Sandbox Test

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/ValidationSandboxTest.java

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+package org.hl7.fhir.r4.validation;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.util.ClasspathUtil;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationResult;
+import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
+import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.PrePopulatedValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class ValidationSandboxTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ValidationSandboxTest.class);
+
+	private static final String CODE_SYSTEMS_DIRECTORY = "/sandbox/code-systems";
+	private static final String VALUE_SETS_DIRECTORY = "/sandbox/value-sets";
+	private static final String STRUCTURE_DEFINITIONS_DIRECTORY = "/sandbox/structure-definitions";
+
+	private static final FhirContext ourFhirContext = FhirContext.forR4Cached();
+	private static FhirValidator myValidator;
+
+	@BeforeAll
+	public static void beforeAll(){
+		configureValidator();
+	}
+
+	@Test
+	public void testValidatorWithCustomProfile() {
+		// Profile defined in /sandbox/structure-definitions/test-observation.json
+		Observation observation = new Observation();
+		observation.getMeta().addProfile("http://example.org/fhir/StructureDefinition/TestObservation");
+
+		// missing code
+		ValidationResult validationResult = myValidator.validateWithResult(observation);
+		List<SingleValidationMessage> validationErrors = getValidationMessagesBySeverity(validationResult.getMessages(), ResultSeverityEnum.ERROR);
+		assertFalse(validationResult.isSuccessful());
+		assertEquals(1, validationErrors.size());
+		String expectedErrorMessage = "Observation.code: minimum required = 1, but only found 0 (from http://example.org/fhir/StructureDefinition/TestObservation)";
+		assertEquals(expectedErrorMessage, validationErrors.get(0).getMessage());
+
+		// valid code from CodeSystem 1 (/sandbox/code-systems/code-system-1.json)
+		observation.getCode().addCoding().setCode("value-1").setSystem("http://acme.org/code-system-1");
+		validationResult = myValidator.validateWithResult(observation);
+		assertTrue(validationResult.isSuccessful());
+
+		// code from CodeSystem 1 not included in the ValueSet (/sandbox/value-sets/value-set-1.json)
+		observation.getCode().getCoding().clear();
+		assertTrue(observation.getCode().getCoding().isEmpty());
+		observation.getCode().addCoding().setCode("value-2").setSystem("http://acme.org/code-system-1");
+		validationResult = myValidator.validateWithResult(observation);
+		assertFalse(validationResult.isSuccessful());
+		validationErrors = getValidationMessagesBySeverity(validationResult.getMessages(), ResultSeverityEnum.ERROR);
+		assertEquals(1, validationErrors.size());
+		expectedErrorMessage = "None of the codings provided are in the value set 'ValueSet 1' (http://acme.org/value-set-1), and a coding from this value set is required) (codes = http://acme.org/code-system-1#value-2)";
+		assertEquals(expectedErrorMessage, validationErrors.get(0).getMessage());
+
+		// valid code from CodeSystem 2 (/sandbox/code-systems/code-system-2.json)
+		observation.getCode().getCoding().clear();
+		assertTrue(observation.getCode().getCoding().isEmpty());
+		observation.getCode().addCoding().setCode("value-2").setSystem("http://acme.org/code-system-2");
+		validationResult = myValidator.validateWithResult(observation);
+		assertTrue(validationResult.isSuccessful());
+	}
+
+	private static List<SingleValidationMessage> getValidationMessagesBySeverity(
+		List<SingleValidationMessage> theValidationMessages, ResultSeverityEnum theSeverity) {
+		return theValidationMessages.stream().filter(m -> m.getSeverity() == theSeverity).collect(Collectors.toList());
+	}
+
+	private static void configureValidator() {
+		ValidationSupportChain supportChain = new ValidationSupportChain();
+		supportChain.addValidationSupport(new DefaultProfileValidationSupport(ourFhirContext));
+		supportChain.addValidationSupport(new SnapshotGeneratingValidationSupport(ourFhirContext));
+		supportChain.addValidationSupport(new InMemoryTerminologyServerValidationSupport(ourFhirContext));
+		supportChain.addValidationSupport(new CommonCodeSystemsTerminologyService(ourFhirContext));
+
+		PrePopulatedValidationSupport prePopulatedSupport = new PrePopulatedValidationSupport(ourFhirContext);
+		IParser parser = ourFhirContext.newJsonParser();
+		addCodeSystems(prePopulatedSupport, parser);
+		addValueSets(prePopulatedSupport, parser);
+		addStructureDefinitions(prePopulatedSupport, parser);
+
+		supportChain.addValidationSupport(prePopulatedSupport);
+
+		FhirInstanceValidator module = new FhirInstanceValidator(supportChain);
+		myValidator = ourFhirContext.newValidator();
+		myValidator.registerValidatorModule(module);
+	}
+
+	private static void addCodeSystems(PrePopulatedValidationSupport prePopulatedSupport, IParser theParser) {
+		List<String> fileNames = getFileNamesFromDirectory(CODE_SYSTEMS_DIRECTORY);
+		for (String fileName : fileNames) {
+			String path = CODE_SYSTEMS_DIRECTORY + "/" + fileName;
+			String json = ClasspathUtil.loadResource(path);
+			CodeSystem codeSystem = theParser.parseResource(CodeSystem.class, json);
+			prePopulatedSupport.addCodeSystem(codeSystem);
+			ourLog.info("Loaded CodeSystem: {}", path);
+		}
+	}
+
+	private static void addValueSets(PrePopulatedValidationSupport prePopulatedSupport, IParser theParser) {
+		List<String> fileNames = getFileNamesFromDirectory(VALUE_SETS_DIRECTORY);
+		for (String fileName : fileNames) {
+			String path = VALUE_SETS_DIRECTORY + "/" + fileName;
+			String json = ClasspathUtil.loadResource(path);
+			ValueSet valueSet = theParser.parseResource(ValueSet.class, json);
+			prePopulatedSupport.addValueSet(valueSet);
+			ourLog.info("Loaded ValueSet: {}", path);
+		}
+	}
+
+	private static void addStructureDefinitions(PrePopulatedValidationSupport prePopulatedSupport, IParser theParser) {
+		List<String> fileNames = getFileNamesFromDirectory(STRUCTURE_DEFINITIONS_DIRECTORY);
+		for (String fileName : fileNames) {
+			String path = STRUCTURE_DEFINITIONS_DIRECTORY + "/" + fileName;
+			String json = ClasspathUtil.loadResource(path);
+			StructureDefinition structureDefinition = theParser.parseResource(StructureDefinition.class, json);
+			prePopulatedSupport.addStructureDefinition(structureDefinition);
+			ourLog.info("Loaded StructureDefinition: {}", path);
+		}
+	}
+	private static List<String> getFileNamesFromDirectory(String theDirectory){
+		List<String> filenames = new ArrayList<>();
+		try (InputStream in = ValidationSandboxTest.class.getResourceAsStream(theDirectory);
+			 BufferedReader br = new BufferedReader(new InputStreamReader(in))){
+			String resource;
+			while ((resource = br.readLine()) != null) {
+				filenames.add(resource);
+			}
+		} catch (IOException e){
+			throw new RuntimeException(e);
+		}
+		return filenames;
+	}
+}

