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models.py
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models.py
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import time
from django.conf import settings
from django.contrib.postgres.fields import ArrayField
from django.core.exceptions import ValidationError
from django.db import models, transaction
from django.db.models import UniqueConstraint, F, QuerySet, Q
from django.utils import timezone
from django.utils.functional import cached_property
from pydash import get, compact
from core.collections.constants import (
COLLECTION_TYPE, REFERENCE_ALREADY_EXISTS, CONCEPT_FULLY_SPECIFIED_NAME_UNIQUE_PER_COLLECTION_AND_LOCALE,
CONCEPT_PREFERRED_NAME_UNIQUE_PER_COLLECTION_AND_LOCALE, COLLECTION_VERSION_TYPE,
REFERENCE_TYPE_CHOICES, CONCEPT_REFERENCE_TYPE, MAPPING_REFERENCE_TYPE, SOURCE_MAPPINGS, SOURCE_TO_CONCEPTS,
TRANSFORM_TO_RESOURCE_VERSIONS, COLLECTION_REFERENCE_TYPE)
from core.collections.parsers import CollectionReferenceParser
from core.collections.utils import is_concept, is_mapping
from core.common.constants import (
DEFAULT_REPOSITORY_TYPE, ACCESS_TYPE_VIEW, ACCESS_TYPE_EDIT,
ES_REQUEST_TIMEOUT, ES_REQUEST_TIMEOUT_ASYNC, HEAD)
from core.common.models import ConceptContainerModel, BaseResourceModel
from core.common.tasks import seed_children_to_expansion, batch_index_resources, index_expansion_concepts, \
index_expansion_mappings
from core.common.utils import drop_version, to_owner_uri, generate_temp_version, es_id_in, \
es_wildcard_search, get_resource_class_from_resource_name, get_exact_search_fields, to_snake_case, \
es_exact_search, es_to_pks, batch_qs, split_list_by_condition, decode_string
from core.concepts.constants import LOCALES_FULLY_SPECIFIED
from core.concepts.models import Concept
from core.mappings.models import Mapping
class Collection(ConceptContainerModel):
OBJECT_TYPE = COLLECTION_TYPE
OBJECT_VERSION_TYPE = COLLECTION_VERSION_TYPE
es_fields = {
'collection_type': {'sortable': True, 'filterable': True, 'facet': True, 'exact': True},
'mnemonic': {'sortable': True, 'filterable': True, 'exact': True},
'name': {'sortable': True, 'filterable': True, 'exact': True},
'last_update': {'sortable': True, 'filterable': False, 'default': 'desc'},
'locale': {'sortable': False, 'filterable': True, 'facet': True},
'owner': {'sortable': True, 'filterable': True, 'facet': True, 'exact': True},
'owner_type': {'sortable': False, 'filterable': True, 'facet': True},
'custom_validation_schema': {'sortable': False, 'filterable': True, 'facet': True},
'canonical_url': {'sortable': True, 'filterable': True},
'experimental': {'sortable': False, 'filterable': False, 'facet': False},
'external_id': {'sortable': False, 'filterable': True, 'facet': False, 'exact': False},
}
class Meta:
db_table = 'collections'
constraints = [
UniqueConstraint(
fields=['mnemonic', 'version', 'organization'],
name="org_collection_unique",
condition=models.Q(user=None),
),
UniqueConstraint(
fields=['mnemonic', 'version', 'user'],
name="user_collection_unique",
condition=models.Q(organization=None),
)
]
indexes = [] + ConceptContainerModel.Meta.indexes
collection_type = models.TextField(blank=True)
preferred_source = models.TextField(blank=True)
repository_type = models.TextField(default=DEFAULT_REPOSITORY_TYPE, blank=True)
custom_resources_linked_source = models.TextField(blank=True)
immutable = models.BooleanField(null=True, blank=True, default=None)
locked_date = models.DateTimeField(null=True, blank=True)
autoexpand_head = models.BooleanField(default=True, null=True)
autoexpand = models.BooleanField(default=True, null=True)
expansion_uri = models.TextField(null=True, blank=True)
def set_active_concepts(self):
expansion = self.expansion
if expansion:
self.active_concepts = expansion.concepts.filter(retired=False, is_active=True).count()
def set_active_mappings(self):
expansion = self.expansion
if expansion:
self.active_mappings = expansion.mappings.filter(retired=False, is_active=True).count()
@staticmethod
def get_search_document():
from core.collections.documents import CollectionDocument
return CollectionDocument
@classmethod
def get_base_queryset(cls, params):
collection = params.pop('collection', None)
contains_uri = params.pop('contains', None)
include_references = params.pop('include_references', None) in [True, 'true']
queryset = super().get_base_queryset(params)
