Improve updating of patients

tests/web/test_patient_api.py

@@ -7,7 +7,10 @@
 from txmatching.database.services.txm_event_service import \
     get_txm_event_complete
 from txmatching.database.sql_alchemy_schema import UploadedFileModel
-from txmatching.patients.patient import DonorType
+from txmatching.patients.hla_model import HLAAntibodies, HLATyping
+from txmatching.patients.patient import DonorType, RecipientRequirements
+from txmatching.utils.blood_groups import BloodGroup
+from txmatching.utils.enums import Sex
 from txmatching.utils.get_absolute_path import get_absolute_path
 from txmatching.web import API_VERSION, PATIENT_NAMESPACE, TXM_EVENT_NAMESPACE
 
@@ -226,3 +229,163 @@ def test_donor_recipient_pair_deletion(self):
                                 headers=self.auth_headers)
         self.assertEqual(400, res.status_code)
         self.assertEqual('application/json', res.content_type)
+
+    def test_update_donor(self):
+        txm_event_db_id = self.fill_db_with_patients(
+            get_absolute_path(PATIENT_DATA_OBFUSCATED))
+        donor_db_id = 10
+
+        # 1. update patient
+        with self.app.test_client() as client:
+            json_data = {
+                'db_id': donor_db_id,
+                'blood_group': 'A',
+                'hla_typing': {
+                    'hla_types_list': []
+                },
+                'sex': 'M',
+                'height': 200,
+                'weight': 100,
+                'year_of_birth': 1990,
+                'active': True
+            }
+            res = client.put(f'{API_VERSION}/{TXM_EVENT_NAMESPACE}/{txm_event_db_id}/'
+                             f'{PATIENT_NAMESPACE}/donor',
+                             headers=self.auth_headers, json=json_data)
+        self.assertEqual(200, res.status_code)
+        self.assertEqual('application/json', res.content_type)
+
+        # Check that update was working
+        txm_event = get_txm_event(txm_event_db_id)
+        donor = txm_event.active_donors_dict[donor_db_id]
+        self.assertEqual(donor.parameters.blood_group, BloodGroup.A)
+        self.assertEqual(donor.parameters.hla_typing, HLATyping([]))
+        self.assertEqual(donor.parameters.sex, Sex.M)
+        self.assertEqual(donor.parameters.height, 200)
+        self.assertEqual(donor.parameters.weight, 100)
+        self.assertEqual(donor.parameters.year_of_birth, 1990)
+        self.assertEqual(donor.active, True)
+
+        # 2. update with unspecified values
+        with self.app.test_client() as client:
+            json_data = {
+                'db_id': donor_db_id,
+                'blood_group': 'B',
+                'hla_typing': {
+                    'hla_types_list': []
+                },
+                'sex': None,
+                'height': None,
+                'weight': None,
+                'year_of_birth': None,
+                'active': False
+            }
+            res = client.put(f'{API_VERSION}/{TXM_EVENT_NAMESPACE}/{txm_event_db_id}/'
+                             f'{PATIENT_NAMESPACE}/donor',
+                             headers=self.auth_headers, json=json_data)
+        self.assertEqual(200, res.status_code)
+        self.assertEqual('application/json', res.content_type)
+
+        # Check that update was working
+        txm_event = get_txm_event(txm_event_db_id)
+        donor = next(donor for donor in txm_event.all_donors if donor.db_id == donor_db_id)
+
+        self.assertEqual(donor.parameters.blood_group, BloodGroup.B)
+        self.assertEqual(donor.parameters.hla_typing, HLATyping([]))
+        self.assertEqual(donor.parameters.sex, None)
+        self.assertEqual(donor.parameters.height, None)
+        self.assertEqual(donor.parameters.weight, None)
+        self.assertEqual(donor.parameters.year_of_birth, None)
+        self.assertEqual(donor.active, False)
+
+    def test_update_recipient(self):
+        txm_event_db_id = self.fill_db_with_patients(
+            get_absolute_path(PATIENT_DATA_OBFUSCATED))
+        recipient_db_id = 10
+
+        # 1. update patient
+        with self.app.test_client() as client:
+            json_data = {
+                'db_id': recipient_db_id,
+                'blood_group': 'A',
+                'hla_typing': {
+                    'hla_types_list': []
+                },
+                'sex': 'M',
+                'height': 200,
+                'weight': 100,
+                'year_of_birth': 1990,
+                'acceptable_blood_groups': ['A', 'B', 'AB'],
+                'hla_antibodies': {
+                    'hla_antibodies_list': []
+                },
+                'recipient_requirements': {
+                    'require_better_match_in_compatibility_index': True,
+                    'require_better_match_in_compatibility_index_or_blood_group': True,
+                    'require_compatible_blood_group': True
+                },
+                'cutoff': 42
+            }
+            res = client.put(f'{API_VERSION}/{TXM_EVENT_NAMESPACE}/{txm_event_db_id}/'
+                             f'{PATIENT_NAMESPACE}/recipient',
+                             headers=self.auth_headers, json=json_data)
+        self.assertEqual(200, res.status_code)
+        self.assertEqual('application/json', res.content_type)
+
+        # Check that update was working
+        txm_event = get_txm_event(txm_event_db_id)
+        recipient = txm_event.active_recipients_dict[recipient_db_id]
+        self.assertEqual(recipient.parameters.blood_group, BloodGroup.A)
+        self.assertEqual(recipient.parameters.hla_typing, HLATyping([]))
+        self.assertEqual(recipient.parameters.sex, Sex.M)
+        self.assertEqual(recipient.parameters.height, 200)
+        self.assertEqual(recipient.parameters.weight, 100)
+        self.assertEqual(recipient.parameters.year_of_birth, 1990)
+        self.assertEqual(recipient.acceptable_blood_groups, [BloodGroup.A, BloodGroup.B, BloodGroup.AB])
+        self.assertEqual(recipient.hla_antibodies, HLAAntibodies())
+        self.assertEqual(recipient.recipient_requirements, RecipientRequirements(True, True, True))
+        self.assertEqual(recipient.recipient_cutoff, 42)
+
+        # 2. update with unspecified values
+        with self.app.test_client() as client:
+            json_data = {
+                'db_id': recipient_db_id,
+                'blood_group': 'B',
+                'hla_typing': {
+                    'hla_types_list': []
+                },
+                'sex': None,
+                'height': None,
+                'weight': None,
+                'year_of_birth': None,
+                'acceptable_blood_groups': ['0'],
+                'hla_antibodies': {
+                    'hla_antibodies_list': []
+                },
+                'recipient_requirements': {
+                    'require_better_match_in_compatibility_index': False,
+                    'require_better_match_in_compatibility_index_or_blood_group': False,
+                    'require_compatible_blood_group': False
+                },
+                'cutoff': None
+            }
+            res = client.put(f'{API_VERSION}/{TXM_EVENT_NAMESPACE}/{txm_event_db_id}/'
+                             f'{PATIENT_NAMESPACE}/recipient',
+                             headers=self.auth_headers, json=json_data)
+        self.assertEqual(200, res.status_code)
+        self.assertEqual('application/json', res.content_type)
+
+        # Check that update was working
+        txm_event = get_txm_event(txm_event_db_id)
+        recipient = next(recipient for recipient in txm_event.all_recipients if recipient.db_id == recipient_db_id)
+
+        self.assertEqual(recipient.parameters.blood_group, BloodGroup.B)
+        self.assertEqual(recipient.parameters.hla_typing, HLATyping([]))
+        self.assertEqual(recipient.parameters.sex, None)
+        self.assertEqual(recipient.parameters.height, None)
+        self.assertEqual(recipient.parameters.weight, None)
+        self.assertEqual(recipient.parameters.year_of_birth, None)
+        self.assertEqual(recipient.acceptable_blood_groups, [BloodGroup.ZERO])
+        self.assertEqual(recipient.hla_antibodies, HLAAntibodies())
+        self.assertEqual(recipient.recipient_requirements, RecipientRequirements(False, False, False))
+        self.assertEqual(recipient.recipient_cutoff, 42)  # Cutoff is unchanged

