test: Use Loinc Terminology Service (#92)

* loinc term

* create core terminology service

* update action yaml to use secret

* only validate once

* revert to false

* update expected nuymber of validation errors

* update expected number of validation errors

Author: JNygaard-Skylight

.github/workflows/test.yml

@@ -12,7 +12,7 @@ on:
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
-  
+
 jobs:
   unit-test-dotnet-fhir-converter-api:
     runs-on: ubuntu-latest
@@ -61,6 +61,8 @@ jobs:
           dotnet-version: "8.0.x"
       - name: Run tests
         run: dotnet test --filter FullyQualifiedName~Converter.FunctionalTests --logger "console;verbosity=detailed"
+        env:
+          VALIDATE_FHIR: false
 
   unit-test-dotnet-fhir-converter-tool:
     runs-on: ubuntu-latest
@@ -84,4 +86,7 @@ jobs:
         with:
           dotnet-version: "8.0.x"
       - name: Run tests
-        run: VALIDATE_FHIR=true dotnet test --filter FullyQualifiedName~Converter.FunctionalTests.ConvertDataTemplateDirectoryProviderFunctionalTests.GivenEcrDocument_WhenConverting_ExpectedFhirResourceShouldBeValid --logger "console;verbosity=detailed"
+        run: dotnet test --filter FullyQualifiedName~Converter.FunctionalTests.ConvertDataTemplateDirectoryProviderFunctionalTests.GivenEcrDocument_WhenConverting_ExpectedFhirResourceShouldBeValid --logger "console;verbosity=detailed"
+        env:
+          VALIDATE_FHIR: true
+          LOINC_AUTH: ${{ secrets.LOINC_AUTH }}

src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs

@@ -241,9 +241,9 @@ public static IEnumerable<object[]> GetDataForEcr()
                 // ]
                 new[] { @"EICR", @"eCR_full.xml", @"eCR_full-expected.json", "validation", "9" },
                 new[] { @"EICR", @"eCR_RR_combined_3_1.xml", @"eCR_RR_combined_3_1-expected.json", "validation", "13" },
-                new[] { @"EICR", @"eCR_EveEverywoman.xml", @"eCR_EveEverywoman-expected.json", "validation", "51" },
+                new[] { @"EICR", @"eCR_EveEverywoman.xml", @"eCR_EveEverywoman-expected.json", "validation", "37" },
                 new[] { @"EICR", @"eicr04152020.xml", @"eicr04152020-expected.json", "validation", "19" },
-                new[] { @"EICR", @"CDAR2_IG_PHCASERPT_R2_D2_SAMPLE.xml", @"CDAR2_IG_PHCASERPT_R2_D2_SAMPLE-expected.json", "validation", "25" },
+                new[] { @"EICR", @"CDAR2_IG_PHCASERPT_R2_D2_SAMPLE.xml", @"CDAR2_IG_PHCASERPT_R2_D2_SAMPLE-expected.json", "validation", "21" },
             };
             return data.Select(item => new[]
             {
@@ -398,6 +398,9 @@ protected void ConvertCCDAMessageAndValidateExpectedResponse(ITemplateProvider t
 
         protected void ValidateConvertCCDAMessageIsValidFHIR(ITemplateProvider templateProvider, string rootTemplate, string inputFile, string validationFailureStep, int numFailures)
         {
+            System.Console.Out.WriteLine("#####################################################################################################");
+            System.Console.Out.WriteLine(inputFile);
+            System.Console.Out.WriteLine("-----------------------------------------------------------------------------------------------------");
             var validateFhir = Environment.GetEnvironmentVariable("VALIDATE_FHIR") ?? "false";
             if (validateFhir.Trim() == "false") return;
 
@@ -420,17 +423,34 @@ protected void ValidateConvertCCDAMessageIsValidFHIR(ITemplateProvider templateP
                     actualContent,
                     serializerOptions
                 );
-                var packageSource = new FhirPackageSource(
+                var ecrSource = new FhirPackageSource(
                     ModelInfo.ModelInspector,
                     "https://packages2.fhir.org/packages",
-                    new string[] {
-                        "hl7.fhir.us.ecr@2.1.2",
-                    }
+                    new string[] { "hl7.fhir.us.ecr@2.1.2", }
                 );
-                var profileSource = new CachedResolver(packageSource);
+                var coreSource = FhirPackageSource.CreateCorePackageSource(
+                    ModelInfo.ModelInspector,
+                    FhirRelease.R4,
+                    "https://packages2.fhir.org/packages"
+                );
+
+                var profileSource = new CachedResolver(ecrSource);
+                var loincClient = new FhirClient("https://fhir.loinc.org");
+                loincClient.RequestHeaders.Authorization =
+                    new System.Net.Http.Headers.AuthenticationHeaderValue(
+                        "Basic",
+                        "am55Z2FhcmQ6M1hTQCFld2NBQWVMc1pN"
+                    );
+                var loincTerminologyService = new ExternalTerminologyService(loincClient);
                 var terminologyService = new LocalTerminologyService(profileSource);
+                var baseTermSer = LocalTerminologyService.CreateDefaultForCore(coreSource);
+                var mulTermSer = new MultiTerminologyService(
+                    terminologyService,
+                    baseTermSer,
+                    loincTerminologyService
+                );
 
-                var validator = new Validator(profileSource, terminologyService);
+                var validator = new Validator(profileSource, mulTermSer);
                 var result = validator.Validate(poco);
                 var outcomeText = result.ToString();
                 var numFailed = result.Issue.Count();