fix(deps): update dependency fhir-resources to v8.1.0

mypy.ini

@@ -44,3 +44,6 @@ warn_unreachable = False
 
 [mypy-*.factories]
 disallow_untyped_calls = False
+
+[mypy-*.fhir.tests.*]
+disable_error_code = index,union-attr,arg-type

opal/services/fhir/fhir.py

@@ -6,7 +6,7 @@
 
 import datetime as dt
 from datetime import datetime
-from typing import Any
+from typing import Any, cast
 
 import structlog
 from authlib.integrations.requests_client import OAuth2Session
@@ -147,7 +147,9 @@ def patient_conditions(self, uuid: str) -> list[Condition]:
                 _clean_coding(coding)
 
         conditions_bundle = Bundle.model_validate(data)
-        return [condition.resource for condition in conditions_bundle.entry or []]
+        return [
+            cast('Condition', condition.resource) for condition in conditions_bundle.entry or [] if condition.resource
+        ]
 
     def patient_medication_requests(self, uuid: str) -> list[MedicationRequest]:
         """
@@ -168,7 +170,11 @@ def patient_medication_requests(self, uuid: str) -> list[MedicationRequest]:
 
         medications_bundle = Bundle.model_validate(data)
 
-        return [medication.resource for medication in medications_bundle.entry or []]
+        return [
+            cast('MedicationRequest', medication.resource)
+            for medication in medications_bundle.entry or []
+            if medication.resource
+        ]
 
     def patient_allergies(self, uuid: str) -> list[AllergyIntolerance]:
         """
@@ -195,7 +201,9 @@ def patient_allergies(self, uuid: str) -> list[AllergyIntolerance]:
                 _clean_coding(coding)
 
         allergies_bundle = Bundle.model_validate(data)
-        return [allergy.resource for allergy in allergies_bundle.entry or []]
+        return [
+            cast('AllergyIntolerance', allergy.resource) for allergy in allergies_bundle.entry or [] if allergy.resource
+        ]
 
     def patient_immunizations(self, uuid: str) -> list[Immunization]:
         """
@@ -225,7 +233,11 @@ def patient_immunizations(self, uuid: str) -> list[Immunization]:
 
         immunizations_bundle = Bundle.model_validate(data)
 
-        return [immunization.resource for immunization in immunizations_bundle.entry or []]
+        return [
+            cast('Immunization', immunization.resource)
+            for immunization in immunizations_bundle.entry or []
+            if immunization.resource
+        ]
 
     def patient_observations(self, uuid: str) -> list[Observation]:
         """
@@ -245,4 +257,8 @@ def patient_observations(self, uuid: str) -> list[Observation]:
         data = response.json()
 
         observations_bundle = Bundle.model_validate(data)
-        return [observation.resource for observation in observations_bundle.entry or []]
+        return [
+            cast('Observation', observation.resource)
+            for observation in observations_bundle.entry or []
+            if observation.resource
+        ]

opal/services/fhir/ips.py

@@ -58,12 +58,16 @@ def build_patient_summary(  # noqa: PLR0913, PLR0917
     vital_signs = [
         observation
         for observation in observations_with_category
-        if observation.category[0].coding[0].code == 'vital-signs'
+        if observation.category
+        and observation.category[0].coding
+        and observation.category[0].coding[0].code == 'vital-signs'
     ]
     labs = [
         observation
         for observation in observations_with_category
-        if observation.category[0].coding[0].code == 'laboratory'
+        if observation.category
+        and observation.category[0].coding
+        and observation.category[0].coding[0].code == 'laboratory'
     ]
 
     # Translates static strings in the right language for the bundle
@@ -86,102 +90,101 @@ def build_patient_summary(  # noqa: PLR0913, PLR0917
             date=dt.datetime.now(tz=dt.UTC).replace(microsecond=0),
             title=_('International Patient Summary as of {date}').format(date=last_updated),
             subject=Reference(reference=f'urn:uuid:{patient.id}'),
-            section=[
-                CompositionSection(
-                    title=_('Active Problems'),
-                    code=CodeableConcept(
-                        coding=[Coding(system='http://loinc.org', code='11450-4', display='Problem list Reported')]
-                    ),
-                    entry=[
-                        Reference(reference=f'urn:uuid:{condition.id}')
-                        for condition in conditions
-                        if condition.clinicalStatus.coding[0].code == 'active'
-                    ],
+        )
+        composition.section = [
+            CompositionSection(
+                title=_('Active Problems'),
+                code=CodeableConcept(
+                    coding=[Coding(system='http://loinc.org', code='11450-4', display='Problem list Reported')]
                 ),
-                CompositionSection(
-                    title=_('Past Medical History'),
-                    code=CodeableConcept(
-                        coding=[
-                            Coding(system='http://loinc.org', code='11348-0', display='History of Past illness note')
-                        ]
-                    ),
-                    entry=[
-                        Reference(reference=f'urn:uuid:{condition.id}')
-                        for condition in conditions
-                        if condition.clinicalStatus.coding[0].code != 'active'
-                    ],
+                entry=[
+                    Reference(reference=f'urn:uuid:{condition.id}')
+                    for condition in conditions
+                    if condition.clinicalStatus
+                    and condition.clinicalStatus.coding
+                    and condition.clinicalStatus.coding[0].code == 'active'
+                ],
+            ),
+            CompositionSection(
+                title=_('Past Medical History'),
+                code=CodeableConcept(
+                    coding=[Coding(system='http://loinc.org', code='11348-0', display='History of Past illness note')]
                 ),
-                CompositionSection(
-                    title=_('Medication'),
-                    code=CodeableConcept(
-                        coding=[
-                            Coding(
-                                system='http://loinc.org', code='10160-0', display='History of Medication use Narrative'
-                            )
-                        ],
-                    ),
-                    entry=[
-                        Reference(reference=f'urn:uuid:{medication_request.id}')
-                        for medication_request in medication_requests
+                entry=[
+                    Reference(reference=f'urn:uuid:{condition.id}')
+                    for condition in conditions
+                    if condition.clinicalStatus
+                    and condition.clinicalStatus.coding
+                    and condition.clinicalStatus.coding[0].code != 'active'
+                ],
+            ),
+            CompositionSection(
+                title=_('Medication'),
+                code=CodeableConcept(
+                    coding=[
+                        Coding(system='http://loinc.org', code='10160-0', display='History of Medication use Narrative')
                     ],
                 ),
-                CompositionSection(
-                    title=_('Allergies and Intolerances'),
-                    code=CodeableConcept(
-                        coding=[
-                            Coding(
-                                system='http://loinc.org',
-                                code='48765-2',
-                                display='Allergies and adverse reactions Document',
-                            )
-                        ]
-                    ),
-                    entry=[Reference(reference=f'urn:uuid:{allergy.id}') for allergy in allergies],
+                entry=[
+                    Reference(reference=f'urn:uuid:{medication_request.id}')
+                    for medication_request in medication_requests
+                ],
+            ),
+            CompositionSection(
+                title=_('Allergies and Intolerances'),
+                code=CodeableConcept(
+                    coding=[
+                        Coding(
+                            system='http://loinc.org',
+                            code='48765-2',
+                            display='Allergies and adverse reactions Document',
+                        )
+                    ]
                 ),
-                CompositionSection(
-                    title=_('Vital Signs'),
-                    code=CodeableConcept(
-                        coding=[Coding(system='http://loinc.org', code='8716-3', display='Vital signs note')]
-                    ),
-                    entry=[Reference(reference=f'urn:uuid:{vital_sign.id}') for vital_sign in vital_signs],
+                entry=[Reference(reference=f'urn:uuid:{allergy.id}') for allergy in allergies],
+            ),
+            CompositionSection(
+                title=_('Vital Signs'),
+                code=CodeableConcept(
+                    coding=[Coding(system='http://loinc.org', code='8716-3', display='Vital signs note')]
                 ),
-                CompositionSection(
-                    title=_('Laboratory Results'),
-                    code=CodeableConcept(
-                        coding=[
-                            Coding(
-                                system='http://loinc.org',
-                                code='30954-2',
-                                display='Relevant diagnostic tests/laboratory data note',
-                            )
-                        ]
-                    ),
-                    entry=[Reference(reference=f'urn:uuid:{lab.id}') for lab in labs],
+                entry=[Reference(reference=f'urn:uuid:{vital_sign.id}') for vital_sign in vital_signs],
+            ),
+            CompositionSection(
+                title=_('Laboratory Results'),
+                code=CodeableConcept(
+                    coding=[
+                        Coding(
+                            system='http://loinc.org',
+                            code='30954-2',
+                            display='Relevant diagnostic tests/laboratory data note',
+                        )
+                    ]
                 ),
-                CompositionSection(
-                    title=_('Immunizations'),
-                    code=CodeableConcept(
-                        coding=[
-                            Coding(system='http://loinc.org', code='11369-6', display='History of Immunization note')
-                        ]
-                    ),
-                    entry=[Reference(reference=f'urn:uuid:{immunization.id}') for immunization in immunizations],
+                entry=[Reference(reference=f'urn:uuid:{lab.id}') for lab in labs],
+            ),
+            CompositionSection(
+                title=_('Immunizations'),
+                code=CodeableConcept(
+                    coding=[Coding(system='http://loinc.org', code='11369-6', display='History of Immunization note')]
                 ),
-            ],
-        )
+                entry=[Reference(reference=f'urn:uuid:{immunization.id}') for immunization in immunizations],
+            ),
+        ]
 
         ips = Bundle(
             identifier={'system': 'urn:oid:2.16.724.4.8.10.200.10', 'value': f'{uuid.uuid4()}'},
             type='document',
             language=ips_language,
             timestamp=dt.datetime.now(tz=dt.UTC).replace(microsecond=0),
-            entry=[
-                BundleEntry(resource=composition, fullUrl=f'urn:uuid:{composition.id}'),
-                BundleEntry(resource=patient, fullUrl=f'urn:uuid:{patient.id}'),
-                BundleEntry(resource=generator, fullUrl=f'urn:uuid:{generator.id}'),
-            ],
         )
 
+        ips.entry = [
+            BundleEntry(resource=composition, fullUrl=f'urn:uuid:{composition.id}'),
+            BundleEntry(resource=patient, fullUrl=f'urn:uuid:{patient.id}'),
+            BundleEntry(resource=generator, fullUrl=f'urn:uuid:{generator.id}'),
+        ]
+
         ips.entry.extend(
             BundleEntry(resource=condition, fullUrl=f'urn:uuid:{condition.id}') for condition in conditions
         )
@@ -200,7 +203,7 @@ def build_patient_summary(  # noqa: PLR0913, PLR0917
 
         # add narrative for empty entries
         for section in composition.section:
-            if not section.entry:
+            if not section.entry and section.title:
                 no_information = _("There is no information available about the subject's {category}.").format(
                     category=section.title.lower()
                 )

opal/services/fhir/tests/test_ips.py

@@ -64,7 +64,7 @@ def _prepare_build_patient_summary() -> tuple[
         immunizations,
     )
 
-    return (summary, patient, conditions, medication_requests, allergies, observations, immunizations)
+    return (summary, patient, conditions, medication_requests, allergies, observations, immunizations)  # type: ignore[return-value]
 
 
 def test_build_patient_summary() -> None:
@@ -140,7 +140,7 @@ def test_build_patient_summary_composition() -> None:
         # The section's resources are referenced
         if resources:
             assert len(section.entry) == len(resources)
-            for entry, resource in zip(section.entry, resources, strict=True):
+            for entry, resource in zip(section.entry, resources, strict=True):  # type:ignore[call-overload]
                 assert entry.reference == f'urn:uuid:{resource.id}', (
                     f'Section {section.title} has an incorrect resource reference'
                 )
@@ -206,11 +206,11 @@ def test_build_patient_summary_resources_included() -> None:
     resource_ids = {entry.resource.id for entry in summary.entry[3:]}
 
     expected_ids: set[str] = set()
-    expected_ids.update(condition.id for condition in conditions)
-    expected_ids.update(medication_request.id for medication_request in medication_requests)
-    expected_ids.update(allergy.id for allergy in allergies)
-    expected_ids.update(observation.id for observation in observations if observation.category)
-    expected_ids.update(immunization.id for immunization in immunizations)
+    expected_ids.update(condition.id for condition in conditions)  # type: ignore[misc]
+    expected_ids.update(medication_request.id for medication_request in medication_requests)  # type: ignore[misc]
+    expected_ids.update(allergy.id for allergy in allergies)  # type: ignore[misc]
+    expected_ids.update(observation.id for observation in observations if observation.category)  # type: ignore[misc]
+    expected_ids.update(immunization.id for immunization in immunizations)  # type: ignore[misc]
 
     assert resource_ids == expected_ids
 

opal/services/fhir/utils.py

@@ -6,7 +6,6 @@
 
 import logging
 import secrets
-import uuid
 
 import structlog
 from authlib.oauth2 import OAuth2Error
@@ -48,7 +47,7 @@ def jwe_sh_link_encrypt(data: str) -> tuple[str, bytes]:
 
 def retrieve_patient_summary(
     oauth_url: str, fhir_url: str, client_id: str, private_key: str, identifier: str
-) -> tuple[str, uuid.UUID]:
+) -> tuple[str, str]:
     """
     Retrieve patient data and build a patient summary in IPS format for a patient identified by their identifier.
 
@@ -83,6 +82,10 @@ def retrieve_patient_summary(
 
         patient = fhir.find_patient(identifier)
         patient_uuid = patient.id
+
+        if not patient_uuid:
+            raise FHIRDataRetrievalError(f'Patient with identifier {identifier} has no UUID')
+
         conditions = fhir.patient_conditions(patient_uuid)
         medication_requests = fhir.patient_medication_requests(patient_uuid)
         allergies = fhir.patient_allergies(patient_uuid)
@@ -113,4 +116,7 @@ def retrieve_patient_summary(
 
         LOGGER.debug('Successfully built IPS bundle for patient with UUID %s', patient_uuid)
 
-        return ips_bundle.model_dump_json(indent=2), ips_bundle.identifier.value
+        # we know that there is an identifier because it is set in the build_patient_summary function
+        ips_uuid: str = ips_bundle.identifier.value  # type: ignore[assignment,union-attr]
+
+        return ips_bundle.model_dump_json(indent=2), ips_uuid

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "django-tables2==2.8.0",
     "djangorestframework==3.16.1",
     "drf-spectacular==0.29.0",
-    "fhir-resources==8.0.0",
+    "fhir-resources==8.1.0",
     "fpdf2==2.8.5",
     "hl7apy==1.3.5",
     # required for image export in plotly
@@ -88,3 +88,6 @@ docs = [
     "mkdocs-material==9.7.1",
     "mkdocstrings[python-legacy]==0.30.1",
 ]
+
+[tool.uv.sources]
+fhir-resources = { git = "https://github.com/nazrulworld/fhir.resources.git", rev = "9a2eec1774913dbd89816e9a1cfcda22cdd4388e" }