Merge pull request #517 from rcpch/perms-tests

*based on PR #510 'Finished KPI Tests'* Finishes first round of testing

epilepsy12/admin.py

@@ -18,7 +18,6 @@ class Epilepsy12UserAdmin(UserAdmin, SimpleHistoryAdmin):
         "email",
         "surname",
         "role",
-        "organisation_employer",
         "is_active",
     )
     list_display = (
@@ -28,7 +27,6 @@ class Epilepsy12UserAdmin(UserAdmin, SimpleHistoryAdmin):
         "first_name",
         "surname",
         "is_active",
-        "twitter_handle",
         "role",
         "organisation_employer",
         "is_superuser",
@@ -52,20 +50,30 @@ class Epilepsy12UserAdmin(UserAdmin, SimpleHistoryAdmin):
             },
         ),
         ("Epilepsy12 Centre", {"fields": ("organisation_employer", "role")}),
-        ("Contacts", {"fields": ("email", "twitter_handle")}),
+        ("Contacts", {"fields": ("email",)}),
         (
             "Permissions",
             {
                 "fields": (
                     "is_active",
                     "is_staff",
+                    "is_rcpch_staff",
                     "is_rcpch_audit_team_member",
                     "is_superuser",
                     "email_confirmed",
                     "view_preference",
                 )
             },
         ),
+        (
+            "Access",
+            {
+                "fields": (
+                    "last_login",
+                    "date_joined",
+                )
+            },
+        ),
         (
             "Group Permissions",
             {
@@ -76,7 +84,6 @@ class Epilepsy12UserAdmin(UserAdmin, SimpleHistoryAdmin):
                 ),
             },
         ),
-        ("Personal", {"fields": ("bio",)}),
     )
     add_fieldsets = (
         (
@@ -89,6 +96,7 @@ class Epilepsy12UserAdmin(UserAdmin, SimpleHistoryAdmin):
                     "first_name",
                     "surname",
                     "is_staff",
+                    "is_rcpch_staff",
                     "is_active",
                     "is_rcpch_audit_team_member",
                     "role",
@@ -114,6 +122,8 @@ def get_form(self, request, obj=None, **kwargs):
             form.base_fields["title"].disabled = True
             form.base_fields["email"].disabled = True
             form.base_fields["is_staff"].disabled = True
+            form.base_fields["is_rcpch_staff"].disabled = True
+            form.base_fields["is_rcpch_audit_team_member"].disabled = True
         return form
 
 

epilepsy12/common_view_functions/aggregate_by.py

@@ -1,6 +1,7 @@
 from typing import Literal
 
 # Django imports
+from django.apps import apps
 from django.contrib.gis.db.models import (
     Q,
     F,
@@ -16,7 +17,8 @@
 
 # E12 imports
 from epilepsy12.constants import ETHNICITIES, SEX_TYPE
-from ..models import Case
+
+# from ..models import Case
 from .report_queries import (
     get_all_organisations,
     get_all_trusts,
@@ -34,12 +36,12 @@
 def cases_aggregated_by_sex(selected_organisation):
     # aggregate queries on trust level cases
 
+    Case = apps.get_model("epilepsy12", "Case")
+
     sex_long_list = [When(sex=k, then=Value(v)) for k, v in SEX_TYPE]
 
     cases_aggregated_by_sex = (
-        Case.objects.filter(
-            organisations__OrganisationName__contains=selected_organisation
-        )
+        Case.objects.filter(organisations=selected_organisation)
         .values("sex")
         .annotate(sex_display=DJANGO_CASE(*sex_long_list, output_field=CharField()))
         .values("sex_display")
@@ -52,34 +54,37 @@ def cases_aggregated_by_sex(selected_organisation):
 
 def cases_aggregated_by_deprivation_score(selected_organisation):
     # aggregate queries on trust level cases
+    Case = apps.get_model("epilepsy12", "Case")
 
-    deprivation_quintiles = ((1, 1), (2, 2), (3, 3), (4, 4), (5, 5), (None, 6))
-
-    imd_long_list = [
-        When(index_of_multiple_deprivation_quintile=k, then=Value(v))
-        for k, v in deprivation_quintiles
-    ]
+    cases_in_selected_organisation = Case.objects.filter(
+        organisations__OrganisationName__contains=selected_organisation
+    )
 
