def test_seed (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.content)
# Test the source
source = random.randint (0,100)
f = setField(p, 'source', source)
f = getField(p, 'source')
assert source == int(f.content)
# Test the cubelocation
cubelocation = random.randint (0,100)
f = setField(p, 'cubelocation', cubelocation)
f = getField(p, 'cubelocation')
assert cubelocation == int(f.content)
# 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.content
def test_wrong(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.content)
# Test the weight
weight = random.random()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert abs(weight - float(f.content)) < 0.001
# Test inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# bad format to a number
url = "https://{}/sd/{}/{}/{}/setField/status/aa/".format(
SITE_HOST, 'unittest', 'unit_anno', p.annoid)
req = getURL(url)
assert (req.status_code >= 400)
# request a missing field
url = "https://{}/sd/{}/{}/{}/getField/othernonesuch/".format(
SITE_HOST, 'unittest', 'unit_anno', p.annoid)
req = getURL(url)
assert (req.status_code >= 400)
def test_organelle (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.content)
# Test the organelleclass
organelleclass = random.randint (0,100)
f = setField(p, 'organelleclass', organelleclass)
f = getField(p, 'organelleclass')
assert organelleclass == int(f.content)
# Test the segment
segment = random.randint (0,65535)
f = setField(p, 'segment', segment)
f = getField(p, 'segment')
assert segment == int(f.content)
# Test status
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# 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.content
def test_wrong ( 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.content)
# Test the weight
weight = random.random ()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert abs(weight - float(f.content)) < 0.001
# Test inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# bad format to a number
url = "https://{}/sd/{}/{}/{}/setField/status/aa/".format(SITE_HOST, 'unittest', 'unit_anno', p.annoid)
req = getURL( url )
assert(req.status_code >= 400)
# request a missing field
url = "https://{}/sd/{}/{}/{}/getField/othernonesuch/".format(SITE_HOST, 'unittest', 'unit_anno', p.annoid)
req = getURL( url )
assert(req.status_code >= 400)
def test_roi (self):
"""Upload an roi and test it's fields"""
# Make a skeleton
makeAnno (p, 9)
# test the parent
parent = random.randint (0,65535)
f = setField(p, 'parent', parent)
f = getField(p, 'parent')
assert parent == int(f.content)
# make a bunch of children ROIs
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
childids = []
for i in range(0,4):
makeAnno ( q, 9)
f = setField(q, 'parent', p.annoid)
childids.append(q.annoid)
# Test children
f = getField(p, 'children')
rchildids = f.content.split(',')
for cid in rchildids:
assert int(cid) in childids
assert len(rchildids) == 4
def test_seed(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.content)
# Test the source
source = random.randint(0, 100)
f = setField(p, 'source', source)
f = getField(p, 'source')
assert source == int(f.content)
# Test the cubelocation
cubelocation = random.randint(0, 100)
f = setField(p, 'cubelocation', cubelocation)
f = getField(p, 'cubelocation')
assert cubelocation == int(f.content)
# 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.content
def test_roi(self):
"""Upload an roi and test it's fields"""
# Make a skeleton
makeAnno(p, 9)
# test the parent
parent = random.randint(0, 65535)
f = setField(p, 'parent', parent)
f = getField(p, 'parent')
assert parent == int(f.content)
# make a bunch of children ROIs
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
childids = []
for i in range(0, 4):
makeAnno(q, 9)
f = setField(q, 'parent', p.annoid)
childids.append(q.annoid)
# Test children
f = getField(p, 'children')
rchildids = f.content.split(',')
for cid in rchildids:
assert int(cid) in childids
assert len(rchildids) == 4
def test_annotation (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.content)
# Test confidence
confidence = random.random ()
f = setField(p, 'confidence', confidence)
f = getField(p, 'confidence')
assert abs(confidence - float(f.content)) < 0.001
def test_annotation(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.content)
# Test confidence
confidence = random.random()
f = setField(p, 'confidence', confidence)
f = getField(p, 'confidence')
assert abs(confidence - float(f.content)) < 0.001
def test_node (self):
"""Upload a skeleton node and test it's fields"""
# Make a node
makeAnno (p, 7)
