feat: DOIs, GA4 and DataSource enhancements

Co-authored-by: ieuans <ieuans@users.noreply.github.com>

Author: JackScanlon

.github/workflows/testing-pipline.yml

@@ -82,13 +82,13 @@ jobs:
 
       - name: Run application
         run: |
-          export $(grep -v '^#' docker/.env/remote.test.env | xargs)
+          export $(grep -v '^#' docker/env/remote.test.env | xargs)
           cd CodeListLibrary_project
           python manage.py runserver 0.0.0.0:8000 > /dev/null &
 
       - name: Run tests
         run: |
-          export $(grep -v '^#' docker/.env/remote.test.env | xargs)
+          export $(grep -v '^#' docker/env/remote.test.env | xargs)
           cd CodeListLibrary_project
           pytest -vv -s --random-order --cov-report xml --cov . --html=report.html --self-contained-html --alluredir=./clinicalcode/tests/allure-results
         env:

.gitignore

@@ -4,7 +4,6 @@ __pycache__
 
 # Py env
 **/env/
-**/.env/
 **/venv/
 **/.venv/
 
@@ -47,7 +46,7 @@ CodeListLibrary_project/staticroot/*
 **/engagelens/.env
 
 # Allow docker env directory
-!**/docker/.env/
+!**/docker/env/
 !**/docker/**/env/
 
 # Platform / OS files

CodeListLibrary_project/clinicalcode/api/views/DataSource.py

@@ -22,7 +22,7 @@ def get_datasources(request):
         | id            | `int/list[int]` | `NULL`  | Match by a single `int` _id_ field, or match by array overlap |
         | name          | `str`           | `NULL`  | Case insensitive direct match of _name_ field                 |
         | uid           | `str/uuid`      | `NULL`  | Case insensitive direct match of _uid_ field                  |
-        | datasource_id | `int`           | `NULL`  | Match by exact _datasource_id_                                |
+        | datasource_id | `int`           | `NULL`  | Match by exact _datasource_id_ (HDRUK ID)                     |
         | url           | `str`           | `NULL`  | Case insensitive direct match of _url_ field                  |
         | source        | `str`           | `NULL`  | Case insensitive direct match of _source_ field               |
     """
@@ -54,7 +54,7 @@ def get_datasources(request):
 @permission_classes([IsAuthenticatedOrReadOnly])
 def get_datasource_internal_detail(request, datasource_id):
     """
-        Get detail of specified datasource by by its internal Id
+        Get detail of specified datasource by by its internal `id`
     """
     query = None
     if gen_utils.parse_int(datasource_id, default=None) is not None:
@@ -134,6 +134,7 @@ def get_datasource_internal_detail(request, datasource_id):
         'url': datasource.url,
         'uid': datasource.uid,
         'description': datasource.description,
+        'datasource_id': datasource.datasource_id,
         'source': datasource.source,
         'phenotypes': list(entities)
     }
@@ -147,13 +148,13 @@ def get_datasource_internal_detail(request, datasource_id):
 @permission_classes([IsAuthenticatedOrReadOnly])
 def get_datasource_detail(request, datasource_id):
     """
-        Get detail of specified datasource by `datasource_id`, _i.e._ the HDRUK DataSource `pid` or its `UUID` for linkage between applications, including associated published entities.
+        Get detail of specified datasource by its internal `id` or its `UUID` for linkage between applications (see HDRUK HealthDataGateway), including associated published entities.
     """
     query = None
     if gen_utils.is_valid_uuid(datasource_id):
         query = { 'uid': datasource_id }
     elif gen_utils.parse_int(datasource_id, default=None) is not None:
-        query = { 'datasource_id': int(datasource_id) }
+        query = { 'id': int(datasource_id) }
 
     if not query:
         return Response(
@@ -228,6 +229,7 @@ def get_datasource_detail(request, datasource_id):
         'url': datasource.url,
         'uid': datasource.uid,
         'description': datasource.description,
+        'datasource_id': datasource.datasource_id,
         'source': datasource.source,
         'phenotypes': list(entities)
     }

CodeListLibrary_project/clinicalcode/context_processors/general.py

@@ -19,5 +19,6 @@ def general_var(request):
         'SHOW_COOKIE_ALERT': settings.SHOW_COOKIE_ALERT,
         'IS_HDRUK_EXT': settings.IS_HDRUK_EXT,
         'CANONICAL_PATH': get_canonical_path(request),
-        'APPROVED_STATUS_DICT': {e.name: e.value for e in constants.APPROVAL_STATUS}
+        'APPROVED_STATUS_DICT': {e.name: e.value for e in constants.APPROVAL_STATUS},
+        'DOI_ACTIVE': settings.DOI_ACTIVE,
     }

CodeListLibrary_project/clinicalcode/entity_utils/constants.py

@@ -623,7 +623,10 @@ class ONTOLOGY_TYPES(int, enum.Enum, metaclass=IterableMeta):
                             'allowed_brands': [3],
                             'allow_null': True,
                         },
-                        'HDRUK': 'allow_null',
+                        'HDRUK': {
+                            'allowed_brands': [1, 2, 3],
+                            'allow_null': True,
+                        },
                         'HDRN': True,
                         'SAIL': False,
                     },

CodeListLibrary_project/clinicalcode/entity_utils/create_utils.py

@@ -1427,7 +1427,16 @@ def compute_brand_context(request, form_data, form_entity=None):
             if len(collections) > 0:
                 related_brands.update(collections)
 
-    return list(related_brands)
+    related_brands = list(related_brands)
+
+    # Ensure brand is first in list (for referral)
+    if brand is not None:
+        idx = next((i for i, x in enumerate(related_brands) if x == brand.id), None)
+        if idx is not None and idx != 0:
+            related_brands[idx] = related_brands[0]
+            related_brands[0] = brand.id
+
+    return related_brands
 
 @transaction.atomic
 def create_or_update_entity_from_form(request, form, errors=[], override_dirty=False):