def _update(Kind, table, nodes, now, user):
if not nodes:
return
# 0: id
# 1: X
# 2: Y
# 3: Z
can_edit_all_or_fail(user, (node[0] for node in nodes.itervalues()), table)
for node in nodes.itervalues():
Kind.objects.filter(id=int(node[0])).update(editor=user,
edition_time=now,
location_x=float(node[1]),
location_y=float(node[2]),
location_z=float(node[3]))
def _update(Kind, table, nodes, now, user):
if not nodes:
return
# 0: id
# 1: X
# 2: Y
# 3: Z
can_edit_all_or_fail(user, (node[0] for node in nodes.itervalues()), table)
for node in nodes.itervalues():
Kind.objects.filter(id=int(node[0])).update(
editor=user,
edition_time=now,
location_x=float(node[1]),
location_y=float(node[2]),
location_z=float(node[3]))
def _update_location(table, nodes, now, user, cursor):
if not nodes:
return
# 0: id
# 1: X
# 2: Y
# 3: Z
can_edit_all_or_fail(user, (node[0] for node in nodes), table)
# Sanitize node details
nodes = [(int(i), float(x), float(y), float(z)) for i, x, y, z in nodes]
node_template = "(" + "),(".join(["%s, %s, %s, %s"] * len(nodes)) + ")"
node_table = [v for k in nodes for v in k]
cursor.execute(
"""
UPDATE location n
SET editor_id = %s, location_x = target.x,
location_y = target.y, location_z = target.z
FROM (SELECT x.id, x.location_x AS old_loc_x,
x.location_y AS old_loc_y, x.location_z AS old_loc_z,
y.new_loc_x AS x, y.new_loc_y AS y, y.new_loc_z AS z
FROM location x
INNER JOIN (VALUES {}) y(id, new_loc_x, new_loc_y, new_loc_z)
ON x.id = y.id FOR NO KEY UPDATE) target
WHERE n.id = target.id
RETURNING n.id, n.edition_time, target.old_loc_x, target.old_loc_y,
target.old_loc_z
""".format(node_template), [user.id] + node_table)
updated_rows = cursor.fetchall()
if len(nodes) != len(updated_rows):
raise ValueError('Coudn\'t update node ' + ','.join(
frozenset([str(r[0]) for r in nodes]) -
frozenset([str(r[0]) for r in updated_rows])))
return updated_rows
def _update_location(table, nodes, now, user, cursor):
if not nodes:
return
# 0: id
# 1: X
# 2: Y
# 3: Z
can_edit_all_or_fail(user, (node[0] for node in nodes), table)
# Sanitize node details
nodes = [(int(i), float(x), float(y), float(z)) for i,x,y,z in nodes]
node_template = "(" + "),(".join(["%s, %s, %s, %s"] * len(nodes)) + ")"
node_table = [v for k in nodes for v in k]
cursor.execute("""
UPDATE location n
SET editor_id = %s, location_x = target.x,
location_y = target.y, location_z = target.z
FROM (SELECT x.id, x.location_x AS old_loc_x,
x.location_y AS old_loc_y, x.location_z AS old_loc_z,
y.new_loc_x AS x, y.new_loc_y AS y, y.new_loc_z AS z
FROM location x
INNER JOIN (VALUES {}) y(id, new_loc_x, new_loc_y, new_loc_z)
ON x.id = y.id FOR NO KEY UPDATE) target
WHERE n.id = target.id
RETURNING n.id, n.edition_time, target.old_loc_x, target.old_loc_y,
target.old_loc_z
""".format(node_template), [user.id] + node_table)
updated_rows = cursor.fetchall()
if len(nodes) != len(updated_rows):
raise ValueError('Coudn\'t update node ' +
','.join(frozenset([str(r[0]) for r in nodes]) -
frozenset([str(r[0]) for r in updated_rows])))
return updated_rows
def delete_neuron(request, project_id=None, neuron_id=None):
""" Deletes a neuron if and only if two things are the case: 1. The user
ownes all treenodes of the skeleton modeling the neuron in question and
2. The neuron is not annotated by other users.
"""
# Make sure the user can edit the neuron in general
can_edit_class_instance_or_fail(request.user, neuron_id, 'neuron')
# Create class and relation dictionaries
classes = dict(
Class.objects.filter(project_id=project_id).values_list(
'class_name', 'id'))
relations = dict(
Relation.objects.filter(project_id=project_id).values_list(
'relation_name', 'id'))
# Make sure the user has permission to edit all treenodes of all skeletons
skeleton_ids = ClassInstanceClassInstance.objects.filter(
class_instance_b=neuron_id,
relation_id=relations['model_of']).values_list('class_instance_a',
flat=True)
for skid in skeleton_ids:
others_nodes = Treenode.objects.filter(skeleton_id=skid).exclude(
user_id=request.user.id).values_list('id', flat=True)
if others_nodes:
try:
can_edit_all_or_fail(request.user, others_nodes, 'treenode')
except Exception:
raise Exception("You don't have permission to remove all " \
"treenodes of skeleton %s modeling this neuron. The " \
"neuron won't be deleted." % skid)
# Make sure the user has permission to edit all annotations of this neuron
annotation_ids = set(
ClassInstanceClassInstance.objects.filter(
class_instance_a_id=neuron_id,
relation_id=relations['annotated_with']).values_list('id',
flat=True))
if annotation_ids:
try:
can_edit_all_or_fail(request.user, annotation_ids,
'class_instance_class_instance')
except Exception:
raise Exception("You don't have permission to remove all " \
"annotations linked to this neuron. The neuron won't " \
"be deleted.")