hapi-fhir-validation/src/test/resources/sandbox/code-systems/code-system-1.json

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+{
+	"resourceType": "CodeSystem",
+	"id": "code-system-1",
+	"url": "http://acme.org/code-system-1",
+	"name": "Code System 1",
+	"title": "Code System 1",
+	"status": "active",
+	"experimental": false,
+	"content": "complete",
+	"concept": [
+		{
+			"code": "value-1",
+			"display": "Value 1"
+		},
+		{
+			"code": "value-2",
+			"display": "Value 2"
+		}
+	]
+}

hapi-fhir-validation/src/test/resources/sandbox/code-systems/code-system-2.json

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+{
+	"resourceType": "CodeSystem",
+	"id": "code-system-2",
+	"url": "http://acme.org/code-system-2",
+	"name": "Code System 2",
+	"title": "Code System 2",
+	"status": "active",
+	"experimental": false,
+	"content": "complete",
+	"concept": [
+		{
+			"code": "value-1",
+			"display": "Value 2"
+		},
+		{
+			"code": "value-2",
+			"display": "Value 2"
+		}
+	]
+}

hapi-fhir-validation/src/test/resources/sandbox/structure-definitions/test-observation.json

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+{
+	"resourceType": "StructureDefinition",
+	"url": "http://example.org/fhir/StructureDefinition/TestObservation",
+	"name": "TestObservation",
+	"status": "draft",
+	"fhirVersion": "4.0.1",
+	"kind": "resource",
+	"abstract": false,
+	"type": "Observation",
+	"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation",
+	"derivation": "constraint",
+	"differential": {
+		"element":  [
+			{
+				"id": "Observation.status",
+				"path": "Observation.status",
+				"min": 0
+			},
+			{
+				"id": "Observation.code",
+				"path": "Observation.code",
+				"binding" : {
+					"extension" : [{
+						"url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
+						"valueString" : "ObservationCode"
+					}],
+					"strength" : "required",
+					"valueSet" : "http://acme.org/value-set-1"
+				}
+			}
+		]
+	}
+}

hapi-fhir-validation/src/test/resources/sandbox/value-sets/value-set-1.json

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+{
+	"resourceType": "ValueSet",
+	"id": "value-set-1",
+	"url": "http://acme.org/value-set-1",
+	"name": "ValueSet 1",
+	"title": "ValueSet 1",
+	"status": "active",
+	"compose": {
+		"include": [
+			{
+				"system": "http://acme.org/code-system-1",
+				"concept": [
+					{
+						"code": "value-1"
+					}
+				]
+			},
+			{
+				"system": "http://acme.org/code-system-2",
+				"concept": [
+					{
+						"code": "value-2"
+					}
+				]
+			}
+		]
+	}
+}