Merge branch 'main' into sachin/extra-feedback-work

Author: sachin-panayil

.snyk

@@ -5,4 +5,5 @@ ignore:
   SNYK-PYTHON-PYGMENTS-15746419:
     - '*' :
         reason: 'No remediation available'
-        expires: '2026-04-04T17:33:45.004Z'
+        expires: '2026-04-04T17:33:45.004Z'
+  

Makefile

@@ -181,6 +181,11 @@ down:
 	@echo "Shutting down all docker compose services..."
 	@docker compose down
 
+.PHONY: test-down
+test-down:
+	@echo "Shutting down all test docker compose services..."
+	@docker compose -f compose.test.yml down
+
 .PHONY: test-setup
 test-setup:
 	@echo "Setting up test database..."
@@ -206,7 +211,7 @@ test: test-setup
 	@$(MAKE) test-frontend
 
 .PHONY: playwright-local
-playwright-local: test-system-setup build-frontend-test-assets
+playwright-local: test-down test-system-setup build-frontend-test-assets
 	@cd playwright; \
 		npx playwright test --project=local
 
@@ -264,7 +269,7 @@ test-system-setup: test-setup
 
 .PHONY: test-server
 test-server: test-system-setup build-frontend-test-assets
-	bin/npr --test --publish 8008:8008 python manage.py runserver 0.0.0.0:8008
+	docker compose -f compose.test.yml up django-web
 
 ###
 # whole project concerns

backend/README.md

@@ -17,7 +17,7 @@ Django backend that provides a FHIR API for accessing data from the npd database
 - [colima](https://github.com/abiosoft/colima) (if using macOS)
 - a postgres database with the npd schema
 
-### Local dev
+### Local Dev
 
 1. Ensure that either colima (if using macOS) or the docker service is running
 2. Create a `.env` file in this directory, following the template of the `.env_template` file

backend/npdfhir/management/commands/seedsystem.py

@@ -72,7 +72,9 @@ def generate_sample_practitioner_roles(self):
                 individual=DefaultIndividual(id="f1579a55-b5e1-4717-988d-6e014acbe348"),
                 npi=DefaultNPI(npi=1000000011),
             ),
-            organization=DefaultOrganization(npi=DefaultNPI(npi=1000000012)),
+            organization=DefaultOrganization(
+                id="893149b6-34de-4030-a2fa-89cc02baccbe", npi=DefaultNPI(npi=1000000012)
+            ),
             location=DefaultLocation(has_endpoint=False),
         )
 
@@ -96,16 +98,18 @@ def generate_sample_practitioner_roles(self):
         DefaultPractitionerRole(
             practitioner=DefaultPractitioner(
                 individual=DefaultIndividual(
-                    names=[DefaultName(first_name="Test", last_name="Practitioner 1")]
-                )
+                    id="9b309f46-115e-4eed-bc6e-0e414d5f1215",
+                    names=[DefaultName(first_name="Test", last_name="Practitioner 1")],
+                ),
             ),
             organization=DefaultOrganization(id="0c1f8f84-0502-4444-b636-8fee4ab76e32"),
         )
         DefaultPractitionerRole(
             practitioner=DefaultPractitioner(
                 individual=DefaultIndividual(
-                    names=[DefaultName(first_name="Test", last_name="Practitioner 2")]
-                )
+                    id="91cc98f8-8f65-4f6c-8ef2-9dbe829ed5c2",
+                    names=[DefaultName(first_name="Test", last_name="Practitioner 2")],
+                ),
             ),
             organization=DefaultOrganization(id="0c1f8f84-0502-4444-b636-8fee4ab76e32"),
         )

backend/npdfhir/mappings.py

@@ -31,3 +31,21 @@ def to_choices(self):
 genderMapping = Mapping({"F": "Female", "M": "Male", "O": "Other"})
 