# Try to get the root node to have a valid location for a log entry
if skeleton_ids:
try:
root_node = Treenode.objects.get(skeleton_id=skeleton_ids[0],
parent=None)
root_location = (root_node.location_x, root_node.location_y,
root_node.location_z)
except (Treenode.DoesNotExist, Treenode.MultipleObjectsReturned):
root_location = None
else:
root_location = None
# Delete neuron (and implicitely all annotation links due to Django's
# cascading deletion)
neuron = get_object_or_404(ClassInstance, pk=neuron_id)
neuron.delete()
# Delete all annotations that are not used anymore
used_annotation_ids = set(
ClassInstanceClassInstance.objects.filter(
class_instance_b_id__in=annotation_ids,
relation_id=relations['annotated_with']).values_list('id',
flat=True))
unused_annotation_ids = annotation_ids.difference(used_annotation_ids)
ClassInstance.objects.filter(id__in=unused_annotation_ids).delete()
# Delete the skeletons (and their treenodes through cascading delete)
cursor = connection.cursor()
for skid in skeleton_ids:
# Because there are constraints used in the database that Django is not
# aware of, it's emulation of cascading deletion doesn't work.
# Therefore, raw SQL needs to be used to use true cascading deletion.
cursor.execute(
'''
BEGIN;
DELETE FROM change_request WHERE treenode_id IN (
SELECT id FROM treenode WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM change_request WHERE connector_id IN (
SELECT id FROM treenode_connector WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM treenode_class_instance WHERE treenode_id IN (
SELECT id FROM treenode WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM treenode WHERE skeleton_id=%s AND project_id=%s;
DELETE FROM treenode_connector WHERE skeleton_id=%s AND project_id=%s;
DELETE FROM class_instance WHERE id=%s AND project_id=%s;
DELETE FROM review WHERE skeleton_id=%s AND project_id=%s;
COMMIT;
''', (skid, project_id) * 7)
# Insert log entry and refer to position of the first skeleton's root node
insert_into_log(
project_id, request.user.id, 'remove_neuron', root_location,
'Deleted neuron %s and skeleton(s) %s.' %
(neuron_id, ', '.join([str(s) for s in skeleton_ids])))
return HttpResponse(json.dumps({
'skeleton_ids': list(skeleton_ids),
'success': "Deleted neuron #%s as well as its skeletons and " \
"annotations." % neuron_id}))
def delete_neuron(request, project_id=None, neuron_id=None):
""" Deletes a neuron if and only if two things are the case: 1. The user
ownes all treenodes of the skeleton modeling the neuron in question and
2. The neuron is not annotated by other users.
"""
# Make sure the user can edit the neuron in general
can_edit_class_instance_or_fail(request.user, neuron_id, 'neuron')
# Create class and relation dictionaries
classes = dict(Class.objects.filter(
project_id=project_id).values_list('class_name', 'id'))
relations = dict(Relation.objects.filter(
project_id=project_id).values_list('relation_name', 'id'))
# Make sure the user has permission to edit all treenodes of all skeletons
skeleton_ids = ClassInstanceClassInstance.objects.filter(
class_instance_b=neuron_id,
relation_id=relations['model_of']).values_list(
'class_instance_a', flat=True)
for skid in skeleton_ids:
others_nodes = Treenode.objects.filter(skeleton_id=skid).exclude(
user_id=request.user.id).values_list('id', flat=True)
if others_nodes:
try:
can_edit_all_or_fail(request.user, others_nodes, 'treenode')
except Exception:
raise Exception("You don't have permission to remove all " \
"treenodes of skeleton %s modeling this neuron. The " \
"neuron won't be deleted." % skid)
# Make sure the user has permission to edit all annotations of this neuron
annotation_ids = set(ClassInstanceClassInstance.objects.filter(
class_instance_a_id=neuron_id,
relation_id=relations['annotated_with']).values_list(
'id', flat=True))
if annotation_ids:
try:
can_edit_all_or_fail(request.user, annotation_ids,
'class_instance_class_instance')
except Exception:
raise Exception("You don't have permission to remove all " \
"annotations linked to this neuron. The neuron won't " \
"be deleted.")