txmatching/data_transfer_objects/configuration/configuration_swagger.py

@@ -1,8 +1,7 @@
 from flask_restx import fields
 
 from txmatching.configuration.configuration import Configuration
-from txmatching.data_transfer_objects.matchings.matching_swagger import \
-    CountryCodeJson
+from txmatching.data_transfer_objects.enums_swagger import CountryCodeJson
 from txmatching.solvers.solver_from_config import SUPPORTED_SOLVERS
 from txmatching.web.api.namespaces import matching_api
 

txmatching/data_transfer_objects/enums_swagger.py

@@ -0,0 +1,27 @@
+from txmatching.patients.patient import DonorType
+from txmatching.utils.blood_groups import BloodGroup
+from txmatching.utils.country_enum import Country
+from txmatching.utils.enums import Sex
+from txmatching.web.api.namespaces import enums_api
+
+CountryCodeJson = enums_api.schema_model('CountryCode', {
+    'enum': [country.value for country in Country],
+    'type': 'string'
+})
+
+BloodGroupEnumJson = enums_api.schema_model('BloodGroupEnum', {
+    'enum': [blood_group.value for blood_group in BloodGroup],
+    'type': 'string'
+})
+
+SexEnumJson = enums_api.schema_model('SexEnum', {
+    'enum': [sex.value for sex in Sex],
+    'type': 'string',
+    'description': 'Sex of the patient.'
+})
+
+DonorTypeEnumJson = enums_api.schema_model('DonorType', {
+    'enum': [donor_type.value for donor_type in DonorType],
+    'type': 'string',
+    'description': 'Type of the donor.'
+})

txmatching/data_transfer_objects/matchings/matching_swagger.py

@@ -2,7 +2,6 @@
 
 from txmatching.data_transfer_objects.hla.hla_swagger import (HLAAntibody,
                                                               HLAType)
-from txmatching.utils.country_enum import Country
 from txmatching.utils.enums import (HLA_GROUPS_NAMES_WITH_OTHER,
                                     AntibodyMatchTypes, HLAGroup, MatchTypes)
 from txmatching.web.api.namespaces import matching_api
@@ -84,11 +83,6 @@
         cls_or_instance=fields.Nested(DetailedScoreForGroupJson))
 })
 
-CountryCodeJson = matching_api.schema_model('CountryCode', {
-    'enum': [country.value for country in Country],
-    'type': 'string'
-})
-
 CountryInRoundJson = matching_api.model('Country', {
     'country_code': fields.String(required=True),
     'donor_count': fields.Integer(required=True),

txmatching/data_transfer_objects/patients/patient_swagger.py

@@ -1,22 +1,23 @@
 from flask_restx import fields
 
+from txmatching.data_transfer_objects.enums_swagger import (BloodGroupEnumJson,
+                                                            CountryCodeJson,
+                                                            DonorTypeEnumJson,
+                                                            SexEnumJson)
 from txmatching.data_transfer_objects.hla.hla_swagger import (
     EXAMPLE_HLA_TYPING, HLAAntibodies, HLATyping)
 from txmatching.data_transfer_objects.matchings.matching_swagger import (
-    DESCRIPTION_DETAILED_SCORE, EXAMPLE_DETAILED_SCORE, CountryCodeJson,
+    DESCRIPTION_DETAILED_SCORE, EXAMPLE_DETAILED_SCORE,
     DetailedScoreForGroupJson)
 from txmatching.data_transfer_objects.txm_event.txm_event_swagger import (
     DonorJsonIn, RecipientJsonIn)
-from txmatching.patients.patient import DonorType
-from txmatching.utils.blood_groups import BloodGroup
-from txmatching.utils.enums import Sex
 from txmatching.web.api.namespaces import patient_api
 