 addressUseMapping = Mapping({1: "home", 2: "work", 3: "temp", 4: "old", 5: "billing"})
+
+
+def other_id_type_to_fhir(other_id_type):
+    fhirIdentifierTypes = {
+        2: {
+            "code": "UPIN",
+            "display": "Medicare/CMS (formerly HCFA)'s Universal Physician Identification numbers",
+        },
+        4: {"code": "MCR", "display": "Practitioner Medicare Number"},
+        5: {"code": "MCD", "display": "Practitioner Medicaid Number"},
+        6: {"code": "MCR", "display": "Practitioner Medicare Number"},
+        7: {"code": "MCR", "display": "Practitioner Medicare Number"},
+        8: {"code": "PPIN", "display": "Medicare/CMS Performing Provider Identification Number"},
+    }
+    if other_id_type in fhirIdentifierTypes.keys():
+        return fhirIdentifierTypes[other_id_type]
+    else:
+        return {"code": "OTHER", "display": "Other"}

backend/npdfhir/models.py

@@ -620,7 +620,7 @@ class OrganizationToOtherId(models.Model):
     npi = models.ForeignKey(ClinicalOrganization, models.DO_NOTHING, db_column="npi")
     other_id = models.CharField(max_length=100)
     other_id_type = models.ForeignKey("OtherIdType", models.DO_NOTHING)
-    state_code = models.CharField(max_length=2)
+    state_code = models.ForeignKey(FipsState, models.DO_NOTHING, db_column="state_code")
     issuer = models.CharField(max_length=200)
 
     class Meta:

backend/npdfhir/serializers.py

@@ -39,7 +39,8 @@
     OrganizationToName,
     ProviderToOrganization,
 )
-from .utils import genReference, get_schema_data, other_id_type_to_fhir
+from .utils import genReference, get_schema_data
+from .mappings import other_id_type_to_fhir
 
 if "runserver" or "test" in sys.argv:
     from .cache import (
@@ -167,9 +168,12 @@ class Meta:
         ]
 
     def to_representation(self, instance):
+        assigner_parts = []
+        if instance.issuer != "" and instance.issuer != " ":
+            assigner_parts.append(instance.issuer)
+        assigner_parts.append(instance.state_code.abbreviation)
         fhir_type = other_id_type_to_fhir(instance.other_id_type.id)
         license_identifier = Identifier(
-            # system="", TODO: Figure out how to associate a system with each identifier
             value=instance.other_id,
             type=CodeableConcept(
                 coding=[
@@ -180,7 +184,7 @@ def to_representation(self, instance):
                     )
                 ]
             ),
-            # use="" TODO: Add use for other identifier
+            assigner=Reference(display=" - ".join(assigner_parts)),
             # period=Period(start=instance.issue_date, end=instance.expiry_date),
         )
         return license_identifier.model_dump()
@@ -235,6 +239,24 @@ class Meta:
         model = Npi
         fields = "__all__"
 
+    def to_representation(self, instance):
+        npi = Identifier(
+            system="http://terminology.hl7.org/NamingSystem/npi",
+            value=str(instance.npi),
+            type=CodeableConcept(
+                coding=[
+                    Coding(
+                        system="http://terminology.hl7.org/CodeSystem/v2-0203",
+                        code="NPI",
+                        display="National Provider Identifier",
+                    )
+                ]
+            ),
+            use="official",
+            period=Period(start=instance.enumeration_date, end=instance.deactivation_date),
+        )
+        return npi
+
 
 class IndividualSerializer(serializers.Serializer):
     name = NameSerializer(source="individualtoname_set", read_only=True, many=True)
@@ -295,17 +317,30 @@ def to_representation(self, instance):
             use="official",
             system=instance.system,
             value=instance.other_id,
-            # TODO: Replace with Organization reference
+            # TODO: Replace with Organization reference?
             assigner=Reference(display=str(instance.issuer_id)),
         )
 
         return endpoint_identifier.model_dump()
 
