fix(release): fixes and updates (#1613)

CodeListLibrary_project/clinicalcode/admin.py

@@ -7,10 +7,15 @@
 from .models.EntityClass import EntityClass
 from .models.GenericEntity import GenericEntity
 from .models.Template import Template
+from .models.OntologyTag import OntologyTag
 from .models.DMD_CODES import DMD_CODES
 from .forms.TemplateForm import TemplateAdminForm
 from .forms.EntityClassForm import EntityAdminForm
 
+@admin.register(OntologyTag)
+class OntologyTag(admin.ModelAdmin):
+ list_display = ['id', 'name', 'type_id', 'atlas_id']
+
 
 @admin.register(CodingSystemFilter)
 class CodingSystemFilterAdmin(admin.ModelAdmin):

CodeListLibrary_project/clinicalcode/api/urls.py

@@ -7,7 +7,11 @@
 from drf_yasg.views import get_schema_view
 from drf_yasg import openapi
 
-from .views import Concept, GenericEntity, Template, DataSource, Tag, Collection
+from .views import (
+ Concept, GenericEntity,
+ Template, DataSource,
+ Tag, Collection, Ontology
+)
 
 """ Router
  Use the default REST API router to access the API details explicitly. These paths will 
@@ -135,19 +139,30 @@ def get_schema(self, request=None, public=False):
 
  # Tags
  url(r'^tags/$',
- Tag.get_tags, 
+ Tag.get_tags,
  name='tag_list'),
  url(r'^tags/(?P<tag_id>\d+)/detail/$',
- Tag.get_tag_detail, 
+ Tag.get_tag_detail,
  name='tag_list_by_id'),
 
  # Collections
  url(r'^collections/$',
- Collection.get_collections, 
+ Collection.get_collections,
  name='collection_list'),
  url(r'^collections/(?P<collection_id>\d+)/detail/$',
- Collection.get_collection_detail, 
- name='collections_list_by_id'), 
+ Collection.get_collection_detail,
+ name='collections_list_by_id'),
+
+ # Ontology
+ url(r'^ontology/$',
+ Ontology.get_ontologies,
+ name='ontology_list'),
+ url(r'^ontology/type/(?P<ontology_id>\d+)/$',
+ Ontology.get_ontology_detail,
+ name='ontology_list_by_type'),
+ url(r'^ontology/node/(?P<node_id>\d+)/$',
+ Ontology.get_ontology_node,
+ name='ontology_node_by_id'),
 ]
 
 """ Create/Update urls """

CodeListLibrary_project/clinicalcode/api/views/GenericEntity.py

@@ -318,7 +318,7 @@ def get_entity_detail(request, phenotype_id, version_id=None, field=None):
  historical_entity, 
  user_authed, 
  target_field=field, 
- return_data=True
+ return_data=False
  )
 
  if field == 'codes':

CodeListLibrary_project/clinicalcode/api/views/Ontology.py

@@ -0,0 +1,81 @@
+from rest_framework.decorators import (api_view, permission_classes)
+from rest_framework.permissions import IsAuthenticatedOrReadOnly
+from rest_framework.response import Response
+from rest_framework import status
+from django.db.models import F
+
+from ...entity_utils import api_utils
+from ...entity_utils import gen_utils
+from ...entity_utils import constants
+
+from ...models.OntologyTag import OntologyTag
+
+@api_view(['GET'])
+@permission_classes([IsAuthenticatedOrReadOnly])
+def get_ontologies(request):
+ """
+ Get all ontology categories and their root nodes, incl. associated data
+ """
+ result = OntologyTag.get_groups([x.value for x in constants.ONTOLOGY_TYPES], default=[])
+ return Response(
+ data=list(result),
+ status=status.HTTP_200_OK
+ )
+
+@api_view(['GET'])
+@permission_classes([IsAuthenticatedOrReadOnly])
+def get_ontology_detail(request, ontology_id):
+ """
+ Get specified ontology group detail by the ontology_id type, including associated
+ data e.g. root nodes, children etc
+ """
+ ontology_id = gen_utils.parse_int(ontology_id, default=None)
+ if not isinstance(ontology_id, int):
+ return Response(
+ data={
+ 'message': 'Invalid ontology id, expected valid integer'
+ },
+ content_type='json',
+ status=status.HTTP_400_BAD_REQUEST
+ )
+
+ result = OntologyTag.get_group_data(ontology_id, default=None)
+ if not isinstance(result, dict):
+ return Response(
+ data={
+ 'message': f'Ontology of id {ontology_id} does not exist'
+ },
+ content_type='json',
+ status=status.HTTP_404_NOT_FOUND
+ )
+
+ return Response(
+ data=result,
+ status=status.HTTP_200_OK
+ )
+
+@api_view(['GET'])
+@permission_classes([IsAuthenticatedOrReadOnly])
+def get_ontology_node(request, node_id):
+ """
+ Get the element details of the specified ontology element by its
+ node_id including associated data
+
+ e.g. tree-related information
+
+ """
+ node_id = gen_utils.parse_int(node_id, default=None)
+ if not isinstance(node_id, int):
+ return Response(
+ data={
+ 'message': 'Invalid node id, expected valid integer'
+ },
+ content_type='json',
+ status=status.HTTP_400_BAD_REQUEST
+ )
+
+ result = OntologyTag.get_node_data(node_id, default=None)
+ return Response(
+ data=result,
+ status=status.HTTP_200_OK
+ )

