def test_annotation_creation(self):
self.fake_authentication()
neuron_ids = [2365, 2381]
# Expect entity 2365 and 2381 to be not annotated
for nid in neuron_ids:
aq = create_annotation_query(self.test_project_id, {'neuron_id': nid})
self.assertEqual(len(aq), 0)
# Annotate both with the same annotation
_annotate_entities(self.test_project_id, neuron_ids,
{'myannotation': {'user_id': self.test_user_id}})
# Expect entity 2365 and 2381 to be annotated
for nid in neuron_ids:
aq = create_annotation_query(self.test_project_id, {'neuron_id': nid})
self.assertEqual(len(aq), 1)
self.assertEqual(aq[0].name, 'myannotation')
# Annotate both with the pattern annotation
_annotate_entities(self.test_project_id, neuron_ids,
{'pattern {n9} test-{n}-annotation': { 'user_id': self.test_user_id}})
# Expect entity 2365 and 2381 to be annotated
aq = create_annotation_query(self.test_project_id, {'neuron_id': 2365}).order_by('name')
self.assertEqual(len(aq), 2)
self.assertEqual(aq[0].name, 'myannotation')
self.assertEqual(aq[1].name, 'pattern 9 test-1-annotation')
aq = create_annotation_query(self.test_project_id, {'neuron_id': 2381}).order_by('name')
self.assertEqual(len(aq), 2)
self.assertEqual(aq[0].name, 'myannotation')
self.assertEqual(aq[1].name, 'pattern 10 test-2-annotation')
def test_rename_neuron_fail(self):
self.fake_authentication()
neuron_id = 362
# Lock this neuron for another user
_annotate_entities(self.test_project_id, [neuron_id],
{'locked': {
'user_id': 1
}})
count_logs = lambda: Log.objects.all().count()
log_count = count_logs()
old_name = ClassInstance.objects.get(id=neuron_id).name
new_name = 'newname'
self.assertFalse(old_name == new_name)
url = '/%d/neurons/%s/rename' % (self.test_project_id, neuron_id)
response = self.client.post(url, {'name': new_name})
self.assertEqual(response.status_code, 200)
parsed_response = json.loads(response.content.decode('utf-8'))
self.assertTrue('error' in parsed_response)
self.assertTrue(parsed_response['error'])
self.assertEqual(old_name,
ClassInstance.objects.get(id=neuron_id).name)
self.assertEqual(log_count, count_logs())
def test_annotation_creation(self):
self.fake_authentication()
neuron_ids = [2365, 2381]
# Expect entity 2365 and 2381 to be not annotated
for nid in neuron_ids:
aq = create_annotation_query(self.test_project_id, {'neuron_id': nid})
self.assertEqual(len(aq), 0)
# Annotate both with the same annotation
_annotate_entities(self.test_project_id, neuron_ids,
{'myannotation': self.test_user_id})
# Expect entity 2365 and 2381 to be annotated
for nid in neuron_ids:
aq = create_annotation_query(self.test_project_id, {'neuron_id': nid})
self.assertEqual(len(aq), 1)
self.assertEqual(aq[0].name, 'myannotation')
# Annotate both with the pattern annotation
_annotate_entities(self.test_project_id, neuron_ids,
{'pattern {n9} test-{n}-annotation': self.test_user_id})
# Expect entity 2365 and 2381 to be annotated
aq = create_annotation_query(self.test_project_id, {'neuron_id': 2365}).order_by('name')
self.assertEqual(len(aq), 2)
self.assertEqual(aq[0].name, 'myannotation')
self.assertEqual(aq[1].name, 'pattern 9 test-1-annotation')
aq = create_annotation_query(self.test_project_id, {'neuron_id': 2381}).order_by('name')
self.assertEqual(len(aq), 2)
self.assertEqual(aq[0].name, 'myannotation')
self.assertEqual(aq[1].name, 'pattern 10 test-2-annotation')
def test_export_compact_skeleton_with_annotations(self):
self.fake_authentication()
skeleton_id = 373
neuron_id = 374
_, new_annotations = _annotate_entities(self.test_project_id, [neuron_id],