 PatientParametersJson = patient_api.model('PatientParameters', {
-    'blood_group': fields.String(required=False, enum=[blood_group.value for blood_group in BloodGroup]),
+    'blood_group': fields.Nested(BloodGroupEnumJson, required=True),
     'hla_typing': fields.Nested(required=False, model=HLATyping),
-    'country_code': fields.Nested(CountryCodeJson, required=False),
-    'sex': fields.String(required=False, enum=[sex.value for sex in Sex]),
+    'country_code': fields.Nested(CountryCodeJson, required=True),
+    'sex': fields.Nested(SexEnumJson, required=False),
     'height': fields.Integer(required=False),
     'weight': fields.Float(required=False),
     'year_of_birth': fields.Integer(required=False),
@@ -33,7 +34,7 @@
     'db_id': fields.Integer(required=True, description='Database id of the patient'),
     'medical_id': fields.String(required=True, description='Medical id of the patient'),
     'parameters': fields.Nested(required=True, model=PatientParametersJson),
-    'donor_type': fields.String(required=True, enum=[donor_type.value for donor_type in DonorType]),
+    'donor_type': fields.Nested(DonorTypeEnumJson, required=True),
     'related_recipient_db_id': fields.Integer(required=False, description='Database id of the related recipient'),
     'score_with_related_recipient': fields.Float(required=False, description='Score calculated with related recipient'),
     'compatible_blood_with_related_recipient': fields.Boolean(
@@ -49,8 +50,7 @@
 
 RecipientJson = patient_api.model('Recipient', {
     'db_id': fields.Integer(required=True, description='Database id of the patient'),
-    'acceptable_blood_groups': fields.List(required=False, cls_or_instance=fields.String(
-        enum=[blood_group.value for blood_group in BloodGroup])),
+    'acceptable_blood_groups': fields.List(required=False, cls_or_instance=fields.Nested(BloodGroupEnumJson)),
     'medical_id': fields.String(required=True, description='Medical id of the patient'),
     'parameters': fields.Nested(required=True, model=PatientParametersJson),
     'hla_antibodies': fields.Nested(required=True, model=HLAAntibodies),
@@ -83,16 +83,28 @@
     'hla_antibodies_list': fields.List(required=True, cls_or_instance=fields.Nested(HLAAntibodyToUpdateJson)),
 })
 
-RecipientToUpdateJson = patient_api.model('RecipientModelToUpdate', {
+PatientToUpdateJson = patient_api.model('PatientModelToUpdate', {
     'db_id': fields.Integer(required=True, description='Database id of the patient', example=1),
-    'acceptable_blood_groups': fields.List(required=False, cls_or_instance=fields.String(
-        enum=[blood_group.value for blood_group in BloodGroup]),
-                                           description='Provide full list of all the acceptable blood groups of the '
-                                                       'patient, not just the change set'),
+    'blood_group': fields.Nested(BloodGroupEnumJson, required=False),
     'hla_typing': fields.Nested(HLATypingToUpdateJson, required=False,
                                 description='Provide full list of all the HLA types of the patient, not just '
                                             'the change set',
                                 example=EXAMPLE_HLA_TYPING),
+    'sex': fields.Nested(SexEnumJson, required=False),
+    'height': fields.Integer(required=False, example=180),
+    'weight': fields.Float(required=False, example=90),
+    'year_of_birth': fields.Integer(required=False, example=1990),
+})
+
+DonorToUpdateJson = patient_api.inherit('DonorModelToUpdate', PatientToUpdateJson, {
+    'active': fields.Boolean(required=False, description='Information, whether or not given donor shall be considered'
+                                                         ' in exchange.')
+})
+
+RecipientToUpdateJson = patient_api.inherit('RecipientModelToUpdate', PatientToUpdateJson, {
+    'acceptable_blood_groups': fields.List(required=False, cls_or_instance=fields.Nested(BloodGroupEnumJson),
+                                           description='Provide full list of all the acceptable blood groups of the '
+                                                       'patient, not just the change set'),
     'hla_antibodies': fields.Nested(HLAAntibodiesToUpdateJson, required=False,
                                     description='Provide full list of all the HLA antibodies of the patient, not just '
                                                 'the change set',
@@ -106,26 +118,23 @@
                                             description='Provide the whole recipients requirements object, it will be'
                                                         ' overwritten',
                                             example={'require_better_match_in_compatibility_index': True}),
+    'waiting_since': fields.Date(required=False,
+                                 example='2015-01-17',
+                                 description='Date since when the patient has been on waiting list. '
+                                             'Use format YYYY-MM-DD.'),
+    'previous_transplants': fields.Integer(required=False,
+                                           example=0,
+                                           description='Number of previous kidney transplants.'),
     'cutoff': fields.Integer(required=False)
 })
 
