Refactor cancel action

cg/exc.py

@@ -60,6 +60,12 @@ class CgDataError(CgError):
     """
 
 
+class SampleNotFoundError(CgDataError):
+    """
+    Exception raised when a sample is not found.
+    """
+
+
 class ChecksumFailedError(CgError):
     """
     Exception raised when the checksums of two files are not equal.

cg/server/admin.py

@@ -1,6 +1,5 @@
 """Module for Flask-Admin views"""
 
-from datetime import datetime
 from gettext import gettext
 
 from flask import flash, redirect, request, session, url_for
@@ -10,8 +9,7 @@
 from markupsafe import Markup
 
 from cg.constants.constants import NG_UL_SUFFIX, CaseActions, DataDelivery, Workflow
-from cg.server.ext import db
-from cg.store.models import Sample
+from cg.server.ext import db, sample_service
 from cg.utils.flask.enum import SelectEnumField
 
 
@@ -598,64 +596,12 @@ def view_sample_link(unused1, unused2, model, unused3):
         "Are you sure you want to cancel the selected samples?",
     )
     def cancel_samples(self, entry_ids: list[str]) -> None:
-        """
-        Action for cancelling samples:
-            - Comments each sample being cancelled with date and user.
-            - Deletes any relationship between the cancelled samples and cases.
-            - Deletes any cases that only contain samples being cancelled.
-        """
-        all_associated_case_ids: set = set()
-
-        for entry_id in entry_ids:
-            sample: Sample = db.get_sample_by_entry_id(entry_id=int(entry_id))
-
-            sample_case_ids: list[str] = [
-                case_sample.case.internal_id for case_sample in sample.links
-            ]
-            all_associated_case_ids.update(sample_case_ids)
-
-            db.delete_relationships_sample(sample=sample)
-            self.write_cancel_comment(sample=sample)
-
-        case_ids: list[str] = list(all_associated_case_ids)
-        db.delete_cases_without_samples(case_internal_ids=case_ids)
-        cases_with_remaining_samples: list[str] = db.filter_cases_with_samples(case_ids=case_ids)
-
-        self.display_cancel_confirmation(
-            sample_entry_ids=entry_ids, remaining_cases=cases_with_remaining_samples
+        user_email: str | None = session.get("user_email")
+        message: str = sample_service.cancel_samples(
+            sample_ids=entry_ids,
+            user_email=user_email,
         )
-
-    def write_cancel_comment(self, sample: Sample) -> None:
-        """Add comment to sample with date and user cancelling the sample."""
-        user_name: str = db.get_user_by_email(session.get("user_email")).name
-        date: str = datetime.now().strftime("%Y-%m-%d")
-        comment: str = f"Cancelled {date} by {user_name}"
-
-        db.update_sample_comment(sample=sample, comment=comment)
-
-    def display_cancel_confirmation(
-        self, sample_entry_ids: list[str], remaining_cases: list[str]
-    ) -> None:
-        """Show a summary of the cancelled samples and any cases in which other samples were present."""
-        samples: str = "sample" if len(sample_entry_ids) == 1 else "samples"
-        cases: str = "case" if len(remaining_cases) == 1 else "cases"
-
-        message: str = f"Cancelled {len(sample_entry_ids)} {samples}. "
-        case_message: str = ""
-
-        for case_id in remaining_cases:
-            case_message = f"{case_message} {case_id},"
-
-        case_message = case_message.strip(",")
-
-        if remaining_cases:
-            message += (
-                f"Found {len(remaining_cases)} {cases} with additional samples: {case_message}."
-            )
-        else:
-            message += "No case contained additional samples."
-
-        flash(message=message)
+        flash(message)
 
 
 class DeliveryView(BaseView):

cg/server/ext.py

@@ -13,6 +13,7 @@
 from cg.services.orders.order_summary_service.order_summary_service import (
     OrderSummaryService,
 )
+from cg.services.sample_service.sample_service import SampleService
 from cg.store.database import initialize_database
 from cg.store.store import Store
 
@@ -81,3 +82,4 @@ def init_app(self, app):
 delivery_message_service = DeliveryMessageService(store=db, trailblazer_api=analysis_client)
 summary_service = OrderSummaryService(store=db, analysis_client=analysis_client)
 order_service = OrderService(store=db, status_service=summary_service)
+sample_service = SampleService(db)

cg/services/sample_service/sample_service.py

@@ -0,0 +1,34 @@
+from cg.services.sample_service.utils import (
+    get_cancel_comment,
+    get_confirmation_message,
+)
+from cg.store.models import User
+from cg.store.store import Store
+
+
+class SampleService:
+
+    def __init__(self, store: Store):
+        self.store = store
+
+    def cancel_sample(self, sample_id: int, user_email: str) -> None:
+        self.store.mark_sample_as_cancelled(sample_id)
+        self.store.decouple_sample_from_cases(sample_id)
+        self._add_cancel_comment(sample_id=sample_id, user_email=user_email)
+
+    def _add_cancel_comment(self, sample_id: int, user_email: str) -> None:
+        if user := self.store.get_user_by_email(user_email):
+            comment = get_cancel_comment(user.name)
+            self.store.update_sample_comment(sample_id=sample_id, comment=comment)
+
+    def cancel_samples(self, sample_ids: list[int], user_email: str) -> str:
+        """Returns a cancellation confirmation message."""
+        case_ids = self.store.get_case_ids_for_samples(sample_ids)
+
+        for sample_id in sample_ids:
+            self.cancel_sample(sample_id=sample_id, user_email=user_email)
+
+        self.store.delete_cases_without_samples(case_ids)
+        remaining_cases = self.store.filter_cases_with_samples(case_ids)
+
+        return get_confirmation_message(sample_ids=sample_ids, case_ids=remaining_cases)

