def test_wrong_field ( self ):
# Make an annotation
makeAnno (p, 2)
# Test the synapse type
synapse_type = random.randint (0,100)
f = setField(p, 'synapse_type', synapse_type)
f = getField(p, 'synapse_type')
assert synapse_type == int(f.read())
# Test the weight
weight = random.random ()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert weight - float(f.read()) < 0.001
# Test inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# bad format to a number
url = "http://{}/ca/{}/{}/{}/setField/status/aa/".format(SITE_HOST, 'unittest', 'unit_anno', p.annoid)
with pytest.raises(urllib2.HTTPError):
req = urllib2.Request ( url )
f = urllib2.urlopen ( url )
# request a missing field
url = "http://{}/ca/{}/{}/{}/getField/othernonesuch/".format(SITE_HOST, 'unittest', 'unit_anno', p.annoid)
with pytest.raises(urllib2.HTTPError):
req = urllib2.Request ( url )
f = urllib2.urlopen ( url )
def test_seed_field (self):
"""Upload a seed and test it's fields"""
# Make a seed
makeAnno (p, 3)
# Test the parent
parent = random.randint (0,100)
f = setField(p, 'parent', parent)
f = getField(p, 'parent')
assert parent == int(f.read())
# Test the source
source = random.randint (0,100)
f = setField(p, 'source', source)
f = getField(p, 'source')
assert source == int(f.read())
# Test the cubelocation
cubelocation = random.randint (0,100)
f = setField(p, 'cubelocation', cubelocation)
f = getField(p, 'cubelocation')
assert cubelocation == int(f.read())
# Test the position
position = [random.randint (0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'position', ','.join([str(i) for i in position]))
f = getField(p, 'position')
assert ','.join([str(i) for i in position]) == f.read()
def test_organelle_field (self):
"""Upload an organelle and test it's fields"""
# Make an organelle
makeAnno ( p, 6 )
# Test the parentseed
parentseed = random.randint (0,100)
f = setField(p, 'parentseed', parentseed)
f = getField(p, 'parentseed')
assert parentseed == int(f.read())
# Test the organelleclass
organelleclass = random.randint (0,100)
f = setField(p, 'organelleclass', organelleclass)
f = getField(p, 'organelleclass')
assert organelleclass == int(f.read())
# Test inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the seeds
seeds = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'seeds', ','.join([str(i) for i in seeds]))
f = getField(p, 'seeds')
assert ','.join([str(i) for i in seeds]) == f.read()
def test_segment_field (self):
"""Upload a segment and test it's fields"""
# Make a segment
makeAnno (p, 4)
# Test the parentseed
parentseed = random.randint (0,100)
f = setField(p, 'parentseed', parentseed)
f = getField(p, 'parentseed')
assert parentseed == int(f.read())
# Test the segmentclass
segmentclass = random.randint (0,100)
f = setField(p, 'segmentclass', segmentclass)
f = getField(p, 'segmentclass')
assert segmentclass == int(f.read())
# Test the neuron
neuron = random.randint (0,100)
f = setField(p, 'neuron', neuron)
f = getField(p, 'neuron')
assert neuron == int(f.read())
# Test inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the synapses
synapses = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'synapses', ','.join([str(i) for i in synapses]))
f = getField(p, 'synapses')
assert ','.join([str(i) for i in synapses]) == f.read()
def test_seed_field(self):
"""Upload a seed and test it's fields"""
# Make a seed
makeAnno(p, 3)
# Test the parent
parent = random.randint(0, 100)
f = setField(p, 'parent', parent)
f = getField(p, 'parent')
assert parent == int(f.read())
# Test the source
source = random.randint(0, 100)
f = setField(p, 'source', source)
f = getField(p, 'source')
assert source == int(f.read())
# Test the cubelocation
cubelocation = random.randint(0, 100)
f = setField(p, 'cubelocation', cubelocation)
f = getField(p, 'cubelocation')
assert cubelocation == int(f.read())
# Test the position
position = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'position', ','.join([str(i) for i in position]))
