def test_get_agent_hgnc():
mek = protein(name='MAP2K1', namespace='HGNC')
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert agent.name == 'MAP2K1'
assert agent.db_refs.get('HGNC') == mek_hgnc_id
assert agent.db_refs.get('UP') == mek_up_id
# Now create an agent with an identifier
mek = protein(name='Foo', namespace='HGNC', identifier='6840')
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert agent.name == 'MAP2K1'
assert agent.db_refs.get('HGNC') == mek_hgnc_id
assert agent.db_refs.get('UP') == mek_up_id
def test_get_agent_up():
mek = protein(namespace='UP', identifier='Q02750')
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert agent.name == 'MAP2K1'
assert agent.db_refs.get('HGNC') == mek_hgnc_id
assert agent.db_refs.get('UP') == mek_up_id
def test_get_agent_mgi():
node = protein(namespace='MGI', name='Nr1h3')
agent = pb._get_agent(node, {})
assert isinstance(agent, Agent)
assert agent.name == 'Nr1h3'
assert len(agent.db_refs) == 1
assert agent.db_refs.get('MGI') == 'Nr1h3'
def test_get_agent_rgd():
node = protein(namespace='RGD', name='Tp53')
agent = pb._get_agent(node, {})
assert isinstance(agent, Agent)
assert agent.name == 'Tp53'
assert len(agent.db_refs) == 1
assert agent.db_refs.get('RGD') == 'Tp53'
def test_get_agent_with_activity():
mek = protein(name='MAP2K1', namespace='HGNC')
agent = pb._get_agent(mek, activity('act'))
assert isinstance(agent, Agent)
assert isinstance(agent.activity, ActivityCondition)
assert agent.activity.activity_type == 'activity'
assert agent.activity.is_active
def test_get_agent_complex_none_agent():
"""If one of the agents in the complex can't be obtained (e.g., an
unhandled namespace), then the complex itself should be None."""
# Prime agent is None
mek = protein(name='MAP2K1', namespace='FOO')
erk = protein(name='MAPK1', namespace='HGNC',
variants=[pmod('Ph', position=185, code='Thr')])
cplx = complex_abundance([mek, erk])
agent = pb._get_agent(cplx)
assert agent is None
# Bound agent is None
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='FOO',
variants=[pmod('Ph', position=185, code='Thr')])
cplx = complex_abundance([mek, erk])
agent = pb._get_agent(cplx)
assert agent is None
def test_get_agent_with_translocation():
node_data = protein(name='MAPK1', namespace='HGNC')
# Some example edge data
edge_data = translocation(from_loc=entity('GOCC', 'intracellular'),
to_loc=entity('GOCC', 'extracellular space'))
agent = pb._get_agent(node_data, edge_data)
assert isinstance(agent, Agent)
assert agent.name == 'MAPK1'
assert agent.location == 'extracellular space'
def test_get_agent_egid():
node_data = {'function': 'Protein', 'name': '5008', 'namespace': 'EGID'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert agent.name == 'OSM'
assert len(agent.db_refs) == 3
assert agent.db_refs['EGID'] == '5008'
assert agent.db_refs['HGNC'] == '8506'
assert agent.db_refs['UP'] == 'P13725'
def test_get_agent_fusion():
node_data = {'function': 'Protein',
'fusion': {
'partner_5p': {'namespace': 'HGNC', 'name': 'BCR'},
'range_5p': {'missing': '?'},
'range_3p': {'missing': '?'},
'partner_3p': {'namespace': 'HGNC', 'name': 'ABL1'}}}
agent = pb._get_agent(node_data)
assert agent is None
def test_get_agent_named_complex_go():
# TODO: Handle named complexes and map to FamPlex where possible
node_data = {
'cname': '0043509',
'function': 'Complex',
'name': '0043509',
'namespace': 'GOCCID'}
agent = pb._get_agent(node_data)
assert agent is None
def test_get_agent_with_muts():
mek = protein(name='MAP2K1', namespace='HGNC',
variants=[hgvs('p.Val600Glu')])
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert len(agent.mutations) == 1
mut = agent.mutations[0]
assert mut.position == '600'
assert mut.residue_from == 'V'
assert mut.residue_to == 'E'
def test_get_agent_schem():
