def test_loadStandoffFile_extraLines(capfd):
scriptDir = os.path.dirname(__file__)
txtPath = os.path.join(scriptDir,'data_extraLines','example.txt')
a1Path = os.path.join(scriptDir,'data_extraLines','example.a1')
a2Path = os.path.join(scriptDir,'data_extraLines','example.a2')
# Run quietly
data = kindred.loadDoc(dataFormat='standoff',txtPath=txtPath,a1Path=a1Path,a2Path=a2Path)
out, err = capfd.readouterr()
assert out.strip() == ""
assert err.strip() == ""
# Run verbose
data = kindred.loadDoc(dataFormat='standoff',txtPath=txtPath,a1Path=a1Path,a2Path=a2Path,verbose=True)
out, err = capfd.readouterr()
assert out.strip() == ""
assert err.strip() == "Unable to process line: *\tEXTRALINE"
assert isinstance(data,kindred.Document)
entities = data.getEntities()
relations = data.getRelations()
sourceEntityIDsToEntityIDs = data.getSourceEntityIDsToEntityIDs()
assertEntity(entities[0],expectedType='disease',expectedText='colorectal cancer',expectedPos=[(4,21)],expectedSourceEntityID="T1")
assertEntity(entities[1],expectedType='gene',expectedText='APC',expectedPos=[(49,52)],expectedSourceEntityID="T2")
assert relations == [kindred.Relation('causes',[sourceEntityIDsToEntityIDs["T1"],sourceEntityIDsToEntityIDs["T2"]],['obj','subj'])], "(%s) not as expected" % relations
def test_loadStandoffFile_missingA2(capfd): scriptDir = os.path.dirname(__file__) txtPath = os.path.join(scriptDir,'data_missingA2','example.txt') a1Path = os.path.join(scriptDir,'data_missingA2','example.a1') a2Path = os.path.join(scriptDir,'data_missingA2','example.a2') # Run quietly data = kindred.loadDoc(dataFormat='standoff',txtPath=txtPath,a1Path=a1Path,a2Path=a2Path) out, err = capfd.readouterr() assert out.strip() == "" assert err.strip() == "" # Run verbose data = kindred.loadDoc(dataFormat='standoff',txtPath=txtPath,a1Path=a1Path,a2Path=a2Path,verbose=True) out, err = capfd.readouterr() assert out.strip() == "" assert err.strip() == 'Note: No A2 file found : example.a2' assert isinstance(data,kindred.Document) entities = data.getEntities() relations = data.getRelations() sourceEntityIDsToEntityIDs = data.getSourceEntityIDsToEntityIDs() assertEntity(entities[0],expectedType='disease',expectedText='colorectal cancer',expectedPos=[(4,21)],expectedSourceEntityID="T1") assertEntity(entities[1],expectedType='gene',expectedText='APC',expectedPos=[(49,52)],expectedSourceEntityID="T2") assert relations == []
def test_loadJsonFile():
scriptDir = os.path.dirname(__file__)
jsonPath = os.path.join(scriptDir, 'data', 'example.json')
data = kindred.loadDoc(dataFormat='json', path=jsonPath)
assert isinstance(data, kindred.Document)
entities = data.getEntities()
relations = data.getRelations()
sourceEntityIDsToEntityIDs = data.getSourceEntityIDsToEntityIDs()
assertEntity(entities[0],
expectedType='disease',
expectedText='colorectal cancer',
expectedPos=[(4, 21)],
expectedSourceEntityID="T1")
assertEntity(entities[1],
expectedType='gene',
expectedText='APC',
expectedPos=[(49, 52)],
expectedSourceEntityID="T2")
assert relations == [
kindred.Relation('causes', [
sourceEntityIDsToEntityIDs["T1"], sourceEntityIDsToEntityIDs["T2"]
], ['obj', 'subj'])
], "(%s) not as expected" % relations
def test_loadStandoffFile_Triple():
scriptDir = os.path.dirname(__file__)
txtPath = os.path.join(scriptDir,'data_triple','example.txt')
a1Path = os.path.join(scriptDir,'data_triple','example.a1')
a2Path = os.path.join(scriptDir,'data_triple','example.a2')
data = kindred.loadDoc(dataFormat='standoff',txtPath=txtPath,a1Path=a1Path,a2Path=a2Path)
assert isinstance(data,kindred.Document)
entities = data.getEntities()
relations = data.getRelations()
sourceEntityIDsToEntityIDs = data.getSourceEntityIDsToEntityIDs()
assertEntity(entities[0],expectedType='drug',expectedText='Erlotinib',expectedPos=[(0,9)],expectedSourceEntityID="T1")
assertEntity(entities[1],expectedType='gene',expectedText='EGFR',expectedPos=[(13,17)],expectedSourceEntityID="T2")
assertEntity(entities[2],expectedType='disease',expectedText='NSCLC',expectedPos=[(49,54)],expectedSourceEntityID="T3")
assert relations == [kindred.Relation('druginfo',[sourceEntityIDsToEntityIDs["T3"],sourceEntityIDsToEntityIDs["T1"],sourceEntityIDsToEntityIDs["T2"]],['disease','drug','gene'])], "(%s) not as expected" % relations
