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 neuron
# the skeleton of the treenode is modeling.
can_edit_treenode_or_fail(request.user, project_id, treenode_id)
#
treenode = Treenode.objects.get(pk=treenode_id)
parent_id = treenode.parent_id
response_on_error = ''
try:
cursor = connection.cursor()
if not parent_id:
# 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 = "Can't delete root node when it has children"
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:
ClassInstance.objects.filter(pk=treenode.skeleton_id).delete() # deletes as well treenodes that refer to the skeleton
else:
return HttpResponse(json.dumps({"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
_delete_if_empty(neuron.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'
Treenode.objects.filter(parent=treenode).update(parent=treenode.parent)
# Remove treenode
response_on_error = 'Could not delete treenode.'
Treenode.objects.filter(pk=treenode_id).delete()
return HttpResponse(json.dumps({'parent_id': parent_id}))
except Exception as e:
raise Exception(response_on_error + ': ' + str(e))
def delete_treenode(request, project_id=None):
""" If the skeleton has a single node, deletes the skeleton, and if so, if the skeleton is a model_of a neuron that was part_of group 'Isolated synaptic terminals', deletes the neuron. Returns the parent_id, if any."""
treenode_id = int(request.POST.get('treenode_id', -1))
# Raise an Exception if the user doesn't own the treenode or is not superuser
can_edit_or_fail(request.user, treenode_id, 'treenode')
#
treenode = Treenode.objects.get(pk=treenode_id)
parent_id = treenode.parent_id
response_on_error = ''
try:
cursor = connection.cursor()
if not parent_id:
# 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 = "Can't delete root node when it has children"
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.")
# 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.
# Fetch the neuron id, if it was a placeholder under 'Isolated synaptic terminals' group
neuron_id = _in_isolated_synaptic_terminals(treenode.skeleton_id)
# 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:
ClassInstance.objects.filter(pk=treenode.skeleton_id).delete() # deletes as well treenodes that refer to the skeleton
else:
return HttpResponse(json.dumps({"error": "Can't delete isolated node: erroneously, its skeleton contains more than one treenode! Check for multiple root nodes."}))
# If the neuron was part of the 'Isolated synaptic terminals' and no other skeleton is a model_of it, delete it
if neuron_id:
response_on_error = 'Could not delete neuron #%s' % neuron_id
if _delete_if_empty(neuron_id):
print >> sys.stderr, "DELETED neuron %s from IST" % neuron_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'
Treenode.objects.filter(parent=treenode).update(parent=treenode.parent)
# Remove treenode
response_on_error = 'Could not delete treenode.'
Treenode.objects.filter(pk=treenode_id).delete()
return HttpResponse(json.dumps({'parent_id': parent_id}))
except Exception as e:
raise Exception(response_on_error + ': ' + str(e))
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))
def _join_skeleton(user, from_treenode_id, to_treenode_id, project_id):
""" Take the IDs of two nodes, each belonging to a different skeleton,
and make to_treenode be a child of from_treenode,
and join the nodes of the skeleton of to_treenode
into the skeleton of from_treenode,
and delete the former skeleton of to_treenode."""
