technical debt( rework order.workflow column) (#3929)(patch)

# Description Solves technical debt on database model
Clinical-Genomics · Nov 12, 2024 · 262bac9 · 262bac9
1 parent 09a5ccc
commit 262bac9
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diff --git a/alembic/versions/2024_11_11_05ffb5e13d7b_remove_order_workflow.py b/alembic/versions/2024_11_11_05ffb5e13d7b_remove_order_workflow.py
@@ -0,0 +1,51 @@
+"""remove_order_workflow
+
+Revision ID: 05ffb5e13d7b
+Revises: 3503b53a9bc3
+Create Date: 2024-11-11 09:35:33.020098
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "05ffb5e13d7b"
+down_revision = "3503b53a9bc3"
+branch_labels = None
+depends_on = None
+workflows = [
+    "balsamic",
+    "balsamic-pon",
+    "balsamic-qc",
+    "balsamic-umi",
+    "demultiplex",
+    "raw-data",
+    "fluffy",
+    "microsalt",
+    "mip-dna",
+    "mip-rna",
+    "mutant",
+    "raredisease",
+    "rnafusion",
+    "rsync",
+    "spring",
+    "taxprofiler",
+    "tomte",
+    "jasen",
+]
+
+
+def upgrade():
+    op.drop_column(table_name="order", column_name="workflow")
+
+
+def downgrade():
+    op.add_column(
+        "order",
+        sa.Column(
+            "workflow",
+            type_=sa.Enum(*workflows),
+        ),
+    )
diff --git a/cg/cli/add.py b/cg/cli/add.py
@@ -292,7 +292,6 @@ def add_case(
         order = Order(
             customer_id=customer.id,
             ticket_id=int(ticket),
-            workflow=data_analysis,
         )
     new_case.orders.append(order)
 

diff --git a/cg/services/orders/order_service/utils.py b/cg/services/orders/order_service/utils.py
@@ -1,3 +1,4 @@
+from cg.constants import Workflow
 from cg.server.dto.orders.orders_response import Order, OrdersResponse, OrderSummary
 from cg.store.models import Order as DatabaseOrder
 
@@ -9,7 +10,7 @@ def create_order_response(order: DatabaseOrder, summary: OrderSummary | None = N
         order_date=str(order.order_date.date()),
         id=order.id,
         is_open=order.is_open,
-        workflow=order.workflow,
+        workflow=order.workflow if Workflow.BALSAMIC not in order.workflow else Workflow.BALSAMIC,
         summary=summary,
     )
 

diff --git a/cg/services/orders/store_order_services/store_case_order.py b/cg/services/orders/store_order_services/store_case_order.py
@@ -164,7 +164,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow(items[0]["data_analysis"]),
         )
         for case in items:
             status_db_case: Case = self.status_db.get_case_by_internal_id(

diff --git a/cg/services/orders/store_order_services/store_fastq_order_service.py b/cg/services/orders/store_order_services/store_fastq_order_service.py
@@ -105,7 +105,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow(submitted_case["data_analysis"]),
         )
         with self.status_db.session.no_autoflush:
             for sample in items:

diff --git a/cg/services/orders/store_order_services/store_metagenome_order.py b/cg/services/orders/store_order_services/store_metagenome_order.py
@@ -90,7 +90,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow(case_dict["data_analysis"]),
         )
         with self.status_db.session.no_autoflush:
             for sample in case_dict["samples"]:

diff --git a/cg/services/orders/store_order_services/store_microbial_fastq_order_service.py b/cg/services/orders/store_order_services/store_microbial_fastq_order_service.py
@@ -66,7 +66,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow.RAW_DATA,
         )
         for sample in items:
             case_name: str = f'{sample["name"]}-case'

diff --git a/cg/services/orders/store_order_services/store_microbial_order.py b/cg/services/orders/store_order_services/store_microbial_order.py
@@ -105,7 +105,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=data_analysis,
         )
 
         with self.status.session.no_autoflush:

diff --git a/cg/services/orders/store_order_services/store_pacbio_order_service.py b/cg/services/orders/store_order_services/store_pacbio_order_service.py
@@ -69,7 +69,6 @@ def _store_samples_in_statusdb(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow.RAW_DATA,
         )
         new_samples = []
         with self.status_db.session.no_autoflush:

diff --git a/cg/services/orders/store_order_services/store_pool_order.py b/cg/services/orders/store_order_services/store_pool_order.py
@@ -128,7 +128,6 @@ def store_items_in_status(
             customer=customer,
             order_date=datetime.now(),
             ticket_id=int(ticket_id),
-            workflow=Workflow(items[0]["data_analysis"]),
         )
         new_pools: list[Pool] = []
         new_samples: list[Sample] = []

diff --git a/cg/store/base.py b/cg/store/base.py
@@ -11,6 +11,7 @@
     Application,
     ApplicationLimitations,
     ApplicationVersion,
+    Order,
 )
 from cg.store.models import Base as ModelBase
 from cg.store.models import (
@@ -85,6 +86,10 @@ def _get_join_sample_case_order_query(self) -> Query:
             self._get_query(table=Sample).join(Case.links).join(CaseSample.sample).join(Case.orders)
         )
 
