def delete_connector(request:HttpRequest, project_id=None) -> JsonResponse:
connector_id = int(request.POST.get("connector_id", 0))
can_edit_or_fail(request.user, connector_id, 'connector')
# Check provided state
cursor = connection.cursor()
state.validate_state(connector_id, request.POST.get('state'),
node=True, c_links=True, lock=True, cursor=cursor)
# Get connector and partner information
connectors = list(Connector.objects.filter(id=connector_id).prefetch_related(
'treenodeconnector_set', 'treenodeconnector_set__relation'))
if 1 != len(connectors):
raise ValueError("Couldn't find exactly one connector with ID #" +
str(connector_id))
connector = connectors[0]
# TODO: Check how many queries here are generated
partners = [{
'id': p.treenode_id,
'edition_time': p.treenode.edition_time,
'rel': p.relation.relation_name,
'rel_id': p.relation.id,
'confidence': p.confidence,
'link_id': p.id
} for p in connector.treenodeconnector_set.all()]
connector.delete()
return JsonResponse({
'message': 'Removed connector and class_instances',
'connector_id': connector_id,
'confidence': connector.confidence,
'x': connector.location_x,
'y': connector.location_y,
'z': connector.location_z,
'partners': partners
})
def test_correct_child_state(self):
ps1 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
state.validate_state(249, s1, children=True)
def test_correct_link_state(self):
ps1 = {
'links': [[360, '2011-12-20T10:46:01.360Z'],
[372, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
state.validate_state(285, s1, links=True)
def delete_link(request, project_id=None):
connector_id = int(request.POST.get('connector_id', 0))
treenode_id = int(request.POST.get('treenode_id', 0))
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state([treenode_id, connector_id],
request.POST.get('state'),
multinode=True,
lock=True,
cursor=cursor)
links = TreenodeConnector.objects.filter(
connector=connector_id,
treenode=treenode_id).select_related('relation')
if links.count() == 0:
raise ValueError('Couldn\'t find link between connector {} '
'and node {}'.format(connector_id, treenode_id))
link = links[0]
# Could be done by filtering above when obtaining the links,
# but then one cannot distinguish between the link not existing
# and the user_id not matching or not being superuser.
can_edit_or_fail(request.user, link.id, 'treenode_connector')
deleted_link_id = link.id
link.delete()
return JsonResponse({
'link_id': deleted_link_id,
'link_type_id': link.relation.id,
'link_type': link.relation.relation_name,
'result': 'Removed treenode to connector link'
})
def update_parent(request, project_id=None, treenode_id=None):
treenode_id = int(treenode_id)
parent_id = int(request.POST.get('parent_id', -1))
can_edit_treenode_or_fail(request.user, project_id, treenode_id)
# Make sure the back-end is in the expected state
state.validate_state(treenode_id,
request.POST.get('state'),
neighborhood=True,
lock=True)
child = get_object_or_404(Treenode, pk=treenode_id, project_id=project_id)
parent = get_object_or_404(Treenode, pk=parent_id, project_id=project_id)
if child.skeleton_id != parent.skeleton_id:
raise Exception("Child node %s is in skeleton %s but parent node %s is in skeleton %s!", \
treenode_id, child.skeleton_id, parent_id, parent.skeleton_id)
child.parent_id = parent_id
child.save()
return JsonResponse({
'success': True,
'node_id': child.id,
'parent_id': child.parent_id,
'skeleton_id': child.skeleton_id
})
def test_correct_child_state(self):
ps1 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
state.validate_state(249, s1, children=True)
def node_update(request, project_id=None):
treenodes = get_request_list(request.POST, "t") or []
connectors = get_request_list(request.POST, "c") or []
cursor = connection.cursor()
nodes = treenodes + connectors
if nodes:
node_ids = [int(n[0]) for n in nodes]
state.validate_state(node_ids,
request.POST.get('state'),
multinode=True,
lock=True,
cursor=cursor)
now = timezone.now()
old_treenodes = _update_location("treenode", treenodes, now, request.user,
cursor)
old_connectors = _update_location("connector", connectors, now,
request.user, cursor)
num_updated_nodes = len(treenodes) + len(connectors)
return JsonResponse({
'updated': num_updated_nodes,
'old_treenodes': old_treenodes,
'old_connectors': old_connectors
})
def delete_connector(request, project_id=None):
connector_id = int(request.POST.get("connector_id", 0))
can_edit_or_fail(request.user, connector_id, 'connector')
# Check provided state
cursor = connection.cursor()
state.validate_state(connector_id, request.POST.get('state'),
node=True, c_links=True, lock=True, cursor=cursor)
# Get connector and partner information
connectors = list(Connector.objects.filter(id=connector_id).prefetch_related(
'treenodeconnector_set', 'treenodeconnector_set__relation'))
if 1 != len(connectors):
raise ValueError("Couldn't find exactly one connector with ID #" +
connector_id)
connector = connectors[0]
# TODO: Check how many queries here are generated
partners = [{
'id': p.treenode_id,
'edition_time': p.treenode.edition_time,
'rel': p.relation.relation_name,
'rel_id': p.relation.id,
'confidence': p.confidence,
'link_id': p.id
} for p in connector.treenodeconnector_set.all()]
connector.delete()
return JsonResponse({
'message': 'Removed connector and class_instances',
'connector_id': connector_id,
'confidence': connector.confidence,
'x': connector.location_x,
'y': connector.location_y,
'z': connector.location_z,
'partners': partners
})
def delete_link(request, project_id=None):
connector_id = int(request.POST.get('connector_id', 0))
treenode_id = int(request.POST.get('treenode_id', 0))
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state([treenode_id, connector_id], request.POST.get('state'),
multinode=True, lock=True, cursor=cursor)
links = TreenodeConnector.objects.filter(
connector=connector_id,
treenode=treenode_id).select_related('relation')
if links.count() == 0:
raise ValueError('Couldn\'t find link between connector {} '
'and node {}'.format(connector_id, treenode_id))
link = links[0]
