fixing unmarshalling/parsing of FHIR code sets & enums.

fastenhealth · Nov 1, 2024 · e1baa08 · e1baa08
1 parent 3319331
commit e1baa08
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Showing 5 changed files with 274 additions and 3 deletions.
diff --git a/clients/internal/base/fhir401_client_test.go b/clients/internal/base/fhir401_client_test.go
@@ -163,6 +163,100 @@ func TestFhir401Client_ProcessResource(t *testing.T) {
 	//require.Equal(t, "A00000000000005", profile.SourceResourceID)
 }
 
+func TestFhir401Client_ProcessEncounterResource_WhichContainsCapitalizedStatusEnum_ShouldParseCorrectly(t *testing.T) {
+	t.Parallel()
+	//setup
+	mockCtrl := gomock.NewController(t)
+	defer mockCtrl.Finish()
+	sc := mock_models.NewMockSourceCredential(mockCtrl)
+	db := mock_models.NewMockDatabaseRepository(mockCtrl)
+	testLogger := logrus.WithFields(logrus.Fields{
+		"type": "test",
+	})
+
+	cernerSandboxDefinition, err := definitions.GetSourceDefinition(definitions.GetSourceConfigOptions{
+		EndpointId: "3290e5d7-978e-42ad-b661-1cf8a01a989c",
+	})
+	require.NoError(t, err)
+
+	client, err := GetSourceClientFHIR401(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, sc, cernerSandboxDefinition, models.WithTestHttpClient(&http.Client{}))
+	require.NoError(t, err)
+	db.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).Return(true, nil).AnyTimes()
+
+	jsonBytes, err := ReadTestFixture("testdata/fixtures/401-R4/document_reference/encounter_resource_broken_parse.json")
+	require.NoError(t, err)
+	referencedResourcesLookup := map[string]bool{}
+	internalFragmentReferenceLookup := map[string]string{}
+	summary := models.UpsertSummary{}
+
+	rawResource := models.RawResourceFhir{
+		SourceResourceID:   "e7vTGSIu3VmPxDxo8hbtSKQ3",
+		SourceResourceType: "Encounter",
+		ResourceRaw:        jsonBytes,
+	}
+
+	// test
+	err = client.ProcessResource(db, rawResource, referencedResourcesLookup, internalFragmentReferenceLookup, &summary)
+
+	//assert
+	require.NoError(t, err)
+	require.Equal(t, 4, len(referencedResourcesLookup))
+	require.Equal(t, map[string]bool{
+		"Encounter/e7vTGSIu3VmPxDxo8hbtSKQ3":                      true,
+		"Location/eq0Zb8k23Hg.GX9aMfavyZg3":                       false,
+		"Patient/etMDDQeIicnivVsdRrZcEQGPqfFlXIbJH5wMZqQ7ZNldGo3": false,
+		"Practitioner/e7y0GLCXTb0rdKZlNSuQhww3":                   false,
+	}, referencedResourcesLookup)
+	//require.Equal(t, "A00000000000005", profile.SourceResourceID)
+}
+
+func TestFhir401Client_ProcessObservationResource_WhichContainsUnicodeCharacters_ShouldParseCorrectly(t *testing.T) {
+	t.Skip("Cannot handle escaped unicode characters")
+	//setup
+	mockCtrl := gomock.NewController(t)
+	defer mockCtrl.Finish()
+	sc := mock_models.NewMockSourceCredential(mockCtrl)
+	db := mock_models.NewMockDatabaseRepository(mockCtrl)
+	testLogger := logrus.WithFields(logrus.Fields{
+		"type": "test",
+	})
+
+	cernerSandboxDefinition, err := definitions.GetSourceDefinition(definitions.GetSourceConfigOptions{
+		EndpointId: "3290e5d7-978e-42ad-b661-1cf8a01a989c",
+	})
+	require.NoError(t, err)
+
+	client, err := GetSourceClientFHIR401(pkg.FastenLighthouseEnvSandbox, context.Background(), testLogger, sc, cernerSandboxDefinition, models.WithTestHttpClient(&http.Client{}))
+	require.NoError(t, err)
+	db.EXPECT().UpsertRawResource(gomock.Any(), gomock.Any(), gomock.Any()).Return(true, nil).AnyTimes()
+
+	jsonBytes, err := ReadTestFixture("testdata/fixtures/401-R4/document_reference/observation_broken_parse.json")
+	require.NoError(t, err)
+	referencedResourcesLookup := map[string]bool{}
+	internalFragmentReferenceLookup := map[string]string{}
+	summary := models.UpsertSummary{}
+
+	rawResource := models.RawResourceFhir{
+		SourceResourceID:   "e7vTGSIu3VmPxDxo8hbtSKQ3",
+		SourceResourceType: "Encounter",
+		ResourceRaw:        jsonBytes,
+	}
+
+	// test
+	err = client.ProcessResource(db, rawResource, referencedResourcesLookup, internalFragmentReferenceLookup, &summary)
+
+	//assert
+	require.NoError(t, err)
+	require.Equal(t, 4, len(referencedResourcesLookup))
+	require.Equal(t, map[string]bool{
+		"Encounter/e7vTGSIu3VmPxDxo8hbtSKQ3":                      true,
+		"Location/eq0Zb8k23Hg.GX9aMfavyZg3":                       false,
+		"Patient/etMDDQeIicnivVsdRrZcEQGPqfFlXIbJH5wMZqQ7ZNldGo3": false,
+		"Practitioner/e7y0GLCXTb0rdKZlNSuQhww3":                   false,
+	}, referencedResourcesLookup)
+	//require.Equal(t, "A00000000000005", profile.SourceResourceID)
+}
+
 func TestFhir401Client_ProcessResourceWithContainedResources(t *testing.T) {
 	t.Parallel()
 	//setup

diff --git a/...nal/base/testdata/fixtures/401-R4/document_reference/encounter_resource_broken_parse.json b/...nal/base/testdata/fixtures/401-R4/document_reference/encounter_resource_broken_parse.json
@@ -0,0 +1,79 @@
+{
+  "class": {
+    "code": "5",
+    "display": "Appointment",
+    "system": "urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260"
+  },
+  "id": "e7vTGSIu3VmPxDxo8hbtSKQ3",
+  "identifier": [
+    {
+      "system": "urn:oid:1.2.840.114350.1.13.44.2.7.3.698084.8",
+      "use": "usual",
+      "value": "247735644"
+    }
+  ],
+  "location": [
+    {
+      "location": {
+        "display": "Adult Orthopedics",
+        "reference": "Location/eq0Zb8k23Hg.GX9aMfavyZg3"
+      }
+    }
+  ],
+  "participant": [
+    {
+      "individual": {
+        "display": "KIRK J. JAMES, MD",
+        "reference": "Practitioner/e7y0GLCXTb0rdKZlNSuQhww3"
+      },
+      "period": {
+        "end": "2019-11-21T18:00:00Z",
+        "start": "2018-11-21T17:40:00Z"
+      }
+    }
+  ],
+  "period": {
+    "end": "2019-11-21T18:00:00Z",
+    "start": "2018-11-21T17:40:00Z"
+  },
+  "reasonCode": [
+    {
+      "coding": [
+        {
+          "code": "494",
+          "display": "Limb Pain",
+          "system": "urn:oid:1.2.840.114350.1.13.44.2.7.2.728286"
+        }
+      ],
+      "text": "Limb Pain"
+    }
+  ],
+  "resourceType": "Encounter",
+  "status": "Finished",
+  "subject": {
+    "display": "Doe, John",
+    "reference": "Patient/etMDDQeIicnivVsdRrZcEQGPqfFlXIbJH5wMZqQ7ZNldGo3"
+  },
+  "type": [
+    {
+      "coding": [
+        {
+          "code": "101",
+          "display": "Office Visit",
+          "system": "urn:oid:1.2.840.114350.1.13.44.2.7.10.698084.30"
+        }
+      ],
+      "text": "Office Visit"
+    },
+    {
+      "coding": [
+        {
+          "code": "36",
+          "display": "Initial Specialty Visit",
+          "system": "urn:oid:1.2.840.114350.1.13.44.2.7.2.808267"
+        }
+      ],
+      "text": "Initial Specialty Visit"
+    }
+  ]
+}
diff --git a/...s/internal/base/testdata/fixtures/401-R4/document_reference/observation_broken_parse.json b/...s/internal/base/testdata/fixtures/401-R4/document_reference/observation_broken_parse.json
@@ -0,0 +1,98 @@
+{
+  "basedOn": [
+    {
+      "display": "HEPATITIS B SURFACE ANTIBODY IMMUNITY QUANTITATIVE",
+      "reference": "ServiceRequest/klsdk3-PBKXHFeY0Q7KMDFz92TYK2nbYKsI3"
+    }
+  ],
+  "category": [
+    {
+      "coding": [
+        {
+          "code": "laboratory",
+          "display": "Laboratory",
+          "system": "http://terminology.hl7.org/CodeSystem/observation-category"
+        }
+      ],
+      "text": "Laboratory"
+    },
+    {
+      "coding": [
+        {
+          "code": "LAB",
+          "display": "LAB",
+          "system": "urn:oid:1.2.840.114350.1.13.44.2.7.10.798268.30"
+        }
+      ],
+      "text": "LAB"
+    }
+  ],
+  "code": {
+    "coding": [
+      {
+        "code": "5193-8",
+        "display": "Hepatitis B virus surface Ab [Units/volume] in Serum or Plasma by Immunoassay",
+        "system": "http://loinc.org"
+      },
+      {
+        "code": "18063",
+        "system": "urn:oid:1.2.840.114350.1.13.44.2.7.5.737384.80113"
+      },
+      {
+        "code": "18063",
+        "display": "HEPATITIS B SURFACE ANTIBODY QUANT",
+        "system": "urn:oid:1.2.840.114350.1.13.44.2.7.2.768282"
+      }
+    ],
+    "text": "HEPATITIS B SURFACE ANTIBODY QUANT"
+  },
+  "effectiveDateTime": "2021-06-07T01:00:00Z",
+  "encounter": {
+    "display": "Lab Visit",
+    "identifier": {
+      "system": "urn:oid:1.2.840.114350.1.13.44.2.7.3.698084.8",
+      "use": "usual",
+      "value": "315534385"
+    },
+    "reference": "Encounter/exxx3In3deguCac1YMmg3"
+  },
+  "id": "eDLs6fOQWxxxxxyRm6L53E5CxAMgXynSZ6fIlFdJM8SeT.qhxNM3",
+  "interpretation": [
+    {
+      "coding": [
+        {
+          "code": "L",
+          "display": "Low",
+          "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"
+        }
+      ],
+      "text": "Low"
+    }
+  ],
+  "issued": "2021-06-07T20:00:00Z",
+  "note": [
+    {
+      "text": "Patient is considered to be Not Immune to infection with HBV."
+    }
+  ],
+  "referenceRange": [
+    {
+      "text": "\u003e=10.00"
+    }
+  ],
+  "resourceType": "Observation",
+  "specimen": {
+    "display": "Specimen XD#DDD-D00420",
+    "reference": "Specimen/xxxxwer-YwClO-82tNgDDI43tkGp2UsGcRs3"
+  },
+  "status": "final",
+  "subject": {
+    "display": "Doe, John",
+    "reference": "Patient/1234"
+  },
+  "valueQuantity": {
+    "comparator": "\u003c",
+    "unit": "mIU/mL",
+    "value": 3.1
+  }
+}
diff --git a/go.mod b/go.mod
@@ -3,7 +3,7 @@ module github.com/fastenhealth/fasten-sources
 go 1.18
 
 require (
-	github.com/fastenhealth/gofhir-models v0.0.6
+	github.com/fastenhealth/gofhir-models v0.0.7
 	github.com/gabriel-vasile/mimetype v1.4.3
 	github.com/go-playground/validator/v10 v10.16.0
 	github.com/golang/mock v1.6.0

diff --git a/go.sum b/go.sum
@@ -1,8 +1,8 @@
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/fastenhealth/gofhir-models v0.0.6 h1:yJYYaV1eJtHiGEfA1rXLsyOm/9hIi6s2cGoZzGfW1tM=
-github.com/fastenhealth/gofhir-models v0.0.6/go.mod h1:xB8ikGxu3bUq2b1JYV+CZpHqBaLXpOizFR0eFBCunis=
+github.com/fastenhealth/gofhir-models v0.0.7 h1:t7Oyvc6eh3z9oaX5e5Krs7LiBT2n32z8yJrn5D0+cJg=
+github.com/fastenhealth/gofhir-models v0.0.7/go.mod h1:xB8ikGxu3bUq2b1JYV+CZpHqBaLXpOizFR0eFBCunis=
 github.com/gabriel-vasile/mimetype v1.4.3 h1:in2uUcidCuFcDKtdcBxlR0rJ1+fsokWf+uqxgUFjbI0=
 github.com/gabriel-vasile/mimetype v1.4.3/go.mod h1:d8uq/6HKRL6CGdk+aubisF/M5GcPfT7nKyLpA0lbSSk=
 github.com/go-playground/assert/v2 v2.2.0 h1:JvknZsQTYeFEAhQwI4qEt9cyV5ONwRHC+lYKSsYSR8s=