SMILE-3459 Implemented -l parameter in validator. (#3983)

* SMILE-3459 Implemented -l parameter in validator. Added SnapshotGeneratingValidationSupport to R4 support chain.

* SMILE-3459 Removed failing test that I added.

* Revert "SMILE-3459 Removed failing test that I added."

This reverts commit d11abc7ad5bc0bc5fa149e83670621959b03a7b9.

* SMILE-3459 Added test cases for loading local R4 profile.

* SMILE-3459 Added when clause to test names.

* SMILE-3459 WIP Logging assert isn't working.

* - changes to test for logging

* - change logging level to error

* - capture all logging events in tests

* SMILE-3459 Ensure validation error is logged when resource doesn't comply with profile.

* SMILE-3459 Added changelog.

* SMILE-3459 Made ValidateCommandTest less brittle.

* SMILE-3459 Changed LocalFileValidationSupport to support all resource types.

* SMILE-3459 Added LocalFileValidationSupportTest

* SMILE-3459 Created ValidationSupportChainCreator.

* SMILE-3459 Added new Msg.code for local profile load failure.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java

@@ -25,7 +25,7 @@ public final class Msg {
 
 	/**
 	 * IMPORTANT: Please update the following comment after you add a new code
-	 * Last used code value: 2140
+	 * Last used code value: 2141
 	 */
 
 	private Msg() {}

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java

@@ -27,6 +27,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationOptions;
 import ca.uhn.fhir.validation.ValidationResult;
 import com.google.common.base.Charsets;
 import com.helger.commons.io.file.FileHelper;
@@ -40,7 +41,6 @@ import org.fusesource.jansi.Ansi.Color;
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -136,40 +136,27 @@ public class ValidateCommand extends BaseCommand {
 		FhirContext ctx = getFhirContext();
 		FhirValidator val = ctx.newValidator();
 
-		IBaseResource localProfileResource = null;
+		ValidationOptions options = new ValidationOptions();
 		if (theCommandLine.hasOption("l")) {
 			String localProfile = theCommandLine.getOptionValue("l");
-			ourLog.info("Loading profile: {}", localProfile);
+			options.addProfile(localProfile);
-			String input = loadFile(localProfile);
-
-			localProfileResource = ca.uhn.fhir.rest.api.EncodingEnum.detectEncodingNoDefault(input).newParser(ctx).parseResource(input);
 		}
 
 		if (theCommandLine.hasOption("p")) {
 			switch (ctx.getVersion().getVersion()) {
 				case DSTU2: {
-					ValidationSupportChain validationSupport = new ValidationSupportChain(
-						new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
-
-					if (theCommandLine.hasOption("r")) {
-						validationSupport.addValidationSupport((IValidationSupport) new LoadingValidationSupportDstu2());
-					}
 					FhirInstanceValidator instanceValidator;
-					instanceValidator = new FhirInstanceValidator(validationSupport);
+					ValidationSupportChain validationSupportChain = ValidationSupportChainCreator.getValidationSupportChainDstu2(ctx, theCommandLine);
+					instanceValidator = new FhirInstanceValidator(validationSupportChain);
 					val.registerValidatorModule(instanceValidator);
-
 					break;
 				}
 				case DSTU3:
 				case R4: {
 					FhirInstanceValidator instanceValidator = new FhirInstanceValidator(ctx);
 					val.registerValidatorModule(instanceValidator);
-					ValidationSupportChain validationSupport = new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
+					ValidationSupportChain validationSupportChain = ValidationSupportChainCreator.getValidationSupportChainR4(ctx, theCommandLine);
-
+					instanceValidator.setValidationSupport(validationSupportChain);
-					if (theCommandLine.hasOption("r")) {
-						validationSupport.addValidationSupport((IValidationSupport) new LoadingValidationSupportDstu3());
-					}
-					instanceValidator.setValidationSupport(validationSupport);
 					break;
 				}
 				default:
@@ -182,7 +169,7 @@ public class ValidateCommand extends BaseCommand {
 
 		ValidationResult results;
 		try {
-			results = val.validateWithResult(contents);
+			results = val.validateWithResult(contents, options);
 		} catch (DataFormatException e) {
 			throw new CommandFailureException(Msg.code(1621) + e.getMessage());
 		}

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidationSupportChainCreator.java

