class IndividualDocument(Document):
"""Individual elastic search document"""
pk = fields.IntegerField(attr='pk')
name = string_field('name')
group = ObjectField(
properties={
'name': string_field('name'),
'pk': fields.IntegerField('pk'),
'count': fields.IntegerField('count')
})
study = string_field('study_name')
ex = ObjectField(properties={'pk': fields.IntegerField('pk')})
characteristica_all_normed = characteristica_object_field
access = string_field('access')
allowed_users = fields.ObjectField(
attr="allowed_users",
properties={'username': string_field("username")},
multi=True)
class Django:
model = Individual
# Ignore auto updating of Elasticsearch when a model is saved/deleted
ignore_signals = True
# Don't perform an index refresh after every update
auto_refresh = False
class Index:
name = 'individuals'
settings = elastic_settings
class GroupDocument(DocType):
"""Individual elastic search document"""
pk = fields.IntegerField(attr='pk')
name = string_field('name')
count = fields.IntegerField(attr='count')
parent = ObjectField(
properties={
'name': string_field('name'),
'pk': fields.IntegerField('pk'),
'count': fields.IntegerField('count')
})
study = ObjectField(
properties={
'name': string_field('name'),
'pk': fields.IntegerField('pk'),
'sid': fields.StringField('sid')
})
ex = ObjectField(properties={'pk': fields.IntegerField('pk')})
characteristica_all_normed = fields.ObjectField(properties={
'pk':
fields.IntegerField(),
'category':
string_field('category_key'),
'choice':
string_field('choice'),
'value':
fields.FloatField('value'),
'mean':
fields.FloatField(),
'median':
fields.FloatField(),
'min':
fields.FloatField(),
'max':
fields.FloatField(),
'se':
fields.FloatField(),
'sd':
fields.FloatField(),
'cv':
fields.FloatField(),
'unit':
string_field('unit'),
'count':
fields.IntegerField('count'),
},
multi=True)
class Meta:
model = Group
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update (overrides global setting):
auto_refresh = False
class GroupDocument(Document):
""" Elastic Group Document """
pk = fields.IntegerField(attr='pk')
name = string_field('name')
count = fields.IntegerField(attr='count')
parent = ObjectField(
properties={
'name': string_field('name'),
'pk': fields.IntegerField('pk'),
'count': fields.IntegerField('count')
})
study = string_field('study_name')
ex = ObjectField(properties={'pk': fields.IntegerField('pk')})
characteristica_all_normed = characteristica_object_field
access = string_field('access')
allowed_users = fields.ObjectField(
attr="allowed_users",
properties={'username': string_field("username")},
multi=True)
class Django:
model = Group
# Ignore auto updating of Elasticsearch when a model is saved
# or deleted:
ignore_signals = True
# Don't perform an index refresh after every update
auto_refresh = False
class Index:
name = 'groups'
settings = elastic_settings
def get_queryset(self):
"""Not mandatory but to improve performance we can select related in one sql request"""
return super(GroupDocument, self).get_queryset().select_related(
'ex__groupset__study',
'parent').prefetch_related("characteristica")
class IndividualCharacteristicaDocument(Document):
""" Characteristica elastic search document. """
study_sid = string_field('study_sid')
study_name = string_field('study_name')
# individual related
individual_pk = fields.IntegerField(attr='individual_pk')
individual_name = fields.StringField(
attr='individual_name',
fields={
'raw': fields.StringField(analyzer='keyword'),
})
individual_group_pk = fields.IntegerField(attr='individual_group_pk', )
characteristica_pk = fields.IntegerField(attr='characteristica_pk', )
count = fields.IntegerField()
measurement_type = fields.StringField(
attr='measurement_type',
fields={
'raw': fields.StringField(analyzer='keyword'),
})
choice = fields.StringField(fields={
'raw': fields.StringField(analyzer='keyword'),
})
unit = fields.StringField(fields={
'raw': fields.StringField(analyzer='keyword'),
})
substance = fields.StringField(attr='substance',
fields={
'raw':
fields.StringField(analyzer='keyword'),
})
value = fields.FloatField(attr='value')
mean = fields.FloatField(attr='mean')
median = fields.FloatField(attr='median')
min = fields.FloatField(attr='min')
max = fields.FloatField(attr='max')
se = fields.FloatField(attr='se')
sd = fields.FloatField(attr='sd')
cv = fields.FloatField(attr='cv')
access = string_field('access')
allowed_users = fields.ObjectField(
attr="allowed_users",
properties={'username': string_field("username")},
multi=True)
class Django:
model = IndividualCharacteristica
# Ignore auto updating of Elasticsearch when a model is saved/deleted:
ignore_signals = True
# Don't perform an index refresh after every update
auto_refresh = False
class Index:
name = "individual_characteristica"
settings = {**elastic_settings, 'max_result_window': 50000}
def get_queryset(self):
"""Not mandatory but to improve performance we can select related in one sql request"""
return super(IndividualCharacteristicaDocument,
self).get_queryset().select_related(
'individual', 'characteristica')
from django_elasticsearch_dsl import Document, fields
from django_elasticsearch_dsl.registries import registry
from pkdb_app.subjects.models import Individual, Characteristica, Group, GroupCharacteristica, IndividualCharacteristica
from pkdb_app.interventions.documents import string_field, ObjectField
from ..documents import elastic_settings
html_strip = analyzer('html_strip',
tokenizer="standard",
filter=["standard", "lowercase", "stop", "snowball"],
char_filter=["html_strip"])
characteristica_object_field = fields.ObjectField(properties={
'pk':
fields.IntegerField(),
'measurement_type':
string_field('measurement_type_name'),
'substance':
string_field('substance_name'),
'choice':
string_field('choice'),
'value':
fields.FloatField('value'),
'mean':
fields.FloatField(),
'median':
fields.FloatField(),
'min':
fields.FloatField(),
'max':
fields.FloatField(),
'se':