if collection:
queryset = queryset.filter(cls.get_exact_or_criteria('mnemonic', collection))
if contains_uri:
queryset = queryset.filter(
references__expression=contains_uri, public_access__in=[ACCESS_TYPE_EDIT, ACCESS_TYPE_VIEW]
)
if include_references:
queryset = queryset.prefetch_related('references')
return queryset
@property
def collection(self):
return self.mnemonic
@staticmethod
def get_resource_url_kwarg():
return 'collection'
def update_version_data(self, head):
super().update_version_data(head)
self.collection_type = head.collection_type
self.preferred_source = head.preferred_source
self.repository_type = head.repository_type
self.custom_resources_linked_source = head.custom_resources_linked_source
self.immutable = head.immutable
self.locked_date = head.locked_date
@property
def should_auto_expand(self):
if self.is_head:
return self.autoexpand_head
return self.autoexpand
def validate(self, reference):
if self.should_auto_expand:
reference.full_clean()
else:
reference.last_resolved_at = None
if reference.expression and self.references.filter(
expression=reference.expression, include=reference.include).exists():
raise ValidationError({reference.expression: [REFERENCE_ALREADY_EXISTS]})
if self.is_openmrs_schema and self.expansion_uri:
if reference._concepts is None or reference._concepts.count() == 0: # pylint: disable=protected-access
return
for concept in reference._concepts: # pylint: disable=protected-access
self.check_concept_uniqueness_in_collection_and_locale_by_name_attribute(
concept, attribute='type__in', value=LOCALES_FULLY_SPECIFIED,
error_message=CONCEPT_FULLY_SPECIFIED_NAME_UNIQUE_PER_COLLECTION_AND_LOCALE
)
self.check_concept_uniqueness_in_collection_and_locale_by_name_attribute(
concept, attribute='locale_preferred', value=True,
error_message=CONCEPT_PREFERRED_NAME_UNIQUE_PER_COLLECTION_AND_LOCALE
)
def check_concept_uniqueness_in_collection_and_locale_by_name_attribute(
self, concept, attribute, value, error_message
):
other_concepts_in_collection = self.expansion.concepts
if not other_concepts_in_collection.exists():
return
matching_names_in_concept = {}
names = concept.names.filter(**{attribute: value})
for name in names:
validation_error = dict(names=[error_message])
# making sure names in the submitted concept meet the same rule
name_key = name.locale + name.name
if name_key in matching_names_in_concept:
raise ValidationError(validation_error)
matching_names_in_concept[name_key] = True
if other_concepts_in_collection.filter(
names__name=name.name, names__locale=name.locale, **{f"names__{attribute}": value}
).exists():
raise ValidationError(validation_error)
@transaction.atomic
def add_expressions(
self, data, user, cascade=False, transform=False):
parser = CollectionReferenceParser(data, transform, cascade, user)
parser.parse()
parser.to_reference_structure()
references = parser.to_objects()
return self.add_references(references, user)
def add_references(self, references, user=None):
errors = {}
added_references = []
for reference in references:
reference.expression = reference.build_expression()
reference.collection = self
reference.created_by = user
try:
self.validate(reference)
reference.save()
except Exception as ex:
errors[reference.expression] = ex.messages if hasattr(ex, 'messages') else ex
continue
if reference.id:
added_references.append(reference)
if self.expansion_uri:
self.expansion.add_references(added_references)
if user and user.is_authenticated:
self.updated_by = user
self.save()
self.update_children_counts()
return added_references, errors
def seed_references(self):
head = self.head
if head:
for reference in head.references.all():
new_reference = reference.clone(last_resolved_at=timezone.now(), collection=self)
new_reference.save()
new_reference.concepts.set(reference.concepts.all())
new_reference.mappings.set(reference.mappings.all())
@staticmethod
def is_validation_necessary():
return False
@property
def expansions_count(self):
return self.expansions.count()
def delete_references(self, expressions):
if expressions == '*': # Deprecated: Old way
references_to_be_deleted = self.references
if self.expansion_uri:
self.expansion.delete_expressions(expressions)
else:
references_to_be_deleted = self.references.filter(expression__in=expressions)
if self.expansion_uri:
self.expansion.delete_references(references_to_be_deleted)
references_to_be_deleted.all().delete()
def get_cascaded_mapping_uris_from_concept_expressions(self, expressions):
mapping_uris = []
if not self.expansion_uri:
return mapping_uris
for expression in expressions:
if is_concept(expression):
mapping_uris += list(
self.expansion.mappings.filter(
from_concept__uri__icontains=drop_version(expression)).values_list('uri', flat=True)
)
return mapping_uris
def cascade_children_to_expansion(self, expansion_data=None, index=True, sync=False): # pylint: disable=arguments-differ
if not expansion_data:
expansion_data = {}
should_auto_expand = self.should_auto_expand
if should_auto_expand and not self.expansions.exists() and not get(expansion_data, 'mnemonic'):
expansion_data['mnemonic'] = Expansion.get_auto_expand_mnemonic(self.version)
expansion_data['is_processing'] = True
expansion = Expansion.persist(index=index, **expansion_data, collection_version=self, sync=sync)
if should_auto_expand and not self.expansion_uri:
self.expansion_uri = expansion.uri
self.save()
return expansion
def index_children(self):
if self.expansion_uri:
from core.concepts.documents import ConceptDocument
from core.mappings.documents import MappingDocument
self.batch_index(self.expansion.concepts, ConceptDocument)
self.batch_index(self.expansion.mappings, MappingDocument)
@property
def expansion(self):
if self.expansion_uri:
return self.expansions.filter(uri=self.expansion_uri).first()
return None
@property
def active_references(self):
return self.references.count()
@property
def last_concept_update(self):
updated_at = None
if self.expansion_uri and self.expansion.concepts.exists():
updated_at = self.expansion.concepts.latest('updated_at').updated_at
return updated_at
@property
def last_mapping_update(self):
updated_at = None
if self.expansion_uri and self.expansion.mappings.exists():
updated_at = self.expansion.mappings.latest('updated_at').updated_at
return updated_at
@property
def expansions_url(self):
return self.uri + 'expansions/'
class ReferencedConcept(models.Model):
reference = models.ForeignKey('collections.CollectionReference', on_delete=models.CASCADE)
concept = models.ForeignKey('concepts.Concept', on_delete=models.CASCADE)
class ReferencedMapping(models.Model):
reference = models.ForeignKey('collections.CollectionReference', on_delete=models.CASCADE)
mapping = models.ForeignKey('mappings.Mapping', on_delete=models.CASCADE)
class CollectionReference(models.Model):
class Meta:
db_table = 'collection_references'
OPERATOR_EQUAL = '='
OPERATOR_IN = 'in'
ALLOWED_FILTER_OPS = [OPERATOR_EQUAL, OPERATOR_IN]
_concepts = None
_mappings = None
original_expression = None
# core
id = models.BigAutoField(primary_key=True)
expression = models.TextField()
created_at = models.DateTimeField(auto_now_add=True)
updated_at = models.DateTimeField(auto_now=True)
last_resolved_at = models.DateTimeField(default=timezone.now, null=True)
reference_type = models.CharField(choices=REFERENCE_TYPE_CHOICES, default=CONCEPT_REFERENCE_TYPE, max_length=10)
created_by = models.ForeignKey('users.UserProfile', null=True, blank=True, on_delete=models.SET_NULL)
# FHIR specs
filter = models.JSONField(null=True, blank=True)
display = models.TextField(null=True, blank=True)
namespace = models.TextField(null=True, blank=True)
code = models.CharField(null=True, blank=True, max_length=255)
system = models.TextField(null=True, blank=True)
version = models.CharField(null=True, blank=True, max_length=255)
valueset = ArrayField(models.TextField(), null=True, blank=True)
cascade = models.JSONField(null=True, blank=True)
transform = models.CharField(null=True, blank=True, max_length=255)
include = models.BooleanField(default=True)
resource_version = models.CharField(null=True, blank=True, max_length=255)
# associations
concepts = models.ManyToManyField('concepts.Concept', related_name='references', through=ReferencedConcept)
mappings = models.ManyToManyField('mappings.Mapping', related_name='references', through=ReferencedMapping)
collection = models.ForeignKey('collections.Collection', related_name='references', on_delete=models.CASCADE)
@property
def resource_type(self):
return COLLECTION_REFERENCE_TYPE
@property
def can_compute_against_other_system_version(self):
return (not self.system or not self.version) and not self.resource_version
def can_compute_against_system_version(self, system_version):
result = False
if self.can_compute_against_other_system_version and system_version:
self_system_version = self.resolve_system_version
if self_system_version:
result = drop_version(self_system_version.uri) == drop_version(system_version.uri)
return result
def clone(self, **kwargs):
return CollectionReference(
expression=self.expression,
reference_type=self.reference_type,
created_by=self.created_by,
filter=self.filter,
display=self.display,
namespace=self.namespace,
code=self.code,
system=self.system,
version=self.version,
valueset=self.valueset,
cascade=self.cascade,
transform=self.transform,
include=self.include,
resource_version=self.resource_version,
**kwargs,
)
def build_expression(self):
if self.expression:
return self.expression
expression = ''
if self.system:
is_canonical = self.system.startswith('http://') or self.system.startswith('https://')
expression = self.system
if self.version:
expression += '|' + self.version if is_canonical else self.version
elif self.valueset and isinstance(self.valueset, list):
expression = self.valueset[0] # pylint: disable=unsubscriptable-object
is_canonical = expression.startswith('https://') or expression.startswith('http://')
if self.code or self.filter or not is_canonical:
if self.is_concept:
expression += 'concepts/' if expression.endswith('/') else '/concepts/'
elif self.is_mapping:
expression += 'mappings/' if expression.endswith('/') else '/mappings/'
if expression:
if self.code:
expression += self.code + '/'
if self.resource_version:
expression += self.resource_version + '/'
elif self.filter:
expression += '?' + self.filter_to_querystring()
return expression
@property
def concepts_count(self):
return self.concepts.count()
@property
def mappings_count(self):
return self.mappings.count()
@cached_property
def uri(self):
return self.calculate_uri(self.collection)
def calculate_uri(self, collection):
if collection:
return f'{collection.uri}references/{self.id}/'
return None
@property
def without_version(self):
return drop_version(self.expression)
def fetch_concepts(self, refetch=False):
if not get(self, '_fetched') or refetch:
self._concepts, self._mappings = self.get_concepts()
self._fetched = True
def fetch_mappings(self, refetch=False):
if not get(self, '_fetched') or refetch:
self._mappings = self.get_mappings()
self._fetched = True
def get_concepts(self, system_version=None):
queryset = self.get_resource_queryset_from_system_and_valueset(Concept, 'concepts', system_version)
mapping_queryset = Mapping.objects.none()
if self.code:
queryset = queryset.filter(mnemonic=decode_string(self.code))
if self.resource_version:
queryset = queryset.filter(version=self.resource_version)
if self.cascade:
cascade_params = self.get_concept_cascade_params()
for concept in queryset:
result = concept.cascade(**cascade_params)
queryset |= result['concepts']
mapping_queryset |= result['mappings']
if self.should_apply_filter():
queryset = self.apply_filters(queryset, Concept)
if self.should_transform_to_latest_version():
queryset = self.transform_to_latest_version(queryset, Concept)
if self.code:
concept = queryset.first()
self.resource_version = concept.version
self.expression = concept.uri
if mapping_queryset.exists():
mapping_queryset = self.transform_to_latest_version(mapping_queryset, Mapping)
return queryset, mapping_queryset
def get_mappings(self, system_version=None):
queryset = self.get_resource_queryset_from_system_and_valueset(Mapping, 'mappings', system_version)
if self.code:
queryset = queryset.filter(mnemonic=self.code)
if self.resource_version:
queryset = queryset.filter(version=self.resource_version)
if self.should_apply_filter():
queryset = self.apply_filters(queryset, Mapping)
if self.should_transform_to_latest_version():
queryset = self.transform_to_latest_version(queryset, Mapping)
if self.code:
mapping = queryset.first()
self.resource_version = mapping.version
self.expression = mapping.uri
return queryset
@staticmethod
def transform_to_latest_version(queryset, klass):
ids = []
resources = klass.objects.filter(id__in=queryset.values_list('id', flat=True))
for resource in resources.filter(id=F('versioned_object_id')):
ids.append(resource.get_latest_version().id)
if ids:
queryset = resources.exclude(id=F('versioned_object_id')) | klass.objects.filter(id__in=ids)
return queryset
def should_transform_to_latest_version(self):
return not self.resource_version and self.transform
def should_apply_filter(self):
return not self.code and self.filter
def get_concept_cascade_params(self):
is_dict = isinstance(self.cascade, dict)
method = get(self.cascade, 'method') if is_dict and 'method' in self.cascade else self.cascade or ''
cascade_params = {
'source_version': get(self.cascade, 'source_version') or self.version or HEAD,
'source_mappings': method.lower() == SOURCE_MAPPINGS,
'source_to_concepts': method.lower() == SOURCE_TO_CONCEPTS,
'cascade_levels': 1 if self.cascade == method else get(self.cascade, 'cascade_levels', '*'),
}
if is_dict:
for attr in ['cascade_mappings', 'cascade_hierarchy', 'include_mappings', 'reverse', 'max_results']:
if attr in self.cascade:
cascade_params[attr] = get(self.cascade, attr)
map_types = get(self.cascade, 'map_types', None)
exclude_map_types = get(self.cascade, 'exclude_map_types', None)
mappings_criteria = Q()
if map_types:
mappings_criteria &= Q(map_type__in=compact(map_types.split(',')))
if exclude_map_types:
mappings_criteria &= ~Q(map_type__in=compact(exclude_map_types.split(',')))
cascade_params['mappings_criteria'] = mappings_criteria
return cascade_params
def __is_exact_search_filter(self):
return bool(next(
(filter_def for filter_def in self.filter if # pylint:disable=not-an-iterable
filter_def['property'] == 'exact_match' and filter_def['value'] == 'on'),
False
))
def apply_filters(self, queryset, resource_klass):
if self.filter:
pks = []
document = resource_klass.get_search_document()
search = document.search()
is_exact_search = self.__is_exact_search_filter()
for filter_def in self.filter: # pylint: disable=not-an-iterable
if to_snake_case(filter_def['property']) == 'exact_match':
continue
val = filter_def['value']
if filter_def['property'] == 'q':
exact_search_fields = get_exact_search_fields(resource_klass)
if is_exact_search:
search = es_exact_search(search, val, exact_search_fields)
else:
name_attr = '_name' if self.is_concept else 'name'
search = es_wildcard_search(search, val, exact_search_fields, name_attr)
else:
search = search.filter("match", **{to_snake_case(filter_def["property"]): filter_def["value"]})
for _queryset in batch_qs(queryset.order_by('id'), 500):
# iterating on queryset because ES has max_clause limit default to 1024
search_within_queryset = es_id_in(search, list(_queryset.values_list('id', flat=True)))
pks += es_to_pks(search_within_queryset.params(request_timeout=ES_REQUEST_TIMEOUT_ASYNC))
if pks:
resource_versions = resource_klass.objects.filter(id__in=set(pks))
if self.version or self.valueset or self.transform:
return resource_versions
return resource_klass.objects.filter(
id__in=resource_versions.values_list('versioned_object_id', flat=True))
return resource_klass.objects.none()
return queryset
# returns intersection of system and valueset resources considering creator permissions
def get_resource_queryset_from_system_and_valueset(self, resource_klass, resource_relation, system_version=None):
system_version = system_version or self.resolve_system_version
valueset_versions = self.resolve_valueset_versions
queryset = None
if system_version and system_version.can_view_all_content(self.created_by):
queryset = get(system_version, resource_relation).filter()
if system_version.is_head and not self.resource_version:
queryset = queryset.filter(
is_latest_version=True
) if self.transform else queryset.filter(id=F('versioned_object_id'))
if valueset_versions:
for valueset in valueset_versions:
if valueset.expansion_uri and valueset.can_view_all_content(self.created_by):
rel = get(valueset.expansion, resource_relation)
if queryset is None:
queryset = rel.all()
else:
queryset &= rel.all()
if not system_version and not valueset_versions and self.expression:
queryset = resource_klass.from_uri_queryset(self.expression)
return queryset
@cached_property
def resolve_system_version(self):
if self.system:
from core.sources.models import Source
version = Source.resolve_reference_expression(self.system, self.namespace, self.version)
if version.id:
return version
return None
@cached_property
def resolve_valueset_versions(self):
versions = []
if isinstance(self.valueset, list):
for valueset in self.valueset: # pylint: disable=not-an-iterable
if valueset:
version = Collection.resolve_reference_expression(valueset, self.namespace)
if version.id:
versions.append(version)
return versions
def clean(self):
if not self.is_valid_filter():
raise ValidationError(dict(filter=['Invalid filter schema.']))
