rework application relationship (#3912) (patch)

### Changed

- application.order_types is a modifiable list

cg/server/admin.py

@@ -77,10 +77,10 @@ def is_external_application(unused1, unused2, model, unused3):
 
 def view_order_types(unused1, unused2, model, unused3):
     del unused1, unused2, unused3
-    order_type_list = "<br>".join([order_type.order_type for order_type in model.order_types])
+    order_type_list = "<br>".join(model.order_types)
     return (
         Markup(f'<div style="display: inline-block; min-width: 200px;">{order_type_list}</div>')
-        if model.order_types
+        if model.order_type_applications
         else ""
     )
 
@@ -168,7 +168,7 @@ class ApplicationView(BaseView):
     }
     column_filters = ["prep_category", "is_accredited"]
     column_searchable_list = ["tag", "prep_category"]
-    form_excluded_columns = ["category", "versions", "order_types"]
+    form_excluded_columns = ["category", "versions", "order_type_applications"]
     form_extra_fields = {
         "suitable_order_types": MultiCheckboxField(
             "Order Types", choices=[(choice, choice.name) for choice in OrderType]
@@ -205,10 +205,7 @@ def edit_form(self, obj=None):
 
         # Pre-select the existing order types for the application
         if obj and request.method != "POST":
-            form.suitable_order_types.data = [
-                order_type.order_type for order_type in obj.order_types
-            ]
-
+            form.suitable_order_types.data = obj.order_types
         return form
 
 

cg/store/base.py

@@ -6,7 +6,12 @@
 from sqlalchemy import and_, func
 from sqlalchemy.orm import Query, Session
 
-from cg.store.models import Analysis, Application, ApplicationLimitations, ApplicationVersion
+from cg.store.models import (
+    Analysis,
+    Application,
+    ApplicationLimitations,
+    ApplicationVersion,
+)
 from cg.store.models import Base as ModelBase
 from cg.store.models import (
     Case,
@@ -82,7 +87,7 @@ def _get_join_sample_case_order_query(self) -> Query:
 
     def _get_join_application_ordertype_query(self) -> Query:
         """Return join application to order type query."""
-        return self._get_query(table=Application).join(Application.order_types)
+        return self._get_query(table=Application).join(Application.order_type_applications)
 
     def _get_join_sample_application_version_query(self) -> Query:
         """Return join sample to application version query."""

cg/store/models.py

@@ -181,10 +181,23 @@ class Application(Base):
     pipeline_limitations: Mapped[list["ApplicationLimitations"]] = orm.relationship(
         back_populates="application"
     )
-    order_types: Mapped[list["OrderTypeApplication"]] = orm.relationship(
-        "OrderTypeApplication", back_populates="application"
+    order_type_applications: Mapped[list["OrderTypeApplication"]] = orm.relationship(
+        "OrderTypeApplication",
+        back_populates="application",
     )
 
+    @property
+    def order_types(self) -> list[OrderType]:
+        return [entry.order_type for entry in self.order_type_applications]
+
+    @order_types.setter
+    def order_types(self, order_types: list[OrderType]) -> None:
+        self.order_type_applications.clear()
+        self.order_type_applications = [
+            OrderTypeApplication(order_type=order_type, application_id=self.id)
+            for order_type in order_types
+        ]
+
     def __str__(self) -> str:
         return self.tag
 
@@ -1205,4 +1218,6 @@ class OrderTypeApplication(Base):
     application_id: Mapped[int] = mapped_column(
         ForeignKey("application.id", ondelete="CASCADE"), primary_key=True
     )
-    application: Mapped[Application] = orm.relationship("Application", back_populates="order_types")
+    application: Mapped[Application] = orm.relationship(
+        "Application", back_populates="order_type_applications"
+    )

tests/store/crud/read/test_read_application.py

@@ -11,7 +11,7 @@ def test_get_active_applications_by_order_type_no_application(store: Store):
     # GIVEN a store with applications without order types
     applications: list[Application] = store.get_applications()
     for application in applications:
-        assert not application.order_types
+        assert not application.order_type_applications
 
     # GIVEN an order type
     order_type: OrderType = OrderType.PACBIO_LONG_READ

tests/store/filters/test_status_order_type_application_filters.py

@@ -1,8 +1,10 @@
 from sqlalchemy.orm import Query
 
 from cg.models.orders.constants import OrderType
-from cg.store.filters.status_ordertype_application_filters import filter_applications_by_order_type
-from cg.store.models import Application, OrderTypeApplication
+from cg.store.filters.status_ordertype_application_filters import (
+    filter_applications_by_order_type,
+)
+from cg.store.models import Application
 from cg.store.store import Store
 from tests.store_helpers import StoreHelpers
 
@@ -26,11 +28,14 @@ def test_filter_applications_by_order_type(applications_store: Store, helpers: S
     )
 
     # WHEN filtering applications by order type
-    order_type_applications: Query = applications_store._get_query(table=OrderTypeApplication)
+    order_type_applications: Query = applications_store._get_query(table=Application).join(
+        Application.order_type_applications
+    )
     filtered_order_type_applications: Query = filter_applications_by_order_type(
         order_type_applications=order_type_applications, order_type=order_type
     )
 
     # THEN assert that only the applications with the given order type are returned
     assert filtered_order_type_applications.count() == 1
-    assert filtered_order_type_applications.first().order_type == order_type
+    application = filtered_order_type_applications.first()
+    assert order_type in application.order_types