Speedup issue confirmation

tests/utils/hla_system/test_code_parser.py

@@ -219,6 +219,9 @@ def test_mfi_extraction(self):
             ).hla_antibodies_per_groups[3].hla_antibody_list))
         # When MFI quite close to each other but one below and one above cutoff
         self._compare_mfi_result(expected_mfi=1500, mfis=[1500, 2900])
+        # no warning in case the values are all quite low:
+        self._compare_mfi_result(expected_mfi=1201, mfis=[1339, 1058, 2058, 1206], has_issue=False)
+        self._compare_mfi_result(expected_mfi=1508, mfis=[3970, 1922, 1422, 1180], has_issue=True)
 
     def test_no_ultra_high_res_with_multiple_splits(self):
         """

txmatching/data_transfer_objects/patients/utils.py

@@ -3,18 +3,19 @@
 
 from txmatching.data_transfer_objects.hla.parsing_issue_dto import (
     ParsingIssue, ParsingIssueConfirmationDTO, ParsingIssuePublicDTO)
-from txmatching.database.sql_alchemy_schema import ParsingIssueModel
 from txmatching.data_transfer_objects.patients.upload_dtos.donor_upload_dto import \
     DonorUploadDTO
 from txmatching.data_transfer_objects.patients.upload_dtos.hla_antibodies_upload_dto import \
     HLAAntibodiesUploadDTO
 from txmatching.data_transfer_objects.patients.upload_dtos.recipient_upload_dto import \
     RecipientUploadDTO
-from txmatching.patients.patient import Donor, Recipient, TxmEvent
+from txmatching.database.sql_alchemy_schema import ParsingIssueModel
+from txmatching.patients.patient import Donor, Recipient, TxmEventBase
 
 logger = logging.getLogger(__name__)
 
-def parsing_issue_to_dto(parsing_issue: ParsingIssue, txm_event: TxmEvent) -> ParsingIssuePublicDTO:
+
+def parsing_issue_to_dto(parsing_issue: ParsingIssue, txm_event: TxmEventBase) -> ParsingIssuePublicDTO:
     return ParsingIssuePublicDTO(
         hla_code_or_group=parsing_issue.hla_code_or_group,
         parsing_issue_detail=parsing_issue.parsing_issue_detail,
@@ -27,13 +28,13 @@ def parsing_issue_to_dto(parsing_issue: ParsingIssue, txm_event: TxmEvent) -> Pa
 
 
 def parsing_issue_model_to_confirmation_dto(parsing_issue: ParsingIssueModel,
-                                            txm_event: TxmEvent) -> ParsingIssueConfirmationDTO:
+                                            txm_event_id: int) -> ParsingIssueConfirmationDTO:
     return ParsingIssueConfirmationDTO(
         db_id=parsing_issue.id,
         hla_code_or_group=parsing_issue.hla_code_or_group,
         parsing_issue_detail=parsing_issue.parsing_issue_detail,
         message=parsing_issue.message,
-        txm_event_id=txm_event.db_id,
+        txm_event_id=txm_event_id,
         confirmed_at=parsing_issue.confirmed_at,
         confirmed_by=parsing_issue.confirmed_by,
         donor_id=parsing_issue.donor_id,

txmatching/database/services/parsing_issue_service.py

@@ -3,20 +3,24 @@
 
 from sqlalchemy import and_
 
-from txmatching.auth.exceptions import InvalidArgumentException, OverridingException
-from txmatching.data_transfer_objects.hla.parsing_issue_dto import ParsingIssue, ParsingIssueConfirmationDTO
-from txmatching.data_transfer_objects.patients.utils import parsing_issue_model_to_confirmation_dto
+from txmatching.auth.exceptions import (InvalidArgumentException,
+                                        OverridingException)
+from txmatching.data_transfer_objects.hla.parsing_issue_dto import (
+    ParsingIssue, ParsingIssueConfirmationDTO)
+from txmatching.data_transfer_objects.patients.utils import \
+    parsing_issue_model_to_confirmation_dto
 from txmatching.database.db import db
 from txmatching.database.sql_alchemy_schema import ParsingIssueModel
-from txmatching.patients.patient import TxmEvent
-from txmatching.utils.hla_system.hla_transformations.parsing_issue_detail import WARNING_PROCESSING_RESULTS
+from txmatching.utils.hla_system.hla_transformations.parsing_issue_detail import \
+    WARNING_PROCESSING_RESULTS
 