self.original_expression = str(self.expression)
if self.transform and self.transform.lower() != TRANSFORM_TO_RESOURCE_VERSIONS:
self.transform = None
self.evaluate()
is_resolved = bool((self._mappings and self._mappings.exists()) or (self._concepts and self._concepts.exists()))
if not is_resolved:
self.last_resolved_at = None
if not self.reference_type:
self.reference_type = MAPPING_REFERENCE_TYPE if self.is_mapping else CONCEPT_REFERENCE_TYPE
if self.expression is None:
self.expression = self.build_expression()
def filter_to_querystring(self):
if self.filter:
queries = []
for filter_def in self.filter: # pylint: disable=not-an-iterable
value = ','.join(filter_def['value']) if isinstance(filter_def['value'], list) else filter_def['value']
queries.append(f'{filter_def["property"]}={value}')
return '&'.join(queries)
return None
@cached_property
def expression_with_filters(self):
querystring = self.filter_to_querystring()
if querystring:
joiner = '&' if '?' in self.expression else '&'
return f"{self.expression}{joiner}{querystring}"
return self.expression
def is_valid_filter(self):
if not self.filter:
return True
if not isinstance(self.filter, list):
return False
if len(self.filter) != len(compact(self.filter)):
return False
return all(map(self.__is_valid_filter_schema, self.filter))
def get_allowed_filter_properties(self):
common = ['q', 'exact_match']
if self.is_concept:
return [*Concept.es_fields.keys(), *common]
if self.is_mapping:
return [*Mapping.es_fields.keys(), *common]
return common
def __is_valid_filter_schema(self, filter_def):
return isinstance(filter_def, dict) and \
sorted(filter_def.keys()) == sorted(['property', 'op', 'value']) and \
{type(val) for val in filter_def.values()} == {str} and \
filter_def['op'] in self.ALLOWED_FILTER_OPS and \
to_snake_case(filter_def['property']) in self.get_allowed_filter_properties()
def save(self, force_insert=False, force_update=False, using=None,
update_fields=None):
super().save(force_insert=force_insert, force_update=force_update, using=using, update_fields=update_fields)
if self.id and get(self, '_fetched'):
if self._concepts is not None and self._concepts.exists():
self.concepts.set(self._concepts)
if self._mappings is not None and self._mappings.exists():
self.mappings.set(self._mappings)
@property
def is_concept(self):
return self.reference_type == 'concepts' or is_concept(self.expression)
@property
def is_mapping(self):
return self.reference_type == 'mappings' or is_mapping(self.expression)
def evaluate(self):
if self.is_concept:
self.fetch_concepts()
elif self.is_mapping:
self.fetch_mappings()
self._fetched = True
def get_related_uris(self):
self.fetch_concepts()
return [*set(self._concepts.values_list('uri', flat=True)), *set(self._mappings.values_list('uri', flat=True))]
def default_expansion_parameters():
return {
"filter": "",
"date": "",
"count": 0,
"offset": 0,
"includeDesignations": True,
"activeOnly": False,
"includeDefinition": False,
"excludeNested": True,
"excludeNotForUI": True,
"excludePostCoordinated": True,
"exclude-system": "",
"system-version": "",
"check-system-version": "",
"force-system-version": ""
}
class Expansion(BaseResourceModel):
class Meta:
db_table = 'collection_expansions'
indexes = [] + BaseResourceModel.Meta.indexes
parameters = models.JSONField(default=default_expansion_parameters)
canonical_url = models.URLField(null=True, blank=True)
text = models.TextField(null=True, blank=True)
concepts = models.ManyToManyField('concepts.Concept', blank=True, related_name='expansion_set')
mappings = models.ManyToManyField('mappings.Mapping', blank=True, related_name='expansion_set')
collection_version = models.ForeignKey(
'collections.Collection', related_name='expansions', on_delete=models.CASCADE)
is_processing = models.BooleanField(default=False)
@property
def is_auto_generated(self):
