import unittest import json import fhirspec_pb2 from fhir_spec_extractor import FhirSpecExtractor from google.protobuf import text_format class FhirSpecExtractorTest(unittest.TestCase): BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION = json.loads(""" { "resourceType" : "Bundle", "id" : "resources", "meta" : { "lastUpdated" : "2019-11-01T09:29:23.356+11:00" }, "type" : "collection", "entry" : [ { "fullUrl" : "http://hl7.org/fhir/CompartmentDefinition/relatedPerson" }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Immunization", "resource" : { "resourceType" : "StructureDefinition", "id" : "Immunization", "meta" : { "lastUpdated" : "2019-11-01T09:29:23.356+11:00" }, "fhirVersion" : "4.0.1", "kind" : "resource", "type" : "Immunization", "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/DomainResource", "snapshot" : { "element" : [{ "id" : "Immunization", "path" : "Immunization", "min" : 0, "max" : "*", "base" : { "path" : "Immunization", "min" : 0, "max" : "*" } }, { "id" : "Immunization.id", "path" : "Immunization.id", "min" : 0, "max" : "1", "base" : { "path" : "Resource.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }] }, { "id" : "Immunization.status", "path" : "Immunization.status", "min" : 1, "max" : "1", "base" : { "path" : "Immunization.status", "min" : 1, "max" : "1" }, "type" : [{ "code" : "code" }] }, { "id" : "Immunization.vaccineCode", "path" : "Immunization.vaccineCode", "min" : 1, "max" : "1", "base" : { "path" : "Immunization.vaccineCode", "min" : 1, "max" : "1" }, "type" : [{ "code" : "CodeableConcept" }] }, { "id" : "Immunization.exampleFieldToTestOneToMany", "path" : "Immunization.exampleFieldToTestOneToMany", "min" : 1, "max" : "*", "base" : { "path" : "Immunization.exampleFieldToTestOneToMany", "min" : 1, "max" : "*" }, "type" : [{ "code" : "CodeableConcept" }] }, { "id" : "Immunization.occurrence[x]", "path" : "Immunization.occurrence[x]", "min" : 1, "max" : "1", "base" : { "path" : "Immunization.occurrence[x]", "min" : 1, "max" : "1" }, "type" : [{ "code" : "dateTime" }, { "code" : "string" }] }, { "id" : "Immunization.performer", "path" : "Immunization.performer", "min" : 0, "max" : "*", "base" : { "path" : "Immunization.performer", "min" : 0, "max" : "*" }, "type" : [{ "code" : "BackboneElement" }] }, { "id" : "Immunization.performer.id", "path" : "Immunization.performer.id", "min" : 0, "max" : "1", "base" : { "path" : "Element.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }] }, { "id" : "Immunization.performer.extension", "path" : "Immunization.performer.extension", "min" : 0, "max" : "*", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }] }, { "id" : "Immunization.performer.actor", "path" : "Immunization.performer.actor", "min" : 1, "max" : "1", "base" : { "path" : "Immunization.performer.actor", "min" : 1, "max" : "1" }, "type" : [{ "code" : "Reference" }] }, { "id" : "Immunization.contained", "path" : "Immunization.contained", "min" : 0, "max" : "*", "base" : { "path" : "DomainResource.contained", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Resource" }] } ] } } }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Patient", "resource" : { "resourceType" : "StructureDefinition", "id" : "Patient", "meta" : { "lastUpdated" : "2019-11-01T09:29:23.356+11:00" }, "url" : "http://hl7.org/fhir/StructureDefinition/Patient", "fhirVersion" : "4.0.1", "kind" : "resource", "type" : "Patient", "snapshot" : { "element" : [{ "id" : "Patient.id", "path" : "Patient.id", "min" : 0, "max" : "1", "base" : { "path" : "Resource.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }] }] } } } ] } """) BUNDLE_WITH_OBSERVATION_STRUCTURE_DEFINITION = json.loads(""" { "resourceType" : "Bundle", "id" : "resources", "meta" : { "lastUpdated" : "2024-12-06T22:01:38.605+00:00" }, "type" : "collection", "entry" : [ { "fullUrl" : "http://hl7.org/fhir/CompartmentDefinition/relatedPerson" }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Observation", "resource" : { "resourceType" : "StructureDefinition", "id" : "Observation", "meta" : { "lastUpdated" : "2024-12-06T22:01:38.605+00:00" }, "fhirVersion" : "4.0.1", "kind" : "resource", "type" : "Observation", "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/DomainResource", "snapshot" : { "element" : [{ "id" : "Observation", "path" : "Observation", "min" : 0, "max" : "*", "base" : { "path" : "Observation", "min" : 0, "max" : "*" } }, { "id" : "Observation.id", "path" : "Observation.id", "min" : 0, "max" : "1", "base" : { "path" : "Resource.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "id" }], "code" : "http://hl7.org/fhirpath/System.String" }] }, { "id" : "Observation.status", "path" : "Observation.status", "min" : 1, "max" : "1", "base" : { "path" : "Observation.status", "min" : 1, "max" : "1" }, "type" : [{ "code" : "code" }] }, { "id" : "Observation.code", "path" : "Observation.code", "min" : 1, "max" : "1", "base" : { "path" : "Observation.code", "min" : 1, "max" : "1" }, "type" : [{ "code" : "CodeableConcept" }] }, { "id" : "Observation.value[x]", "path" : "Observation.value[x]", "min" : 0, "max" : "1", "base" : { "path" : "Observation.value[x]", "min" : 1, "max" : "1" }, "type" : [{ "code": "Quantity" }, { "code": "CodeableConcept" }, { "code": "string" }, { "code": "boolean" }, { "code": "integer" }, { "code": "SampledData" }, { "code": "dateTime" }] } ] } } } ] } """) BUNDLE_WITH_TYPE_STRUCTURE_DEFINITIONS = json.loads(""" { "resourceType": "Bundle", "id": "types", "meta": { "lastUpdated": "2019-11-01T09:29:23.356+11:00" }, "type": "collection", "entry": [ { "fullUrl": "http://hl7.org/fhir/StructureDefinition/boolean", "resource": { "resourceType": "StructureDefinition", "id": "boolean", "url": "http://hl7.org/fhir/StructureDefinition/boolean", "name": "boolean", "fhirVersion": "4.0.1", "kind": "primitive-type", "abstract": false, "type": "boolean", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element", "snapshot": { "element": [ { "id": "boolean", "path": "boolean", "min": 0, "max": "*", "base": { "path": "boolean", "min": 0, "max": "*" }, "isModifier": false, "isSummary": false }, { "id": "boolean.id", "path": "boolean.id", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "string" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "isModifier": false, "isSummary": false }, { "id": "boolean.extension", "path": "boolean.extension", "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "isModifier": false, "isSummary": false }, { "id": "boolean.value", "path": "boolean.value", "representation": [ "xmlAttr" ], "short": "Primitive value for boolean", "definition": "The actual value", "min": 0, "max": "1", "base": { "path": "boolean.value", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "boolean" }, { "url": "http://hl7.org/fhir/StructureDefinition/regex", "valueString": "true|false" } ], "code": "http://hl7.org/fhirpath/System.Boolean" } ], "isModifier": false, "isSummary": false } ] } } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/integer", "resource": { "resourceType": "StructureDefinition", "id": "integer", "url": "http://hl7.org/fhir/StructureDefinition/integer", "version": "4.0.1", "name": "integer", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "type": "integer" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/id", "resource": { "resourceType": "StructureDefinition", "id": "id", "url": "http://hl7.org/fhir/StructureDefinition/id", "version": "4.0.1", "name": "id", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "type": "id" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/string", "resource": { "resourceType": "StructureDefinition", "id": "string", "url": "http://hl7.org/fhir/StructureDefinition/string", "version": "4.0.1", "name": "string", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "abstract": false, "type": "string" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/code", "resource": { "resourceType": "StructureDefinition", "id": "code", "url": "http://hl7.org/fhir/StructureDefinition/code", "version": "4.0.1", "name": "code", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "abstract": false, "type": "code", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/string" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/dateTime", "resource": { "resourceType": "StructureDefinition", "id": "dateTime", "url": "http://hl7.org/fhir/StructureDefinition/dateTime", "version": "4.0.1", "name": "dateTime", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "abstract": false, "type": "dateTime", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/uri", "resource": { "resourceType": "StructureDefinition", "id": "uri", "url": "http://hl7.org/fhir/StructureDefinition/uri", "version": "4.0.1", "name": "uri", "status": "active", "fhirVersion": "4.0.1", "kind": "primitive-type", "abstract": false, "type": "uri", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element" } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/CodeableConcept", "resource": { "resourceType": "StructureDefinition", "id": "CodeableConcept", "url": "http://hl7.org/fhir/StructureDefinition/CodeableConcept", "version": "4.0.1", "name": "CodeableConcept", "contact": [ { "telecom": [ { "system": "url", "value": "http://hl7.org/fhir" } ] } ], "fhirVersion": "4.0.1", "kind": "complex-type", "abstract": false, "type": "CodeableConcept", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element", "derivation": "specialization", "snapshot": { "element": [ { "id": "CodeableConcept", "path": "CodeableConcept", "min": 0, "max": "*", "base": { "path": "CodeableConcept", "min": 0, "max": "*" }, "isModifier": false }, { "id": "CodeableConcept.id", "path": "CodeableConcept.id", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "string" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "isModifier": false }, { "id": "CodeableConcept.extension", "path": "CodeableConcept.extension", "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "isModifier": false }, { "id": "CodeableConcept.coding", "path": "CodeableConcept.coding", "min": 0, "max": "*", "base": { "path": "CodeableConcept.coding", "min": 0, "max": "*" }, "type": [ { "code": "Coding" } ], "isModifier": false }, { "id": "CodeableConcept.text", "path": "CodeableConcept.text", "min": 0, "max": "1", "base": { "path": "CodeableConcept.text", "min": 0, "max": "1" }, "type": [ { "code": "string" } ], "isModifier": false, "isSummary": true } ] } } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/Element", "resource": { "resourceType": "StructureDefinition", "id": "Element", "url": "http://hl7.org/fhir/StructureDefinition/Element", "version": "4.0.1", "name": "BElement", "status": "active", "fhirVersion": "4.0.1", "kind": "complex-type", "abstract": true, "type": "Element", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element", "snapshot": { "element": [ { "id": "Element", "path": "Element", "min": 0, "max": "*", "base": { "path": "Element", "min": 0, "max": "*" }, "isModifier": false }, { "id": "Element.id", "path": "Element.id", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "string" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "isModifier": false, "isSummary": false }, { "id": "Element.extension", "path": "Element.extension", "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "isModifier": false, "isSummary": false } ] } } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/Quantity", "resource": { "resourceType": "StructureDefinition", "id": "Quantity", "url": "http://hl7.org/fhir/StructureDefinition/Quantity", "version": "4.0.1", "name": "Quantity", "fhirVersion": "4.0.1", "kind": "complex-type", "type": "Quantity", "snapshot": { "element": [] } } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/SampledData", "resource": { "resourceType": "StructureDefinition", "id": "SampledData", "url": "http://hl7.org/fhir/StructureDefinition/SampledData", "version": "4.0.1", "name": "SampledData", "fhirVersion": "4.0.1", "kind": "complex-type", "type": "SampledData", "snapshot": { "element": [] } } }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Extension", "resource" : { "resourceType" : "StructureDefinition", "id" : "Extension", "url" : "http://hl7.org/fhir/StructureDefinition/Extension", "version" : "4.0.1", "name" : "Extension", "fhirVersion" : "4.0.1", "kind" : "complex-type", "type" : "Extension", "snapshot" : { "element" : [{ "id" : "Extension", "path" : "Extension", "min" : 0, "max" : "*", "base" : { "path" : "Extension", "min" : 0, "max" : "*" } }, { "id" : "Extension.id", "path" : "Extension.id", "min" : 0, "max" : "1", "base" : { "path" : "Element.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }] }, { "id" : "Extension.extension", "path" : "Extension.extension", "min" : 0, "max" : "*", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }] }, { "id" : "Extension.url", "path" : "Extension.url", "min" : 1, "max" : "1", "base" : { "path" : "Extension.url", "min" : 1, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "uri" }], "code" : "http://hl7.org/fhirpath/System.String" }] }, { "id" : "Extension.value[x]", "path" : "Extension.value[x]", "min" : 0, "max" : "1", "base" : { "path" : "Extension.value[x]", "min" : 0, "max" : "1" }, "type" : [{ "code" : "boolean" }, { "code" : "code" }, { "code" : "CodeableConcept" }, { "code" : "Coding" }] }] } } }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Coding", "resource" : { "resourceType" : "StructureDefinition", "id" : "Coding", "url" : "http://hl7.org/fhir/StructureDefinition/Coding", "version" : "4.0.1", "name" : "Coding", "fhirVersion" : "4.0.1", "kind" : "complex-type", "type" : "Coding", "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Element", "snapshot" : { "element" : [ { "id" : "Coding.system", "path" : "Coding.system", "min" : 0, "max" : "1", "base" : { "path" : "Coding.system", "min" : 0, "max" : "1" }, "type" : [{ "code" : "uri" }] }, { "id" : "Coding.code", "path" : "Coding.code", "min" : 0, "max" : "1", "base" : { "path" : "Coding.code", "min" : 0, "max" : "1" }, "type" : [{ "code" : "code" }] } ] } } }, { "fullUrl" : "http://hl7.org/fhir/StructureDefinition/Reference", "resource" : { "resourceType" : "StructureDefinition", "id" : "Reference", "url" : "http://hl7.org/fhir/StructureDefinition/Reference", "version" : "4.0.1", "name" : "Reference", "fhirVersion" : "4.0.1", "kind" : "complex-type", "type" : "Reference", "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Element", "snapshot" : { "element" : [ { "id" : "Reference.reference", "path" : "Reference.reference", "min" : 0, "max" : "1", "base" : { "path" : "Reference.reference", "min" : 0, "max" : "1" }, "type" : [{ "code" : "string" }] } ] } } }, { "fullUrl": "http://hl7.org/fhir/StructureDefinition/OtherType", "resource": { "resourceType": "StructureDefinition", "id": "OtherType", "url": "http://hl7.org/fhir/StructureDefinition/OtherType", "version": "4.0.1", "name": "OtherType", "status": "active", "fhirVersion": "4.0.1", "kind": "complex-type", "abstract": false, "type": "OtherType", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Element", "snapshot": { "element": [ { "id": "CodeableConcept.id", "path": "CodeableConcept.id", "representation": [ "xmlAttr" ], "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "string" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "isModifier": false, "isSummary": false } ] } } } ] } """) IMMUNIZATION_RESOURCE_TYPE_INT = 1 OBSERVATION_RESOURCE_TYPE_INT = 3 PATIENT_RESOURCE_TYPE_INT = 9 def test_fhir_spec_extractor_immunization_resource_produces_expected_resource_config(self): fhir_spec_extractor = FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"Immunization"}) # we expect each top level field to be present, and one ofs that are represented in the spec # as e.g. occurrence[x] should be expanded into the individual fields such as # occurrenceDateTime and occurrenceString. Fields with a cardinality of 0..* or 1..* should # have is_array = true set in their config. expected_required_fields = {"status", "vaccineCode", "exampleFieldToTestOneToMany"} expected_multi_type_config = fhirspec_pb2.MultiTypeFieldConfig( name="occurrence[x]", typed_field_names=["occurrenceDateTime", "occurrenceString"], is_required=True ) expected_field_names_to_config = { "resourceType": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_ID ), "status": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODE ), "vaccineCode": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT ), "exampleFieldToTestOneToMany": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT ), "occurrenceDateTime": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_DATE_TIME ), "occurrenceString": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "performer": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_IMMUNIZATION_PERFORMER ), "contained": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_RESOURCE ), } generated_spec = fhir_spec_extractor.generate_r4_fhir_spec_proto_message( self.BUNDLE_WITH_TYPE_STRUCTURE_DEFINITIONS ) # Check that exactly one Immunization config is present self.assertEqual(len(generated_spec.resource_type_to_config.keys()), 1) immunization_config = ( generated_spec.resource_type_to_config[self.IMMUNIZATION_RESOURCE_TYPE_INT]) # Check that the list of required fields is as expected self.assertEqual(set(immunization_config.required_fields), expected_required_fields) # Check that the list of multi type configs is as expected self.assertEqual(len(immunization_config.multi_type_fields), 1) received_multi_type_config = immunization_config.multi_type_fields[0] self.assertEqual(received_multi_type_config.name, expected_multi_type_config.name) self.assertEqual(received_multi_type_config.typed_field_names, expected_multi_type_config.typed_field_names) self.assertEqual(received_multi_type_config.is_required, expected_multi_type_config.is_required) # Check that the field names to config map is as expected self.assertEqual(set(expected_field_names_to_config.keys()), set(immunization_config.allowed_field_names_to_config.keys())) for expected_field, expected_config in expected_field_names_to_config.items(): self.assertEqual( immunization_config.allowed_field_names_to_config[expected_field], expected_config, "Mismatching config for field " + expected_field ) def test_fhir_spec_extractor_immunization_and_patient_contains_two_entries(self): fhir_spec_extractor = FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"Immunization", "Patient"}) generated_spec = fhir_spec_extractor.generate_r4_fhir_spec_proto_message( self.BUNDLE_WITH_TYPE_STRUCTURE_DEFINITIONS ) self.assertEqual(len(generated_spec.resource_type_to_config), 2) def test_fhir_spec_extractor_unsupported_resource_raises_exception(self): with self.assertRaises(ValueError): FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"UnsupportedResource"}) def test_fhir_spec_extractor_missing_resource_raises_exception(self): with self.assertRaises(ValueError): FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"Observation"}) def test_fhir_spec_extractor_observation_resource_produces_expected_resource_config(self): fhir_spec_extractor = FhirSpecExtractor( self.BUNDLE_WITH_OBSERVATION_STRUCTURE_DEFINITION, {"Observation"}) # we expect each top level field to be present, and one ofs that are represented in the spec # as e.g. value[x] should be expanded into the individual fields such as # valueString and valueInteger. Fields with a cardinality of 0..* or 1..* should # have is_array = true set in their config. expected_required_fields = {"status", "code"} expected_multi_type_config = fhirspec_pb2.MultiTypeFieldConfig( name="value[x]", typed_field_names=[ "valueQuantity", "valueCodeableConcept", "valueString", "valueBoolean", "valueInteger", "valueSampledData", "valueDateTime"], is_required=False ) expected_field_names_to_config = { "resourceType": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_ID ), "status": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODE ), "code": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT ), "valueQuantity": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_QUANTITY ), "valueCodeableConcept": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT ), "valueString": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "valueBoolean": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_BOOLEAN ), "valueInteger": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_INTEGER ), "valueSampledData": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_SAMPLED_DATA ), "valueDateTime": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_DATE_TIME ), } generated_spec = fhir_spec_extractor.generate_r4_fhir_spec_proto_message( self.BUNDLE_WITH_TYPE_STRUCTURE_DEFINITIONS ) # Check that exactly one Observation config is present self.assertEqual(len(generated_spec.resource_type_to_config.keys()), 1) observation_config = ( generated_spec.resource_type_to_config[self.OBSERVATION_RESOURCE_TYPE_INT]) # Check that the list of required fields is as expected self.assertEqual(set(observation_config.required_fields), expected_required_fields) # Check that the list of multi type configs is as expected self.assertEqual(len(observation_config.multi_type_fields), 1) received_multi_type_config = observation_config.multi_type_fields[0] self.assertEqual(received_multi_type_config.name, expected_multi_type_config.name) self.assertEqual(received_multi_type_config.typed_field_names, expected_multi_type_config.typed_field_names) self.assertEqual(received_multi_type_config.is_required, expected_multi_type_config.is_required) # Check that the field names to config map is as expected self.assertEqual(set(expected_field_names_to_config.keys()), set(observation_config.allowed_field_names_to_config.keys())) for expected_field, expected_config in expected_field_names_to_config.items(): self.assertEqual( observation_config.allowed_field_names_to_config[expected_field], expected_config, "Mismatching config for field " + expected_field ) def test_fhir_spec_extractor_immunization_produces_expected_type_configs(self): fhir_spec_extractor = FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"Immunization"}) expected_complex_type_configs = [ fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_RESOURCE, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, ), fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODE, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "extension": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_EXTENSION ), "coding": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODING ), "text": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ) }), ), # Expected because this is added for primitive type extension validation fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_ELEMENT, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "extension": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_EXTENSION ), }), ), # Expected because Coding is a nested type used in CodeableConcept fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODING, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "system": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_URI ), "code": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODE ) }), ), # Expected because Extension is a nested type used in CodeableConcept fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_EXTENSION, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "extension": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_EXTENSION ), "url": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_URI ), "valueBoolean": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_BOOLEAN ), "valueCode": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODE ), "valueCodeableConcept": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODEABLE_CONCEPT ), "valueCoding": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_CODING ), }, multi_type_fields=[fhirspec_pb2.MultiTypeFieldConfig( name="value[x]", typed_field_names=[ "valueBoolean", "valueCode", "valueCodeableConcept", "valueCoding"], is_required=False, )], required_fields=["url"]), ), fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_DATE_TIME, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_ID, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), # Expected because it is used in the Extension definition fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_BOOLEAN, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), # Expected because URI is the type of "Coding.system" fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_URI, kind=fhirspec_pb2.Kind.KIND_PRIMITIVE_TYPE, ), # Expected because this is the definition of the BackboneElement child type, defined in # the Immunization resource "performer" field. fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_IMMUNIZATION_PERFORMER, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "id": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ), "extension": fhirspec_pb2.FhirFieldConfig( is_array=True, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_EXTENSION ), "actor": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_REFERENCE ), }, required_fields=["actor"]), ), # Expected because this is a type required by the IMMUNIZATION_PERFORMER child type. fhirspec_pb2.FhirDataType( fhir_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_REFERENCE, kind=fhirspec_pb2.Kind.KIND_COMPLEX_TYPE, fhir_complex_type_config=fhirspec_pb2.FhirComplexTypeConfig( allowed_field_names_to_config={ "reference": fhirspec_pb2.FhirFieldConfig( is_array=False, r4_type=fhirspec_pb2.R4FhirType.R4_FHIR_TYPE_STRING ) }), ), ] generated_spec = fhir_spec_extractor.generate_r4_fhir_spec_proto_message( self.BUNDLE_WITH_TYPE_STRUCTURE_DEFINITIONS) self.assertEqual(set(config.fhir_type for config in expected_complex_type_configs), set(config.fhir_type for config in generated_spec.fhir_data_type_configs)) self.assertEqual(len(expected_complex_type_configs), len(generated_spec.fhir_data_type_configs)) self.assertEqual(set(str(config) for config in expected_complex_type_configs), set(str(config) for config in generated_spec.fhir_data_type_configs)) def test_fhir_spec_extractor_missing_type_structure_definition_raises_exception(self): fhir_spec_extractor = FhirSpecExtractor( self.BUNDLE_WITH_IMMUNIZATION_AND_PATIENT_STRUCTURE_DEFINITION, {"Immunization"}) type_definitions_bundle_without_any_definitions = json.loads(""" { "resourceType": "Bundle", "id": "types", "meta": { "lastUpdated": "2019-11-01T09:29:23.356+11:00" }, "type": "collection", "entry": [] } """) with self.assertRaises(ValueError): fhir_spec_extractor.generate_r4_fhir_spec_proto_message( type_definitions_bundle_without_any_definitions) if __name__ == '__main__': unittest.main()