     cases_aggregated_by_deprivation = (
-        Case.objects.filter(
-            organisations__OrganisationName__contains=selected_organisation
-        )
+        # Filter just Cases in selected org
+        cases_in_selected_organisation
+        # Get list of IMD quintiles
         .values("index_of_multiple_deprivation_quintile")
+        # Converting 'None' to 6 in a new index_of_multiple_deprivation_quintile_display "column"
         .annotate(
             index_of_multiple_deprivation_quintile_display=DJANGO_CASE(
-                *imd_long_list, output_field=PositiveSmallIntegerField()
+                When(index_of_multiple_deprivation_quintile=None, then=Value(6)),
+                default="index_of_multiple_deprivation_quintile",
+                output_field=PositiveSmallIntegerField(),
             )
         )
+        # Keeps only the new column
         .values("index_of_multiple_deprivation_quintile_display")
+        # Value count the new column
         .annotate(
             cases_aggregated_by_deprivation=Count(
-                "index_of_multiple_deprivation_quintile"
-            )
+                "index_of_multiple_deprivation_quintile_display"
+            ),
         )
-        .order_by("index_of_multiple_deprivation_quintile")
+        .order_by('index_of_multiple_deprivation_quintile_display')
+
     )
-
-    # map quintile num to string repr
+
     deprivation_quintile_str_map = {
         1: "1st quintile",
         2: "2nd quintile",
@@ -89,19 +94,23 @@ def cases_aggregated_by_deprivation_score(selected_organisation):
         6: "Not known",
     }
 
-    for index, q in enumerate(cases_aggregated_by_deprivation):
-        q[
-            "index_of_multiple_deprivation_quintile_display"
-        ] = deprivation_quintile_str_map.get(
-            q.get("index_of_multiple_deprivation_quintile_display")
-        )
+    for aggregate in cases_aggregated_by_deprivation:
+        quintile = aggregate["index_of_multiple_deprivation_quintile_display"]
+
+        str_map = deprivation_quintile_str_map.get(quintile)
 
+        aggregate.update(
+            {"index_of_multiple_deprivation_quintile_display_str": str_map}
+        )
+
     return cases_aggregated_by_deprivation
 
 
 def cases_aggregated_by_ethnicity(selected_organisation):
     # aggregate queries on trust level cases
 
+    Case = apps.get_model("epilepsy12", "Case")
+
     ethnicity_long_list = [When(ethnicity=k, then=Value(v)) for k, v in ETHNICITIES]
 
     cases_aggregated_by_ethnicity = (
@@ -219,6 +228,7 @@ def return_all_aggregated_kpis_for_cohort_and_abstraction_level_annotated_by_sub
     """
     Returns aggregated KPIS for given cohort annotated by sublevel of abstraction (eg kpis in each NHS England region, labelled by region)
     """
+    Case = apps.get_model("epilepsy12", "Case")
 
     if abstraction_level == "organisation":
         abstraction_sublevels = get_all_organisations()

epilepsy12/common_view_functions/calculate_kpi_functions/score_kpi_3.py

@@ -2,10 +2,11 @@
 
 # django imports
 from django.contrib.gis.db.models import Q
+from django.apps import apps
 
 # E12 imports
 from epilepsy12.constants import KPI_SCORE
-from epilepsy12.models import AntiEpilepsyMedicine, Episode
+
 
 def score_kpi_3(registration_instance, age_at_first_paediatric_assessment) -> int:
     """3. tertiary_input
@@ -20,6 +21,9 @@ def score_kpi_3(registration_instance, age_at_first_paediatric_assessment) -> in
 
     assessment = registration_instance.assessment
 
+    AntiEpilepsyMedicine = apps.get_model("epilepsy12", "AntiEpilepsyMedicine")
+    Episode = apps.get_model("epilepsy12", "Episode")
+
     # EVALUATE ELIGIBILITY CRITERIA
 
     # first gather relevant data
@@ -69,6 +73,7 @@ def score_kpi_3(registration_instance, age_at_first_paediatric_assessment) -> in
     else:
         return KPI_SCORE["FAIL"]
 
+
 def score_kpi_3b(registration_instance) -> int:
     """3b. epilepsy_surgery_referral
 

epilepsy12/common_view_functions/calculate_kpi_functions/score_kpi_5.py

@@ -2,9 +2,10 @@
 
 # django imports
 from django.contrib.gis.db.models import Q
+from django.apps import apps
 
 # E12 imports
-from epilepsy12.models import Syndrome
+# from epilepsy12.models import Syndrome
 from epilepsy12.constants import KPI_SCORE
 
 
@@ -20,6 +21,8 @@ def score_kpi_5(registration_instance, age_at_first_paediatric_assessment) -> in
     multiaxial_diagnosis = registration_instance.multiaxialdiagnosis
     investigations = registration_instance.investigations
 