if from_treenode_id is None or to_treenode_id is None:
raise Exception('Missing arguments to _join_skeleton')
response_on_error = ''
try:
to_treenode_id = int(to_treenode_id)
cursor = connection.cursor()
cursor.execute('''
SELECT class_instance.user_id,
treenode.skeleton_id,
treenode.user_id
FROM class_instance,
treenode
WHERE treenode.id = %s
AND treenode.skeleton_id = class_instance.id
''' % to_treenode_id)
to_skeleton_user_id, to_skid, to_treenode_user_id = cursor.fetchone()
# Check if joining is allowed
if 0 == Treenode.objects.filter(parent_id=to_treenode_id).count() and Treenode.objects.filter(pk=to_treenode_id).values_list('parent_id')[0][0] is None:
# Is an isolated node, so it can be joined freely
pass
# If the treenode is not isolated, must own the skeleton or be superuser
elif user.is_superuser or user.id == to_skeleton_user_id:
pass
# If the skeleton is a model_of a neuron that is part_of the 'Fragments' group
# or the 'Isolated synaptic terminals' group, then it can be joined
elif _under_fragments(to_skid):
pass
# Else, if the user owns the node (but not the skeleton), the join is possible only if all other nodes also belong to the user (such a situation occurs when the user ows both skeletons to join, or when part of a skeleton is split away from a larger one that belongs to someone else)
elif user.id == to_treenode_user_id and 0 == Treenode.objects.filter(skeleton_id=to_skid).exclude(user=user).count():
pass
else:
raise Exception("User %s with id #%s cannot join skeleton #%s, because the user doesn't own the skeleton or the skeleton contains nodes that belong to someone else." % (user.username, user.id, to_skid))
from_treenode_id = int(from_treenode_id)
from_treenode = Treenode.objects.get(pk=from_treenode_id)
from_skid = from_treenode.skeleton_id
if from_skid == to_skid:
raise Exception('Cannot join treenodes of the same skeleton, this would introduce a loop.')
from_neuron = _get_neuronname_from_skeletonid( project_id, from_skid )
to_neuron = _get_neuronname_from_skeletonid( project_id, to_skid )
# Reroot to_skid at to_treenode if necessary
response_on_error = 'Could not reroot at treenode %s' % to_treenode_id
_reroot_skeleton(to_treenode_id, project_id)
# The target skeleton is removed and its treenode assumes
# the skeleton id of the from-skeleton.
response_on_error = 'Could not update Treenode table with new skeleton id for joined treenodes.'
Treenode.objects.filter(skeleton=to_skid).update(skeleton=from_skid)
response_on_error = 'Could not update TreenodeConnector table.'
TreenodeConnector.objects.filter(
skeleton=to_skid).update(skeleton=from_skid)
# Determine if the neuron is part_of group 'Isolated synaptic terminals'
response_on_error = 'Could not find neuron of skeleton #%s.' % to_skid
neuron_id = _in_isolated_synaptic_terminals(to_skid)
# Remove skeleton of to_id (deletes cicic part_of to neuron by cascade,
# leaving the parent neuron dangling in the object tree).
response_on_error = 'Could not delete skeleton with ID %s.' % to_skid
ClassInstance.objects.filter(pk=to_skid).delete()
# Remove the neuron if it belongs to 'Isolated synaptic terminals'
# It is ok if the request.user doesn't match with the neuron's user_id or is not superuser.
if neuron_id:
response_on_error = 'Could not delete neuron with id %s.' % neuron_id
if _delete_if_empty(neuron_id):
print >> sys.stderr, "DELETED neuron %s from IST" % neuron_id
# Update the parent of to_treenode.
response_on_error = 'Could not update parent of treenode with ID %s' % to_treenode_id
Treenode.objects.filter(id=to_treenode_id).update(parent=from_treenode_id, editor=user)
insert_into_log(project_id, user.id, 'join_skeleton', from_treenode.location, 'Joined skeleton with ID %s (neuron: %s) into skeleton with ID %s (neuron: %s)' % (to_skid, to_neuron['neuronname'], from_skid, from_neuron['neuronname']) )
except Exception as e:
raise Exception(response_on_error + ':' + str(e))
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 _join_skeleton(user, from_treenode_id, to_treenode_id, project_id,
annotation_set):
""" Take the IDs of two nodes, each belonging to a different skeleton, and
make to_treenode be a child of from_treenode, and join the nodes of the
skeleton of to_treenode into the skeleton of from_treenode, and delete the
former skeleton of to_treenode. All annotations in annotation_set will be
linked to the skeleton of to_treenode."""