node_data = {
'cname': 'Promegestone',
'function': 'Abundance',
'name': 'Promegestone',
'namespace': 'SCHEM'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert agent.name == 'Promegestone'
assert len(agent.db_refs) == 1
assert agent.db_refs['SCHEM'] == 'Promegestone'
def test_get_agent_mirna():
node_data = {
'cname': 'MIR218-1',
'function': 'miRNA',
'name': 'MIR218-1',
'namespace': 'HGNC'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert agent.name == 'MIR218-1'
assert len(agent.db_refs) == 1
assert agent.db_refs['HGNC'] == '31595'
def test_get_agent_sdis():
node_data = {
'cname': 'metastasis',
'function': 'Pathology',
'name': 'metastasis',
'namespace': 'SDIS'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert agent.name == 'metastasis'
assert len(agent.db_refs) == 1
assert agent.db_refs['SDIS'] == 'metastasis'
def test_get_agent_chebi():
node_data = {
'cname': 'nitric oxide',
'function': 'Abundance',
'name': 'nitric oxide',
'namespace': 'CHEBI'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert agent.name == 'nitric oxide'
assert len(agent.db_refs) == 1
assert agent.db_refs['CHEBI'] == 'CHEBI:16480'
def test_get_agent_sfam():
node_data = {
'cname': 'PRKC Family',
'function': 'Protein',
'name': 'PRKC Family',
'namespace': 'SFAM'}
agent = pb._get_agent(node_data)
assert isinstance(agent, Agent)
assert len(agent.db_refs) == 2
assert agent.db_refs['SFAM'] == 'PRKC Family'
assert agent.db_refs['FPLX'] == 'PKC'
assert agent.name == 'PKC'
def test_get_agent_with_mods():
mek = protein(name='MAP2K1', namespace='HGNC',
variants=[pmod('Ph')])
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert len(agent.mods) == 1
mod = agent.mods[0]
assert mod.mod_type == 'phosphorylation'
assert not mod.residue
assert not mod.position
mek = protein(name='MAP2K1', namespace='HGNC',
variants=[pmod('Ph', code='Ser')])
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert len(agent.mods) == 1
mod = agent.mods[0]
assert mod.mod_type == 'phosphorylation'
assert mod.residue == 'S'
assert not mod.position
mek = protein(name='MAP2K1', namespace='HGNC',
variants=[pmod('Ph', position=218)])
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert len(agent.mods) == 1
mod = agent.mods[0]
assert mod.mod_type == 'phosphorylation'
assert not mod.residue
assert mod.position == '218'
mek = protein(name='MAP2K1', namespace='HGNC',
variants=[pmod('Ph', position=218, code='Ser')])
agent = pb._get_agent(mek, {})
assert isinstance(agent, Agent)
assert len(agent.mods) == 1
mod = agent.mods[0]
assert mod.mod_type == 'phosphorylation'
assert mod.residue == 'S'
assert mod.position == '218'
def test_get_agent_complex():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC',
variants=[pmod('Ph', position=185, code='Thr')])
cplx = complex_abundance([mek, erk])
agent = pb._get_agent(cplx)
assert isinstance(agent, Agent)
assert agent.name == 'MAP2K1'
assert len(agent.bound_conditions) == 1
bc = agent.bound_conditions[0]
assert isinstance(bc, BoundCondition)
assert bc.is_bound is True
bc_agent = bc.agent
assert bc_agent.name == 'MAPK1'
assert len(bc_agent.mods) == 1
assert bc_agent.mods[0].mod_type == 'phosphorylation'
assert bc_agent.mods[0].residue == 'T'
assert bc_agent.mods[0].position == '185'
def test_get_agent_up_no_id():
mek = protein(name='MAP2K1', namespace='UP')
agent = pb._get_agent(mek, {})
assert agent is None
def test_get_agent_meshpp():
apoptosis = bioprocess(name='Apoptosis', namespace='MESHPP')
agent = pb._get_agent(apoptosis)
assert isinstance(agent, Agent)
assert agent.name == 'Apoptosis'
assert agent.db_refs == {}
def test_get_agent_meshd():
hyperoxia = bioprocess(name='Hyperoxia', namespace='MESHD')
agent = pb._get_agent(hyperoxia)
assert isinstance(agent, Agent)
assert agent.name == 'Hyperoxia'
assert agent.db_refs == {}
