fix: change blaze service constructor to use specific instances inste…

…ad of factory

main.py

@@ -2,6 +2,9 @@
 import logging
 import sys
 from service.blaze_service import BlazeService
+from service.condition_service import ConditionService
+from service.patient_service import PatientService
+from service.sample_service import SampleService
 from util.config import BLAZE_URL
 from util.custom_logger import setup_logger
 from util.http_util import is_endpoint_available
@@ -13,7 +16,14 @@
     logger.info("Starting FHIR_Module...")
     if is_endpoint_available(endpoint_url=BLAZE_URL, wait_time=10, max_attempts=5):
         repository_factory = get_repository_factory()
-        blaze_service = BlazeService(repository_factory=repository_factory, blaze_url=BLAZE_URL)
+        patient_service = PatientService(repository_factory.create_sample_donor_repository())
+        condition_service = ConditionService(repository_factory.create_condition_repository())
+        sample_service = SampleService(repository_factory.create_sample_repository())
+        sample_collection_repository = repository_factory.create_sample_collection_repository()
+        blaze_service = BlazeService(patient_service=patient_service, condition_service=condition_service,
+                                     sample_service=sample_service, blaze_url=BLAZE_URL,
+                                     sample_collection_repository=sample_collection_repository)
+        blaze_service.sync_samples()
         blaze_service.sync()
     else:
         logger.error("Exiting FHIR_Module.")

service/blaze_service.py

@@ -9,7 +9,6 @@
 from exception.patient_not_found import PatientNotFoundError
 from model.sample import Sample
 from model.sample_donor import SampleDonor
-from persistence.factories.repository_factory import RepositoryFactory
 from persistence.sample_collection_repository import SampleCollectionRepository
 from service.condition_service import ConditionService
 from service.patient_service import PatientService
@@ -24,26 +23,22 @@
 class BlazeService:
     """Service class for business operations/interactions with a Blaze FHIR server."""
 
-    def __init__(self, repository_factory: RepositoryFactory,
-                 # patient_service: PatientService, condition_service: ConditionService,
-                 # sample_service: SampleService
+    def __init__(self,
+                 patient_service: PatientService, condition_service: ConditionService,
+                 sample_service: SampleService,
                  blaze_url: str,
-                 # sample_collection_repository: SampleCollectionRepository
+                 sample_collection_repository: SampleCollectionRepository
                  ):
         """
         Class for interacting with a Blaze Store FHIR server
         :param blaze_url: Base url of the FHIR server
         Must be without a trailing /.
         """
-        self._patient_service = PatientService(repository_factory.create_sample_donor_repository())
-        self._condition_service = ConditionService(repository_factory.create_condition_repository())
-        self._sample_service = SampleService(repository_factory.create_sample_repository())
-        self._sample_collection_repository = repository_factory.create_sample_collection_repository()
-        # self._patient_service = patient_service
-        # self._condition_service = condition_service
-        # self._sample_service = sample_service
+        self._patient_service = patient_service
+        self._condition_service = condition_service
+        self._sample_service = sample_service
         self._blaze_url = blaze_url
-        # self._sample_collection_repository = sample_collection_repository
+        self._sample_collection_repository = sample_collection_repository
         self._credentials = BLAZE_AUTH
 
     def sync(self):

test/integration/test_blaze.py

@@ -63,26 +63,15 @@ def get_all(self) -> Generator[SampleCollection, None, None]:
         yield from self.sample_collections
 
 
-class RepositoryFactoryStub(RepositoryFactory):
-
-    def create_condition_repository(self) -> ConditionRepository:
-        return ConditionRepoStub()
-
-    def create_sample_collection_repository(self) -> SampleCollectionRepository:
-        return SampleCollectionRepoStub()
-
-    def create_sample_repository(self) -> SampleRepository:
-        return SampleRepoStub()
-
-    def create_sample_donor_repository(self) -> SampleDonorRepository:
-        return SampleDonorRepoStub()
-
-
 class TestBlazeStore(unittest.TestCase):
 
     @pytest.fixture(autouse=True)
     def run_around_tests(self):
-        self.blaze_service = BlazeService(RepositoryFactoryStub(), blaze_url='http://localhost:8080/fhir')
+        self.blaze_service = BlazeService(patient_service=PatientService(SampleDonorRepoStub()),
+                                          condition_service=ConditionService(ConditionRepoStub()),
+                                          sample_service=SampleService(SampleRepoStub()),
+                                          blaze_url='http://localhost:8080/fhir',
+                                          sample_collection_repository=SampleCollectionRepoStub())
         yield  # run test
         try:
             for donor in SampleDonorRepoStub().get_all():
@@ -112,7 +101,11 @@ def test_delete_nonexistent_resource_404(self):
         self.assertEqual(404, self.blaze_service.delete_fhir_resource("Patient", "newId"))
 
     def test_upload_all_patients_when_blaze_unreachable(self):
-        self.blaze_service = BlazeService(RepositoryFactoryStub(), blaze_url='http://localhost:44/wrong')
+        self.blaze_service = BlazeService(PatientService(SampleDonorRepoStub()),
+                                          blaze_url='http://localhost:44/wrong',
+                                          condition_service=ConditionService(ConditionRepoStub()),
+                                          sample_service=SampleService(SampleRepoStub()),
+                                          sample_collection_repository=SampleCollectionRepoStub())
         self.assertEqual(404, self.blaze_service.initial_upload_of_all_patients())
 
     def test_is_present_in_blaze(self):
@@ -127,7 +120,11 @@ def test_sync_one_new_patient(self):
         self.blaze_service.initial_upload_of_all_patients()
         num_of_patients_before_sync = self.blaze_service.get_number_of_resources("Patient")
         donor_repo.add(SampleDonor("uniqueNewPatient5"))
-        self.blaze_service = BlazeService(RepositoryFactoryStub(), blaze_url='http://localhost:8080/fhir')
+        self.blaze_service = BlazeService(PatientService(donor_repo),
+                                          blaze_url='http://localhost:8080/fhir',
+                                          condition_service=ConditionService(ConditionRepoStub()),
+                                          sample_service=SampleService(SampleRepoStub()),
+                                          sample_collection_repository=SampleCollectionRepoStub())
         self.blaze_service.sync_patients()
         self.assertEqual(num_of_patients_before_sync + 1, self.blaze_service.get_number_of_resources("Patient"))
 
@@ -152,7 +149,11 @@ def test_sync_one_new_condition(self):
         self.blaze_service.sync_conditions()
         self.assertFalse(self.blaze_service.patient_has_condition("fakeId", "C50.6"))
         condition_repo.add(Condition(patient_id="fakeId", icd_10_code="C50.6"))
-        self.blaze_service = BlazeService(RepositoryFactoryStub(), blaze_url='http://localhost:8080/fhir')
+        self.blaze_service = BlazeService(PatientService(SampleDonorRepoStub()),
+                                          blaze_url='http://localhost:8080/fhir',
+                                          condition_service=ConditionService(condition_repo),
+                                          sample_service=SampleService(SampleRepoStub()),
+                                          sample_collection_repository=SampleCollectionRepoStub())
         self.blaze_service.sync_conditions()
         self.assertTrue(self.blaze_service.patient_has_condition("fakeId", "C50.6"))