class Spike(BlockBasedPermissionsMixin, BaseInfo, DataObject):
"""
NEO Spike @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
time = models.FloatField()
time__unit = TimeUnitField('time__unit',
default=DEFAULTS['default_time_unit'])
sampling_rate = models.FloatField('sampling_rate', blank=True, null=True)
sampling_rate__unit = SamplingUnitField('sampling_rate__unit',
blank=True,
null=True)
left_sweep = models.FloatField('left_sweep', blank=True, null=True)
left_sweep__unit = TimeUnitField('left_sweep__unit', blank=True, null=True)
# NEO data arrays
waveform = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
waveform__unit = SignalUnitField('waveform__unit',
default=DEFAULTS['default_data_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
unit = VersionedForeignKey(Unit, blank=True, null=True)
def save(self, *args, **kwargs):
self.block = self.segment.block
super(Spike, self).save(*args, **kwargs)
class AnalogSignal(BlockBasedPermissionsMixin, BaseInfo, DataObject):
"""
NEO AnalogSignal @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
sampling_rate = models.FloatField('sampling_rate')
sampling_rate__unit = SamplingUnitField(
'sampling_rate__unit', default=DEFAULTS['default_samp_unit'])
t_start = models.FloatField('t_start')
t_start__unit = TimeUnitField('t_start__unit',
default=DEFAULTS['default_time_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
recordingchannel = VersionedForeignKey(RecordingChannel,
blank=True,
null=True)
# NEO data arrays
signal = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
signal__unit = SignalUnitField('signal__unit',
default=DEFAULTS['default_data_unit'])
def save(self, *args, **kwargs):
self.block = self.segment.block
super(AnalogSignal, self).save(*args, **kwargs)
class EpochArray(BlockBasedPermissionsMixin, BaseInfo, DataObject):
"""
NEO EpochArray @ G-Node.
"""
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
# NEO data arrays
labels = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
times = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
times__unit = TimeUnitField('times__unit',
default=DEFAULTS['default_time_unit'])
durations = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
durations__unit = TimeUnitField('durations__unit',
default=DEFAULTS['default_time_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
def save(self, *args, **kwargs):
self.block = self.segment.block
super(EpochArray, self).save(*args, **kwargs)
class ACLFakeModel(BaseGnodeObject):
""" simple versioned model """
test_attr = models.IntegerField()
test_str_attr = models.CharField(max_length=50, blank=True)
test_ref = VersionedForeignKey(
ACLFakeOwnedModel, blank=True, null=True, on_delete=models.SET_NULL
)
class BaseInfo(BaseGnodeObject):
""" Base abstract class for any NEO object (except Block) """
# block reference is used to determine access to an object
block = VersionedForeignKey(Block)
metadata = VersionedForeignKey(Section, null=True, blank=True)
description = models.CharField(max_length=1024, blank=True, null=True)
class Meta:
abstract = True
@property
def has_data(self):
return False # no data by default
@property
def size(self):
raise NotImplementedError()
class Value(DocumentBasedPermissionsMixin, BaseGnodeObject):
"""
Class implemented metadata Value.
"""
data = models.TextField('data')
uncertainty = models.CharField(max_length=100, blank=True, null=True)
unit = models.CharField(max_length=100, blank=True, null=True)
reference = models.CharField(max_length=100, blank=True, null=True)
definition = models.CharField(max_length=100, blank=True, null=True)
filename = models.CharField(max_length=100, blank=True, null=True)
encoder = models.CharField(max_length=100, blank=True, null=True)
checksum = models.CharField(max_length=100, blank=True, null=True)
property = VersionedForeignKey(Property, on_delete=models.CASCADE)
document = VersionedForeignKey(Document)
def save(self, *args, **kwargs):
self.document = self.property.document
super(Value, self).save(*args, **kwargs)
class Property(DocumentBasedPermissionsMixin, BaseGnodeObject):
"""
Class represents a metadata "Property". Defines any kind of metadata
property and may be linked to the Section.