# test the nodetype
nodetype = random.randint (0,100)
f = setField(p, 'nodetype', nodetype)
f = getField(p, 'nodetype')
assert nodetype == int(f.content)
# test the skeletonid
skeletonid = random.randint (0,65535)
f = setField(p, 'skeletonid', skeletonid)
f = getField(p, 'skeletonid')
assert skeletonid == int(f.content)
# test the pointid
pointid = random.randint (0,65535)
f = setField(p, 'pointid', pointid)
f = getField(p, 'pointid')
assert pointid == int(f.content)
# test the parentid
parentid = random.randint (0,65535)
f = setField(p, 'parentid', parentid)
f = getField(p, 'parentid')
assert parentid == int(f.content)
# test the radius
radius = random.random()
f = setField(p, 'radius', radius)
f = getField(p, 'radius')
assert abs(radius - float(f.content)) < 0.001
# test the location
location = [random.random(), random.random(), random.random()]
f = setField(p, 'location', ','.join([str(i) for i in location]))
f = getField(p, 'location')
assert ','.join([str(i) for i in location]) == f.content
# make a bunch of children
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
childids = []
for i in range(0,4):
makeAnno ( q, 9)
f = setField(q, 'parent', p.annoid)
childids.append(q.annoid)
# Test children
f = getField(p, 'children')
rchildids = f.content.split(',')
for cid in rchildids:
assert int(cid) in childids
assert len(rchildids) == 4
def test_node(self):
"""Upload a skeleton node and test it's fields"""
# Make a node
makeAnno(p, 7)
# test the nodetype
nodetype = random.randint(0, 100)
f = setField(p, 'nodetype', nodetype)
f = getField(p, 'nodetype')
assert nodetype == int(f.content)
# test the skeletonid
skeletonid = random.randint(0, 65535)
f = setField(p, 'skeletonid', skeletonid)
f = getField(p, 'skeletonid')
assert skeletonid == int(f.content)
# test the pointid
pointid = random.randint(0, 65535)
f = setField(p, 'pointid', pointid)
f = getField(p, 'pointid')
assert pointid == int(f.content)
# test the parentid
parentid = random.randint(0, 65535)
f = setField(p, 'parentid', parentid)
f = getField(p, 'parentid')
assert parentid == int(f.content)
# test the radius
radius = random.random()
f = setField(p, 'radius', radius)
f = getField(p, 'radius')
assert abs(radius - float(f.content)) < 0.001
# test the location
location = [random.random(), random.random(), random.random()]
f = setField(p, 'location', ','.join([str(i) for i in location]))
f = getField(p, 'location')
assert ','.join([str(i) for i in location]) == f.content
# make a bunch of children
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
childids = []
for i in range(0, 4):
makeAnno(q, 9)
f = setField(q, 'parent', p.annoid)
childids.append(q.annoid)
# Test children
f = getField(p, 'children')
rchildids = f.content.split(',')
for cid in rchildids:
assert int(cid) in childids
assert len(rchildids) == 4
def test_synapse (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.content)
# Test the weight
weight = random.random ()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert abs(weight - float(f.content)) < 0.001
# Test the inheritance
status = random.randint (0,100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# 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.content
# test the centroid
centroid = [random.randint(0,65535), random.randint(0,65535), random.randint(0,65535)]
f = setField(p, 'centroid', ','.join([str(i) for i in centroid]))
f = getField(p, 'centroid')
assert ','.join([str(i) for i in centroid]) == f.content
# Test the segments
segments = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'segments', ','.join([str(i) for i in segments]))
f = getField(p, 'segments')
assert ','.join([str(i) for i in segments]) == f.content
# Test the presegments
presegments = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'presegments', ','.join([str(i) for i in presegments]))
f = getField(p, 'presegments')
assert ','.join([str(i) for i in presegments]) == f.content
# Test the postsegments
postsegments = [random.randint(0,100), random.randint(0,100), random.randint(0,100)]
f = setField(p, 'postsegments', ','.join([str(i) for i in postsegments]))
f = getField(p, 'postsegments')
assert ','.join([str(i) for i in postsegments]) == f.content
def test_kvpairs(self):
# do a general kv test for each annotation type
for i in range(1,10):
makeAnno (p, i)
key = ''.join(random.choice(string.ascii_letters + string.digits) for _ in range(random.randint(1,128)))
value = ''.join(random.choice(string.ascii_letters + string.digits) for _ in range(random.randint(1,1024)))
setField( p, key, value )
f = getField ( p, key )