+    def _get_join_order_case_query(self) -> Query:
+        """Return a query joining sample, cases_sample, case and order. Selects from sample."""
+        return self._get_query(table=Order).join(Order.cases)
+
     def _get_join_application_ordertype_query(self) -> Query:
         """Return join application to order type query."""
         return self._get_query(table=Application).join(Application.order_type_applications)

diff --git a/cg/store/crud/read.py b/cg/store/crud/read.py
@@ -1391,10 +1391,15 @@ def get_all_pools_to_deliver(self) -> list[Pool]:
 
     def get_orders(self, orders_request: OrdersRequest) -> tuple[list[Order], int]:
         """Filter, sort and paginate orders based on the provided request."""
-        orders: Query = apply_order_filters(
-            orders=self._get_query(Order),
-            filters=[OrderFilter.BY_WORKFLOW, OrderFilter.BY_SEARCH, OrderFilter.BY_OPEN],
+        order_case: Query = self._get_join_order_case_query()
+        order_for_workflow: Query = apply_case_filter(
+            cases=order_case,
+            filter_functions=[CaseFilter.WITH_WORKFLOW],
             workflow=orders_request.workflow,
+        )
+        orders: Query = apply_order_filters(
+            orders=order_for_workflow,
+            filters=[OrderFilter.BY_SEARCH, OrderFilter.BY_OPEN],
             search=orders_request.search,
             is_open=orders_request.is_open,
         )

diff --git a/cg/store/filters/status_order_filters.py b/cg/store/filters/status_order_filters.py
@@ -9,12 +9,6 @@
 from cg.store.models import Customer, Order
 
 
-def filter_orders_by_workflow(orders: Query, workflow: str | None, **kwargs) -> Query:
-    if workflow == Workflow.BALSAMIC:
-        return orders.filter(Order.workflow.startswith(workflow))
-    return orders.filter(Order.workflow == workflow) if workflow else orders
-
-
 def filter_orders_by_id(orders: Query, id: int | None, **kwargs) -> Query:
     return orders.filter(Order.id == id) if id else orders
 
@@ -65,7 +59,6 @@ class OrderFilter(Enum):
     BY_IDS: Callable = filter_orders_by_ids
     BY_SEARCH: Callable = filter_orders_by_search
     BY_TICKET_ID: Callable = filter_orders_by_ticket_id
-    BY_WORKFLOW: Callable = filter_orders_by_workflow
     BY_OPEN: Callable = filter_orders_by_is_open
     PAGINATE: Callable = apply_pagination
     SORT: Callable = apply_sorting
@@ -77,7 +70,6 @@ def apply_order_filters(
     id: int = None,
     ids: list[int] = None,
     ticket_id: int = None,
-    workflow: SortOrder = None,
     page: int = None,
     page_size: int = None,
     sort_field: OrderSortField = None,
@@ -90,7 +82,6 @@ def apply_order_filters(
             orders=orders,
             id=id,
             ids=ids,
-            workflow=workflow,
             page=page,
             page_size=page_size,
             ticket_id=ticket_id,

diff --git a/cg/store/models.py b/cg/store/models.py
@@ -991,9 +991,12 @@ class Order(Base):
     customer: Mapped[Customer] = orm.relationship(foreign_keys=[customer_id])
     order_date: Mapped[datetime] = mapped_column(default=datetime.now)
     ticket_id: Mapped[int] = mapped_column(unique=True, index=True)
-    workflow: Mapped[str] = mapped_column(types.Enum(*(workflow.value for workflow in Workflow)))
     is_open: Mapped[bool] = mapped_column(default=True)
 