"""
# odML fields
name = models.CharField('name', max_length=100)
definition = models.CharField(max_length=100, blank=True, null=True)
mapping = models.CharField(max_length=100, blank=True, null=True)
dependency = models.CharField(max_length=100, blank=True, null=True)
dependencyvalue = models.CharField(max_length=100, blank=True, null=True)
section = VersionedForeignKey(Section, on_delete=models.CASCADE)
document = VersionedForeignKey(Document)
def save(self, *args, **kwargs):
self.document = self.section.document
super(Property, self).save(*args, **kwargs)
class IrregularlySampledSignal(BlockBasedPermissionsMixin, BaseInfo,
DataObject):
"""
NEO IrregularlySampledSignal @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
t_start = models.FloatField('t_start')
t_start__unit = TimeUnitField('t_start__unit',
default=DEFAULTS['default_time_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
recordingchannel = VersionedForeignKey(RecordingChannel,
blank=True,
null=True)
# NEO data arrays
signal = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
signal__unit = SignalUnitField('signal__unit',
default=DEFAULTS['default_data_unit'])
times = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
times__unit = TimeUnitField('times__unit',
default=DEFAULTS['default_time_unit'])
def full_clean(self, *args, **kwargs):
""" Add some validation to keep 'signal' and 'times' dimensions
consistent. Currently switched off. """
super(IrregularlySampledSignal, self).full_clean(*args, **kwargs)
def save(self, *args, **kwargs):
self.block = self.segment.block
super(IrregularlySampledSignal, self).save(*args, **kwargs)
class Unit(BlockBasedPermissionsMixin, BaseInfo):
"""
NEO Unit @ G-Node.
"""
name = models.CharField(max_length=DEFAULTS['name_max_length'])
# NEO relationships
recordingchannelgroup = VersionedForeignKey(RecordingChannelGroup)
def save(self, *args, **kwargs):
self.block = self.recordingchannelgroup.block
super(Unit, self).save(*args, **kwargs)
class SpikeTrain(BlockBasedPermissionsMixin, BaseInfo, DataObject):
"""
NEO SpikeTrain @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
t_start = models.FloatField('t_start')
t_start__unit = TimeUnitField('t_start__unit',
default=DEFAULTS['default_time_unit'])
t_stop = models.FloatField('t_stop')
t_stop__unit = TimeUnitField('t_stop__unit',
default=DEFAULTS['default_time_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
unit = VersionedForeignKey(Unit, blank=True, null=True)
# NEO data arrays
times = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
times__unit = TimeUnitField('times__unit',
default=DEFAULTS['default_time_unit'])
waveforms = models.FileField(storage=fs,
upload_to=make_upload_path,
blank=True,
null=True)
waveforms__unit = SignalUnitField('waveforms__unit', blank=True, null=True)
# rewrite the size property when waveforms are supported
def compute_size(self):
return self.times.size
def save(self, *args, **kwargs):
self.block = self.segment.block
super(SpikeTrain, self).save(*args, **kwargs)
class Block(BasePermissionsMixin, BaseGnodeObject):
"""
NEO Block @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'])
description = models.CharField(max_length=1024, blank=True, null=True)
filedatetime = models.DateTimeField(null=True, blank=True)
index = models.IntegerField(null=True, blank=True)
metadata = VersionedForeignKey(Section, null=True, blank=True)
@property
def size(self):
return sum([s.size for s in self.segment_set.all()])
class Event(BlockBasedPermissionsMixin, BaseInfo):
"""
NEO Event @ G-Node.