assert ( f.content == value )
def test_organelle(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.content)
# Test the organelleclass
organelleclass = random.randint(0, 100)
f = setField(p, 'organelleclass', organelleclass)
f = getField(p, 'organelleclass')
assert organelleclass == int(f.content)
# Test the segment
segment = random.randint(0, 65535)
f = setField(p, 'segment', segment)
f = getField(p, 'segment')
assert segment == int(f.content)
# Test status
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# 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.content
def test_kvpairs(self):
# do a general kv test for each annotation type
for i in range(1, 10):
makeAnno(p, i)
key = ''.join(
random.choice(string.ascii_letters + string.digits)
for _ in range(random.randint(1, 128)))
value = ''.join(
random.choice(string.ascii_letters + string.digits)
for _ in range(random.randint(1, 1024)))
setField(p, key, value)
f = getField(p, key)
assert (f.content == value)
def test_neuron(self):
"""Upload a neuron and test it's fields"""
# Make a neuron
makeAnno(p, 5)
# make a bunch of segments and add to the neuron
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
segids = []
for i in range(0, 5):
makeAnno(q, 4)
f = setField(q, 'neuron', p.annoid)
segids.append(q.annoid)
# Test segments
f = getField(p, 'segments')
rsegids = f.content.split(',')
for sid in rsegids:
assert int(sid) in segids
assert len(rsegids) == 5
def test_neuron (self):
"""Upload a neuron and test it's fields"""
# Make a neuron
makeAnno (p, 5)
# make a bunch of segments and add to the neuron
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
segids = []
for i in range(0,5):
makeAnno ( q, 4)
f = setField(q, 'neuron', p.annoid)
segids.append(q.annoid)
# Test segments
f = getField(p, 'segments')
rsegids = f.content.split(',')
for sid in rsegids:
assert int(sid) in segids
assert len(rsegids) == 5
def test_skeleton (self):
"""Upload a skeleton and test it's fields"""
# Make a node
makeAnno (p, 8)
# test the nodetype
skeletontype = random.randint (0,100)
f = setField(p, 'skeletontype', skeletontype)
f = getField(p, 'skeletontype')
assert skeletontype == int(f.content)
# test the rootnode
rootnode = random.randint (0,65535)
f = setField(p, 'rootnode', rootnode)
f = getField(p, 'rootnode')
assert rootnode == int(f.content)
# add some nodes to the skeleton and query them
# make a bunch of children cnodes
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
r = Params()
r.token = 'unittest'
r.resolution = 0
r.channels = ['unit_anno']
# make a root node
s = Params()
s.token = 'unittest'
s.resolution = 0
s.channels = ['unit_anno']
# make a root node
skelids = []
# make a root node
makeAnno ( q, 7)
setField(p, 'rootnode', q.annoid)
setField(q, 'skeleton', p.annoid)
skelids.append(q.annoid)
# Make 2 children and four grandchildren
for i in range(0,2):
makeAnno ( r, 7)
f = setField(r, 'parent', q.annoid)
f = setField(r, 'skeleton', p.annoid)
skelids.append(r.annoid)
for i in range(0,2):
makeAnno ( s, 7)
f = setField(s, 'parent', r.annoid)
f = setField(s, 'skeleton', p.annoid)
skelids.append(s.annoid)
# Test skeleton
f = getField(p, 'nodes')
rskelids = f.content.split(',')
for sid in rskelids:
assert int(sid) in skelids
assert len(rskelids) == 7
def test_test_segment (self):
"""Upload a segment and test it's fields"""
for i in range(1,10):
makeAnno (p, 1)
# Make a segment
makeAnno (p, 4)
# make a bunch of synapses
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
synids = []
presynids = []
postsynids = []
for i in range(0,8):
makeAnno ( q, 2)
f = setField(q, 'segments', ','.join([str(p.annoid),str(random.randint(500,1000))]))
# f = setField(q, 'presegments', ','.join([str(p.annoid),str(random.randint(500,1000))]))
f = setField(q, 'presegments', ','.join([str(p.annoid)]))
f = setField(q, 'postsegments', ','.join([str(p.annoid)]))
synids.append(q.annoid)
presynids.append(q.annoid)
postsynids.append(q.annoid)
# make one more segment
makeAnno ( q, 2)
f = setField(q, 'segments', p.annoid)
synids.append(q.annoid)
# Test synapses
f = getField(p, 'synapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in synids
assert len(rsynids) == 9
# Test presynapses
f = getField(p, 'presynapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in presynids
assert len(rsynids) == 8
# Test postsynapses
f = getField(p, 'postsynapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in postsynids
assert len(rsynids) == 8
# make a bunch of organelles
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
orgids = []
for i in range(0,8):
makeAnno ( q, 6 )