return self.mnemonic == self.auto_generated_mnemonic
@property
def auto_generated_mnemonic(self):
return self.get_auto_expand_mnemonic(get(self, 'collection_version.version'))
@staticmethod
def get_auto_expand_mnemonic(version):
return f"autoexpand-{version}"
@staticmethod
def get_resource_url_kwarg():
return Expansion.get_url_kwarg()
@staticmethod
def get_url_kwarg():
return 'expansion'
@property
def is_default(self):
return self.uri == self.collection_version.expansion_uri
@property
def expansion(self):
return self.mnemonic
@property
def active_concepts(self):
return self.concepts.count()
@property
def active_mappings(self):
return self.mappings.count()
@property
def owner_url(self):
return to_owner_uri(self.uri)
def apply_parameters(self, queryset, is_concept_queryset):
parameters = ExpansionParameters(self.parameters, is_concept_queryset)
return parameters.apply(queryset)
def index_concepts(self):
if self.concepts.exists():
if get(settings, 'TEST_MODE', False):
index_expansion_concepts(self.id)
else:
index_expansion_concepts.apply_async((self.id, ), queue='indexing')
def index_mappings(self):
if self.mappings.exists():
if get(settings, 'TEST_MODE', False):
index_expansion_mappings(self.id)
else:
index_expansion_mappings.apply_async((self.id, ), queue='indexing')
@staticmethod
def to_ref_list(references):
if isinstance(references, CollectionReference):
return [references]
if isinstance(references, list):
return references
return references.all()
@classmethod
def to_ref_list_separated(cls, references):
refs = cls.to_ref_list(references)
if isinstance(refs, QuerySet):
return refs.filter(include=True), refs.exclude(include=True)
return split_list_by_condition(refs, lambda ref: ref.include)
def delete_references(self, references):
refs, _ = self.to_ref_list_separated(references)
index_concepts = False
index_mappings = False
for reference in refs:
concepts = reference.concepts
if concepts.exists():
index_concepts = True
filters = dict(id__in=list(concepts.values_list('id', flat=True)))
self.concepts.set(self.concepts.exclude(**filters))
batch_index_resources.apply_async(('concept', filters), queue='indexing')
mappings = reference.mappings
if mappings.exists():
index_mappings = True
filters = dict(id__in=list(mappings.values_list('id', flat=True)))
self.mappings.set(self.mappings.exclude(**filters))
batch_index_resources.apply_async(('mapping', filters), queue='indexing')
if index_concepts:
self.index_concepts()
if index_mappings:
self.index_mappings()
references_to_readd = self.collection_version.references.exclude(
id__in=[ref.id for ref in self.to_ref_list(references)])
self.add_references(references_to_readd, True, True, False)
def delete_expressions(self, expressions): # Deprecated: Old way, must use delete_references instead
concepts_filters = None
mappings_filters = None
if expressions == '*':
if self.concepts.exists():
concepts_filters = dict(id__in=list(self.concepts.values_list('id', flat=True)))
self.concepts.clear()
if self.mappings.exists():
mappings_filters = dict(id__in=list(self.mappings.values_list('id', flat=True)))
self.mappings.clear()
else:
concepts_filters = dict(uri__in=expressions)
mappings_filters = dict(uri__in=expressions)
self.concepts.set(self.concepts.exclude(**concepts_filters))
self.mappings.set(self.mappings.exclude(**mappings_filters))
if not get(settings, 'TEST_MODE', False):
batch_index_resources.apply_async(('concept', concepts_filters), queue='indexing')
batch_index_resources.apply_async(('mapping', mappings_filters), queue='indexing')
def add_references(self, references, index=True, is_adding_all_references=False, attempt_reevaluate=True): # pylint: disable=too-many-locals,too-many-branches
include_refs, exclude_refs = self.to_ref_list_separated(references)
if not is_adding_all_references:
existing_exclude_refs = self.collection_version.references.exclude(include=True)