CodeListLibrary_project/clinicalcode/entity_utils/api_utils.py

@@ -385,13 +385,14 @@ def get_entity_detail_from_layout(
  validation = template_utils.get_field_item(
  constants.metadata, field, 'validation', {}
  )
- is_source = validation.get('source')
 
+ is_source = validation.get('source')
  if is_source:
- value = template_utils.get_metadata_value_from_source(
- entity, field, default=None
- )
- if value is None:
+ if template_utils.is_metadata(entity, field=field):
+ value = template_utils.get_metadata_value_from_source(
+ entity, field, default=None
+ )
+ else:
  value = template_utils.get_entity_field(entity, field)
 
  result[field] = value

CodeListLibrary_project/clinicalcode/entity_utils/concept_utils.py

@@ -1,3 +1,4 @@
+
 from django.db import connection
 from django.db.models import ForeignKey
 from django.http.request import HttpRequest
@@ -745,8 +746,8 @@ def get_clinical_concept_data(concept_id, concept_history_id, include_reviewed_c
  aggregate_component_codes=False, include_component_codes=True,
  include_attributes=False, strippable_fields=None,
  remove_userdata=False, hide_user_details=False,
- derive_access_from=None, format_for_api=False,
- include_source_data=False):
+ derive_access_from=None, requested_entity_id=None,
+ format_for_api=False, include_source_data=False):
  """
  [!] Note: This method ignores permissions to derive data - it should only be called from a
  a method that has previously considered accessibility
@@ -878,21 +879,21 @@ def get_clinical_concept_data(concept_id, concept_history_id, include_reviewed_c
  concept_data['code_attribute_header'] = attribute_headers
 
  # Set phenotype owner
- phenotype_owner = concept.phenotype_owner
+ phenotype_owner = concept.phenotype_owner 
  if phenotype_owner:
  concept_data['phenotype_owner'] = phenotype_owner.id
- entity_from_concept = GenericEntity.history.filter(
- id=phenotype_owner.id
- )
- template_data = entity_from_concept.values_list('template_data',flat=True)
 
- #Iterate through the concept_information to find the phenotype owner history
- for index, value in enumerate(template_data):
- history_ids_concept = [j['concept_version_id'] for j in value['concept_information']]
- if concept_history_id in history_ids_concept:
- concept_data['phenotype_owner_history_id'] = entity_from_concept.values_list('history_id',flat=True)[index]
-
+ latest_version_id = permission_utils.get_latest_owner_version_from_concept(
+ phenotype_id=phenotype_owner.id,
+ concept_id=historical_concept.id,
+ concept_version_id=historical_concept.history_id
+ )
 
+ if latest_version_id is not None:
+ concept_data['phenotype_owner_history_id'] = latest_version_id
+
+ # Set the requested entity id
+ concept_data['requested_entity_id'] = requested_entity_id
 
  # Set base
  if not format_for_api:

CodeListLibrary_project/clinicalcode/entity_utils/constants.py

@@ -125,6 +125,26 @@ class FORM_METHODS(int, enum.Enum, metaclass=IterableMeta):
  CREATE = 1
  UPDATE = 2
 
+class ONTOLOGY_TYPES(int, enum.Enum, metaclass=IterableMeta):
+ """
+ Defines the ontology internal type id,
+ which describes the ontology type
+
+ """
+ CLINICAL_DISEASE = 0
+ CLINICAL_DOMAIN = 1
+ CLINICAL_FUNCTIONAL_ANATOMY = 2
+
+"""
+ Used to define the labels for each
+ known ontology type
+
+"""
+ONTOLOGY_LABELS = {
+ ONTOLOGY_TYPES.CLINICAL_DOMAIN: 'Clinical Domain',
+ ONTOLOGY_TYPES.CLINICAL_DISEASE: 'Clinical Disease Category (ICD-10)',
+ ONTOLOGY_TYPES.CLINICAL_FUNCTIONAL_ANATOMY: 'Functional Anatomy',
+}
 
 """
  The excepted X-Requested-With header if a fetch request is made
@@ -476,7 +496,7 @@ class FORM_METHODS(int, enum.Enum, metaclass=IterableMeta):
  "citation_requirements": {
  "title": "Citation Requirements",
  "description": "A request for how this phenotype is referenced if used in other work.",
- "field_type": "textarea_markdown",
+ "field_type": "citation_requirements",
  "active": True,
  "validation": {
  "type": "string",
@@ -699,6 +719,12 @@ class FORM_METHODS(int, enum.Enum, metaclass=IterableMeta):
  'output_type': 'list_of_inputboxes'
  },
 
+ 'citation_requirements': {
+ 'data_type': 'string',
+ 'input_type': 'markdown',
+ 'output_type': 'citation_requirements'
+ },
+
  'enum': {
  'data_type': 'int',
  'input_type': 'dropdown-list',
@@ -712,6 +738,11 @@ class FORM_METHODS(int, enum.Enum, metaclass=IterableMeta):
  'apply_badge_style': True
  },
 
+ 'ontology': {
+ 'input_type': 'generic/ontology',
+ 'output_type': 'generic/ontology'
+ },
+
  'enum_radio_badge': {
  'data_type': 'int',
  'input_type': 'radiobutton',