-DonorToUpdateJson = patient_api.model('DonorModelToUpdate', {
-    'db_id': fields.Integer(required=True, description='Database id of the patient', example=1),
-    'hla_typing': fields.Nested(HLATypingToUpdateJson, required=False,
-                                description='Provide full list of all the HLA types of the patient, not just '
-                                            'the change set',
-                                example=EXAMPLE_HLA_TYPING),
-    'active': fields.Boolean(required=False, description='Information, whether or not given donor shall be considered'
-                                                         ' in exchange.')
-})
-
 HLAAntibodyPairInJson = patient_api.model('HLAAntibodyPairIn', {
     'name': fields.String(required=True, example='A32', description='HLA antibody name.'),
     'mfi': fields.Integer(required=True, example=2350, description='Mean fluorescence intensity. Use exact value.'),
 })
 
 DonorModelPairInJson = patient_api.model('DonorModelPairIn', {
-    'country_code': fields.Nested(CountryCodeJson, required=False),
+    'country_code': fields.Nested(CountryCodeJson, required=True),
     'donor': fields.Nested(required=True, model=DonorJsonIn),
     'recipient': fields.Nested(required=False, model=RecipientJsonIn)
 })

txmatching/data_transfer_objects/patients/update_dtos/patient_update_dto.py

@@ -6,14 +6,24 @@
 from txmatching.data_transfer_objects.patients.update_dtos.hla_code_update_dtos import \
     HLATypingUpdateDTO
 from txmatching.patients.hla_model import HLAType
+from txmatching.patients.patient_parameters import Centimeters, Kilograms
+from txmatching.utils.blood_groups import BloodGroup
+from txmatching.utils.enums import Sex
 from txmatching.utils.hla_system.hla_transformations import \
     preprocess_hla_code_in
 
 
 @dataclass
 class PatientUpdateDTO:
+    # pylint: disable=too-many-instance-attributes
+    # It is reasonable to have many attributes here
     db_id: int
+    blood_group: Optional[BloodGroup] = None
     hla_typing: Optional[HLATypingUpdateDTO] = None
+    sex: Optional[Sex] = None
+    height: Optional[Centimeters] = None
+    weight: Optional[Kilograms] = None
+    year_of_birth: Optional[int] = None
 
     def __post_init__(self):
         """

txmatching/data_transfer_objects/patients/update_dtos/recipient_update_dto.py

@@ -17,6 +17,8 @@ class RecipientUpdateDTO(PatientUpdateDTO):
     hla_antibodies: Optional[HLAAntibodiesDTO] = None
     recipient_requirements: Optional[RecipientRequirements] = None
     cutoff: Optional[int] = None
+    waiting_since: Optional[str] = None
+    previous_transplants: Optional[int] = None
 
     def __post_init__(self):
         super().__post_init__()