def test_process_row_stab():
test_row_stab = SignorRow(ENTITYA='UCHL5',
TYPEA='protein',
IDA='Q9Y5K5',
DATABASEA='UNIPROT',
ENTITYB='TGFBR1',
TYPEB='protein',
IDB='P36897',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='stabilization',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='17052192',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-150135')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_stab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
def test_process_row_dephos_nores_down():
test_row = _SignorRow_(ENTITYA='CSNK1D', TYPEA='protein', IDA='P48730',
DATABASEA='UNIPROT', ENTITYB='LEF1', TYPEB='protein', IDB='Q9UJU2',
DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='15747065', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-134494')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == True
def test_process_row_dephos_nores_down():
test_row = SignorRow(ENTITYA='CSNK1D', TYPEA='protein', IDA='P48730',
DATABASEA='UNIPROT', ENTITYB='LEF1', TYPEB='protein', IDB='Q9UJU2',
DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='15747065', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-134494')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == True
def test_process_row_dephos_up():
test_row = _SignorRow_(ENTITYA='CHEK2', TYPEA='protein', IDA='O96017',
DATABASEA='UNIPROT', ENTITYB='CHEK2', TYPEB='protein', IDB='O96017',
DATABASEB='UNIPROT', EFFECT='up-regulates activity',
MECHANISM='dephosphorylation', RESIDUE='Thr387',
SEQUENCE='LMRTLCGtPTYLAPE', TAX_ID='9606', CELL_DATA='BTO:0000007',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='11901158', DIRECT='YES', NOTES='', ANNOTATOR='gcesareni',
SENTENCE='', SIGNOR_ID='SIGNOR-116131')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'T'
assert stmts[1].position == '387'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'T'
assert mc.position == '387'
assert af.is_active == False
def test_process_row_chem_inh():
test_row_chem_inh = SignorRow(ENTITYA='722544-51-6',
TYPEA='chemical',
IDA='CID:16007391',
DATABASEA='PUBCHEM',
ENTITYB='AURKB',
TYPEB='protein',
IDB='Q96GD4',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='chemical inhibition',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='Other',
DIRECT='YES',
NOTES='Selleck',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-190245')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_inh)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Inhibition)
def test_process_row_dephos_down():
test_row = _SignorRow_(ENTITYA='PRKCD', TYPEA='protein', IDA='Q05655',
DATABASEA='UNIPROT', ENTITYB='PTPN22', TYPEB='protein',
IDB='Q9Y2R2', DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='Ser35',
SEQUENCE='FLKLKRQsTKYKADK', TAX_ID='9606', CELL_DATA='BTO:0000782',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='18056643', DIRECT='YES', NOTES='', ANNOTATOR='llicata',
SENTENCE='', SIGNOR_ID='SIGNOR-159591')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'S'
assert stmts[1].position == '35'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '35'
assert af.is_active == True
def test_process_row_chem_act():
test_row_chem_act = SignorRow(ENTITYA='Prostaglandin E2',
TYPEA='smallmolecule',
IDA='CID:5280360',
DATABASEA='PUBCHEM',
ENTITYB='GNG12',
TYPEB='protein',
IDB='Q9UBI6',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='chemical activation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='16293724',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-141820')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_act)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Activation)
def test_process_row_complex_up():