 
-def confirm_a_parsing_issue(user_id: int, parsing_issue_id: int, txm_event: TxmEvent) -> ParsingIssueConfirmationDTO:
+def confirm_a_parsing_issue(user_id: int, parsing_issue_id: int,
+                            txm_event_id: int) -> ParsingIssueConfirmationDTO:
     parsing_issue = ParsingIssueModel.query.get(parsing_issue_id)
 
-    if parsing_issue is None or parsing_issue.txm_event_id != txm_event.db_id:
-        raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} not found in txm event {txm_event.db_id}')
+    if parsing_issue is None or parsing_issue.txm_event_id != txm_event_id:
+        raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} not found in txm event {txm_event_id}')
 
     if parsing_issue.parsing_issue_detail not in WARNING_PROCESSING_RESULTS:
         raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} is not a warning')
@@ -28,14 +32,14 @@ def confirm_a_parsing_issue(user_id: int, parsing_issue_id: int, txm_event: TxmE
     parsing_issue.confirmed_at = datetime.now()
 
     db.session.commit()
-    return parsing_issue_model_to_confirmation_dto(parsing_issue, txm_event)
+    return parsing_issue_model_to_confirmation_dto(parsing_issue, txm_event_id)
 
 
-def unconfirm_a_parsing_issue(parsing_issue_id: int, txm_event: TxmEvent) -> ParsingIssueConfirmationDTO:
+def unconfirm_a_parsing_issue(parsing_issue_id: int, txm_event_id: int) -> ParsingIssueConfirmationDTO:
     parsing_issue = ParsingIssueModel.query.get(parsing_issue_id)
 
-    if parsing_issue is None or parsing_issue.txm_event_id != txm_event.db_id:
-        raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} not found in txm event {txm_event.db_id}')
+    if parsing_issue is None or parsing_issue.txm_event_id != txm_event_id:
+        raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} not found in txm event {txm_event_id}')
 
     if parsing_issue.parsing_issue_detail not in WARNING_PROCESSING_RESULTS:
         raise InvalidArgumentException(f'Parsing issue {parsing_issue_id} is not a warning')
@@ -47,7 +51,7 @@ def unconfirm_a_parsing_issue(parsing_issue_id: int, txm_event: TxmEvent) -> Par
     parsing_issue.confirmed_at = None
 
     db.session.commit()
-    return parsing_issue_model_to_confirmation_dto(parsing_issue, txm_event)
+    return parsing_issue_model_to_confirmation_dto(parsing_issue, txm_event_id)
 
 
 def parsing_issues_to_models(

txmatching/utils/hla_system/hla_transformations/get_mfi_from_multiple_hla_codes.py

@@ -8,11 +8,13 @@
 
 RELATIVE_DIFFERENCE_THRESHOLD_FOR_SUSPICIOUS_MFI = 3 / 4
 
-RELATIVE_CLOSENESS_TO_CUTOFF_FROM_BELOW = 0.5
+RELATIVE_CLOSENESS_TO_CUTOFF_FROM_BELOW = 3 / 4
 RELATIVE_CLOSENESS_TO_CUTOFF_FROM_ABOVE = 1.25
 RELATIVE_CLOSENESS_TO_MINIMUM = 1 / 2
 DIFFERENCE_THRESHOLD_RATIO = 1 / 4
 
+MAX_MFI_RATIO_TO_BE_JUST_BELOW_CUTOFF = 7 / 8
+
 
 def get_mfi_from_multiple_hla_codes(mfis: List[int],
                                     cutoff: int,
@@ -73,15 +75,16 @@ def get_mfi_from_multiple_hla_codes(mfis: List[int],
     else:
         relevant_mean = int(np.mean(mfis))
 
-    if RELATIVE_CLOSENESS_TO_CUTOFF_FROM_BELOW * cutoff < relevant_mean < cutoff:
+    if RELATIVE_CLOSENESS_TO_CUTOFF_FROM_BELOW * cutoff < relevant_mean < cutoff and \
+            max_mfi > cutoff * MAX_MFI_RATIO_TO_BE_JUST_BELOW_CUTOFF:
         parsing_issues.append(
             ParsingIssue(
                 hla_code_or_group=raw_code,
                 parsing_issue_detail=ParsingIssueDetail.MFI_PROBLEM,
                 message=f'Dropping {raw_code} antibody: '
                         f'Calculated MFI: {int(relevant_mean)}, Cutoff: {cutoff}, MFI values: {mfis}. '
-                        f'To be consulted with immunologist, because the antibody is dropped even though it has some '
-                        f'high MFI values.'
+                        f'To be consulted with immunologist, the estimated overall MFI is below cutoff, but the '
+                        f'value is close to cutoff.'
             )
         )
 