# Could be done by filtering above when obtaining the links,
# but then one cannot distinguish between the link not existing
# and the user_id not matching or not being superuser.
can_edit_or_fail(request.user, link.id, 'treenode_connector')
deleted_link_id = link.id
link.delete()
return JsonResponse({
'link_id': deleted_link_id,
'link_type_id': link.relation.id,
'link_type': link.relation.relation_name,
'result': 'Removed treenode to connector link'
})
def test_wrong_child_state(self):
ps1 = {
'children': [[247, '2011-12-05T13:51:36.955Z']],
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(249, s1, children=True))
ps2 = {
'children': [[251, '1011-12-05T13:51:36.955Z']],
}
s2 = json.dumps(ps2)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(249, s2, children=True))
ps3 = {
'children': [],
}
s3 = json.dumps(ps3)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(249, s3, children=True))
ps4 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
}
s4 = json.dumps(ps4)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(251, s4, children=True))
def test_correct_link_state(self):
ps1 = {
'links': [[360, '2011-12-20T10:46:01.360Z'],
[372, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
state.validate_state(285, s1, links=True)
def test_wrong_child_state(self):
ps1 = {
'children': [[247, '2011-12-05T13:51:36.955Z']],
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError, lambda: state.validate_state(249, s1, children=True))
ps2 = {
'children': [[251, '1011-12-05T13:51:36.955Z']],
}
s2 = json.dumps(ps2)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError, lambda: state.validate_state(249, s2, children=True))
ps3 = {
'children': [],
}
s3 = json.dumps(ps3)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError, lambda: state.validate_state(249, s3, children=True))
ps4 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
}
s4 = json.dumps(ps4)
# Expect this state to validate cleanly
self.assertRaises(state.StateMatchingError, lambda: state.validate_state(251, s4, children=True))
def update_parent(request, project_id=None, treenode_id=None):
treenode_id = int(treenode_id)
parent_id = int(request.POST.get('parent_id', -1))
can_edit_treenode_or_fail(request.user, project_id, treenode_id)
# Make sure the back-end is in the expected state
state.validate_state(treenode_id, request.POST.get('state'),
neighborhood=True, lock=True)
child = get_object_or_404(Treenode, pk=treenode_id, project_id=project_id)
parent = get_object_or_404(Treenode, pk=parent_id, project_id=project_id)
if child.skeleton_id != parent.skeleton_id:
raise Exception("Child node %s is in skeleton %s but parent node %s is in skeleton %s!", \
treenode_id, child.skeleton_id, parent_id, parent.skeleton_id)
child.parent_id = parent_id
child.save()
return JsonResponse({
'success': True,
'node_id': child.id,
'parent_id': child.parent_id,
'skeleton_id': child.skeleton_id
})
def test_correct_edge_state(self):
ps1 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
'edition_time': '2011-12-05T13:51:36.955Z'
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
state.validate_state(249, s1, node=True, children=[251])
def test_correct_edge_state(self):
ps1 = {
'children': [[251, '2011-12-05T13:51:36.955Z']],
'edition_time': '2011-12-05T13:51:36.955Z'
}
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
state.validate_state(249, s1, node=True, children=[251])
def test_correct_neighborhood_state(self):
ps1 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [[360, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
state.validate_state(285, s1, neighborhood=True)
def test_correct_neighborhood_state(self):
ps1 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [[360, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
state.validate_state(285, s1, neighborhood=True)
def test_correct_clink_state(self):
ps1 = {
'c_links': [[360, '2011-12-20T10:46:01.360Z'],
[372, '3011-12-20T10:46:01.360Z'],
[382, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
self.assertRaises(ValueError, lambda: state.validate_state(356, s1, links=True))
self.assertRaises(ValueError, lambda: state.validate_state(358, s1, links=True))
def test_correct_parent_state(self):
ps1 = {'parent': [249, '2011-12-05T13:51:36.955Z']}
s1 = json.dumps(ps1)
state.validate_state(251, s1, is_parent=True, parent_edittime=True)
state.validate_state(251, s1, is_parent=True, parent_edittime=False)
state.validate_state(251, s1, is_parent=False, parent_edittime=True)
state.validate_state(247, s1, is_parent=False, parent_edittime=True)
self.assertRaises(
state.StateMatchingError, lambda: state.validate_state(
247, s1, is_parent=True, parent_edittime=True))
def test_correct_parent_state(self):
ps1 = {
'parent': [249, '2011-12-05T13:51:36.955Z']
}
s1 = json.dumps(ps1)
state.validate_state(251, s1, is_parent=True, parent_edittime=True)
state.validate_state(251, s1, is_parent=True, parent_edittime=False)
state.validate_state(251, s1, is_parent=False, parent_edittime=True)
state.validate_state(247, s1, is_parent=False, parent_edittime=True)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(247, s1, is_parent=True, parent_edittime=True))
def test_wrong_parent_state(self):
ps1 = {
'parent': [249, '1011-12-05T13:51:36.955Z']
}
s1 = json.dumps(ps1)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(251, s1, is_parent=True, parent_edittime=True))
s2 = json.dumps([])
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(251, s1, is_parent=True, parent_edittime=True))
s3 = json.dumps({})
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(251, s3, is_parent=True, parent_edittime=True))
def test_wrong_link_state(self):
ps1 = {
'links': [[360, '1011-12-20T10:46:01.360Z'],
[372, '2011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
self.assertRaises(state.StateMatchingError, lambda: state.validate_state(285, s1, links=True))
def test_wrong_multinode_shared_state(self):
ps1 = {
'edition_time': '2011-12-05T13:51:00.000Z'
}
s1 = json.dumps(ps1)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state([247, 249, 251], s1, multinode=False, node=True))
def update_radii(request, project_id=None):
"""Update the radius of one or more nodes"""
treenode_ids = [int(v) for k,v in request.POST.items() \
if k.startswith('treenode_ids[')]
radii = [float(v) for k,v in request.POST.items() \
if k.startswith('treenode_radii[')]
# Make sure the back-end is in the expected state
cursor = connection.cursor()
state.validate_state(treenode_ids, request.POST.get('state'),
multinode=True, lock=True, cursor=cursor)
updated_nodes = update_node_radii(treenode_ids, radii, cursor)
return JsonResponse({
'success': True,
'updated_nodes': updated_nodes
})
def test_wrong_multinode_state(self):
ps1 = [
[247, '2011-12-05T13:51:36.955Z'],
[249, '3011-12-05T13:51:36.955Z'],
[251, '2011-12-05T13:51:36.955Z']
]
s1 = json.dumps(ps1)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state([247, 249, 251], s1, multinode=True))
s2 = json.dumps([])
self.assertRaises(ValueError,
lambda: state.validate_state([247, 249, 251], s2, multinode=True))
s3 = json.dumps({})
self.assertRaises(ValueError,
lambda: state.validate_state([247, 249, 251], s3, multinode=True))
def update_radii(request, project_id=None):
"""Update the radius of one or more nodes"""
treenode_ids = [int(v) for k,v in six.iteritems(request.POST) \
if k.startswith('treenode_ids[')]
radii = [float(v) for k,v in six.iteritems(request.POST) \
if k.startswith('treenode_radii[')]
# Make sure the back-end is in the expected state
cursor = connection.cursor()
state.validate_state(treenode_ids,
request.POST.get('state'),
multinode=True,
lock=True,
cursor=cursor)
updated_nodes = update_node_radii(treenode_ids, radii, cursor)
return JsonResponse({'success': True, 'updated_nodes': updated_nodes})
def test_correct_multinode_state(self):
ps1 = [
[247, '2011-12-05T13:51:36.955Z'],
[249, '2011-12-05T13:51:36.955Z'],
[251, '2011-12-05T13:51:36.955Z']
]
s1 = json.dumps(ps1)