{'myannotation': {'user_id': self.test_user_id}})
new_annotation_link_id = new_annotations.pop()
url = '/%d/%d/1/1/compact-skeleton' % (self.test_project_id, skeleton_id)
response = self.client.get(url, {
'with_annotations': True
})
self.assertEqual(response.status_code, 200)
parsed_response = json.loads(response.content.decode('utf-8'))
expected_response = [
[[377, None, 3, 7620.0, 2890.0, 0.0, -1.0, 5],
[403, 377, 3, 7840.0, 2380.0, 0.0, -1.0, 5],
[405, 377, 3, 7390.0, 3510.0, 0.0, -1.0, 5],
[407, 405, 3, 7080.0, 3960.0, 0.0, -1.0, 5],
[409, 407, 3, 6630.0, 4330.0, 0.0, -1.0, 5]],
[[377, 356, 1, 6730.0, 2700.0, 0.0],
[409, 421, 1, 6260.0, 3990.0, 0.0]],
{"uncertain end": [403]},
[],
[[new_annotation_link_id]]]
self.assertEqual(len(parsed_response), len(expected_response))
six.assertCountEqual(self, parsed_response[0], expected_response[0])
six.assertCountEqual(self, parsed_response[1], expected_response[1])
self.assertEqual(parsed_response[2], expected_response[2])
self.assertEqual(parsed_response[3], expected_response[3])
self.assertEqual(parsed_response[4], expected_response[4])
def test_export_compact_skeleton_with_annotations(self):
self.fake_authentication()
skeleton_id = 373
neuron_id = 374
_, new_annotations = _annotate_entities(
self.test_project_id, [neuron_id],
{'myannotation': {
'user_id': self.test_user_id
}})
new_annotation_link_id = new_annotations.pop()
url = '/%d/%d/1/1/compact-skeleton' % (self.test_project_id,
skeleton_id)
response = self.client.get(url, {'with_annotations': True})
self.assertEqual(response.status_code, 200)
parsed_response = json.loads(response.content.decode('utf-8'))
expected_response = [[[377, None, 3, 7620.0, 2890.0, 0.0, -1.0, 5],
[403, 377, 3, 7840.0, 2380.0, 0.0, -1.0, 5],
[405, 377, 3, 7390.0, 3510.0, 0.0, -1.0, 5],
[407, 405, 3, 7080.0, 3960.0, 0.0, -1.0, 5],
[409, 407, 3, 6630.0, 4330.0, 0.0, -1.0, 5]],
[[377, 356, 1, 6730.0, 2700.0, 0.0],
[409, 421, 1, 6260.0, 3990.0, 0.0]], {
"uncertain end": [403]
}, [], [[new_annotation_link_id]]]
self.assertEqual(len(parsed_response), len(expected_response))
six.assertCountEqual(self, parsed_response[0], expected_response[0])
six.assertCountEqual(self, parsed_response[1], expected_response[1])
self.assertEqual(parsed_response[2], expected_response[2])
self.assertEqual(parsed_response[3], expected_response[3])
self.assertEqual(parsed_response[4], expected_response[4])
def test_rename_neuron_fail(self):
self.fake_authentication()
neuron_id = 362
# Lock this neuron for another user
_annotate_entities(self.test_project_id, [neuron_id], {'locked': 1})
count_logs = lambda: Log.objects.all().count()
log_count = count_logs()
old_name = ClassInstance.objects.get(id=neuron_id).name
new_name = 'newname'
self.assertFalse(old_name == new_name)
url = '/%d/neurons/%s/rename' % (self.test_project_id, neuron_id)
response = self.client.post(url, {'name': new_name})
self.assertEqual(response.status_code, 200)
parsed_response = json.loads(response.content)
self.assertTrue('error' in parsed_response)
self.assertTrue(parsed_response['error'])
self.assertEqual(old_name, ClassInstance.objects.get(id=neuron_id).name)
self.assertEqual(log_count, count_logs())
def split_skeleton(request, project_id=None):
""" The split is only possible if the neuron is not locked or if it is
locked by the current user or if the current user belongs to the group
of the user who locked it. Of course, the split is also possible if
the current user is a super-user.