test_row = _SignorRow_(ENTITYA='NONO', TYPEA='protein', IDA='Q15233',
DATABASEA='UNIPROT', ENTITYB='TOP1', TYPEB='protein', IDB='P11387',
DATABASEB='UNIPROT', EFFECT='up-regulates', MECHANISM='binding',
RESIDUE='', SEQUENCE='', TAX_ID='9606', CELL_DATA='BTO:0000017',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='9756848', DIRECT='YES', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-60557')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert af.is_active
def test_process_row_dephos_up():
test_row = SignorRow(ENTITYA='CHEK2', TYPEA='protein', IDA='O96017',
DATABASEA='UNIPROT', ENTITYB='CHEK2', TYPEB='protein', IDB='O96017',
DATABASEB='UNIPROT', EFFECT='up-regulates activity',
MECHANISM='dephosphorylation', RESIDUE='Thr387',
SEQUENCE='LMRTLCGtPTYLAPE', TAX_ID='9606', CELL_DATA='BTO:0000007',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='11901158', DIRECT='YES', NOTES='', ANNOTATOR='gcesareni',
SENTENCE='', SIGNOR_ID='SIGNOR-116131')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'T'
assert stmts[1].position == '387'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'T'
assert mc.position == '387'
assert af.is_active == False
def test_process_row_complex_up():
test_row = SignorRow(ENTITYA='NONO', TYPEA='protein', IDA='Q15233',
DATABASEA='UNIPROT', ENTITYB='TOP1', TYPEB='protein', IDB='P11387',
DATABASEB='UNIPROT', EFFECT='up-regulates', MECHANISM='binding',
RESIDUE='', SEQUENCE='', TAX_ID='9606', CELL_DATA='BTO:0000017',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='9756848', DIRECT='YES', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-60557')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert af.is_active
def test_process_row_dephos_down():
test_row = SignorRow(ENTITYA='PRKCD', TYPEA='protein', IDA='Q05655',
DATABASEA='UNIPROT', ENTITYB='PTPN22', TYPEB='protein',
IDB='Q9Y2R2', DATABASEB='UNIPROT', EFFECT='down-regulates',
MECHANISM='dephosphorylation', RESIDUE='Ser35',
SEQUENCE='FLKLKRQsTKYKADK', TAX_ID='9606', CELL_DATA='BTO:0000782',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='18056643', DIRECT='YES', NOTES='', ANNOTATOR='llicata',
SENTENCE='', SIGNOR_ID='SIGNOR-159591')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue == 'S'
assert stmts[1].position == '35'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '35'
assert af.is_active == True
def test_process_row_phos_multi_res():
test_row = SignorRow(ENTITYA='RAF1', TYPEA='protein', IDA='P04049',
DATABASEA='UNIPROT', ENTITYB='MAP2K2', TYPEB='protein',
IDB='P36507', DATABASEB='UNIPROT', EFFECT='up-regulates',
MECHANISM='phosphorylation', RESIDUE='Ser218;Ser222',
SEQUENCE='VSGQLIDsMANSFVG;LIDSMANsFVGTRSY', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='8157000', DIRECT='YES',
NOTES='', ANNOTATOR='gcesareni', SENTENCE='',
SIGNOR_ID='SIGNOR-36553')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 4
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].position == '218'
assert isinstance(stmts[2], Phosphorylation)
assert stmts[2].position == '222'
af = stmts[3]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 2
mc0 = af.agent.mods[0]
assert mc0.mod_type == 'phosphorylation'
assert mc0.residue == 'S'
assert mc0.position == '218'
mc1 = af.agent.mods[1]
assert mc1.mod_type == 'phosphorylation'
assert mc1.residue == 'S'
assert mc1.position == '222'
assert af.is_active == True
def test_process_row_complex_down():
test_row = _SignorRow_(ENTITYA='XIAP', TYPEA='protein', IDA='P98170',
DATABASEA='UNIPROT', ENTITYB='CASP3', TYPEB='protein',
IDB='P42574', DATABASEB='UNIPROT', EFFECT='down-regulates activity',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='10548111', DIRECT='YES', NOTES='',
ANNOTATOR='amattioni', SENTENCE='', SIGNOR_ID='SIGNOR-71954')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert not af.is_active
def test_process_row_complex_down():
test_row = SignorRow(ENTITYA='XIAP', TYPEA='protein', IDA='P98170',
DATABASEA='UNIPROT', ENTITYB='CASP3', TYPEB='protein',
IDB='P42574', DATABASEB='UNIPROT', EFFECT='down-regulates activity',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='10548111', DIRECT='YES', NOTES='',
ANNOTATOR='amattioni', SENTENCE='', SIGNOR_ID='SIGNOR-71954')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert not af.is_active
def test_process_row_phos_multi_res():
test_row = _SignorRow_(ENTITYA='RAF1', TYPEA='protein', IDA='P04049',
DATABASEA='UNIPROT', ENTITYB='MAP2K2', TYPEB='protein',
IDB='P36507', DATABASEB='UNIPROT', EFFECT='up-regulates',
MECHANISM='phosphorylation', RESIDUE='Ser218;Ser222',
SEQUENCE='VSGQLIDsMANSFVG;LIDSMANsFVGTRSY', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='8157000', DIRECT='YES',
NOTES='', ANNOTATOR='gcesareni', SENTENCE='',
SIGNOR_ID='SIGNOR-36553')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 4
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].position == '218'
assert isinstance(stmts[2], Phosphorylation)
assert stmts[2].position == '222'
af = stmts[3]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 2
mc0 = af.agent.mods[0]
assert mc0.mod_type == 'phosphorylation'
assert mc0.residue == 'S'
assert mc0.position == '218'
mc1 = af.agent.mods[1]
assert mc1.mod_type == 'phosphorylation'
assert mc1.residue == 'S'
assert mc1.position == '222'
assert af.is_active == True
def test_process_row_dephos_nores_up():
test_row = SignorRow(ENTITYA='STK11', TYPEA='protein', IDA='Q15831',
DATABASEA='UNIPROT', ENTITYB='AMPK', TYPEB='complex',
IDB='SIGNOR-C15', DATABASEB='SIGNOR',
EFFECT='up-regulates activity', MECHANISM='dephosphorylation',
RESIDUE='', SEQUENCE='', TAX_ID='-1', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='14976552',
DIRECT='YES', NOTES='', ANNOTATOR='lperfetto',
SENTENCE='', SIGNOR_ID='SIGNOR-242602')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == False
def test_process_row_dephos_nores_up():
test_row = _SignorRow_(ENTITYA='STK11', TYPEA='protein', IDA='Q15831',
DATABASEA='UNIPROT', ENTITYB='AMPK', TYPEB='complex',
IDB='SIGNOR-C15', DATABASEB='SIGNOR',
EFFECT='up-regulates activity', MECHANISM='dephosphorylation',
RESIDUE='', SEQUENCE='', TAX_ID='-1', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='14976552',
DIRECT='YES', NOTES='', ANNOTATOR='lperfetto',
SENTENCE='', SIGNOR_ID='SIGNOR-242602')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Dephosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == False
def test_process_row():
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
assert stmts[0].agent_list()[0].activity.activity_type == 'transcription'
def test_recursively_expand_complex_constituents():
complex_map = {
'SIGNOR-C87': ['P61964', 'Q9UBL3', 'Q9C005', 'Q15291'],
'SIGNOR-C88': ['SIGNOR-C87', 'O14686'],
'SIGNOR-C91': ['SIGNOR-C88', 'P23759']}
sp = SignorProcessor([test_row], complex_map)
constituents = sp._recursively_lookup_complex('SIGNOR-C91')
assert constituents == ['P23759', 'O14686', 'P61964', 'Q9UBL3', 'Q9C005',
'Q15291']
def test_recursively_expand_complex_constituents():
complex_map = {
'SIGNOR-C87': ['P61964', 'Q9UBL3', 'Q9C005', 'Q15291'],
'SIGNOR-C88': ['SIGNOR-C87', 'O14686'],
'SIGNOR-C91': ['SIGNOR-C88', 'P23759']}
sp = SignorProcessor([test_row], complex_map)
constituents = sp._recursively_lookup_complex('SIGNOR-C91')
assert(constituents == ['P23759', 'O14686', 'P61964', 'Q9UBL3', 'Q9C005',
'Q15291'])
def test_process_row():
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
assert stmts[0].agent_list()[0].activity.activity_type == 'transcription'
def test_process_row_chem_act():
test_row_chem_act = _SignorRow_(ENTITYA='Prostaglandin E2',
TYPEA='smallmolecule', IDA='CID:5280360', DATABASEA='PUBCHEM',
ENTITYB='GNG12', TYPEB='protein', IDB='Q9UBI6', DATABASEB='UNIPROT',
EFFECT='up-regulates', MECHANISM='chemical activation', RESIDUE='',
SEQUENCE='', TAX_ID='9606', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='16293724', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-141820')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_act)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Activation)
def test_process_row_stab():
test_row_stab = _SignorRow_(ENTITYA='UCHL5', TYPEA='protein', IDA='Q9Y5K5',
DATABASEA='UNIPROT', ENTITYB='TGFBR1', TYPEB='protein',
IDB='P36897', DATABASEB='UNIPROT', EFFECT='up-regulates',
MECHANISM='stabilization', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='17052192', DIRECT='YES', NOTES='',
ANNOTATOR='gcesareni', SENTENCE='', SIGNOR_ID='SIGNOR-150135')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_stab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
def test_signor_complexes():
test_row = SignorRow(ENTITYA='NFY',
TYPEA='complex',
IDA='SIGNOR-C1',
DATABASEA='SIGNOR',
ENTITYB='ID1',
TYPEB='protein',
IDB='P41134',
DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional activation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000972',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18025157',
DIRECT='NO',
NOTES='',
ANNOTATOR='',
SENTENCE='',
SIGNOR_ID='SIGNOR-255746')
complex_map = {'SIGNOR-C1': ['P23511', 'P25208', 'Q13952']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
s0 = sp.statements[0]
assert (isinstance(s0, IncreaseAmount))
assert (s0.subj.db_refs['UP'] == 'P23511')
assert (s0.subj.db_refs['HGNC'] == '7804')
assert (s0.subj.name == 'NFYA')
assert (s0.subj.bound_conditions[0].agent.db_refs['UP'] == 'P25208')
assert (s0.subj.bound_conditions[0].agent.name == 'NFYB')
assert (s0.subj.bound_conditions[0].agent.db_refs['HGNC'] == '7805')
assert (s0.subj.bound_conditions[1].agent.db_refs['UP'] == 'Q13952')
assert (s0.subj.bound_conditions[1].agent.name == 'NFYC')
assert (s0.subj.bound_conditions[1].agent.db_refs['HGNC'] == '7806')
s1 = sp.statements[1]
assert (isinstance(s1, Complex))
assert len(s1.evidence) == 1
assert s1.evidence[0].source_api == 'signor'
assert s1.evidence[0].source_id == 'SIGNOR-C1'
assert s1.evidence[0].text
correct_up_ids = set(['P23511', 'Q13952', 'P25208'])
correct_hgnc_ids = set(['7804', '7805', '7806'])
correct_names = set(['NFYA', 'NFYC', 'NFYB'])
actual_up_ids = set([m.db_refs['UP'] for m in s1.members])
actual_hgnc_ids = set([m.db_refs['HGNC'] for m in s1.members])
actual_names = set([m.name for m in s1.members])
assert (actual_up_ids == correct_up_ids)
assert (actual_hgnc_ids == correct_hgnc_ids)
assert (actual_names == correct_names)
def test_complexes_with_families():
test_row = SignorRow(ENTITYA='MAPK1', TYPEA='protein',
IDA='P27361', DATABASEA='UNIPROT', ENTITYB='CDO/JLP/P38',
TYPEB='complex', IDB='SIGNOR-C22', DATABASEB='SIGNOR',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='22863532', DIRECT='NO', NOTES='',
ANNOTATOR='miannu', SENTENCE='', SIGNOR_ID='SIGNOR-198641')
complex_map = {'SIGNOR-C22' : ['O60271', 'Q4KMG0', 'SIGNOR-PF14']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 2
assert(isinstance(sp.statements[0], IncreaseAmount))
obj = sp.statements[0].obj
assert(obj.db_refs['UP'] == 'O60271')
assert(len(obj.bound_conditions) == 2)
assert(obj.bound_conditions[0].agent.db_refs['UP'] == 'Q4KMG0')
assert(obj.bound_conditions[1].agent.db_refs['SIGNOR'] == 'SIGNOR-PF14')
assert(obj.bound_conditions[1].agent.db_refs['FPLX'] == 'ROBO')
s1 = sp.statements[1]
assert(isinstance(s1, Complex))
members = s1.members
assert(members[0].db_refs['UP'] == 'O60271')
assert(members[1].db_refs['UP'] == 'Q4KMG0')
assert(members[2].db_refs['SIGNOR'] == 'SIGNOR-PF14')
assert(members[2].db_refs['FPLX'] == 'ROBO')
def test_process_row_chem_inh():
test_row_chem_inh = _SignorRow_(ENTITYA='722544-51-6', TYPEA='chemical',
IDA='CID:16007391', DATABASEA='PUBCHEM', ENTITYB='AURKB',
TYPEB='protein', IDB='Q96GD4', DATABASEB='UNIPROT',
EFFECT='down-regulates', MECHANISM='chemical inhibition', RESIDUE='',
SEQUENCE='', TAX_ID='9606', CELL_DATA='', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='',
MODIFICATIONB='', MODBSEQ='', PMID='Other', DIRECT='YES',
NOTES='Selleck', ANNOTATOR='gcesareni', SENTENCE='',
SIGNOR_ID='SIGNOR-190245')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_chem_inh)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Inhibition)
def test_process_row_binding_complex():
test_row = _SignorRow_(ENTITYA='ATG5', TYPEA='protein', IDA='Q9H1Y0',
DATABASEA='UNIPROT', ENTITYB='ATG12/5/16L1', TYPEB='complex',
IDB='SIGNOR-C109', DATABASEB='SIGNOR', EFFECT='form complex',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='BTO:0000007', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='18321988', DIRECT='YES', NOTES='',
ANNOTATOR='lperfetto', SENTENCE='', SIGNOR_ID='SIGNOR-226693')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Complex)
assert len(stmts[0].agent_list()) == 2
def test_process_row_binding_complex():
test_row = SignorRow(ENTITYA='ATG5', TYPEA='protein', IDA='Q9H1Y0',
DATABASEA='UNIPROT', ENTITYB='ATG12/5/16L1', TYPEB='complex',
IDB='SIGNOR-C109', DATABASEB='SIGNOR', EFFECT='form complex',
MECHANISM='binding', RESIDUE='', SEQUENCE='', TAX_ID='9606',
CELL_DATA='', TISSUE_DATA='BTO:0000007', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='18321988', DIRECT='YES', NOTES='',
ANNOTATOR='lperfetto', SENTENCE='', SIGNOR_ID='SIGNOR-226693')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Complex)
assert len(stmts[0].agent_list()) == 2
def test_get_agent():
# Protein/gene
# Create an empty Signor processor
sp = SignorProcessor([])
test_ag = Agent('RELA',
db_refs={
'HGNC': hgnc_client.get_hgnc_id('RELA'),
'UP': 'Q04206'
})
sp_ag = sp._get_agent(test_row.ENTITYA, test_row.TYPEA, test_row.IDA,
test_row.DATABASEA)
assert test_ag.matches(sp_ag)
# Chemical
test_ag = Agent('AZD1480', db_refs={'PUBCHEM': 'CID:16659841'})
sp_ag = sp._get_agent('AZD1480', 'chemical', 'CID:16659841', 'PUBCHEM')
assert test_ag.matches(sp_ag)
# Signor phenotype
test_ag = Agent('Cell cycle progr.', db_refs={'SIGNOR': 'SIGNOR-PH42'})
sp_ag = sp._get_agent('Cell cycle progr.', 'phenotype', 'SIGNOR-PH42',
'SIGNOR')
assert test_ag.matches(sp_ag)
# Ungrounded -- couldn't find a real example in the dataset
test_ag = Agent('Foobar', db_refs={})
sp_ag = sp._get_agent('Foobar', 'pathway', None, None)
assert test_ag.matches(sp_ag)
sp_ag = sp._get_agent('Foobar', 'antibody', None, None)
assert test_ag.matches(sp_ag)
def test_process_row_destab():
test_row_destab = _SignorRow_(ENTITYA='INS', TYPEA='protein', IDA='P01308',
DATABASEA='UNIPROT', ENTITYB='APOB', TYPEB='protein', IDB='P04114',
DATABASEB='UNIPROT',
EFFECT='down-regulates quantity by destabilization',
MECHANISM='destabilization', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0000575', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='23721961',
DIRECT='NO', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-252114')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_destab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], DecreaseAmount)
def test_mod_unknown_effect():
test_row = _SignorRow_(ENTITYA='JAK2', TYPEA='protein', IDA='O60674',
DATABASEA='UNIPROT', ENTITYB='JAK2', TYPEB='protein', IDB='O60674',
DATABASEB='UNIPROT', EFFECT='unknown', MECHANISM='phosphorylation',
RESIDUE='Tyr1007', SEQUENCE='VLPQDKEyYKVKEPG', TAX_ID='-1',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='9111318', DIRECT='YES', NOTES='', ANNOTATOR='',
SENTENCE='', SIGNOR_ID='SIGNOR-251358')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Phosphorylation)
assert stmts[0].residue == 'Y'
assert stmts[0].position == '1007'
def test_process_row_destab():
test_row_destab = SignorRow(ENTITYA='INS', TYPEA='protein', IDA='P01308',
DATABASEA='UNIPROT', ENTITYB='APOB', TYPEB='protein', IDB='P04114',
DATABASEB='UNIPROT',
EFFECT='down-regulates quantity by destabilization',
MECHANISM='destabilization', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0000575', TISSUE_DATA='',
MODULATOR_COMPLEX='', TARGET_COMPLEX='', MODIFICATIONA='',
MODASEQ='', MODIFICATIONB='', MODBSEQ='', PMID='23721961',
DIRECT='NO', NOTES='', ANNOTATOR='miannu',
SENTENCE='', SIGNOR_ID='SIGNOR-252114')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row_destab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], DecreaseAmount)
def test_mod_unknown_effect():
test_row = SignorRow(ENTITYA='JAK2', TYPEA='protein', IDA='O60674',
DATABASEA='UNIPROT', ENTITYB='JAK2', TYPEB='protein', IDB='O60674',
DATABASEB='UNIPROT', EFFECT='unknown', MECHANISM='phosphorylation',
RESIDUE='Tyr1007', SEQUENCE='VLPQDKEyYKVKEPG', TAX_ID='-1',
CELL_DATA='', TISSUE_DATA='', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='9111318', DIRECT='YES', NOTES='', ANNOTATOR='',
SENTENCE='', SIGNOR_ID='SIGNOR-251358')
# Create an empty Signor processor
sp = SignorProcessor([])
stmts, no_mech = sp._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Phosphorylation)
assert stmts[0].residue == 'Y'
assert stmts[0].position == '1007'
def test_get_agent():
# Protein/gene
# Create an empty Signor processor
sp = SignorProcessor([])
test_ag = Agent('RELA', db_refs={'HGNC': hgnc_client.get_hgnc_id('RELA'),
'UP': 'Q04206'})
sp_ag = sp._get_agent(test_row.ENTITYA, test_row.TYPEA,
test_row.IDA, test_row.DATABASEA)
assert test_ag.matches(sp_ag)
# Chemical
test_ag = Agent('AZD1480', db_refs={'PUBCHEM': '16659841'})
sp_ag = sp._get_agent('AZD1480', 'chemical', 'CID: 16659841',
'PUBCHEM')
assert test_ag.matches(sp_ag)
# Signor phenotype
test_ag = Agent('Cell cycle progr.', db_refs={'SIGNOR': 'SIGNOR-PH42'})
sp_ag = sp._get_agent('Cell cycle progr.', 'phenotype',
'SIGNOR-PH42', 'SIGNOR')
assert test_ag.matches(sp_ag)
# Ungrounded -- couldn't find a real example in the dataset
test_ag = Agent('Foobar', db_refs={})
sp_ag = sp._get_agent('Foobar', 'pathway', None, None)
assert test_ag.matches(sp_ag)
sp_ag = sp._get_agent('Foobar', 'antibody', None, None)
assert test_ag.matches(sp_ag)
def test_signor_family_famplex_mapping():
test_row = SignorRow(ENTITYA='TLRs', TYPEA='proteinfamily',
IDA='SIGNOR-PF20', DATABASEA='SIGNOR',
ENTITYB='Interferon Production', TYPEB='phenotype',
IDB='SIGNOR-PH16', DATABASEB='SIGNOR', EFFECT='up-regulates',
MECHANISM='', RESIDUE='', SEQUENCE='', TAX_ID='9606', CELL_DATA='',
TISSUE_DATA='', MODULATOR_COMPLEX='', TARGET_COMPLEX='',
MODIFICATIONA='', MODASEQ='', MODIFICATIONB='', MODBSEQ='',
PMID='20404851', DIRECT='NO', NOTES='', ANNOTATOR='lperfetto',
SENTENCE='', SIGNOR_ID='SIGNOR-216310')
complex_map = {}
sp = SignorProcessor([test_row], complex_map)
statements = sp.statements
assert(len(statements) == 1)
s0 = statements[0]
assert(s0.subj.db_refs['FPLX'] == 'TLR')
assert s0.subj.db_refs['SIGNOR'] == 'SIGNOR-PF20'
assert(s0.subj.name == 'TLR')