# Expect this state to validate cleanly
state.validate_state([247, 249, 251], s1, multinode=True)
# Expect wrong input list to cause error
self.assertRaises(ValueError,
lambda: state.validate_state([247, 249], s1, multinode=True))
self.assertRaises(ValueError,
lambda: state.validate_state([247, 249, 253], s1, multinode=True))
self.assertRaises(ValueError,
lambda: state.validate_state([247, 249, 251, 253], s1, multinode=True))
def node_update(request, project_id=None):
treenodes = get_request_list(request.POST, "t") or []
connectors = get_request_list(request.POST, "c") or []
cursor = connection.cursor()
nodes = treenodes + connectors
if nodes:
node_ids = [int(n[0]) for n in nodes]
state.validate_state(node_ids, request.POST.get('state'),
multinode=True, lock=True, cursor=cursor)
now = timezone.now()
old_treenodes = _update_location("treenode", treenodes, now, request.user, cursor)
old_connectors = _update_location("connector", connectors, now, request.user, cursor)
num_updated_nodes = len(treenodes) + len(connectors)
return JsonResponse({
'updated': num_updated_nodes,
'old_treenodes': old_treenodes,
'old_connectors': old_connectors
})
def update_parent(request, project_id=None, treenode_id=None):
treenode_id = int(treenode_id)
parent_id = int(request.POST.get('parent_id', -1))
# Make sure the back-end is in the expected state
state.validate_state(treenode_id, request.POST.get('state'),
neighborhood=True, lock=True, cursor=cursor)
child = Treenode.objects.get(pk=treenode_id)
parent = Treenode.objects.get(pk=parent_id)
if (child.skeleton_id != parent.skeleton_id):
raise Exception("Child node %s is in skeleton %s but parent node %s is in skeleton %s!", \
treenode_id, child.skeleton_id, parent_id, parent.skeleton_id)
child.parent_id = parent_id
child.save()
return JsonResponse({
'success': True,
'node_id': child.id,
'parent_id': child.parent_id,
'skeleton_id': child.skeleton_id
})
def test_wrong_neighborhood_state(self):
ps1 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [[360, '3011-12-20T10:46:01.360Z']],
}
s1 = json.dumps(ps1)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(285, s1, neighborhood=True))
ps2 = {
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [[360, '3011-12-20T10:46:01.360Z']],
}
s2 = json.dumps(ps2)
self.assertRaises(ValueError,
lambda: state.validate_state(285, s2, neighborhood=True))
ps3 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [[360, '3011-12-20T10:46:01.360Z']],
}
s3 = json.dumps(ps3)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(285, s3, neighborhood=True))
ps4 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'links': [[360, '3011-12-20T10:46:01.360Z']],
}
s4 = json.dumps(ps4)
self.assertRaises(ValueError,
lambda: state.validate_state(285, s4, neighborhood=True))
ps5 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
}
s5 = json.dumps(ps5)
self.assertRaises(ValueError,
lambda: state.validate_state(285, s5, neighborhood=True))
ps6 = {
'edition_time': '2011-12-04T13:51:36.955Z',
'parent': [283, '2011-12-15T13:51:36.955Z'],
'children': [[289, '2011-11-06T13:51:36.955Z']],
'links': [],
}
s6 = json.dumps(ps6)
self.assertRaises(state.StateMatchingError,
lambda: state.validate_state(285, s6, neighborhood=True))
def test_correct_multinode_shared_state(self):
ps1 = {'edition_time': '2011-12-05T13:51:36.955Z'}
s1 = json.dumps(ps1)
state.validate_state([247, 249, 251], s1, multinode=False, node=True)
def create_link(request, project_id=None):
""" Create a link between a connector and a treenode
Currently the following link types (relations) are supported:
presynaptic_to, postsynaptic_to, abutting, gapjunction_with.
"""
from_id = int(request.POST.get('from_id', 0))
to_id = int(request.POST.get('to_id', 0))
link_type = request.POST.get('link_type', 'none')
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state([from_id, to_id],
request.POST.get('state'),
multinode=True,
lock=True,
cursor=cursor)
try:
project = Project.objects.get(id=project_id)
relation = Relation.objects.get(project=project,
relation_name=link_type)
from_treenode = Treenode.objects.get(id=from_id)
to_connector = Connector.objects.get(id=to_id, project=project)
links = TreenodeConnector.objects.filter(connector=to_id,
treenode=from_id,
relation=relation.id)
except ObjectDoesNotExist as e:
return JsonResponse({'error': str(e)})
if links.count() > 0:
return JsonResponse({
'error':
"A relation '%s' between these two elements already exists!" %
link_type
})
related_skeleton_count = ClassInstance.objects.filter(
project=project, id=from_treenode.skeleton.id).count()
if related_skeleton_count > 1:
# Can never happen. What motivated this check for an error of this kind? Would imply that a treenode belongs to more than one skeleton, which was possible when skeletons owned treendoes via element_of relations rather than by the skeleton_id column.
return JsonResponse({
'error':
'Multiple rows for treenode with ID #%s found' % from_id
})
elif related_skeleton_count == 0:
return JsonResponse({
'error':
'Failed to retrieve skeleton id of treenode #%s' % from_id
})
if link_type == 'presynaptic_to':
# Enforce only one presynaptic link
presyn_links = TreenodeConnector.objects.filter(project=project,
connector=to_connector,
relation=relation)
if (presyn_links.count() != 0):
return JsonResponse({
'error':
'Connector %s does not have zero presynaptic connections.' %
to_id
})
# The object returned in case of success
result = {}
if link_type == 'postsynaptic_to':
# Warn if there is already a link from the source skeleton to the
# target skeleton. This can happen and is not necessarely wrong, but
# worth to double check, because it is likely a mistake.
post_links_to_skeleton = TreenodeConnector.objects.filter(
project=project,
connector=to_connector,
relation=relation,
skeleton_id=from_treenode.skeleton_id).count()
if post_links_to_skeleton == 1:
result['warning'] = 'There is already one post-synaptic ' \
'connection to the target skeleton'
elif post_links_to_skeleton > 1:
result['warning'] = 'There are already %s post-synaptic ' \
'connections to the target skeleton' % post_links_to_skeleton
# Enforce only synaptic links
gapjunction_links = TreenodeConnector.objects.filter(
project=project,
connector=to_connector,
relation__relation_name='gapjunction_with')
if (gapjunction_links.count() != 0):
return JsonResponse({
'error':
'Connector %s cannot have both a gap junction and a postsynaptic node.'
% to_id
})
if link_type == 'gapjunction_with':
# Enforce only two gap junction links
gapjunction_links = TreenodeConnector.objects.filter(
project=project, connector=to_connector, relation=relation)
synapse_links = TreenodeConnector.objects.filter(
project=project,
connector=to_connector,
relation__relation_name__endswith='synaptic_to')
if (gapjunction_links.count() > 1):
return JsonResponse({
'error':
'Connector %s can only have two gap junction connections.' %
to_id
})
if (synapse_links.count() != 0):
return JsonResponse({
'error':
'Connector %s is part of a synapse, and gap junction can not be added.'
% to_id
})
link = TreenodeConnector(
user=request.user,
project=project,
relation=relation,
treenode=from_treenode, # treenode_id = from_id
skeleton=from_treenode.
skeleton, # treenode.skeleton_id where treenode.id = from_id
connector=to_connector # connector_id = to_id
)
link.save()
result['message'] = 'success'
result['link_id'] = link.id
result['link_edition_time'] = link.edition_time
result['relation_id'] = link.relation_id
return JsonResponse(result)
def update_confidence(request, project_id=None, treenode_id=None):
"""Update confidence of edge between a node to either its parent or its
connectors.
The connection between a node and its parent or the connectors it is linked
to can be rated with a confidence value in the range 1-5. If connector links
should be updated, one can limit the affected connections to a specific
connector. Returned is an object, mapping updated partners to their old
confidences.
---
parameters:
- name: new_confidence
description: New confidence, value in range 1-5
type: integer
required: true
- name: to_connector
description: Whether all linked connectors instead of parent should be updated
type: boolean
required: false
- name: partner_ids
description: Limit update to a set of connectors if to_connector is true
type: array
items: integer
required: false
- name: partner_confidences
description: Set different confidences to connectors in <partner_ids>
type: array
items: integer
required: false
type:
message:
type: string
required: true
updated_partners:
type: object
required: true
"""
tnid = int(treenode_id)
can_edit_treenode_or_fail(request.user, project_id, tnid)
cursor = connection.cursor()
state.validate_state(tnid, request.POST.get('state'),
node=True, lock=True, cursor=cursor)
to_connector = get_request_bool(request.POST, 'to_connector', False)
partner_ids = get_request_list(request.POST, 'partner_ids', None, int)
partner_confidences = get_request_list(request.POST, 'partner_confidences',
None, int)
new_confidence = int(request.POST.get('new_confidence', 0))
# If partner confidences are specified, make sure there are exactly as many
# as there are partners. Otherwise validate passed in confidence
if partner_ids and partner_confidences:
if len(partner_confidences) != len(partner_ids):
raise ValueError("There have to be as many partner confidences as"
"there are partner IDs")
else:
if new_confidence < 1 or new_confidence > 5:
raise ValueError('Confidence not in range 1-5 inclusive.')
if partner_ids:
# Prepare new confidences for connector query
partner_confidences = (new_confidence,) * len(partner_ids)
if to_connector:
if partner_ids:
partner_template = ",".join(("(%s,%s)",) * len(partner_ids))
partner_data = [p for v in zip(partner_ids, partner_confidences) for p in v]
cursor.execute('''
UPDATE treenode_connector tc
SET confidence = target.new_confidence
FROM (SELECT x.id, x.confidence AS old_confidence,
new_values.confidence AS new_confidence
FROM treenode_connector x
JOIN (VALUES {}) new_values(cid, confidence)
ON x.connector_id = new_values.cid
WHERE x.treenode_id = %s) target
WHERE tc.id = target.id
RETURNING tc.connector_id, tc.edition_time, target.old_confidence
'''.format(partner_template), partner_data + [tnid])
else:
cursor.execute('''
UPDATE treenode_connector tc
SET confidence = %s
FROM (SELECT x.id, x.confidence AS old_confidence
FROM treenode_connector x
WHERE treenode_id = %s) target
WHERE tc.id = target.id
RETURNING tc.connector_id, tc.edition_time, target.old_confidence
''', (new_confidence, tnid))
else:
cursor.execute('''
UPDATE treenode t
SET confidence = %s, editor_id = %s
FROM (SELECT x.id, x.confidence AS old_confidence
FROM treenode x
WHERE id = %s) target
WHERE t.id = target.id
RETURNING t.parent_id, t.edition_time, target.old_confidence
''', (new_confidence, request.user.id, tnid))
updated_partners = cursor.fetchall()
if len(updated_partners) > 0:
location = Location.objects.filter(id=tnid).values_list(
'location_x', 'location_y', 'location_z')[0]
insert_into_log(project_id, request.user.id, "change_confidence",
location, "Changed to %s" % new_confidence)
return JsonResponse({
'message': 'success',
'updated_partners': {
r[0]: {
'edition_time': r[1],
'old_confidence': r[2]
} for r in updated_partners
}
})
# Else, signal error
if to_connector:
raise ValueError('Failed to update confidence between treenode %s and '
'connector.' % tnid)
else:
raise ValueError('Failed to update confidence at treenode %s.' % tnid)
def update_confidence(request, project_id=None, treenode_id=None):
"""Update confidence of edge between a node to either its parent or its
connectors.
The connection between a node and its parent or the connectors it is linked
to can be rated with a confidence value in the range 1-5. If connector links
should be updated, one can limit the affected connections to a specific
connector. Returned is an object, mapping updated partners to their old
confidences.
---
parameters:
- name: new_confidence
description: New confidence, value in range 1-5
type: integer
required: true
- name: to_connector
description: Whether all linked connectors instead of parent should be updated
type: boolean
required: false
- name: partner_ids
description: Limit update to a set of connectors if to_connector is true
type: array
items: integer
required: false
- name: partner_confidences
description: Set different confidences to connectors in <partner_ids>
type: array
items: integer
required: false
type:
message:
type: string
required: true
updated_partners:
type: object
required: true
"""
tnid = int(treenode_id)
can_edit_treenode_or_fail(request.user, project_id, tnid)
cursor = connection.cursor()
state.validate_state(tnid,
request.POST.get('state'),
node=True,
lock=True,
cursor=cursor)
to_connector = request.POST.get('to_connector', 'false') == 'true'
partner_ids = get_request_list(request.POST, 'partner_ids', None, int)
partner_confidences = get_request_list(request.POST, 'partner_confidences',
None, int)
new_confidence = int(request.POST.get('new_confidence', 0))
# If partner confidences are specified, make sure there are exactly as many
# as there are partners. Otherwise validate passed in confidence
if partner_ids and partner_confidences:
if len(partner_confidences) != len(partner_ids):
raise ValueError("There have to be as many partner confidences as"
"there are partner IDs")
else:
if new_confidence < 1 or new_confidence > 5:
raise ValueError('Confidence not in range 1-5 inclusive.')
if partner_ids:
# Prepare new confidences for connector query
partner_confidences = (new_confidence, ) * len(partner_ids)
if to_connector:
if partner_ids:
partner_template = ",".join(("(%s,%s)", ) * len(partner_ids))
partner_data = [
p for v in zip(partner_ids, partner_confidences) for p in v
]
cursor.execute(
'''
UPDATE treenode_connector tc
SET confidence = target.new_confidence
FROM (SELECT x.id, x.confidence AS old_confidence,
new_values.confidence AS new_confidence
FROM treenode_connector x
JOIN (VALUES {}) new_values(cid, confidence)
ON x.connector_id = new_values.cid
WHERE x.treenode_id = %s) target
WHERE tc.id = target.id
RETURNING tc.connector_id, tc.edition_time, target.old_confidence
'''.format(partner_template), partner_data + [tnid])
else:
cursor.execute(
'''
UPDATE treenode_connector tc
SET confidence = %s
FROM (SELECT x.id, x.confidence AS old_confidence
FROM treenode_connector x
WHERE treenode_id = %s) target
WHERE tc.id = target.id
RETURNING tc.connector_id, tc.edition_time, target.old_confidence
''', (new_confidence, tnid))
else:
cursor.execute(
'''
UPDATE treenode t
SET confidence = %s, editor_id = %s
FROM (SELECT x.id, x.confidence AS old_confidence
FROM treenode x
WHERE id = %s) target
WHERE t.id = target.id
RETURNING t.parent_id, t.edition_time, target.old_confidence
''', (new_confidence, request.user.id, tnid))
updated_partners = cursor.fetchall()
if len(updated_partners) > 0:
location = Location.objects.filter(id=tnid).values_list(
'location_x', 'location_y', 'location_z')[0]
insert_into_log(project_id, request.user.id, "change_confidence",
location, "Changed to %s" % new_confidence)
return JsonResponse({
'message': 'success',
'updated_partners': {
r[0]: {
'edition_time': r[1],
'old_confidence': r[2]
}
for r in updated_partners
}
})
# Else, signal error
if to_connector:
raise ValueError('Failed to update confidence between treenode %s and '
'connector.' % tnid)
else:
raise ValueError('Failed to update confidence at treenode %s.' % tnid)
def create_treenode(request, project_id=None):
"""
Add a new treenode to the database
----------------------------------
1. Add new treenode for a given skeleton id. Parent should not be empty.
return: new treenode id
If the parent's skeleton has a single node and belongs to the
'Isolated synaptic terminals' group, then reassign ownership
of the skeleton and the neuron to the user. The treenode remains
property of the original user who created it.
2. Add new treenode (root) and create a new skeleton (maybe for a given
neuron) return: new treenode id and skeleton id.
If a neuron id is given, use that one to create the skeleton as a model of
it.