 
+class ClinicalOrganizationSerializer(serializers.Serializer):
+    other_identifier = OtherIdentifierSerializer(
+        source="organizationtootherid_set", many=True, read_only=True
+    )
+    npi = NPISerializer()
+
+    class Meta:
+        fields = ["other_identifier", "npi"]
+
+
 class OrganizationSerializer(serializers.Serializer):
     name = OrganizationNameSerializer(source="organizationtoname_set", many=True, read_only=True)
     authorized_official = IndividualSerializer(read_only=True)
     address = AddressSerializer(source="organizationtoaddress_set", many=True, read_only=True)
+    clinical_organization = ClinicalOrganizationSerializer(
+        source="clinicalorganization", read_only=True
+    )
 
     class Meta:
         model = Organization
@@ -315,7 +350,6 @@ def to_representation(self, instance):
         request = self.context.get("request")
         instance = instance.organization
         representation = super().to_representation(instance)
-
         organization = FHIROrganization()
         organization.id = str(instance.id)
         organization.meta = Meta(
@@ -325,82 +359,39 @@ def to_representation(self, instance):
         identifiers = []
 
         taxonomies = []
-        # if instance.ein:
-        #    ein_identifier = Identifier(
-        #        system="https://terminology.hl7.org/NamingSystem-USEIN.html",
-        #        value=str(instance.ein.ein_id),
-        #        type=CodeableConcept(
-        #            coding=[Coding(
-        #                system="http://terminology.hl7.org/CodeSystem/v2-0203",
-        #                code="TAX",
-        #                display="Tax ID number"
-        #            )]
-        #        )
-        #    )
-        #    identifiers.append(ein_identifier)
 
         if hasattr(instance, "clinicalorganization"):
-            clinical_org = instance.clinicalorganization
-            if clinical_org and clinical_org.npi:
-                npi_identifier = Identifier(
-                    system="http://terminology.hl7.org/NamingSystem/npi",
-                    value=str(clinical_org.npi.npi),
-                    type=CodeableConcept(
-                        coding=[
-                            Coding(
-                                system="http://terminology.hl7.org/CodeSystem/v2-0203",
-                                code="NPI",
-                                display="National provider identifier",
-                            )
-                        ]
-                    ),
-                    use="official",
-                    period=Period(
-                        start=clinical_org.npi.enumeration_date,
-                        end=clinical_org.npi.deactivation_date,
-                    ),
-                )
+            clinical_org_instance = instance.clinicalorganization
+            if "clinical_organization" in representation.keys():
+                clinical_org = representation["clinical_organization"]
+                npi_identifier = clinical_org["npi"]
                 identifiers.append(npi_identifier)
+                if "other_identifier" in clinical_org.keys():
+                    identifiers += clinical_org["other_identifier"]
 
-                for other_id in clinical_org.organizationtootherid_set.all():
-                    other_identifier = Identifier(
-                        system=str(other_id.other_id_type_id),
-                        value=other_id.other_id,
-                        type=CodeableConcept(
-                            coding=[
-                                Coding(
-                                    system="http://terminology.hl7.org/CodeSystem/v2-0203",
-                                    code="test",  # do we define this based on the type of id it is?
-                                    display="test",  # same as above ^
-                                )
-                            ]
-                        ),
-                    )
-                    identifiers.append(other_identifier)
-
-                for taxonomy in clinical_org.organizationtotaxonomy_set.all():
-                    code = CodeableConcept(
-                        coding=[
-                            Coding(
-                                system="http://nucc.org/provider-taxonomy",
-                                code=taxonomy.nucc_code_id,
-                                display=nucc_taxonomy_codes[str(taxonomy.nucc_code_id)],
-                            )
-                        ]
-                    )
+            for taxonomy in clinical_org_instance.organizationtotaxonomy_set.all():
+                code = CodeableConcept(
+                    coding=[
+                        Coding(
+                            system="http://nucc.org/provider-taxonomy",
+                            code=taxonomy.nucc_code_id,
+                            display=nucc_taxonomy_codes[str(taxonomy.nucc_code_id)],
+                        )
+                    ]
+                )
 
-                    # Extend the Organization class
-                    # NOTE: fhir.resources really doesn't like when you try to subclass their Pydantic models
+                # Extend the Organization class
+                # NOTE: fhir.resources really doesn't like when you try to subclass their Pydantic models
 
-                    qualification_ext = Extension(
-                        url="https://build.fhir.org/organization-definitions.html#Organization.qualification",
-                        valueCodeableConcept=code,
-                    )
+                qualification_ext = Extension(
+                    url="https://build.fhir.org/organization-definitions.html#Organization.qualification",
+                    valueCodeableConcept=code,
+                )
 
-                    taxonomies.append(qualification_ext)
+                taxonomies.append(qualification_ext)
 
-                if taxonomies:
-                    organization.extension = taxonomies
+            if taxonomies:
+                organization.extension = taxonomies
 
         organization.identifier = identifiers
 
@@ -475,12 +466,6 @@ def to_representation(self, instance):
         )
         organization_affiliation.participatingOrganization.display = str(instance.organization_name)
 
-        # NOTE: Period for OrganizationAffiliation cannot currently be fetched so its blank
-
-        # NOTE: Network here means insurance network, per the FHIR spec. We have not begun to incorporate insurance networks
-        # organization_affiliation.network = [genReference("fhir-organization-detail", instance.id, request)]
-        # organization_affiliation.network[0].display = str(instance.organization_name)
-
         organization_affiliation.code = [
             CodeableConcept(
                 coding=[
@@ -493,10 +478,6 @@ def to_representation(self, instance):
             )
         ]
 
-        # NOTE: not sure how to do specialty yet
-
-        endpoints = []
-
         locations = [
             genReference("fhir-location-detail", loc_id, request)
             for loc_id in instance.location_ids
@@ -539,21 +520,7 @@ def to_representation(self, instance):
         practitioner.meta = Meta(
             profile=["http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"]
         )
-        npi_identifier = Identifier(
-            system="http://terminology.hl7.org/NamingSystem/npi",
-            value=str(instance.npi.npi),
-            type=CodeableConcept(
-                coding=[
-                    Coding(
-                        system="http://terminology.hl7.org/CodeSystem/v2-0203",
-                        code="NPI",
-                        display="National provider identifier",
-                    )
-                ]
-            ),
-            use="official",
-            period=Period(start=instance.npi.enumeration_date, end=instance.npi.deactivation_date),
-        )
+        npi_identifier = representation["npi"]
         if representation["individual"]["telecom"] != []:
             practitioner.telecom = representation["individual"]["telecom"]
         if (
@@ -593,8 +560,8 @@ def to_representation(self, instance):
         else:
             location.status = "inactive"
         location.name = instance.name
-        # if 'phone' in representation.keys():
-        #    location.telecom = representation['phone']
+        if "phone" in representation.keys() and representation["phone"] is not None:
+            location.telecom = [representation["phone"]]
         if "address" in representation.keys():
             location.address = representation["address"]
             if (
@@ -701,13 +668,6 @@ def to_representation(self, instance):
                 code=instance.endpoint_connection_type.id,
                 display=instance.endpoint_connection_type.display,
             )
-        # TODO THIS IS TEMPORARY DUE TO INSUFFICIENT DATA
-        else:
-            connection_type = Coding(
-                system="http://terminology.hl7.org/CodeSystem/endpoint-connection-type",
-                code="hl7-fhir-rest",
-                display="HL7 FHIR",
-            )
 
         ## TODO extend base fhir spec to ndh spec
         # if instance.environment_type:

backend/npdfhir/tests/fixtures/organization.py

@@ -107,7 +107,7 @@ def create_if_not_exists(self):
                         npi=clinical_organization,
                         other_id=id.other_id,
                         other_id_type_id=id.other_id_type,
-                        state_code=state_code.id,
+                        state_code=state_code,
                     )
                 for taxonomy in self.taxonomies:
                     OrganizationToTaxonomy.objects.create(