cg/services/sample_service/utils.py

@@ -0,0 +1,16 @@
+from datetime import datetime
+
+
+def get_cancel_comment(user_name: str) -> str:
+    date: str = datetime.now().strftime("%Y-%m-%d")
+    return f"Cancelled {date} by {user_name}"
+
+
+def get_confirmation_message(sample_ids: list[str], case_ids: list[str]) -> str:
+    message = f"Cancelled {len(sample_ids)} samples. "
+    if case_ids:
+        cases = ", ".join(case_ids)
+        message += f"Found {len(case_ids)} cases with additional samples: {cases}."
+    else:
+        message += "No case contained additional samples."
+    return message

cg/store/crud/delete.py

@@ -13,13 +13,6 @@ def __init__(self, session: Session):
         super().__init__(session=session)
         self.session = session
 
-    def delete_relationships_sample(self, sample: Sample) -> None:
-        """Delete relationships between all cases and the provided sample."""
-        if sample and sample.links:
-            for case_sample in sample.links:
-                self.session.delete(case_sample)
-            self.session.commit()
-
     def delete_cases_without_samples(self, case_internal_ids: list[str]) -> None:
         """Delete any cases specified in case_ids without samples."""
         for case_internal_id in case_internal_ids:
@@ -36,3 +29,9 @@ def delete_illumina_flow_cell(self, internal_id: str):
             self.session.commit()
         else:
             raise ValueError(f"Illumina flow cell with internal id {internal_id} not found.")
+
+    def decouple_sample_from_cases(self, sample_id: int) -> None:
+        sample: Sample = self.get_sample_by_entry_id(sample_id)
+        for case_sample in sample.links:
+            self.session.delete(case_sample)
+        self.session.commit()

cg/store/crud/read.py

@@ -9,7 +9,7 @@
 
 from cg.constants import SequencingRunDataAvailability, Workflow
 from cg.constants.constants import CaseActions, CustomerId, PrepCategory, SampleType
-from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError
+from cg.exc import CaseNotFoundError, CgError, OrderNotFoundError, SampleNotFoundError
 from cg.server.dto.orders.orders_request import OrdersRequest
 from cg.store.base import BaseHandler
 from cg.store.filters.status_analysis_filters import AnalysisFilter, apply_analysis_filter
@@ -1009,12 +1009,17 @@ def get_cases_to_compress(self, date_threshold: datetime) -> list[Case]:
 
     def get_sample_by_entry_id(self, entry_id: int) -> Sample:
         """Return a sample by entry id."""
-        return apply_sample_filter(
+        sample: Sample | None = apply_sample_filter(
             filter_functions=[SampleFilter.BY_ENTRY_ID],
             samples=self._get_query(table=Sample),
             entry_id=entry_id,
         ).first()
 
+        if not sample:
+            LOG.error(f"Could not find sample with entry id {entry_id}")
+            raise SampleNotFoundError(f"Could not find sample with entry id {entry_id}")
+        return sample
+
     def get_sample_by_internal_id(self, internal_id: str) -> Sample | None:
         """Return a sample by lims id."""
         return apply_sample_filter(
@@ -1463,3 +1468,14 @@ def get_cases_for_sequencing_qc(self) -> list[Case]:
                 CaseFilter.HAS_SEQUENCE,
             ],
         ).all()
+
+    def get_case_ids_with_sample(self, sample_id: int) -> list[str]:
+        """Return all case ids with a sample."""
+        sample: Sample = self.get_sample_by_entry_id(sample_id)
+        return [link.case.internal_id for link in sample.links] if sample else []
+
+    def get_case_ids_for_samples(self, sample_ids: list[int]) -> list[str]:
+        case_ids: list[str] = []
+        for sample_id in sample_ids:
+            case_ids.extend(self.get_case_ids_with_sample(sample_id))
+        return list(set(case_ids))

cg/store/crud/update.py

@@ -21,12 +21,10 @@ def __init__(self, session: Session):
         super().__init__(session=session)
         self.session = session
 
-    def update_sample_comment(self, sample: Sample, comment: str) -> None:
+    def update_sample_comment(self, sample_id: int, comment: str) -> None:
         """Update comment on sample with the provided comment."""
-        if sample.comment:
-            sample.comment = sample.comment + " " + comment
-        else:
-            sample.comment = comment
+        sample: Sample = self.get_sample_by_entry_id(sample_id)
+        sample.comment = f"{sample.comment} {comment}" if sample.comment else comment
         self.session.commit()
 
     def update_order_delivery(self, order_id: int, delivered: bool) -> Order:
@@ -71,3 +69,8 @@ def update_sample_sequenced_at(self, internal_id: str, date: datetime):
         sample: Sample = self.get_sample_by_internal_id(internal_id)
         sample.last_sequenced_at = date
         self.session.commit()
+
+    def mark_sample_as_cancelled(self, sample_id: int) -> None:
+        sample: Sample = self.get_sample_by_entry_id(sample_id)
+        sample.is_cancelled = True
+        self.session.commit()

tests/store/crud/delete/test_delete.py

@@ -23,7 +23,7 @@ def test_store_api_delete_relationships_between_sample_and_cases(
     assert sample_in_multiple_cases
 
     # WHEN removing the relationships between one sample and its cases
-    store_with_multiple_cases_and_samples.delete_relationships_sample(sample=sample_in_single_case)
+    store_with_multiple_cases_and_samples.decouple_sample_from_cases(sample_in_single_case.id)
 
     # THEN it should no longer be associated with any cases, but other relationships should remain
     results: list[CaseSample] = (