# Try to get the root node to have a valid location for a log entry
if skeleton_ids:
try:
root_node = Treenode.objects.get(
skeleton_id=skeleton_ids[0], parent=None)
root_location = (root_node.location_x, root_node.location_y,
root_node.location_z)
except (Treenode.DoesNotExist, Treenode.MultipleObjectsReturned):
root_location = None
else:
root_location = None
# Delete neuron (and implicitely all annotation links due to Django's
# cascading deletion)
neuron = get_object_or_404(ClassInstance, pk=neuron_id)
neuron.delete()
# Delete all annotations that are not used anymore
used_annotation_ids = set(ClassInstanceClassInstance.objects.filter(
class_instance_b_id__in=annotation_ids,
relation_id=relations['annotated_with']).values_list(
'id', flat=True))
unused_annotation_ids = annotation_ids.difference(used_annotation_ids)
ClassInstance.objects.filter(id__in=unused_annotation_ids).delete()
# Delete the skeletons (and their treenodes through cascading delete)
cursor = connection.cursor()
for skid in skeleton_ids:
# Because there are constraints used in the database that Django is not
# aware of, it's emulation of cascading deletion doesn't work.
# Therefore, raw SQL needs to be used to use true cascading deletion.
cursor.execute('''
BEGIN;
DELETE FROM change_request WHERE treenode_id IN (
SELECT id FROM treenode WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM change_request WHERE connector_id IN (
SELECT id FROM treenode_connector WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM treenode_class_instance WHERE treenode_id IN (
SELECT id FROM treenode WHERE skeleton_id=%s AND project_id=%s);
DELETE FROM treenode WHERE skeleton_id=%s AND project_id=%s;
DELETE FROM treenode_connector WHERE skeleton_id=%s AND project_id=%s;
DELETE FROM class_instance WHERE id=%s AND project_id=%s;
DELETE FROM review WHERE skeleton_id=%s AND project_id=%s;
COMMIT;
''', (skid, project_id) * 7)
# Insert log entry and refer to position of the first skeleton's root node
insert_into_log(project_id, request.user.id, 'remove_neuron', root_location,
'Deleted neuron %s and skeleton(s) %s.' % (neuron_id,
', '.join([str(s) for s in skeleton_ids])))
return HttpResponse(json.dumps({
'skeleton_ids': list(skeleton_ids),
'success': "Deleted neuron #%s as well as its skeletons and " \
"annotations." % neuron_id}))
def rename_neurons(request: HttpRequest, project_id=None) -> JsonResponse:
"""Rename a neuron.
If a neuron is not locked by a user on which the current user has no
permission, the name of neuron can be changed through this endpoint. Neuron
names are currently not allowed to contain pipe characters ("|").
---
parameters:
- name: neuron_names
description: A list of two-element tuples, containing of neuron ID and new name each.
required: true
type: array
paramType: form
type:
success:
description: If renaming was successful
type: boolean
required: true
renamed_neurons:
description: IDs of the renamed neurons
type: integer
required: true
old_names:
description: Old names of the renamed neurons
type: string
required: true
"""
neuron_name_pairs = get_request_list(request.POST, 'names')
if not neuron_name_pairs:
raise ValueError('Need at least one neuron ID / name mapping')
neuron_ids = [int(k) for k, _ in neuron_name_pairs]
neuron_names = [v for _, v in neuron_name_pairs]
# Make sure the user can edit the neuron
can_edit_all_or_fail(request.user, neuron_ids, 'class_instance')
# Do not allow '|' in name because it is used as string separator in NeuroHDF export
for new_name in neuron_names:
if '|' in new_name:
raise ValueError('New name should not contain pipe character')
cursor = connection.cursor()
cursor.execute(
"""
UPDATE class_instance ci
SET name = new_data.name
FROM UNNEST(
%(neuron_ids)s::bigint[],
%(neuron_names)s::text[]) new_data(id, name)
JOIN class_instance ci_old
ON ci_old.id = new_data.id
WHERE ci.id = new_data.id
AND ci.project_id = %(project_id)s
RETURNING ci.id, ci_old.name, ci.name
""", {
'project_id': project_id,
'neuron_ids': neuron_ids,
'neuron_names': neuron_names,
})
rows = cursor.fetchall()
updated_ids = [r[0] for r in rows]
old_names = [r[1] for r in rows]
new_names = [r[2] for r in rows]
# Insert log entry and return successfully
if len(updated_ids) == 1:
insert_into_log(
project_id, request.user.id, "rename_neuron", None,
f"Renamed neuron with ID {neuron_ids[0]} from {old_names[0]} to {neuron_names[0]}"
)
else:
insert_into_log(
project_id, request.user.id, "rename_neuron", None,
f"Renamed {len(neuron_ids)} neurons. IDs: {', '.join(str(uid) for uid in updated_ids)} Old names: {', '.join(old_names)} New names: {', '.join(new_names)}"
)
return JsonResponse({
'success': True,
'renamed_neurons': updated_ids,
'old_names': old_names
})