"""
params = {}
float_values = {
'x': 0,
'y': 0,
'z': 0,
'radius': 0}
int_values = {
'confidence': 0,
'useneuron': -1,
'parent_id': -1}
string_values = {}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
for p in string_values.keys():
params[p] = request.POST.get(p, string_values[p])
# Get optional initial links to connectors, expect each entry to be a list
# of connector ID, relation ID and confidence.
links = get_request_list(request.POST, 'links', [], map_fn=int)
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = int(params['parent_id'])
has_parent = parent_id and parent_id != -1
if has_parent:
state.validate_state(parent_id, request.POST.get('state'),
parent_edittime=has_parent, lock=True)
new_treenode = _create_treenode(project_id, request.user, request.user,
params['x'], params['y'], params['z'], params['radius'],
params['confidence'], params['useneuron'], params['parent_id'],
neuron_name=request.POST.get('neuron_name', None))
# Create all initial links
if links:
created_links = create_connector_link(project_id, request.user.id,
new_treenode.treenode_id, new_treenode.skeleton_id, links)
else:
created_links = []
return JsonResponse({
'treenode_id': new_treenode.treenode_id,
'skeleton_id': new_treenode.skeleton_id,
'edition_time': new_treenode.edition_time,
'parent_edition_time': new_treenode.parent_edition_time,
'created_links': created_links
})
except Exception, e:
raise ValueError("Couldn't parse list parameter: {}".format(e))
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = params.get('parent_id')
child_id = params.get('child_id')
if parent_id not in (-1, None):
s = request.POST.get('state')
# Testing egular edge insertion is assumed if a child ID is provided
partial_child_checks = [] if child_id in (-1, None) else [child_id]
if takeover_child_ids:
partial_child_checks.extend(takeover_child_ids)
state.validate_state(parent_id,
s,
node=True,
children=partial_child_checks or False,
lock=True),
# Find child and parent of new treenode
child = Treenode.objects.get(pk=params['child_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
# Make sure both nodes are actually child and parent
if not child.parent == parent:
raise ValueError('The provided nodes need to be child and parent')
# Make sure the requested location for the new node is on the edge between
# both existing nodes if the user has no edit permissions on the neuron.
try:
can_edit_treenode_or_fail(request.user, project_id, parent.id)
def insert_treenode(request, project_id=None):
"""
Create a new treenode between two existing nodes. Its creator and
creation_date information will be set to information of child node. No node
will be created, if the node on the edge between the given child and parent
node.
"""
# Use creation time, if part of parameter set
params = {}
float_values = {
'x': 0,
'y': 0,
'z': 0,
'radius': 0
}
int_values = {
'confidence': 0,
'parent_id': -1,
'child_id': -1
}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
# If siblings should be taken over, all children of the parent node will be
# come children of the inserted node. This requires extra state
# information: the child state for the paren.
takeover_child_ids = get_request_list(request.POST,
'takeover_child_ids', None, int)
# Get optional initial links to connectors, expect each entry to be a list
# of connector ID and relation ID.
try:
links = get_request_list(request.POST, 'links', [], int)
except Exception as e:
raise ValueError("Couldn't parse list parameter: {}".format(e))
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = params.get('parent_id')
child_id = params.get('child_id')
if parent_id not in (-1, None):
s = request.POST.get('state')
# Testing egular edge insertion is assumed if a child ID is provided
partial_child_checks = [] if child_id in (-1, None) else [child_id]
if takeover_child_ids:
partial_child_checks.extend(takeover_child_ids)
state.validate_state(parent_id, s, node=True,
children=partial_child_checks or False, lock=True),
# Find child and parent of new treenode
child = Treenode.objects.get(pk=params['child_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
# Make sure both nodes are actually child and parent
if not child.parent == parent:
raise ValueError('The provided nodes need to be child and parent')
# Make sure the requested location for the new node is on the edge between
# both existing nodes if the user has no edit permissions on the neuron.
try:
can_edit_treenode_or_fail(request.user, project_id, parent.id)
user, time = request.user, None
except:
child_loc = Point3D(child.location_x, child.location_y, child.location_z)
parent_loc = Point3D(parent.location_x, parent.location_y, parent.location_z)
new_node_loc = Point3D(params['x'], params['y'], params['z'])
if not is_collinear(child_loc, parent_loc, new_node_loc, True, 0.001):
raise ValueError('New node location has to be between child and parent')
# Use creator and creation time for neighboring node that was created last.
if child.creation_time < parent.creation_time:
user, time = parent.user, parent.creation_time
else:
user, time = child.user, child.creation_time
# Create new treenode
new_treenode = _create_treenode(project_id,
user, request.user, params['x'], params['y'], params['z'],
params['radius'], params['confidence'], -1, params['parent_id'], time)
# Update parent of child to new treenode, do this in raw SQL to also get the
# updated edition time Update also takeover children
cursor = connection.cursor()
params = [new_treenode.treenode_id, child.id]
if takeover_child_ids:
params.extend(takeover_child_ids)
child_template = ",".join(("%s",) * (len(takeover_child_ids) + 1))
else:
child_template = "%s"
cursor.execute("""
UPDATE treenode SET parent_id = %s
WHERE id IN ({})
RETURNING id, edition_time
""".format(child_template), params)
result = cursor.fetchall()
if not result or (len(params) - 1) != len(result):
raise ValueError("Couldn't update parent of inserted node's child: " + child.id)
child_edition_times = [[k,v] for k,v in result]
# Create all initial links
if links:
created_links = create_connector_link(project_id, request.user.id,
new_treenode.treenode_id, new_treenode.skeleton_id, links)
else:
created_links = []
return JsonResponse({
'treenode_id': new_treenode.treenode_id,
'skeleton_id': new_treenode.skeleton_id,
'edition_time': new_treenode.edition_time,
'parent_edition_time': new_treenode.parent_edition_time,
'child_edition_times': child_edition_times,
'created_links': created_links
})
def insert_treenode(request, project_id=None):
"""
Create a new treenode between two existing nodes. Its creator and
creation_date information will be set to information of child node. No node
will be created, if the node on the edge between the given child and parent
node.
"""
# Use creation time, if part of parameter set
params = {}
float_values = {'x': 0, 'y': 0, 'z': 0, 'radius': 0}
int_values = {'confidence': 0, 'parent_id': -1, 'child_id': -1}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
# If siblings should be taken over, all children of the parent node will be
# come children of the inserted node. This requires extra state
# information: the child state for the paren.
takeover_child_ids = get_request_list(request.POST, 'takeover_child_ids',
None, int)
# Get optional initial links to connectors, expect each entry to be a list
# of connector ID and relation ID.
try:
links = get_request_list(request.POST, 'links', [], int)
except Exception as e:
raise ValueError("Couldn't parse list parameter: {}".format(e))
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = params.get('parent_id')
child_id = params.get('child_id')
if parent_id not in (-1, None):
s = request.POST.get('state')
# Testing egular edge insertion is assumed if a child ID is provided
partial_child_checks = [] if child_id in (-1, None) else [child_id]
if takeover_child_ids:
partial_child_checks.extend(takeover_child_ids)
state.validate_state(parent_id,
s,
node=True,
children=partial_child_checks or False,
lock=True),
# Find child and parent of new treenode
child = Treenode.objects.get(pk=params['child_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
# Make sure both nodes are actually child and parent
if not child.parent == parent:
raise ValueError('The provided nodes need to be child and parent')
# Make sure the requested location for the new node is on the edge between
# both existing nodes if the user has no edit permissions on the neuron.
try:
can_edit_treenode_or_fail(request.user, project_id, parent.id)
user, time = request.user, None
except:
child_loc = Point3D(child.location_x, child.location_y,
child.location_z)
parent_loc = Point3D(parent.location_x, parent.location_y,
parent.location_z)
new_node_loc = Point3D(params['x'], params['y'], params['z'])
if not is_collinear(child_loc, parent_loc, new_node_loc, True, 0.001):
raise ValueError(
'New node location has to be between child and parent')
