Merge pull request #1417 from SwanseaUniversityMedical/Development

DFTM - Concept Library v2.0.0

.github/workflows/issues_close_projects.yml

@@ -13,9 +13,9 @@ jobs:
   action:
     runs-on: ubuntu-latest
     steps:
-      - uses: dessant/issue-states@v3
+      - uses: dessant/issue-states@v2
         with:
             github-token: ${{ github.token }}
             open-issue-columns: ''
-            closed-issue-columns: 'Current Sprint: Deploy to Demo / Waiting Deployment to Live / In Production'
+            closed-issue-columns: 'Done / Deployed'
             log-output: false

.github/workflows/release.yaml

@@ -11,6 +11,7 @@ env:
   HARBOR_REPO: ${{ vars.HARBOR_REPO }}
   HARBOR_USER: ${{ vars.HARBOR_USER }}
   HARBOR_TOKEN: ${{ secrets.HARBOR_TOKEN }}
+  SERVER_NAME: 'conceptlibrary.saildatabank.com'
 
 jobs:
   release-container:
@@ -26,7 +27,7 @@ jobs:
 
       - name: build container
         run: |
-          docker build -t image -f "Dockerfile" .
+          docker build -t image -f "docker/production/build.Dockerfile" --build-arg server_name="$SERVER_NAME" .
 
       - name: registry login
         run: |

.gitignore

@@ -1,10 +1,25 @@
 *.pyc
+__pycache__
 .project
 .pydevproject
 .DS_Store
-docker/
 CodeListLibrary_project/.settings/org.eclipse.core.resources.prefs
 .settings/org.eclipse.ltk.core.refactoring.prefs
 requirements/base - Django2.txt
 docs/~$plication Guide.docx
+**/docker/**/backup
+*.backup
+git.token
+CodeListLibrary_project/debug.log
+.vscode
+.settings/org.eclipse.core.resources.prefs
+venv
+**/dump.rdb
+CodeListLibrary_project/staticroot/*
+CodeListLibrary_project/media/*
+docker/development/db/postgresql.conf
+docker/CodeListLibrary_project
+
+# macOS system files
+.DS_Stores
 .idea

CodeListLibrary_project/clinicalcode/admin.py

@@ -1,13 +1,15 @@
 from django.contrib import admin
-from django.contrib.auth.models import Group, User
+from django.utils import timezone
 
-from .models import (Brand, CodingSystem, CodingSystemFilter, DataSource, Operator, Tag)
+import datetime
 
-# from forms import GroupAdminForm
-# from django import forms
-# from django.forms.models import inlineformset_factory, ModelChoiceField
+from .models import (Brand, CodingSystem, CodingSystemFilter, DataSource, Operator, Tag)
+from .models.EntityClass import EntityClass
+from .models.GenericEntity import GenericEntity
+from .models.Template import Template
+from .forms.TemplateForm import TemplateAdminForm
+from .forms.EntityClassForm import EntityAdminForm
 
-# Register your models here.
 
 @admin.register(CodingSystemFilter)
 class CodingSystemFilterAdmin(admin.ModelAdmin):
@@ -21,7 +23,7 @@ class OperatorAdmin(admin.ModelAdmin):
 
 @admin.register(Tag)
 class TagAdmin(admin.ModelAdmin):
-    list_display = ['id', 'description', 'display', 'tag_type', 'collection_brand']  #'updated_by' 'created_by' , 'created', 'modified'
+    list_display = ['id', 'description', 'display', 'tag_type', 'collection_brand']
     list_filter = ['collection_brand', 'tag_type', 'display']
     search_fields = ['description']
     exclude = ['created_by', 'updated_by']
@@ -34,13 +36,13 @@ def save_model(self, request, obj, form, change):
             instance.created_by = user
 
         instance.updated_by = user
+        instance.modified = datetime.datetime.now()
         instance.save()
         form.save_m2m()
 
         return instance
 
 
-#admin.site.register(Brand)
 @admin.register(Brand)
 class BrandAdmin(admin.ModelAdmin):
     list_display = ['name', 'id', 'logo_path', 'owner', 'description']
@@ -56,6 +58,7 @@ class DataSourceAdmin(admin.ModelAdmin):
     search_fields = ['name', 'url', 'uid']
     exclude = []
 