@@ -92,8 +95,8 @@ def get_mfi_from_multiple_hla_codes(mfis: List[int],
                 parsing_issue_detail=ParsingIssueDetail.MFI_PROBLEM,
                 message=f'Not dropping {raw_code} antibody: '
                         f'Calculated MFI: {int(relevant_mean)}, Cutoff: {cutoff}, MFI values: {mfis}. '
-                        f'To be consulted with immunologist, because the antibody is NOT dropped even though there are'
-                        f' some MFI values below cutoff.'
+                        f'To be consulted with immunologist, because the antibody is NOT dropped even though '
+                        f'there are some MFI values below cutoff.'
             )
         )
 
@@ -104,9 +107,9 @@ def get_mfi_from_multiple_hla_codes(mfis: List[int],
                 parsing_issue_detail=ParsingIssueDetail.MFI_PROBLEM,
                 message=f'Dropping {raw_code} antibody: '
                         f'Calculated MFI: {int(relevant_mean)}, Cutoff: {cutoff}, MFI values: {mfis}. '
-                        f'To be consulted with immunologist, because the antibody is dropped even though only one MFI '
-                        f'value was identified as relevant for the MFI calculation and therefore the final calculated '
-                        f'mean is less relevant.'
+                        f'To be consulted with immunologist, because the antibody is dropped even though only'
+                        f' one MFI value was identified as relevant for the MFI calculation and therefore '
+                        f'the final calculated mean is less relevant.'
             )
         )
 

txmatching/web/api/patient_api.py

@@ -22,7 +22,8 @@
     ConfigIdPathParamDefinition
 from txmatching.data_transfer_objects.external_patient_upload.swagger import \
     PatientUploadSuccessJson
-from txmatching.data_transfer_objects.hla.parsing_issue_swagger import ParsingIssueConfirmationJson
+from txmatching.data_transfer_objects.hla.parsing_issue_swagger import \
+    ParsingIssueConfirmationJson
 from txmatching.data_transfer_objects.patients.out_dtos.conversions import (
     donor_to_donor_dto_out, recipient_to_recipient_dto_out, to_lists_for_fe)
 from txmatching.data_transfer_objects.patients.out_dtos.donor_dto_out import \
@@ -45,7 +46,8 @@
 from txmatching.database.services.config_service import \
     get_configuration_parameters_from_db_id_or_default
 from txmatching.database.services.parsing_issue_service import (
-    confirm_a_parsing_issue, get_parsing_issues_confirmation_dto_for_patients, unconfirm_a_parsing_issue)
+    confirm_a_parsing_issue, get_parsing_issues_confirmation_dto_for_patients,
+    unconfirm_a_parsing_issue)
 from txmatching.database.services.patient_service import (
     delete_donor_recipient_pair, get_donor_recipient_pair,
     recompute_hla_and_antibodies_parsing_for_all_patients_in_txm_event,
@@ -300,8 +302,7 @@ class ConfirmWarning(Resource):
     @require_role(UserRole.ADMIN)
     def put(self, txm_event_id: int, parsing_issue_id: int):
         user_id = get_current_user_id()
-        txm_event = get_txm_event_complete(txm_event_id)
-        result = confirm_a_parsing_issue(user_id, parsing_issue_id, txm_event)
+        result = confirm_a_parsing_issue(user_id, parsing_issue_id, txm_event_id)
         return response_ok(result)
 
 
@@ -326,6 +327,5 @@ class UnconfirmWarning(Resource):
     @require_valid_txm_event_id()
     @require_role(UserRole.ADMIN)
     def put(self, txm_event_id: int, parsing_issue_id: int):
-        txm_event = get_txm_event_complete(txm_event_id)
-        result = unconfirm_a_parsing_issue(parsing_issue_id, txm_event)
+        result = unconfirm_a_parsing_issue(parsing_issue_id, txm_event_id)
         return response_ok(result)