# Use creator and creation time for neighboring node that was created last.
if child.creation_time < parent.creation_time:
user, time = parent.user, parent.creation_time
else:
user, time = child.user, child.creation_time
# Create new treenode
new_treenode = _create_treenode(project_id, user, request.user,
params['x'], params['y'], params['z'],
params['radius'], params['confidence'], -1,
params['parent_id'], time)
# Update parent of child to new treenode, do this in raw SQL to also get the
# updated edition time Update also takeover children
cursor = connection.cursor()
params = [new_treenode.treenode_id, child.id]
if takeover_child_ids:
params.extend(takeover_child_ids)
child_template = ",".join(("%s", ) * (len(takeover_child_ids) + 1))
else:
child_template = "%s"
cursor.execute(
"""
UPDATE treenode SET parent_id = %s
WHERE id IN ({})
RETURNING id, edition_time
""".format(child_template), params)
result = cursor.fetchall()
if not result or (len(params) - 1) != len(result):
raise ValueError("Couldn't update parent of inserted node's child: " +
child.id)
child_edition_times = [[k, v] for k, v in result]
# Create all initial links
if links:
created_links = create_connector_link(project_id, request.user.id,
new_treenode.treenode_id,
new_treenode.skeleton_id, links)
else:
created_links = []
return JsonResponse({
'treenode_id': new_treenode.treenode_id,
'skeleton_id': new_treenode.skeleton_id,
'edition_time': new_treenode.edition_time,
'parent_edition_time': new_treenode.parent_edition_time,
'child_edition_times': child_edition_times,
'created_links': created_links
})
def delete_treenode(request, project_id=None):
""" Deletes a treenode. If the skeleton has a single node, deletes the
skeleton and its neuron. Returns the parent_id, if any."""
treenode_id = int(request.POST.get('treenode_id', -1))
# Raise an exception if the user doesn't have permission to edit the
# treenode.
can_edit_or_fail(request.user, treenode_id, 'treenode')
# Raise an Exception if the user doesn't have permission to edit the neuron
# the skeleton of the treenode is modeling.
can_edit_treenode_or_fail(request.user, project_id, treenode_id)
# Make sure the back-end is in the expected state
state.validate_state(treenode_id, request.POST.get('state'), lock=True,
neighborhood=True)
treenode = Treenode.objects.get(pk=treenode_id)
parent_id = treenode.parent_id
# Get information about linked connectors
links = list(TreenodeConnector.objects.filter(project_id=project_id,
treenode_id=treenode_id).values_list('id', 'relation_id',
'connector_id', 'confidence'))
n_sampler_refs = SamplerInterval.objects.filter(start_node=treenode).count() + \
SamplerInterval.objects.filter(end_node=treenode).count()
if (n_sampler_refs > 0):
raise ValueError("Can't delete node, it is used in at least one sampler interval")
response_on_error = ''
deleted_neuron = False
cursor = connection.cursor()
try:
if not parent_id:
children = []
# This treenode is root.
response_on_error = 'Could not retrieve children for ' \
'treenode #%s' % treenode_id
n_children = Treenode.objects.filter(parent=treenode).count()
response_on_error = "Could not delete root node"
if n_children > 0:
# TODO yes you can, the new root is the first of the children,
# and other children become independent skeletons
raise Exception("You can't delete the root node when it "
"has children.")
# Get the neuron before the skeleton is deleted. It can't be
# accessed otherwise anymore.
neuron = ClassInstance.objects.get(project_id=project_id,
cici_via_b__relation__relation_name='model_of',
cici_via_b__class_instance_a=treenode.skeleton)
# Remove the original skeleton. It is OK to remove it if it only had
# one node, even if the skeleton's user does not match or the user
# is not superuser. Delete the skeleton, which triggers deleting
# the ClassInstanceClassInstance relationship with neuron_id
response_on_error = 'Could not delete skeleton.'
# Extra check for errors, like having two root nodes
count = Treenode.objects.filter(skeleton_id=treenode.skeleton_id) \
.count()
if 1 == count:
# deletes as well treenodes that refer to the skeleton
ClassInstance.objects.filter(pk=treenode.skeleton_id) \
.delete()
else:
return JsonResponse({"error": "Can't delete " \
"isolated node: erroneously, its skeleton contains more " \
"than one treenode! Check for multiple root nodes."})
# If the neuron modeled by the skeleton of the treenode is empty,
# delete it.
response_on_error = 'Could not delete neuron #%s' % neuron.id
deleted_neuron = _delete_if_empty(neuron.id)
if deleted_neuron:
# Insert log entry for neuron deletion
insert_into_log(project_id, request.user.id, 'remove_neuron',
(treenode.location_x, treenode.location_y, treenode.location_z),
'Deleted neuron %s and skeleton(s) %s.' % (neuron.id, treenode.skeleton_id))
else:
# Treenode is not root, it has a parent and perhaps children.
# Reconnect all the children to the parent.
response_on_error = 'Could not update parent id of children nodes'
cursor.execute("""
UPDATE treenode SET parent_id = %s
WHERE project_id = %s AND parent_id = %s
RETURNING id, edition_time
""", (treenode.parent_id, project_id, treenode.id))
# Children will be a list of two-element lists, just what we want to
# return as child info.
children = cursor.fetchall()
# Remove treenode. Set the current user name in a transaction local
# variable. This is done to communicate the current user to the trigger
# that updates the skeleton summary table.
response_on_error = 'Could not delete treenode.'
cursor.execute("SET LOCAL catmaid.user_id=%(user_id)s", {
'user_id': request.user.id,
})
Treenode.objects.filter(project_id=project_id, pk=treenode_id).delete()
return JsonResponse({
'x': treenode.location_x,
'y': treenode.location_y,
'z': treenode.location_z,
'parent_id': parent_id,
'children': children,
'links': links,
'radius': treenode.radius,
'confidence': treenode.confidence,
'skeleton_id': treenode.skeleton_id,
'deleted_neuron': deleted_neuron,
'success': "Removed treenode successfully."
})
except Exception as e:
raise Exception(response_on_error + ': ' + str(e))
def update_radius(request, project_id=None, treenode_id=None):
treenode_id = int(treenode_id)
radius = float(request.POST.get('radius', -1))
if math.isnan(radius):
raise Exception("Radius '%s' is not a number!" %
request.POST.get('radius'))
option = int(request.POST.get('option', 0))
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state(treenode_id,
request.POST.get('state'),
node=True,
lock=True,
cursor=cursor)
def create_update_response(updated_nodes, radius):
return JsonResponse({
'success': True,
'updated_nodes': updated_nodes,
'new_radius': radius
})
if 0 == option:
# Update radius only for the passed in treenode and return the old
# radius.
old_radii = update_node_radii(treenode_id, radius, cursor)
return create_update_response(old_radii, radius)
cursor.execute('''
SELECT id, parent_id, radius
FROM treenode
WHERE skeleton_id = (SELECT t.skeleton_id FROM treenode t WHERE id = %s)
''' % treenode_id)
if 1 == option:
# Update radius from treenode_id to next branch or end node (included)
children = defaultdict(list)
for row in cursor.fetchall():
children[row[1]].append(row[0])
include = [treenode_id]
c = children[treenode_id]
while 1 == len(c):
child = c[0]
include.append(child)
c = children[child]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 2 == option:
# Update radius from treenode_id to prev branch node or root (excluded)
parents = {}
children = defaultdict(list)
for row in cursor.fetchall():
parents[row[0]] = row[1]
children[row[1]].append(row[0])
include = [treenode_id]
parent = parents[treenode_id]
while parent and parents[parent] and 1 == len(children[parent]):
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 3 == option:
# Update radius from treenode_id to prev node with radius (excluded)
parents = {}
for row in cursor.fetchall():
if row[2] < 0 or row[
0] == treenode_id: # DB default radius is 0 but is initialized to -1 elsewhere
parents[row[0]] = row[1]
include = [treenode_id]
parent = parents[treenode_id]
while parent in parents:
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 4 == option:
# Update radius from treenode_id to root (included)
parents = {row[0]: row[1] for row in cursor.fetchall()}
include = [treenode_id]
parent = parents[treenode_id]
while parent:
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 5 == option:
# Update radius of all nodes (in a single query)
skeleton_id = Treenode.objects.filter(
pk=treenode_id).values('skeleton_id')
include = list(Treenode.objects.filter(skeleton_id=skeleton_id) \
.values_list('id', flat=True))
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
def test_correct_multinode_shared_state(self):
ps1 = {
'edition_time': '2011-12-05T13:51:36.955Z'
}
s1 = json.dumps(ps1)
state.validate_state([247, 249, 251], s1, multinode=False, node=True)
def create_treenode(request, project_id=None):
"""
Add a new treenode to the database
----------------------------------
1. Add new treenode for a given skeleton id. Parent should not be empty.
return: new treenode id
If the parent's skeleton has a single node and belongs to the
'Isolated synaptic terminals' group, then reassign ownership
of the skeleton and the neuron to the user. The treenode remains
property of the original user who created it.
2. Add new treenode (root) and create a new skeleton (maybe for a given
neuron) return: new treenode id and skeleton id.
If a neuron id is given, use that one to create the skeleton as a model of
it.
"""
params = {}
float_values = {'x': 0, 'y': 0, 'z': 0, 'radius': 0}
int_values = {'confidence': 0, 'useneuron': -1, 'parent_id': -1}
string_values = {}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
for p in string_values.keys():
params[p] = request.POST.get(p, string_values[p])
# Get optional initial links to connectors, expect each entry to be a list
# of connector ID, relation ID and confidence.
links = get_request_list(request.POST, 'links', [], map_fn=int)
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = int(params['parent_id'])
has_parent = parent_id and parent_id != -1
if has_parent:
state.validate_state(parent_id,
request.POST.get('state'),
parent_edittime=has_parent,
lock=True)
new_treenode = _create_treenode(project_id,
request.user,
request.user,
params['x'],
params['y'],
params['z'],
params['radius'],
params['confidence'],
params['useneuron'],
params['parent_id'],
neuron_name=request.POST.get(
'neuron_name', None))
# Create all initial links
if links:
created_links = create_connector_link(project_id, request.user.id,
new_treenode.treenode_id,
new_treenode.skeleton_id, links)
else:
created_links = []
return JsonResponse({
'treenode_id': new_treenode.treenode_id,
'skeleton_id': new_treenode.skeleton_id,
'edition_time': new_treenode.edition_time,
'parent_edition_time': new_treenode.parent_edition_time,
'created_links': created_links
})
def create_link(request, project_id=None):
""" Create a link between a connector and a treenode
Currently the following link types (relations) are supported:
presynaptic_to, postsynaptic_to, abutting, gapjunction_with,
tightjunction_with, desmosome_with.
"""
from_id = int(request.POST.get('from_id', 0))
to_id = int(request.POST.get('to_id', 0))
link_type = request.POST.get('link_type', 'none')
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state([from_id, to_id], request.POST.get('state'),
multinode=True, lock=True, cursor=cursor)
try:
project = Project.objects.get(id=project_id)
relation = Relation.objects.get(project=project, relation_name=link_type)
from_treenode = Treenode.objects.get(id=from_id)
to_connector = Connector.objects.get(id=to_id, project=project)
links = TreenodeConnector.objects.filter(
connector=to_id,
treenode=from_id,
relation=relation.id)
except ObjectDoesNotExist as e:
return JsonResponse({'error': str(e)})
if links.count() > 0:
return JsonResponse({'error': "A relation '%s' between these two elements already exists!" % link_type})
related_skeleton_count = ClassInstance.objects.filter(project=project, id=from_treenode.skeleton.id).count()
if related_skeleton_count > 1:
# Can never happen. What motivated this check for an error of this kind? Would imply that a treenode belongs to more than one skeleton, which was possible when skeletons owned treendoes via element_of relations rather than by the skeleton_id column.
return JsonResponse({'error': 'Multiple rows for treenode with ID #%s found' % from_id})
elif related_skeleton_count == 0:
return JsonResponse({'error': 'Failed to retrieve skeleton id of treenode #%s' % from_id})
if link_type == 'presynaptic_to':
# Enforce only one presynaptic link
presyn_links = TreenodeConnector.objects.filter(project=project, connector=to_connector, relation=relation)
if (presyn_links.count() != 0):
return JsonResponse({'error': 'Connector %s does not have zero presynaptic connections.' % to_id})
# The object returned in case of success
result = {}
if link_type == 'postsynaptic_to':
# Warn if there is already a link from the source skeleton to the
# target skeleton. This can happen and is not necessarely wrong, but
# worth to double check, because it is likely a mistake.
post_links_to_skeleton = TreenodeConnector.objects.filter(project=project,
connector=to_connector, relation=relation, skeleton_id=from_treenode.skeleton_id).count()
if post_links_to_skeleton == 1:
result['warning'] = 'There is already one post-synaptic ' \
'connection to the target skeleton'
elif post_links_to_skeleton > 1:
result['warning'] = 'There are already %s post-synaptic ' \
'connections to the target skeleton' % post_links_to_skeleton
# Enforce only synaptic links
gapjunction_links = TreenodeConnector.objects.filter(project=project, connector=to_connector,
relation__relation_name='gapjunction_with')
if (gapjunction_links.count() != 0):
return JsonResponse({'error': 'Connector %s cannot have both a gap junction and a postsynaptic node.' % to_id})
if link_type in UNDIRECTED_BINARY_LINK_TYPES:
# Enforce only two gap junction links
undirected_links = TreenodeConnector.objects.filter(project=project, connector=to_connector, relation=relation)
synapse_links = TreenodeConnector.objects.filter(project=project, connector=to_connector, relation__relation_name__endswith='synaptic_to')
name = LINKS_BY_RELATION[link_type]['name'].lower();
if (undirected_links.count() > 1):
return JsonResponse({'error': 'Connector {} can only have two {} connections.'.format(to_id, name)})
if (synapse_links.count() != 0):
return JsonResponse({'error': 'Connector {} is part of a synapse, and {} can not be added.'.format(to_id, name)})
link = TreenodeConnector(
user=request.user,
project=project,
relation=relation,
treenode=from_treenode, # treenode_id = from_id
skeleton=from_treenode.skeleton, # treenode.skeleton_id where treenode.id = from_id
connector=to_connector # connector_id = to_id
)
link.save()
result['message'] = 'success'
result['link_id'] = link.id
result['link_edition_time'] = link.edition_time
result['relation_id'] = link.relation_id
return JsonResponse(result)
def delete_treenode(request, project_id=None):
""" Deletes a treenode. If the skeleton has a single node, deletes the
skeleton and its neuron. Returns the parent_id, if any."""