"""
treenode_id = int(request.POST['treenode_id'])
treenode = Treenode.objects.get(pk=treenode_id)
skeleton_id = treenode.skeleton_id
upstream_annotation_set = frozenset([v for k,v in request.POST.iteritems()
if k.startswith('upstream_annotation_set[')])
downstream_annotation_set = frozenset([v for k,v in request.POST.iteritems()
if k.startswith('downstream_annotation_set[')])
cursor = connection.cursor()
# Check if the treenode is root!
if not treenode.parent:
return HttpResponse(json.dumps({'error': 'Can\'t split at the root node: it doesn\'t have a parent.'}))
# Check if annotations are valid
if not check_annotations_on_split(project_id, skeleton_id,
upstream_annotation_set, downstream_annotation_set):
raise Exception("Annotation distribution is not valid for splitting. " \
"One part has to keep the whole set of annotations!")
skeleton = ClassInstance.objects.select_related('user').get(pk=skeleton_id)
project_id=int(project_id)
# retrieve neuron of this skeleton
neuron = ClassInstance.objects.get(
cici_via_b__relation__relation_name='model_of',
cici_via_b__class_instance_a_id=skeleton_id)
# Make sure the user has permissions to edit
can_edit_class_instance_or_fail(request.user, neuron.id, 'neuron')
# retrieve the id, parent_id of all nodes in the skeleton
# with minimal ceremony
cursor.execute('''
SELECT id, parent_id FROM treenode WHERE skeleton_id=%s
''' % skeleton_id) # no need to sanitize
# build the networkx graph from it
graph = nx.DiGraph()
for row in cursor.fetchall():
graph.add_node( row[0] )
if row[1]:
# edge from parent_id to id
graph.add_edge( row[1], row[0] )
# find downstream nodes starting from target treenode_id
# and generate the list of IDs to change, starting at treenode_id (inclusive)
change_list = nx.bfs_tree(graph, treenode_id).nodes()
if not change_list:
# When splitting an end node, the bfs_tree doesn't return any nodes,
# which is surprising, because when the splitted tree has 2 or more nodes
# the node at which the split is made is included in the list.
change_list.append(treenode_id)
# create a new skeleton
new_skeleton = ClassInstance()
new_skeleton.name = 'Skeleton'
new_skeleton.project_id = project_id
new_skeleton.user = skeleton.user # The same user that owned the skeleton to split
new_skeleton.class_column = Class.objects.get(class_name='skeleton', project_id=project_id)
new_skeleton.save()
new_skeleton.name = 'Skeleton {0}'.format( new_skeleton.id ) # This could be done with a trigger in the database
new_skeleton.save()
# Create new neuron
new_neuron = ClassInstance()
new_neuron.name = 'Neuron'
new_neuron.project_id = project_id
new_neuron.user = skeleton.user
new_neuron.class_column = Class.objects.get(class_name='neuron',
project_id=project_id)
new_neuron.save()
new_neuron.name = 'Neuron %s' % str(new_neuron.id)
new_neuron.save()
# Assign the skeleton to new neuron
cici = ClassInstanceClassInstance()
cici.class_instance_a = new_skeleton
cici.class_instance_b = new_neuron
cici.relation = Relation.objects.get(relation_name='model_of', project_id=project_id)
cici.user = skeleton.user # The same user that owned the skeleton to split
cici.project_id = project_id
cici.save()
# update skeleton_id of list in treenode table
# This creates a lazy QuerySet that, upon calling update, returns a new QuerySet
# that is then executed. It does NOT create an update SQL query for every treenode.
tns = Treenode.objects.filter(id__in=change_list).update(skeleton=new_skeleton)
# update the skeleton_id value of the treenode_connector table
tc = TreenodeConnector.objects.filter(
relation__relation_name__endswith = 'synaptic_to',
treenode__in=change_list,
).update(skeleton=new_skeleton)
# setting new root treenode's parent to null
Treenode.objects.filter(id=treenode_id).update(parent=None, editor=request.user)
# Update annotations of existing neuron to have only over set
_update_neuron_annotations(project_id, request.user, neuron.id,
upstream_annotation_set)
# Update annotations of under skeleton
_annotate_entities(project_id, request.user, [new_neuron.id],
downstream_annotation_set)
# Log the location of the node at which the split was done
insert_into_log( project_id, request.user.id, "split_skeleton", treenode.location, "Split skeleton with ID {0} (neuron: {1})".format( skeleton_id, neuron.name ) )
return HttpResponse(json.dumps({}), mimetype='text/json')