Python process_xml Examples

Example #1

File: test_sparser.py Project: reynoldsm88/indra

def test_phosphorylation():
    sp = sparser.process_xml(xml_str1)
    assert len(sp.statements) == 1
    assert sp.statements[0].enz.name == 'MAP2K1'
    assert sp.statements[0].sub.name == 'MAPK3'
    assert len(sp.statements[0].evidence) == 1
    ev = sp.statements[0].evidence[0]
    assert ev.pmid == '54321'
    assert ev.text
    assert ev.source_api == 'sparser'

Example #2

File: test_sparser.py Project: johnbachman/indra

def test_phosphorylation():
    sp = sparser.process_xml(xml_str1)
    assert len(sp.statements) == 1
    assert sp.statements[0].enz.name == 'MAP2K1'
    assert sp.statements[0].sub.name == 'MAPK3'
    assert len(sp.statements[0].evidence) == 1
    ev = sp.statements[0].evidence[0]
    assert ev.pmid == '54321'
    assert ev.text
    assert ev.source_api == 'sparser'

Example #3

File: test_sparser.py Project: reynoldsm88/indra

def test_phosphorylation2():
    sp = sparser.process_xml(xml_str2)
    assert len(sp.statements) == 1
    assert sp.statements[0].enz.name == 'MAPK1'
    assert sp.statements[0].sub.name == 'TP53BP2'
    assert sp.statements[0].residue == 'S'
    assert sp.statements[0].position == '827'
    assert (len(sp.statements[0].evidence) == 1)
    ev = sp.statements[0].evidence[0]
    assert (ev.pmid == '12345')
    assert (ev.text)
    assert (ev.source_api == 'sparser')

Example #4

File: test_sparser.py Project: johnbachman/indra

def test_phosphorylation2():
    sp = sparser.process_xml(xml_str2)
    assert len(sp.statements) == 1
    assert sp.statements[0].enz.name == 'MAPK1'
    assert sp.statements[0].sub.name == 'TP53BP2'
    assert sp.statements[0].residue == 'S'
    assert sp.statements[0].position == '827'
    assert (len(sp.statements[0].evidence) == 1)
    ev = sp.statements[0].evidence[0]
    assert (ev.pmid == '12345')
    assert (ev.text)
    assert (ev.source_api == 'sparser')

Example #5

File: test_sparser.py Project: reynoldsm88/indra

def test_invalid_xml():
    sp = sparser.process_xml('xyz')
    assert sp is None

Example #6

File: test_sparser.py Project: johnbachman/indra

def test_invalid_xml():
    sp = sparser.process_xml('xyz')
    assert sp is None