treenode_id = int(request.POST.get('treenode_id', -1))
# Raise an exception if the user doesn't have permission to edit the
# treenode.
can_edit_or_fail(request.user, treenode_id, 'treenode')
# Raise an Exception if the user doesn't have permission to edit the neuron
# the skeleton of the treenode is modeling.
can_edit_treenode_or_fail(request.user, project_id, treenode_id)
# Make sure the back-end is in the expected state
state.validate_state(treenode_id,
request.POST.get('state'),
lock=True,
neighborhood=True)
treenode = Treenode.objects.get(pk=treenode_id)
parent_id = treenode.parent_id
# Get information about linked connectors
links = list(
TreenodeConnector.objects.filter(project_id=project_id,
treenode_id=treenode_id).values_list(
'id', 'relation_id',
'connector_id', 'confidence'))
n_sampler_refs = SamplerInterval.objects.filter(start_node=treenode).count() + \
SamplerInterval.objects.filter(end_node=treenode).count()
if (n_sampler_refs > 0):
raise ValueError(
"Can't delete node, it is used in at least one sampler interval")
response_on_error = ''
deleted_neuron = False
try:
if not parent_id:
children = []
# This treenode is root.
response_on_error = 'Could not retrieve children for ' \
'treenode #%s' % treenode_id
n_children = Treenode.objects.filter(parent=treenode).count()
response_on_error = "Could not delete root node"
if n_children > 0:
# TODO yes you can, the new root is the first of the children,
# and other children become independent skeletons
raise Exception("You can't delete the root node when it "
"has children.")
# Get the neuron before the skeleton is deleted. It can't be
# accessed otherwise anymore.
neuron = ClassInstance.objects.get(
project_id=project_id,
cici_via_b__relation__relation_name='model_of',
cici_via_b__class_instance_a=treenode.skeleton)
# Remove the original skeleton. It is OK to remove it if it only had
# one node, even if the skeleton's user does not match or the user
# is not superuser. Delete the skeleton, which triggers deleting
# the ClassInstanceClassInstance relationship with neuron_id
response_on_error = 'Could not delete skeleton.'
# Extra check for errors, like having two root nodes
count = Treenode.objects.filter(skeleton_id=treenode.skeleton_id) \
.count()
if 1 == count:
# deletes as well treenodes that refer to the skeleton
ClassInstance.objects.filter(pk=treenode.skeleton_id) \
.delete()
else:
return JsonResponse({"error": "Can't delete " \
"isolated node: erroneously, its skeleton contains more " \
"than one treenode! Check for multiple root nodes."})
# If the neuron modeled by the skeleton of the treenode is empty,
# delete it.
response_on_error = 'Could not delete neuron #%s' % neuron.id
deleted_neuron = _delete_if_empty(neuron.id)
if deleted_neuron:
# Insert log entry for neuron deletion
insert_into_log(
project_id, request.user.id, 'remove_neuron',
(treenode.location_x, treenode.location_y,
treenode.location_z),
'Deleted neuron %s and skeleton(s) %s.' %
(neuron.id, treenode.skeleton_id))
else:
# Treenode is not root, it has a parent and perhaps children.
# Reconnect all the children to the parent.
response_on_error = 'Could not update parent id of children nodes'
cursor = connection.cursor()
cursor.execute(
"""
UPDATE treenode SET parent_id = %s
WHERE project_id = %s AND parent_id = %s
RETURNING id, edition_time
""", (treenode.parent_id, project_id, treenode.id))
# Children will be a list of two-element lists, just what we want to
# return as child info.
children = cursor.fetchall()
# Remove treenode
response_on_error = 'Could not delete treenode.'
Treenode.objects.filter(project_id=project_id, pk=treenode_id).delete()
return JsonResponse({
'x': treenode.location_x,
'y': treenode.location_y,
'z': treenode.location_z,
'parent_id': parent_id,
'children': children,
'links': links,
'radius': treenode.radius,
'confidence': treenode.confidence,
'skeleton_id': treenode.skeleton_id,
'deleted_neuron': deleted_neuron,
'success': "Removed treenode successfully."
})
except Exception as e:
raise Exception(response_on_error + ': ' + str(e))
try:
links = get_request_list(request.POST, 'links', [], lambda x: int(x))
except Exception, e:
raise ValueError("Couldn't parse list parameter: {}".format(e))
# Make sure the back-end is in the expected state if the node should have a
# parent and will therefore become part of another skeleton.
parent_id = params.get('parent_id')
child_id = params.get('child_id')
if parent_id not in (-1, None):
s = request.POST.get('state')
# Testing egular edge insertion is assumed if a child ID is provided
partial_child_checks = [] if child_id in (-1, None) else [child_id]
if takeover_child_ids:
partial_child_checks.extend(takeover_child_ids)
state.validate_state(parent_id, s, node=True,
children=partial_child_checks or False, lock=True),
# Find child and parent of new treenode
child = Treenode.objects.get(pk=params['child_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
# Make sure both nodes are actually child and parent
if not child.parent == parent:
raise ValueError('The provided nodes need to be child and parent')
# Make sure the requested location for the new node is on the edge between
# both existing nodes if the user has no edit permissions on the neuron.
try:
can_edit_treenode_or_fail(request.user, project_id, parent.id)
except:
child_loc = Point3D(child.location_x, child.location_y, child.location_z)
def update_radius(request, project_id=None, treenode_id=None):
treenode_id = int(treenode_id)
radius = float(request.POST.get('radius', -1))
if math.isnan(radius):
raise Exception("Radius '%s' is not a number!" % request.POST.get('radius'))
option = int(request.POST.get('option', 0))
cursor = connection.cursor()
# Make sure the back-end is in the expected state
state.validate_state(treenode_id, request.POST.get('state'),
node=True, lock=True, cursor=cursor)
def create_update_response(updated_nodes, radius):
return JsonResponse({
'success': True,
'updated_nodes': updated_nodes,
'new_radius': radius
})
if 0 == option:
# Update radius only for the passed in treenode and return the old
# radius.
old_radii = update_node_radii(treenode_id, radius, cursor)
return create_update_response(old_radii, radius)
cursor.execute('''
SELECT id, parent_id, radius
FROM treenode
WHERE skeleton_id = (SELECT t.skeleton_id FROM treenode t WHERE id = %s)
''' % treenode_id)
if 1 == option:
# Update radius from treenode_id to next branch or end node (included)
children = defaultdict(list)
for row in cursor.fetchall():
children[row[1]].append(row[0])
include = [treenode_id]
c = children[treenode_id]
while 1 == len(c):
child = c[0]
include.append(child)
c = children[child]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 2 == option:
# Update radius from treenode_id to prev branch node or root (excluded)
parents = {}
children = defaultdict(list)
for row in cursor.fetchall():
parents[row[0]] = row[1]
children[row[1]].append(row[0])
include = [treenode_id]
parent = parents[treenode_id]
while parent and parents[parent] and 1 == len(children[parent]):
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 3 == option:
# Update radius from treenode_id to prev node with radius (excluded)
parents = {}
for row in cursor.fetchall():
if row[2] < 0 or row[0] == treenode_id: # DB default radius is 0 but is initialized to -1 elsewhere
parents[row[0]] = row[1]
include = [treenode_id]
parent = parents[treenode_id]
while parent in parents:
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 4 == option:
# Update radius from treenode_id to root (included)
parents = {row[0]: row[1] for row in cursor.fetchall()}
include = [treenode_id]
parent = parents[treenode_id]
while parent:
include.append(parent)
parent = parents[parent]
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
if 5 == option:
# Update radius of all nodes (in a single query)
skeleton_id = Treenode.objects.filter(pk=treenode_id).values('skeleton_id')
include = list(Treenode.objects.filter(skeleton_id=skeleton_id) \
.values_list('id', flat=True))
old_radii = update_node_radii(include, radius, cursor)
return create_update_response(old_radii, radius)