f = getField(p, 'position')
assert ','.join([str(i) for i in position]) == f.read()
def test_synapse_field (self):
"""Upload a synapse and test it's fields"""
# Make a synapse
makeAnno (p, 2)
# Test synapse type
synapse_type = random.randint (0,100)
f = setField(p, 'synapse_type', synapse_type)
f = getField(p, 'synapse_type')
assert synapse_type == int(f.read())
# Test the weight
weight = random.random ()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert weight - float(f.read()) < 0.001
# Test the inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the seeds
seeds = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'seeds', ','.join([str(i) for i in seeds]))
f = getField(p, 'seeds')
assert ','.join([str(i) for i in seeds]) == f.read()
def test_organelle_field(self):
"""Upload an organelle and test it's fields"""
# Make an organelle
makeAnno(p, 6)
# Test the parentseed
parentseed = random.randint(0, 100)
f = setField(p, 'parentseed', parentseed)
f = getField(p, 'parentseed')
assert parentseed == int(f.read())
# Test the organelleclass
organelleclass = random.randint(0, 100)
f = setField(p, 'organelleclass', organelleclass)
f = getField(p, 'organelleclass')
assert organelleclass == int(f.read())
# Test inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the seeds
seeds = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'seeds', ','.join([str(i) for i in seeds]))
f = getField(p, 'seeds')
assert ','.join([str(i) for i in seeds]) == f.read()
def test_synapse_field(self):
"""Upload a synapse and test it's fields"""
# Make a synapse
makeAnno(p, 2)
# Test synapse type
synapse_type = random.randint(0, 100)
f = setField(p, 'synapse_type', synapse_type)
f = getField(p, 'synapse_type')
assert synapse_type == int(f.read())
# Test the weight
weight = random.random()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert weight - float(f.read()) < 0.001
# Test the inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the seeds
seeds = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'seeds', ','.join([str(i) for i in seeds]))
f = getField(p, 'seeds')
assert ','.join([str(i) for i in seeds]) == f.read()
def test_neuron_field (self):
"""Upload a neuron and test it's fields"""
# Make a neuron
makeAnno (p, 5)
# Test inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test segments
status = [random.randint (0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'segments', ",".join([str(i) for i in status]))
f = getField(p, 'segments')
assert ",".join([str(i) for i in status]) == f.read()
def test_annotation_field (self):
"""Upload an annotation and test it's fields"""
# Make an annotation
makeAnno (p, 1)
# Test Status
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test confidence
confidence = random.random ()
f = setField(p, 'confidence', confidence)
f = getField(p, 'confidence')
assert confidence - float(f.read()) < 0.001
def test_annotation_field(self):
"""Upload an annotation and test it's fields"""
# Make an annotation
makeAnno(p, 1)
# Test Status
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test confidence
confidence = random.random()
f = setField(p, 'confidence', confidence)
f = getField(p, 'confidence')
assert confidence - float(f.read()) < 0.001
def test_neuron_field(self):
"""Upload a neuron and test it's fields"""
# Make a neuron
makeAnno(p, 5)
# Test inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test segments
status = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'segments', ",".join([str(i) for i in status]))
f = getField(p, 'segments')
assert ",".join([str(i) for i in status]) == f.read()
def test_segment_field(self):
"""Upload a segment and test it's fields"""
# Make a segment
makeAnno(p, 4)
# Test the parentseed
parentseed = random.randint(0, 100)
f = setField(p, 'parentseed', parentseed)
f = getField(p, 'parentseed')
assert parentseed == int(f.read())
# Test the segmentclass
segmentclass = random.randint(0, 100)
f = setField(p, 'segmentclass', segmentclass)
f = getField(p, 'segmentclass')
assert segmentclass == int(f.read())
# Test the neuron
neuron = random.randint(0, 100)
f = setField(p, 'neuron', neuron)
f = getField(p, 'neuron')
assert neuron == int(f.read())
# Test inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# Test the synapses
synapses = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'synapses', ','.join([str(i) for i in synapses]))
f = getField(p, 'synapses')
assert ','.join([str(i) for i in synapses]) == f.read()
def test_wrong_field(self):
# Make an annotation
makeAnno(p, 2)
# Test the synapse type
synapse_type = random.randint(0, 100)
f = setField(p, 'synapse_type', synapse_type)
f = getField(p, 'synapse_type')
assert synapse_type == int(f.read())
# Test the weight
weight = random.random()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert weight - float(f.read()) < 0.001
# Test inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.read())
# bad format to a number
url = "http://{}/ca/{}/{}/{}/setField/status/aa/".format(
SITE_HOST, 'unittest', 'unit_anno', p.annoid)
with pytest.raises(urllib2.HTTPError):
req = urllib2.Request(url)
f = urllib2.urlopen(url)
# request a missing field
url = "http://{}/ca/{}/{}/{}/getField/othernonesuch/".format(
SITE_HOST, 'unittest', 'unit_anno', p.annoid)
with pytest.raises(urllib2.HTTPError):
req = urllib2.Request(url)
f = urllib2.urlopen(url)
def test_query_objects(self):
"""Test the function that lists objects of different types."""
# synapse annotations
p.anntype = 2
status = random.randint(0, 100)
confidence = random.random() * 0.3 + 0.1 # number between 0.1 and 0.4
synapse_type = random.randint(0, 100)
synapse_weight = random.random(
) * 0.9 + 0.1 # number between 0.1 and 0.9
for i in range(10):
# Make an annotation
#annid = makeAnno ( anntype, SITE_HOST )
makeAnno(p, p.anntype)
#H5AnnotationFile(p)
# set some fields in the even annotations
if i % 2 == 0:
setField(p, 'status', status)
# set the confidence
setField(p, 'confidence', confidence)
# set the type
setField(p, 'synapse_type', synapse_type)
# set some fields in the even annotations
if i % 2 == 1:
# set the confidence
setField(p, 'confidence', 1.0 - confidence)
# check the status
h5 = queryField(p, 'status', status)
assert (h5['ANNOIDS'].shape[0] == 5)
# check all the confidence variants
field_value = '/'.join(['lt', str(1.0 - confidence - 0.0001), ''])
h5 = queryField(p, 'confidence', field_value)
assert (h5['ANNOIDS'].shape[0] == 5)
field_value = '/'.join(['gt', str(confidence + 0.0001), ''])
h5 = queryField(p, 'confidence', field_value)
assert (h5['ANNOIDS'].shape[0] == 5)
def test_query_objects (self):
"""Test the function that lists objects of different types."""
# synapse annotations
p.anntype = 2
status = random.randint(0,100)
confidence = random.random()*0.3+0.1 # number between 0.1 and 0.4
synapse_type = random.randint(0,100)
synapse_weight = random.random()*0.9+0.1 # number between 0.1 and 0.9
for i in range (10):
# Make an annotation
#annid = makeAnno ( anntype, SITE_HOST )
makeAnno( p, p.anntype)
#H5AnnotationFile(p)
# set some fields in the even annotations
if i % 2 == 0:
setField(p, 'status', status)
# set the confidence
setField(p, 'confidence', confidence)
# set the type
setField(p, 'synapse_type', synapse_type)
# set some fields in the even annotations
if i % 2 == 1:
# set the confidence
setField(p, 'confidence', 1.0 - confidence)
# check the status
h5 = queryField(p, 'status', status)
assert ( h5['ANNOIDS'].shape[0] == 5 )
# check all the confidence variants
field_value = '/'.join( ['lt',str(1.0-confidence-0.0001), ''] )
h5 = queryField(p, 'confidence', field_value)
assert ( h5['ANNOIDS'].shape[0] == 5 )
field_value = '/'.join( ['gt',str(confidence+0.0001), ''] )
h5 = queryField(p, 'confidence', field_value)
assert ( h5['ANNOIDS'].shape[0] == 5 )
