific DNA binding' in n1['synonym']
assert 'microtubule/chromatin interaction' in n1['synonym']
assert 'plasmid binding' in n1['synonym']
assert 'GO slim generic' in n1['provided_by']
n2 = nodes['GO:0005575']
assert n2['id'] == 'GO:0005575'
assert n2['name'] == 'cellular_component'
assert (
n2['description'] ==
'A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).'
)
assert n2['category'] == ['biolink:CellularComponent']
assert n2['xref'] == ['NIF_Subcellular:sao1337158144']
assert 'goslim_chembl' in n2['subsets']
assert 'goslim_generic' in n2['subsets']
assert 'GO slim generic' in n2['provided_by']
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")