if from_treenode_id is None or to_treenode_id is None:
raise Exception('Missing arguments to _join_skeleton')
response_on_error = ''
try:
from_treenode_id = int(from_treenode_id)
to_treenode_id = int(to_treenode_id)
try:
from_treenode = Treenode.objects.get(pk=from_treenode_id)
except Treenode.DoesNotExist:
raise Exception("Could not find a skeleton for treenode #%s" % from_treenode_id)
try:
to_treenode = Treenode.objects.get(pk=to_treenode_id)
except Treenode.DoesNotExist:
raise Exception("Could not find a skeleton for treenode #%s" % to_treenode_id)
from_skid = from_treenode.skeleton_id
from_neuron = _get_neuronname_from_skeletonid( project_id, from_skid )
to_skid = to_treenode.skeleton_id
to_neuron = _get_neuronname_from_skeletonid( project_id, to_skid )
# Make sure the user has permissions to edit both neurons
can_edit_class_instance_or_fail(
user, from_neuron['neuronid'], 'neuron')
can_edit_class_instance_or_fail(
user, to_neuron['neuronid'], 'neuron')
# Check if annotations are valid
if not check_annotations_on_join(project_id, user,
from_neuron['neuronid'], to_neuron['neuronid'], annotation_set):
raise Exception("Annotation distribution is not valid for joining. " \
"Annotations for which you don't have permissions have to be kept!")
if from_skid == to_skid:
raise Exception('Cannot join treenodes of the same skeleton, this would introduce a loop.')
# Reroot to_skid at to_treenode if necessary
response_on_error = 'Could not reroot at treenode %s' % to_treenode_id
_reroot_skeleton(to_treenode_id, project_id)
# The target skeleton is removed and its treenode assumes
# the skeleton id of the from-skeleton.
response_on_error = 'Could not update Treenode table with new skeleton id for joined treenodes.'
Treenode.objects.filter(skeleton=to_skid).update(skeleton=from_skid)
response_on_error = 'Could not update TreenodeConnector table.'
TreenodeConnector.objects.filter(
skeleton=to_skid).update(skeleton=from_skid)
# Remove skeleton of to_id (deletes cicic part_of to neuron by cascade,
# leaving the parent neuron dangling in the object tree).
response_on_error = 'Could not delete skeleton with ID %s.' % to_skid
ClassInstance.objects.filter(pk=to_skid).delete()
# Remove the 'losing' neuron if it is empty
_delete_if_empty(to_neuron['neuronid'])
# Update the parent of to_treenode.
response_on_error = 'Could not update parent of treenode with ID %s' % to_treenode_id
Treenode.objects.filter(id=to_treenode_id).update(parent=from_treenode_id, editor=user)
# Update linked annotations of neuron
response_on_error = 'Could not update annotations of neuron ' \
'with ID %s' % from_neuron['neuronid']
_update_neuron_annotations(project_id, user, from_neuron['neuronid'],
annotation_set)
insert_into_log(project_id, user.id, 'join_skeleton',
from_treenode.location, 'Joined skeleton with ID %s (neuron: ' \
'%s) into skeleton with ID %s (neuron: %s, annotations: %s)' % \
(to_skid, to_neuron['neuronname'], from_skid,
from_neuron['neuronname'], ', '.join(annotation_set)))
except Exception as e:
raise Exception(response_on_error + ':' + str(e))
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)
treenode = Treenode.objects.get(pk=treenode_id)
parent_id = treenode.parent_id
response_on_error = ''
deleted_neuron = False
try:
if not parent_id:
# 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 HttpResponse(json.dumps({"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)
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'
Treenode.objects.filter(parent=treenode) \
.update(parent=treenode.parent)
# Remove treenode
response_on_error = 'Could not delete treenode.'
Treenode.objects.filter(pk=treenode_id).delete()
return HttpResponse(
json.dumps({
'deleted_neuron': deleted_neuron,
'parent_id': parent_id,
'skeleton_id': treenode.skeleton_id,
'success': "Removed treenode successfully."
}))
except Exception as e:
raise Exception(response_on_error + ': ' + str(e))