+    Syndrome = apps.get_model("epilepsy12", "Syndrome")
+
     # not scored
     if (age_at_first_paediatric_assessment >= 2) and (
         multiaxial_diagnosis.syndrome_present is None

epilepsy12/common_view_functions/calculate_kpi_functions/score_kpi_8.py

@@ -1,13 +1,16 @@
 # python imports
 
 # django imports
-from epilepsy12.models import AntiEpilepsyMedicine, MedicineEntity
+from django.apps import apps
 
 # E12 imports
 from epilepsy12.constants import KPI_SCORE
 
 
 def score_kpi_8(registration_instance, age_at_first_paediatric_assessment) -> int:
+    AntiEpilepsyMedicine = apps.get_model("epilepsy12", "AntiEpilepsyMedicine")
+    MedicineEntity = apps.get_model("epilepsy12", "MedicineEntity")
+
     """8. Sodium Valproate
 
     Percentage of all females 12 years and above currently on valproate treatment with annual risk acknowledgement form completed

epilepsy12/common_view_functions/calculate_kpis.py

@@ -2,6 +2,7 @@
 
 # django imports
 from django.contrib.gis.db.models import Sum
+from django.apps import apps
 
 # E12 imports
 from ..general_functions import has_all_attributes
@@ -30,7 +31,8 @@
     calculate_age_at_first_paediatric_assessment_in_years,
     check_is_registered,
 )
-from epilepsy12.models import KPI
+
+# from epilepsy12.models import KPI
 from epilepsy12.constants import KPI_SCORE
 
 
@@ -45,7 +47,9 @@ def calculate_kpis(registration_instance):
     2 - measure not applicable (eg ECG in nonconvulsive seizure)
     None - measure not scored yet
     """
-
+
+    KPI = apps.get_model("epilepsy12", "KPI")
+
     # first set default value 'NOT_SCORED' to all KPIs
     paediatrician_with_expertise_in_epilepsies = KPI_SCORE["NOT_SCORED"]
     epilepsy_specialist_nurse = KPI_SCORE["NOT_SCORED"]

epilepsy12/common_view_functions/group_for_group.py

@@ -4,24 +4,20 @@
 
 # rcpch
 from epilepsy12.constants.user_types import (
-    ROLES,
-    TITLES,
-    AUDIT_CENTRE_LEAD_CLINICIAN,
-    TRUST_AUDIT_TEAM_FULL_ACCESS,
-    AUDIT_CENTRE_CLINICIAN,
-    TRUST_AUDIT_TEAM_EDIT_ACCESS,
+    # groups
     AUDIT_CENTRE_ADMINISTRATOR,
+    AUDIT_CENTRE_CLINICIAN,
+    AUDIT_CENTRE_LEAD_CLINICIAN,
+    RCPCH_AUDIT_TEAM,
+    RCPCH_AUDIT_PATIENT_FAMILY,
+    # permissions
+    TRUST_AUDIT_TEAM_VIEW_ONLY,
     TRUST_AUDIT_TEAM_EDIT_ACCESS,
-    RCPCH_AUDIT_LEAD,
+    TRUST_AUDIT_TEAM_FULL_ACCESS,
     EPILEPSY12_AUDIT_TEAM_FULL_ACCESS,
-    RCPCH_AUDIT_ANALYST,
-    EPILEPSY12_AUDIT_TEAM_EDIT_ACCESS,
-    RCPCH_AUDIT_ADMINISTRATOR,
-    EPILEPSY12_AUDIT_TEAM_VIEW_ONLY,
-    RCPCH_AUDIT_PATIENT_FAMILY,
     PATIENT_ACCESS,
-    TRUST_AUDIT_TEAM_VIEW_ONLY,
-    AUDIT_CENTRE_MANAGER,
+    # preferences in the view
+    VIEW_PREFERENCES,
 )
 
 
@@ -38,14 +34,10 @@ def group_for_role(role_key):
         group = Group.objects.get(name=TRUST_AUDIT_TEAM_EDIT_ACCESS)
     elif role_key == AUDIT_CENTRE_ADMINISTRATOR:
         group = Group.objects.get(name=TRUST_AUDIT_TEAM_VIEW_ONLY)
-    elif role_key == AUDIT_CENTRE_MANAGER:
-        group = Group.objects.get(name=TRUST_AUDIT_TEAM_VIEW_ONLY)
-    elif role_key == RCPCH_AUDIT_LEAD:
+
+    elif role_key == RCPCH_AUDIT_TEAM:
         group = Group.objects.get(name=EPILEPSY12_AUDIT_TEAM_FULL_ACCESS)
-    elif role_key == RCPCH_AUDIT_ANALYST:
-        group = Group.objects.get(name=EPILEPSY12_AUDIT_TEAM_EDIT_ACCESS)
-    elif role_key == RCPCH_AUDIT_ADMINISTRATOR:
-        group = Group.objects.get(name=EPILEPSY12_AUDIT_TEAM_VIEW_ONLY)
+
     elif role_key == RCPCH_AUDIT_PATIENT_FAMILY:
         group = Group.objects.get(name=PATIENT_ACCESS)
     else: