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',