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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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():
# 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():
# 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_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_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_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_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_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'