if isinstance(exclude_refs, QuerySet):
exclude_refs |= existing_exclude_refs
else:
exclude_refs += [*existing_exclude_refs.all()]
index_concepts = False
index_mappings = False
should_reevaluate = attempt_reevaluate and not self.is_auto_generated
include_system_version = None
if should_reevaluate and self.parameters.get(ExpansionParameters.INCLUDE_SYSTEM):
system_version = self.parameters.get(ExpansionParameters.INCLUDE_SYSTEM)
include_system_version = ConceptContainerModel.resolve_reference_expression(system_version)
if not include_system_version.id:
include_system_version = None
def get_ref_results(ref):
# attempt_reevaluate is False for delete reference(s)
if should_reevaluate:
_system_version = include_system_version if ref.can_compute_against_system_version(
include_system_version) else None
_concepts, _mappings = ref.get_concepts(_system_version)
_mappings |= ref.get_mappings(_system_version)
else:
_concepts = ref.concepts.all()
_mappings = ref.mappings.all()
return _concepts, _mappings
for reference in include_refs:
concepts, mappings = get_ref_results(reference)
if concepts.exists():
self.concepts.add(*self.apply_parameters(concepts, True))
index_concepts = True
if mappings.exists():
self.mappings.add(*self.apply_parameters(mappings, False))
index_mappings = True
for reference in exclude_refs:
concepts, mappings = get_ref_results(reference)
if concepts.exists():
self.concepts.remove(*concepts)
index_concepts = True
if mappings.exists():
self.mappings.remove(*mappings)
index_mappings = True
if index:
if index_concepts:
self.index_concepts()
if index_mappings:
self.index_mappings()
def seed_children(self, index=True):
return self.add_references(self.collection_version.references, index, True)
def wait_until_processed(self): # pragma: no cover
processing = self.is_processing
while processing:
print("Expansion is still processing, sleeping for 5 secs...")
time.sleep(5)
self.refresh_from_db()
processing = self.is_processing
if not processing:
print("Expansion processed, waking up...")
def calculate_uri(self):
version = self.collection_version
if version.is_head:
return self.collection_version.uri + f'HEAD/expansions/{self.mnemonic}/'
return self.collection_version.uri + f'expansions/{self.mnemonic}/'
def clean(self):
if not self.parameters:
self.parameters = default_expansion_parameters()
super().clean()
@classmethod
def persist(cls, index, **kwargs):
sync = kwargs.pop('sync', False)
expansion = cls(**kwargs)
temp_version = not bool(expansion.mnemonic)
if temp_version:
expansion.mnemonic = generate_temp_version()
expansion.clean()
expansion.full_clean()
expansion.save()
if temp_version and expansion.id:
expansion.mnemonic = expansion.id
expansion.save()
if get(settings, 'TEST_MODE', False) or sync:
seed_children_to_expansion(expansion.id, index)
else:
seed_children_to_expansion.delay(expansion.id, index)
return expansion
def get_mappings_for_concept(self, concept, include_indirect=False):
concept_criteria = [concept.uri, drop_version(concept.uri)]
criteria = models.Q(from_concept__uri__in=concept_criteria)
if include_indirect:
criteria |= models.Q(to_concept__uri__in=concept_criteria)
return self.mappings.filter(criteria)
class ExpansionParameters:
ACTIVE = 'activeOnly'
TEXT_FILTER = 'filter'
EXCLUDE_SYSTEM = 'exclude-system'
INCLUDE_SYSTEM = 'system-version'
DATE = 'date'
def __init__(self, parameters, is_concept_queryset=True):
self.parameters = parameters
self.parameter_classes = {}
self.before_filters = {}
self.is_concept_queryset = is_concept_queryset
self.to_parameter_classes()
def to_parameter_classes(self):
for parameter, value in self.parameters.items():
parameter = parameter.replace(' ', '')
if parameter == self.ACTIVE:
self.parameter_classes[parameter] = ExpansionActiveParameter(value=value)
elif parameter == self.TEXT_FILTER: