Python IncrementalModel.add_statements Examples

Example #1

File: test_incremental_model.py Project: reynoldsm88/indra

def test_grounding_all():
    im = IncrementalModel()
    stmt = Complex([Agent('A', db_refs={'UP': 'ABCD'}), 
                   Agent('B', db_refs={'HGNC': '1234'})])
    im.add_statements('12345', [stmt])
    im.preassemble(filters=['grounding'])
    assert len(im.assembled_stmts) == 1

Example #2

def test_add_stmts_prior_all():
    im = IncrementalModel()
    im.stmts['prior'] = [stmts[0]]
    im.prior_genes = ['MAPK1', 'MAPK3']
    im.add_statements('12345', [stmts[1]])
    im.preassemble(filters=['prior_all'])
    assert len(im.assembled_stmts) == 1

Example #3

File: test_incremental_model.py Project: johnbachman/indra

def test_add_stmts_prior_all():
    im = IncrementalModel()
    im.stmts['prior'] = [stmts[0]]
    im.prior_genes = ['MAPK1', 'MAPK3']
    im.add_statements('12345', [stmts[1]])
    im.preassemble(filters=['prior_all'])
    assert len(im.assembled_stmts) == 1

Example #4

def test_add_stmts_prior_all():
    im = IncrementalModel()
    # Start out with MAPK1 and MAPK3
    im.stmts['prior'] = [stmts[0]]
    im.prior_genes = ['MAPK1', 'MAPK3']
    # Try to add MAP2K1 and MAPK3
    im.add_statements('12345', [stmts[1]])
    im.preassemble(filters=['prior_all'])
    assert len(im.assembled_stmts) == 1, im.assembled_stmts

Example #5

def test_human_only():
    im = IncrementalModel()
    stmt1 = Phosphorylation(None, Agent('BRAF', db_refs={'UP': 'P15056'}))
    stmt2 = Phosphorylation(None, Agent('BRAF', db_refs={'UP': 'P28028'}))
    stmt3 = Phosphorylation(None, Agent('BRAF', db_refs={'HGNC': 'BRAF'}))
    stmt4 = Phosphorylation(None, Agent('BRAF', db_refs={}))
    im.add_statements('12345', [stmt1], filters=['human_only'])
    assert(len(im.get_statements()) == 1)
    im.add_statements('12346', [stmt2], filters=['human_only'])
    assert(len(im.get_statements()) == 1)
    im.add_statements('12346', [stmt3], filters=['human_only'])
    assert (len(im.get_statements()) == 2)
    im.add_statements('12346', [stmt4], filters=['human_only'])
    assert (len(im.get_statements()) == 3)

Example #6

File: test_incremental_model.py Project: reynoldsm88/indra

def test_human_only():
    im = IncrementalModel()
    stmt1 = Phosphorylation(None, Agent('BRAF', db_refs={'UP': 'P15056'}))
    stmt2 = Phosphorylation(None, Agent('BRAF', db_refs={'UP': 'P28028'}))
    stmt3 = Phosphorylation(None, Agent('BRAF', db_refs={'HGNC': 'BRAF'}))
    stmt4 = Phosphorylation(None, Agent('BRAF', db_refs={}))
    im.add_statements('12345', [stmt1])
    im.preassemble(filters=['human_only'])
    assert len(im.assembled_stmts) == 1
    im.add_statements('12346', [stmt2])
    im.preassemble(filters=['human_only'])
    assert len(im.assembled_stmts) == 1
    im.add_statements('12346', [stmt3])
    im.preassemble(filters=['human_only'])
    assert (len(im.assembled_stmts) == 2)
    im.add_statements('12346', [stmt4])
    im.preassemble(filters=['human_only'])
    assert (len(im.assembled_stmts) == 3)

Example #7

def test_add_stmts_blank_noprior2():
    im = IncrementalModel()
    im.add_statements('12345', stmts, filters=['prior_all'])
    assert(len(im.get_statements()) == 2)

Example #8

def test_add_stmts_model_all():
    im = IncrementalModel()
    im.add_statements('12345', [stmts[0]])
    im.add_statements('23456', [stmts[1]], filters=['model_all'])
    assert(len(im.get_statements()) == 1)

Example #9

def test_add_stmts_blank():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    assert(len(im.get_statements()) == 2)

Example #10

def test_add_stmts_blank_emptyfilter():
    im = IncrementalModel()
    im.add_statements('12345', stmts, filters=[])
    assert(len(im.get_statements()) == 2)

Example #11

File: test_incremental_model.py Project: johnbachman/indra

def test_add_stmts_blank():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    assert len(im.get_statements()) == 2
    im.preassemble()
    assert len(im.assembled_stmts) == 2

Example #12

def test_grounding_none_agent():
    im = IncrementalModel()
    im.add_statements('12345', stmts2)
    im.preassemble(filters=['grounding'])
    assert len(im.assembled_stmts) == 1

Example #13

File: test_incremental_model.py Project: lijielife/indra

def test_add_stmts_blank_nofilter():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=None)
    assert (len(im.assembled_stmts) == 2)

Example #14

def test_add_stmts_blank_noprior2():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=['prior_all'])
    assert len(im.assembled_stmts) == 2

Example #15

def test_grounding_none_agent():
    im = IncrementalModel()
    im.add_statements('12345', stmts2, filters=['grounding'])
    assert(len(im.get_statements()) == 1)

Example #16

def test_add_stmts_prior_all():
    im = IncrementalModel()
    im.stmts['prior'] = [stmts[0]]
    im.add_statements('12345', [stmts[1]], filters=['prior_all'])
    assert(len(im.get_statements()) == 1)

Example #17

File: test_incremental_model.py Project: johnbachman/indra

def test_grounding_none_agent():
    im = IncrementalModel()
    im.add_statements('12345', stmts2)
    im.preassemble(filters=['grounding'])
    assert len(im.assembled_stmts) == 1

Example #18

File: test_incremental_model.py Project: johnbachman/indra

def test_add_stmts_blank_emptyfilter():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=[])
    assert len(im.assembled_stmts) == 2

Example #19

File: test_incremental_model.py Project: johnbachman/indra

def test_add_stmts_blank_noprior2():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=['prior_all'])
    assert len(im.assembled_stmts) == 2

Example #20

def test_grounding_not_all():
    im = IncrementalModel()
    stmt = Complex([Agent('A', db_refs={'UP': 'ABCD'}), 
                   Agent('B')])
    im.add_statements('12345', [stmt], filters=['grounding'])
    assert(len(im.get_statements()) == 0)

Example #21

def test_add_stmts_blank():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    assert len(im.get_statements()) == 2
    im.preassemble()
    assert len(im.assembled_stmts) == 2

Example #22

def test_add_stmts_blank_emptyfilter():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=[])
    assert len(im.assembled_stmts) == 2

Example #23

File: test_incremental_model.py Project: jmuhlich/indra

def test_add_stmts_blank_nofilter():
    im = IncrementalModel()
    im.add_statements('12345', stmts)
    im.preassemble(filters=None)
    assert(len(im.assembled_stmts) == 2)