+    @property
+    def workflow(self) -> Workflow:
+        return self.cases[0].data_analysis
+
     def to_dict(self):
         return to_dict(model_instance=self)
 

diff --git a/tests/meta/archive/conftest.py b/tests/meta/archive/conftest.py
@@ -286,7 +286,6 @@ def archive_store(
     order = Order(
         customer_id=customer_ddn.id,
         ticket_id=new_samples[0].original_ticket,
-        workflow=case.data_analysis,
     )
     base_store.session.add(order)
     base_store.session.add(case)

diff --git a/tests/server/conftest.py b/tests/server/conftest.py
@@ -51,7 +51,6 @@ def order(
         customer_id=customer.id,
         ticket_id=1,
         order_date=datetime.now(),
-        workflow=Workflow.MIP_DNA,
     )
     order.cases.append(server_case)
     order.cases.append(server_case_in_same_order)
@@ -60,21 +59,26 @@ def order(
 
 @pytest.fixture
 def order_another(helpers: StoreHelpers, customer_another: Customer) -> Order:
+    case: Case = helpers.add_case(name="another_case", store=store, data_analysis=Workflow.MIP_DNA)
     order: Order = helpers.add_order(
         store=store, customer_id=customer_another.id, ticket_id=2, order_date=datetime.now()
     )
+    order.cases.append(case)
     return order
 
 
 @pytest.fixture
 def order_balsamic(helpers: StoreHelpers, customer_another: Customer) -> Order:
+    case: Case = helpers.add_case(
+        name="balsamic_case", store=store, data_analysis=Workflow.BALSAMIC
+    )
     order: Order = helpers.add_order(
         store=store,
         customer_id=customer_another.id,
         ticket_id=3,
         order_date=datetime.now(),
-        workflow=Workflow.BALSAMIC,
     )
+    order.cases.append(case)
     return order
 
 

diff --git a/tests/store/crud/conftest.py b/tests/store/crud/conftest.py
@@ -456,27 +456,37 @@ def three_pool_names() -> list[str]:
 
 @pytest.fixture
 def order(helpers: StoreHelpers, store: Store) -> Order:
+    case: Case = helpers.add_case(data_analysis=Workflow.MIP_DNA, store=store, name="order_case")
     order: Order = helpers.add_order(
         store=store, customer_id=1, ticket_id=1, order_date=datetime.now()
     )
+    order.cases.append(case)
     return order
 
 
 @pytest.fixture
 def order_another(helpers: StoreHelpers, store: Store) -> Order:
+    case: Case = helpers.add_case(
+        data_analysis=Workflow.MIP_DNA, store=store, name="order_another_case"
+    )
     order: Order = helpers.add_order(
         store=store, customer_id=2, ticket_id=2, order_date=datetime.now()
     )
+    order.cases.append(case)
     return order
 
 
 @pytest.fixture
 def order_balsamic(helpers: StoreHelpers, store: Store) -> Order:
+    case: Case = helpers.add_case(
+        data_analysis=Workflow.BALSAMIC, store=store, name="order_balsamic_case"
+    )
     order: Order = helpers.add_order(
         store=store,
         customer_id=2,
         ticket_id=3,
         order_date=datetime.now(),
         workflow=Workflow.BALSAMIC,
     )
+    order.cases.append(case)
     return order
diff --git a/tests/store/filters/test_status_order_filters.py b/tests/store/filters/test_status_order_filters.py
@@ -13,7 +13,6 @@ def test_filter_orders_by_ticket_no_matching_ticket(base_store: Store, non_exist
         id=1,
         customer_id=1,
         ticket_id=1,
-        workflow=Workflow.MIP_DNA,
     )
     base_store.session.add(order)
     base_store.session.commit()
@@ -33,7 +32,6 @@ def test_filter_orders_by_ticket_id_matching_ticket(base_store: Store, ticket_id
         id=1,
         customer_id=1,
         ticket_id=int(ticket_id),
-        workflow=Workflow.MIP_DNA,
     )
     base_store.session.add(order)
     base_store.session.commit()

diff --git a/tests/store_helpers.py b/tests/store_helpers.py
@@ -516,7 +516,9 @@ def add_order(
         workflow: Workflow = Workflow.MIP_DNA,
     ) -> Order:
         order = Order(
-            customer_id=customer_id, ticket_id=ticket_id, order_date=order_date, workflow=workflow
+            customer_id=customer_id,
+            ticket_id=ticket_id,
+            order_date=order_date,
         )
         store.session.add(order)
         store.session.commit()
@@ -568,7 +570,6 @@ def ensure_case_from_dict(
         order = store.get_order_by_ticket_id(ticket_id=int(case_info["tickets"])) or Order(
             ticket_id=int(case_info["tickets"]),
             customer_id=customer_obj.id,
-            workflow=case_info.get("data_analysis", Workflow.MIP_DNA),
         )
         case = Case(
             name=case_info["name"],