def post(self, request, collection):
"""Create a new collection
View to create a new collection and an associated bosskey for that collection
Args:
request: DRF Request object
collection : Collection name
Returns:
Collection
"""
col_data = request.data.copy()
col_data['name'] = collection
# Save the object
serializer = CollectionSerializer(data=col_data)
if serializer.is_valid():
serializer.save(creator=self.request.user)
collection_obj = Collection.objects.get(name=col_data['name'])
# Assign permissions to the users primary group and admin group
BossPermissionManager.add_permissions_primary_group(self.request.user, collection_obj)
BossPermissionManager.add_permissions_admin_group(collection_obj)
lookup_key = str(collection_obj.pk)
boss_key = collection_obj.name
LookUpKey.add_lookup(lookup_key, boss_key, collection_obj.name)
return Response(serializer.data, status=status.HTTP_201_CREATED)
else:
return BossHTTPError("{}".format(serializer.errors), ErrorCodes.INVALID_POST_ARGUMENT)
def post(self, request, collection, experiment):
"""Create a new experiment
View to create a new experiment and an associated bosskey for that experiment
Args:
request: DRF Request object
collection : Collection name
experiment : Experiment name
Returns:
Experiment
"""
experiment_data = request.data.copy()
experiment_data['name'] = experiment
try:
# Get the collection information
collection_obj = Collection.objects.get(name=collection)
if request.user.has_perm("add", collection_obj):
experiment_data['collection'] = collection_obj.pk
# Update the coordinate frame
if 'coord_frame' not in experiment_data:
return BossHTTPError("This request requires a valid coordinate frame",
ErrorCodes.INVALID_POST_ARGUMENT)
coord_frame_obj = CoordinateFrame.objects.get(name=experiment_data['coord_frame'])
experiment_data['coord_frame'] = coord_frame_obj.pk
serializer = ExperimentSerializer(data=experiment_data)
if serializer.is_valid():
serializer.save(creator=self.request.user)
experiment_obj = Experiment.objects.get(name=experiment_data['name'], collection=collection_obj)
# Assign permissions to the users primary group and admin group
BossPermissionManager.add_permissions_primary_group(self.request.user, experiment_obj)
BossPermissionManager.add_permissions_admin_group(experiment_obj)
lookup_key = str(collection_obj.pk) + '&' + str(experiment_obj.pk)
boss_key = collection_obj.name + '&' + experiment_obj.name
LookUpKey.add_lookup(lookup_key, boss_key, collection_obj.name, experiment_obj.name)
serializer = ExperimentReadSerializer(experiment_obj)
return Response(serializer.data, status=status.HTTP_201_CREATED)
else:
return BossHTTPError("{}".format(serializer.errors), ErrorCodes.INVALID_POST_ARGUMENT)
else:
return BossPermissionError('add', collection)
except Collection.DoesNotExist:
return BossResourceNotFoundError(collection)
except CoordinateFrame.DoesNotExist:
return BossResourceNotFoundError(experiment_data['coord_frame'])
except ValueError:
return BossHTTPError("Value Error.Collection id {} in post data needs to be an integer"
.format(experiment_data['collection']), ErrorCodes.TYPE_ERROR)
def post(self, request, collection, experiment, channel):
"""
Post a new Channel
Args:
request: DRF Request object
collection: Collection name
experiment: Experiment name
channel: Channel name
Returns :
Channel
"""
channel_data = request.data.copy()
channel_data['name'] = channel
try:
# Get the collection and experiment
collection_obj = Collection.objects.get(name=collection)
experiment_obj = Experiment.objects.get(name=experiment, collection=collection_obj)
# Check for add permissions
if request.user.has_perm("add", experiment_obj):
channel_data['experiment'] = experiment_obj.pk
# The source and related channels are names and need to be removed from the dict before serialization
source_channels = channel_data.pop('sources', [])
related_channels = channel_data.pop('related', [])
# Source channels have to be included for new annotation channels
if 'type' in channel_data and channel_data['type'] == 'annotation' and len(source_channels) == 0:
return BossHTTPError("Annotation channels require the source channel to be set. "
"Specify a valid source channel in the post", ErrorCodes.INVALID_POST_ARGUMENT)
# Validate the source and related channels if they are incuded
channels = self.validate_source_related_channels(experiment_obj, source_channels, related_channels)
source_channels_objs = channels[0]
related_channels_objs = channels[1]
# Validate and create the channel
serializer = ChannelSerializer(data=channel_data)
if serializer.is_valid():
serializer.save(creator=self.request.user)
channel_obj = Channel.objects.get(name=channel_data['name'], experiment=experiment_obj)
# Save source and related channels if they are valid
channel_obj = self.add_source_related_channels(channel_obj, experiment_obj, source_channels_objs,
related_channels_objs)
# Assign permissions to the users primary group and admin group
BossPermissionManager.add_permissions_primary_group(self.request.user, channel_obj)
BossPermissionManager.add_permissions_admin_group(channel_obj)
# Add Lookup key
lookup_key = str(collection_obj.pk) + '&' + str(experiment_obj.pk) + '&' + str(channel_obj.pk)
boss_key = collection_obj.name + '&' + experiment_obj.name + '&' + channel_obj.name
LookUpKey.add_lookup(lookup_key, boss_key, collection_obj.name, experiment_obj.name,
channel_obj.name)
serializer = ChannelReadSerializer(channel_obj)
return Response(serializer.data, status=status.HTTP_201_CREATED)
else:
return BossHTTPError("{}".format(serializer.errors), ErrorCodes.INVALID_POST_ARGUMENT)
else:
return BossPermissionError('add', experiment)
except Collection.DoesNotExist:
return BossResourceNotFoundError(collection)
except Experiment.DoesNotExist:
return BossResourceNotFoundError(experiment)
except Channel.DoesNotExist:
return BossResourceNotFoundError(channel)
except BossError as err:
return err.to_http()
except ValueError:
return BossHTTPError("Value Error in post data", ErrorCodes.TYPE_ERROR)
def post(self, request, collection, experiment, channel):
"""
Post a new Channel
Args:
request: DRF Request object
collection: Collection name
experiment: Experiment name
channel: Channel name
Returns :
Channel
"""
channel_data = request.data.copy()
channel_data['name'] = channel
try:
is_admin = BossPermissionManager.is_in_group(
request.user, ADMIN_GRP)
if 'bucket' in channel_data and channel_data[
'bucket'] and not is_admin:
return BossHTTPError('Only admins can set bucket name',
ErrorCodes.MISSING_PERMISSION)
if 'cv_path' in channel_data and channel_data[
'cv_path'] and not is_admin:
return BossHTTPError('Only admins can set cv_path',
ErrorCodes.MISSING_PERMISSION)
# Get the collection and experiment
collection_obj = Collection.objects.get(name=collection)
experiment_obj = Experiment.objects.get(name=experiment,
collection=collection_obj)
# Check for add permissions
if request.user.has_perm("add", experiment_obj):
channel_data['experiment'] = experiment_obj.pk
use_cloudvol = channel_data.get(
'storage_type', None) == Channel.StorageType.CLOUD_VOLUME
cv_path = channel_data.get('cv_path', None)
if use_cloudvol and (cv_path is None or cv_path == ''):
channel_data[
'cv_path'] = f'/{collection}/{experiment}/{channel}'
if use_cloudvol:
# DX NOTE: For now we assume that cloudvolume channels are downsampled. This means
# that the num_hierarchy_levels in the experiment should be limited to the available
# mip levels in the cloudvolume layer.
channel_data['downsample_status'] = 'DOWNSAMPLED'
# The source and related channels are names and need to be removed from the dict before serialization
source_channels = channel_data.pop('sources', [])
related_channels = channel_data.pop('related', [])
# TODO: Removed source channel requirement for annotation channels. Future update should allow source channel from
# different collections.
# Source channels have to be included for new annotation channels
# if 'type' in channel_data and channel_data['type'] == 'annotation' and len(source_channels) == 0:
# return BossHTTPError("Annotation channels require the source channel to be set. "
# "Specify a valid source channel in the post", ErrorCodes.INVALID_POST_ARGUMENT)
# Validate the source and related channels if they are incuded
channels = self.validate_source_related_channels(
experiment_obj, source_channels, related_channels)
source_channels_objs = channels[0]
related_channels_objs = channels[1]
# Validate and create the channel
serializer = ChannelSerializer(data=channel_data)
if serializer.is_valid():
serializer.save(creator=self.request.user)
channel_obj = Channel.objects.get(
name=channel_data['name'], experiment=experiment_obj)
# Save source and related channels if they are valid
channel_obj = self.add_source_related_channels(
channel_obj, experiment_obj, source_channels_objs,
related_channels_objs)
# Assign permissions to the users primary group and admin group
BossPermissionManager.add_permissions_primary_group(
self.request.user, channel_obj)
BossPermissionManager.add_permissions_admin_group(
channel_obj)
# Add Lookup key
lookup_key = str(collection_obj.pk) + '&' + str(
experiment_obj.pk) + '&' + str(channel_obj.pk)
boss_key = collection_obj.name + '&' + experiment_obj.name + '&' + channel_obj.name
LookUpKey.add_lookup(lookup_key, boss_key,
collection_obj.name,
experiment_obj.name, channel_obj.name)
serializer = ChannelReadSerializer(channel_obj)
return Response(serializer.data,
status=status.HTTP_201_CREATED)
else:
return BossHTTPError("{}".format(serializer.errors),
ErrorCodes.INVALID_POST_ARGUMENT)
else:
return BossPermissionError('add', experiment)
except Collection.DoesNotExist:
return BossResourceNotFoundError(collection)
except Experiment.DoesNotExist:
return BossResourceNotFoundError(experiment)
except Channel.DoesNotExist:
return BossResourceNotFoundError(channel)
except BossError as err:
return err.to_http()
except ValueError:
return BossHTTPError("Value Error in post data",
ErrorCodes.TYPE_ERROR)
def post(self, request, collection, experiment, channel_layer):
"""
Post a new Channel
Args:
request: DRF Request object
collection: Collection name
experiment: Experiment name
channel_layer: Channel or Layer name
Returns :
ChannelLayer
"""
channel_layer_data = request.data.copy()
channel_layer_data['name'] = channel_layer
try:
if 'channels' in channel_layer_data:
channels = dict(channel_layer_data)['channels']
else:
channels = []
collection_obj = Collection.objects.get(name=collection)
experiment_obj = Experiment.objects.get(name=experiment, collection=collection_obj)
# Check for add permissions
if request.user.has_perm("add", experiment_obj):
channel_layer_data['experiment'] = experiment_obj.pk
channel_layer_data['is_channel'] = self.get_bool(channel_layer_data['is_channel'])
# layers require at least 1 channel
if (channel_layer_data['is_channel'] is False) and (len(channels) == 0):
return BossHTTPError("Invalid Request.Please specify a valid channel for the layer",
ErrorCodes.INVALID_POST_ARGUMENT)
serializer = ChannelLayerSerializer(data=channel_layer_data)
if serializer.is_valid():
serializer.save(creator=self.request.user)
channel_layer_obj = ChannelLayer.objects.get(name=channel_layer_data['name'],
experiment=experiment_obj)
# Layer?
if not channel_layer_obj.is_channel:
# Layers must map to at least 1 channel
for channel_id in channels:
# Is this a valid channel?
channel_obj = ChannelLayer.objects.get(pk=channel_id)
if channel_obj:
channel_layer_map = {'channel': channel_id, 'layer': channel_layer_obj.pk}
map_serializer = ChannelLayerMapSerializer(data=channel_layer_map)
if map_serializer.is_valid():
map_serializer.save()
# Assign permissions to the users primary group
BossPermissionManager.add_permissions_primary_group(self.request.user, channel_layer_obj)
# Add Lookup key
lookup_key = str(collection_obj.pk) + '&' + str(experiment_obj.pk) + '&' + str(channel_layer_obj.pk)
boss_key = collection_obj.name + '&' + experiment_obj.name + '&' + channel_layer_obj.name
LookUpKey.add_lookup(lookup_key, boss_key, collection_obj.name, experiment_obj.name,
channel_layer_obj.name)
return Response(serializer.data, status=status.HTTP_201_CREATED)
else:
return BossHTTPError("{}".format(serializer.errors), ErrorCodes.INVALID_POST_ARGUMENT)
else:
return BossPermissionError('add', experiment)
except Collection.DoesNotExist:
return BossResourceNotFoundError(collection)
except Experiment.DoesNotExist:
return BossResourceNotFoundError(experiment)
except ChannelLayer.DoesNotExist:
return BossResourceNotFoundError(channel_layer)
except ValueError:
return BossHTTPError("Value Error in post data", ErrorCodes.TYPE_ERROR)