def test_recursive_complexes():
test_row = SignorRow(ENTITYA='PAX7/MLL2 complex', TYPEA='complex',
IDA='SIGNOR-C91', DATABASEA='SIGNOR', ENTITYB='MYF5',
TYPEB='protein', IDB='P13349', DATABASEB='UNIPROT',
EFFECT='up-regulates quantity by expression',
MECHANISM='transcriptional regulation', RESIDUE='', SEQUENCE='',
TAX_ID='9606', CELL_DATA='BTO:0002314',
TISSUE_DATA='BTO:0000887;BTO:0001103', MODULATOR_COMPLEX='',
TARGET_COMPLEX='', MODIFICATIONA='', MODASEQ='', MODIFICATIONB='',
MODBSEQ='', PMID='22863532', DIRECT='NO', NOTES='',
ANNOTATOR='miannu', SENTENCE='', SIGNOR_ID='SIGNOR-198641')
complex_map = {
'SIGNOR-C87': ['P61964', 'Q9UBL3', 'Q9C005', 'Q15291'],
'SIGNOR-C88': ['SIGNOR-C87', 'O14686'],
'SIGNOR-C91': ['SIGNOR-C88', 'P23759']}
sp = SignorProcessor([test_row], complex_map)
assert isinstance(sp.statements, list)
assert len(sp.statements) == 4
s0 = sp.statements[0]
assert(isinstance(s0, IncreaseAmount))
bc = s0.subj.bound_conditions
assert(bc[0].agent.db_refs['UP'] == 'O14686')
assert(bc[1].agent.db_refs['UP'] == 'P61964')
assert(bc[2].agent.db_refs['UP'] == 'Q9UBL3')
assert(bc[3].agent.db_refs['UP'] == 'Q9C005')
assert(bc[4].agent.db_refs['UP'] == 'Q15291')
assert(isinstance(sp.statements[1], Complex))
correct_complex_ups_1 = {'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_1 = {m.db_refs['UP'] for m in sp.statements[1].members}
assert(correct_complex_ups_1 == actual_complex_ups_1)
assert(isinstance(sp.statements[2], Complex))
correct_complex_ups_2 = {'O14686', 'P61964', 'Q9UBL3', 'Q9C005', 'Q15291'}
actual_complex_ups_2 = {m.db_refs['UP'] for m in sp.statements[2].members}
assert(correct_complex_ups_2 == actual_complex_ups_2)
assert(isinstance(sp.statements[3], Complex))
correct_complex_ups_3 = {'P23759', 'O14686', 'P61964', 'Q9UBL3', 'Q9C005',
'Q15291'}
actual_complex_ups_3 = {m.db_refs['UP'] for m in sp.statements[3].members}
assert(correct_complex_ups_3 == actual_complex_ups_3)
def test_get_evidence():
ev = SignorProcessor._get_evidence(test_row)
assert isinstance(ev, Evidence)
assert ev.pmid == '19530226'
assert ev.annotations == {
'SEQUENCE': None,
'MODULATOR_COMPLEX': None,
'TARGET_COMPLEX': None,
'MODIFICATIONA': None,
'MODASEQ': None,
'MODIFICATIONB': None,
'MODBSEQ': None,
'NOTES': None,
'ANNOTATOR': 'gcesareni',
}
assert ev.context.species.db_refs['TAXONOMY'] == '10090'
assert ev.context.cell_type.db_refs['BTO'] == '0002895'
assert ev.epistemics['direct']
assert ev.source_api == 'signor'
assert ev.source_id == 'SIGNOR-241929'
assert ev.text == "Together, these results indicate that the Met gene " \
"is a direct target of NFkappaB and that Met " \
"participates in NFkappaB-mediated cell survival."
def test_get_evidence():
ev = SignorProcessor._get_evidence(test_row)
assert isinstance(ev, Evidence)
assert ev.pmid == '19530226'
assert ev.annotations == {
'SEQUENCE': None,
'MODULATOR_COMPLEX': None,
'TARGET_COMPLEX': None,
'MODIFICATIONA': None,
'MODASEQ': None,
'MODIFICATIONB': None,
'MODBSEQ': None,
'NOTES': None,
'ANNOTATOR': 'gcesareni',
}
assert ev.context.species.db_refs['TAXONOMY'] == '10090'
assert ev.context.cell_type.db_refs['BTO'] == '0002895'
assert ev.epistemics['direct']
assert ev.source_api == 'signor'
assert ev.source_id == 'SIGNOR-241929'
assert ev.text == "Together, these results indicate that the Met gene " \
"is a direct target of NFkappaB and that Met " \
"participates in NFkappaB-mediated cell survival."
def test_get_agent_keyerror():
# Create an empty Signor processor
sp = SignorProcessor([])
sp_ag = sp._get_agent('foo', 'bar', None, None)
def test_get_agent_keyerror():
# Create an empty Signor processor
sp = SignorProcessor([])
sp_ag = sp._get_agent('foo', 'bar', None, None)