"""
# NEO attributes
name = models.CharField(max_length=DEFAULTS['name_max_length'],
blank=True,
null=True)
label = models.CharField('label', max_length=DEFAULTS['name_max_length'])
time = models.FloatField('time')
time__unit = TimeUnitField('time__unit',
default=DEFAULTS['default_time_unit'])
# NEO relationships
segment = VersionedForeignKey(Segment)
def save(self, *args, **kwargs):
self.block = self.segment.block
super(Event, self).save(*args, **kwargs)
class parent_fake(VersionedM2M):
""" M2M relationship class """
parent = VersionedForeignKey(FakeParentModel)
fake = VersionedForeignKey(FakeModel)
class FakeChildModel(BaseGnodeObject):
""" simple versioned model with parent """
test_attr = models.IntegerField()
test_ref = VersionedForeignKey(
FakeParentModel, blank=True, null=True, on_delete=models.SET_NULL
)
class recordingchannel_rcg(VersionedM2M):
recordingchannelgroup = VersionedForeignKey(RecordingChannelGroup)
recordingchannel = VersionedForeignKey(RecordingChannel)
class Section(DocumentBasedPermissionsMixin, BaseGnodeObject):
"""
Class represents a metadata "Section". Used to organize metadata
(properties - values), Datafiles and NEO Blocks in a tree-like structure.
May be recursively linked to itself.
May be made public or shared with specific users via sharing of the related
Document.
Document field is always set, even for low-level Sections in the odML
hierarchy. This is done to avoid recursive SQL-calls to fetch appropriate
Section permissions.
"""
# odML fields
name = models.CharField(max_length=100)
type = models.CharField(max_length=50, blank=True, null=True)
reference = models.CharField(max_length=100, blank=True, null=True)
definition = models.CharField(max_length=100, blank=True, null=True)
link = models.CharField(max_length=100, blank=True, null=True)
include = models.CharField(max_length=100, blank=True, null=True)
repository = models.CharField(max_length=100, blank=True, null=True)
mapping = models.CharField(max_length=100, blank=True, null=True)
section = VersionedForeignKey(
'self', blank=True, null=True, related_name='section_set',
on_delete=models.CASCADE
)
document = VersionedForeignKey(
Document, blank=True, null=True, on_delete=models.CASCADE
)
# position in the list on the same level in the tree
tree_position = models.IntegerField(default=0)
# field indicates whether it is a "template" section
is_template = models.BooleanField(default=False)
# manager that proxies correct QuerySet
objects = SectionManager()
@property
def sections(self):
return self.section_set.order_by("-tree_position")
def fetch_deep_ids(self, ids):
""" return all section ids located inside sections with given ids. This
function as many sql calls as there are levels of the section tree """
qs = self.__class__.objects.filter(parent_section_id__in=ids)
down_one_level = list(qs.values_list('pk', flat=True))
if down_one_level:
return ids + self.fetch_deep_ids(down_one_level)
return ids
def stats(self, cascade=False):
""" Section statistics """
sec_ids = [self.pk]
if cascade: # recursively traverse a tree of child sections
sec_ids = self.fetch_deep_ids(sec_ids)
stats = {} # calculate section statistics
for rm in self._meta.get_all_related_objects():
if not rm.model == self.__class__:
kwargs = {rm.field.name + '_id__in': sec_ids}
v = rm.model.objects.filter(**kwargs).count()
else:
v = len(sec_ids) - 1 # exclude self
stats[rm.name] = v
return stats
def _get_next_tree_pos(self):
""" Returns the next tree index "inside" self. """
if self.sections:
return int(self.sections[0].tree_position) + 1
return 1
def save(self, *args, **kwargs):
def obj_has_changed(old, new):
return (old is None and new is not None) or \
(new is None and old is not None) or \
(old is not None and new is not None and not old.pk == new.pk)
if self.pk is not None and self.pk != "": # update case
old = self.__class__.objects.get(pk=self.pk)
if obj_has_changed(old.section, self.section):
if not self.section is None:
self.document = self.section.document
elif obj_has_changed(old.document, self.document):
if not old.section is None:
raise ValueError("Clean parent section to change Document")
else: # create case
# section has a priority. if section is set, the document of the new
# section will be taken from the parent section, not from the
# current 'document' attribute
if self.section is None and self.document is None:
raise ValidationError("Either document or section must present")
if self.section is not None:
self.document = self.section.document
self.full_clean()
super(Section, self).save(*args, **kwargs)