+
 @admin.register(CodingSystem)
 class CodingSystemAdmin(admin.ModelAdmin):
     list_display = ['id', 'codingsystem_id', 'name', 'description'] 
@@ -64,19 +67,60 @@ class CodingSystemAdmin(admin.ModelAdmin):
     exclude = []
 
 
-#admin.site.register(CodingSystem)
-
-# ############################################
-# # Unregister the original Group admin.
-# admin.site.unregister(Group)
-#
-# # Create a new Group admin.
-# class GroupAdmin(admin.ModelAdmin):
-#     # Use our custom form.
-#     form = GroupAdminForm
-#     #form_class = GroupAdminForm
-#     # Filter permissions horizontal as well.
-#     filter_horizontal = ['permissions']
-#
-# # Register the new Group ModelAdmin.
-# admin.site.register(Group, GroupAdmin)
+@admin.register(Template)
+class TemplateAdmin(admin.ModelAdmin):
+    readonly_fields = ['template_version']
+    list_display = ['id', 'name', 'description', 'template_version']
+    list_filter = ['name']
+    search_fields = ['name']
+    exclude = ['created_by', 'updated_by']
+    form = TemplateAdminForm
+
+    def save_model(self, request, obj, form, change):
+        """
+            - Responsible for version history
+                -> template_version computed from JSONB data, never updated unless dictdiff and/or purposefully changed
+            - Responsible for computing the 'layout_order' field within the template definition
+                -> Iterates through the template prior to JSONB reordering and creates a 'layout_order' key [array, def. order] (Postgres stores arrays in semantic order)
+                -> Adds 'order' field to the template's individual fields
+        """
+        if obj.definition is not None and 'fields' in obj.definition:
+            order = []
+            for field in obj.definition['fields']:
+                obj.definition['fields'][field]['order'] = len(order)
+                order.append(field)
+            obj.definition['layout_order'] = order
+
+            details = obj.definition.get('template_details') or { }
+            version = details.get('version', None)
+            if version != obj.template_version:
+                obj.template_version = version
+
+        if not change or not obj.created_by:
+            obj.created_by = request.user
+
+        obj.updated_by = request.user
+        obj.modified = datetime.datetime.now()
+
+        obj.save()
+
+
+@admin.register(GenericEntity)
+class GenericEntityAdmin(admin.ModelAdmin):
+    readonly_fields = ['template_version']
+    list_display = ['id', 'name', 'template', 'template_version']
+    exclude = []
+
+
+@admin.register(EntityClass)
+class EntityClassAdmin(admin.ModelAdmin):
+    list_display = ['id', 'name', 'entity_prefix', 'entity_count', 'modified_by', 'modified']
+    exclude = []
+    form = EntityAdminForm
+
+    def save_model(self, request, obj, form, change):
+        if not obj.created_by or not obj.created_by.id:
+            obj.created_by = request.user
+        obj.modified_by = request.user
+        obj.modified = timezone.now()
+        obj.save()

CodeListLibrary_project/clinicalcode/api/serializers.py

@@ -9,51 +9,38 @@
 
 from ..models import (Code, Concept, DataSource, Tag, CodingSystem)
 
-
 class ConceptSerializer(serializers.ModelSerializer):
-
     class Meta:
         model = Concept
         fields = '__all__'
 
 
 class CodeSerializer(serializers.ModelSerializer):
-
     class Meta:
         model = Code
-        #fields = ('id', 'code', 'description', 'code_list')
         fields = '__all__'
 
 
 class TagSerializer(serializers.ModelSerializer):
-
     class Meta:
         model = Tag
-        #fields = '__all__'
         fields = (
             'id', 'description', 'display', 'get_display_display', 'tag_type',
             'get_tag_type_display', 'collection_brand'
-            #' ,  'created_by' , 'updated_by'
         )
 
 
 class DataSourceSerializer(serializers.ModelSerializer):
-
     class Meta:
         model = DataSource
         fields = (
             'id', 'name', 'uid', 'url', 'description', 'datasource_id'
-            # ,  'created_by' , 'updated_by'
         )
 
 
 class CodingSystemSerializer(serializers.ModelSerializer):
-
     class Meta:
         model = CodingSystem
         fields = (
             'id', 'name', 'description', 'codingsystem_id'
         )
-
-
-