f = setField(q, 'segment', p.annoid)
orgids.append(q.annoid)
# Test synapses
f = getField(p, 'organelles')
rorgids = f.content.split(',')
for cid in rorgids:
assert int(cid) in orgids
assert len(rorgids) == 8
def test_test_segment(self):
"""Upload a segment and test it's fields"""
for i in range(1, 10):
makeAnno(p, 1)
# Make a segment
makeAnno(p, 4)
# make a bunch of synapses
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
synids = []
presynids = []
postsynids = []
for i in range(0, 8):
makeAnno(q, 2)
f = setField(
q, 'segments',
','.join([str(p.annoid),
str(random.randint(500, 1000))]))
# f = setField(q, 'presegments', ','.join([str(p.annoid),str(random.randint(500,1000))]))
f = setField(q, 'presegments', ','.join([str(p.annoid)]))
f = setField(q, 'postsegments', ','.join([str(p.annoid)]))
synids.append(q.annoid)
presynids.append(q.annoid)
postsynids.append(q.annoid)
# make one more segment
makeAnno(q, 2)
f = setField(q, 'segments', p.annoid)
synids.append(q.annoid)
# Test synapses
f = getField(p, 'synapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in synids
assert len(rsynids) == 9
# Test presynapses
f = getField(p, 'presynapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in presynids
assert len(rsynids) == 8
# Test postsynapses
f = getField(p, 'postsynapses')
rsynids = f.content.split(',')
for sid in rsynids:
assert int(sid) in postsynids
assert len(rsynids) == 8
# make a bunch of organelles
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
orgids = []
for i in range(0, 8):
makeAnno(q, 6)
f = setField(q, 'segment', p.annoid)
orgids.append(q.annoid)
# Test synapses
f = getField(p, 'organelles')
rorgids = f.content.split(',')
for cid in rorgids:
assert int(cid) in orgids
assert len(rorgids) == 8
def test_synapse(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.content)
# Test the weight
weight = random.random()
f = setField(p, 'weight', weight)
f = getField(p, 'weight')
assert abs(weight - float(f.content)) < 0.001
# Test the inheritance
status = random.randint(0, 100)
f = setField(p, 'status', status)
f = getField(p, 'status')
assert status == int(f.content)
# 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.content
# test the centroid
centroid = [
random.randint(0, 65535),
random.randint(0, 65535),
random.randint(0, 65535)
]
f = setField(p, 'centroid', ','.join([str(i) for i in centroid]))
f = getField(p, 'centroid')
assert ','.join([str(i) for i in centroid]) == f.content
# Test the segments
segments = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'segments', ','.join([str(i) for i in segments]))
f = getField(p, 'segments')
assert ','.join([str(i) for i in segments]) == f.content
# Test the presegments
presegments = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'presegments', ','.join([str(i) for i in presegments]))
f = getField(p, 'presegments')
assert ','.join([str(i) for i in presegments]) == f.content
# Test the postsegments
postsegments = [
random.randint(0, 100),
random.randint(0, 100),
random.randint(0, 100)
]
f = setField(p, 'postsegments',
','.join([str(i) for i in postsegments]))
f = getField(p, 'postsegments')
assert ','.join([str(i) for i in postsegments]) == f.content
def test_skeleton(self):
"""Upload a skeleton and test it's fields"""
# Make a node
makeAnno(p, 8)
# test the nodetype
skeletontype = random.randint(0, 100)
f = setField(p, 'skeletontype', skeletontype)
f = getField(p, 'skeletontype')
assert skeletontype == int(f.content)
# test the rootnode
rootnode = random.randint(0, 65535)
f = setField(p, 'rootnode', rootnode)
f = getField(p, 'rootnode')
assert rootnode == int(f.content)
# add some nodes to the skeleton and query them
# make a bunch of children cnodes
q = Params()
q.token = 'unittest'
q.resolution = 0
q.channels = ['unit_anno']
r = Params()
r.token = 'unittest'
r.resolution = 0
r.channels = ['unit_anno']
# make a root node
s = Params()
s.token = 'unittest'
s.resolution = 0
s.channels = ['unit_anno']
# make a root node
skelids = []
# make a root node
makeAnno(q, 7)
setField(p, 'rootnode', q.annoid)
setField(q, 'skeleton', p.annoid)
skelids.append(q.annoid)
# Make 2 children and four grandchildren
for i in range(0, 2):
makeAnno(r, 7)
f = setField(r, 'parent', q.annoid)
f = setField(r, 'skeleton', p.annoid)
skelids.append(r.annoid)
for i in range(0, 2):
makeAnno(s, 7)
f = setField(s, 'parent', r.annoid)
f = setField(s, 'skeleton', p.annoid)
skelids.append(s.annoid)
# Test skeleton
f = getField(p, 'nodes')
rskelids = f.content.split(',')
for sid in rskelids:
assert int(sid) in skelids
assert len(rskelids) == 7