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
+import ca.uhn.fhir.i18n.Msg;
+import org.apache.commons.cli.CommandLine;
+import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.LocalFileValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+
+import java.io.IOException;
+
+public class ValidationSupportChainCreator {
+
+	public static ValidationSupportChain getValidationSupportChainR4(FhirContext ctx, CommandLine commandLine) {
+		ValidationSupportChain chain = new ValidationSupportChain(
+			new DefaultProfileValidationSupport(ctx),
+			new InMemoryTerminologyServerValidationSupport(ctx));
+
+		if (commandLine.hasOption("l")) {
+			try {
+				String localProfile = commandLine.getOptionValue("l");
+				LocalFileValidationSupport localFileValidationSupport = new LocalFileValidationSupport(ctx);
+
+				localFileValidationSupport.loadFile(localProfile);
+
+				chain.addValidationSupport(localFileValidationSupport);
+				chain.addValidationSupport(new SnapshotGeneratingValidationSupport(ctx));
+			} catch (IOException e) {
+				throw new RuntimeException(Msg.code(2141) + "Failed to load local profile.", e);
+			}
+		}
+		if (commandLine.hasOption("r")) {
+			chain.addValidationSupport(new LoadingValidationSupportDstu3());
+		}
+
+		return chain;
+	}
+
+	public static ValidationSupportChain getValidationSupportChainDstu2(FhirContext ctx, CommandLine commandLine) {
+		ValidationSupportChain chain = new ValidationSupportChain(
+			new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
+
+		if (commandLine.hasOption("r")) {
+			chain.addValidationSupport(new LoadingValidationSupportDstu2());
+		}
+
+		return chain;
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ValidateCommandTest.java

@@ -1,10 +1,46 @@
 package ca.uhn.fhir.cli;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
+import ch.qos.logback.classic.joran.JoranConfigurator;
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.joran.spi.JoranException;
+import ch.qos.logback.core.read.ListAppender;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.ParseException;
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class ValidateCommandTest {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateCommandTest.class);
+
+	private final Logger ourLog = (Logger) LoggerFactory.getLogger(ValidateCommand.class);
+	private ValidateCommand myValidateCommand = new ValidateCommand();
+	private ListAppender<ILoggingEvent> myListAppender = new ListAppender<>();
+
+
+	@BeforeEach
+	public void beforeEach() {
+		ourLog.setLevel(Level.ALL);
+		myListAppender = new ListAppender<>();
+		myListAppender.start();
+		ourLog.addAppender(myListAppender);
+	}
+
+	@AfterEach
+	public void afterEach() {
+		myListAppender.stop();
+	}
+
 
 	@BeforeEach
 	public void before() {
@@ -14,9 +50,8 @@ public class ValidateCommandTest {
 	@Test
 	public void testValidateLocalProfileDstu3() {
 		String resourcePath = ValidateCommandTest.class.getResource("/patient-uslab-example1.xml").getFile();
-		ourLog.info(resourcePath);
 
-		App.main(new String[] {
+		App.main(new String[]{
 			"validate",
 			"-v", "dstu3",
 			"-p",
@@ -28,10 +63,23 @@ public class ValidateCommandTest {
 		String resourcePath = ValidateCommandTest.class.getResource("/patient-uslab-example1.xml").getFile();
 		ourLog.info(resourcePath);
 
-		App.main(new String[] {
+		App.main(new String[]{
 			"validate",
 			"-v", "R4",
 			"-p",
 			"-n", resourcePath});
 	}
+
+	@Test
+	public void validate_withLocalProfileR4_shouldPass_whenResourceCompliesWithProfile() {
+		String patientJson = ValidateCommandTest.class.getResource("/validate/Patient.json").getFile();
+		String patientProfile = ValidateCommandTest.class.getResource("/validate/PatientIn-Profile.json").getFile();
+
+		App.main(new String[]{
+			"validate",
+			"--fhir-version", "r4",
+			"--profile",
+			"--file", patientJson,
+			"-l", patientProfile});
+	}
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ValidationSupportChainCreatorTest.java

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.ParseException;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class ValidationSupportChainCreatorTest {
+
+	private static FhirContext myContextDstu2 = FhirContext.forDstu2();
+	private static FhirContext myContextR4 = FhirContext.forR4();
+
+	private ValidateCommand myValidateCommand = new ValidateCommand();
+
+	@Test
+	public void getR4Chain_shouldProvideExpectedValidationSupport() throws ParseException {
+		String patientJson = ValidateCommandTest.class.getResource("/validate/Patient-no-identifier.json").getFile();
+		String patientProfile = ValidateCommandTest.class.getResource("/validate/PatientIn-Profile.json").getFile();
+
+		String[] args = new String[]{
+			"validate",
+			"--fhir-version", "r4",
+			"--profile",
+			"--file", patientJson,
+			"-l", patientProfile
+		};
+
+		CommandLine commandLine = new DefaultParser().parse(myValidateCommand.getOptions(), args);
+		ValidationSupportChain chain = ValidationSupportChainCreator.getValidationSupportChainR4(myContextR4, commandLine);
+		StructureDefinition structureDefinition = (StructureDefinition) chain.fetchStructureDefinition("https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient");
+
+		assertEquals(structureDefinition.getName(), "Profile_MII_Patient_PatientIn");
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/validate/Patient-no-identifier.json

@@ -0,0 +1,9 @@
+{
+    "resourceType": "Patient",
+    "id": "ExamplePatientPatientFull",
+    "meta": {
+        "profile":  [
+            "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
+        ]
+    }
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/validate/Patient.json

@@ -0,0 +1,24 @@
+{
+    "resourceType": "Patient",
+    "id": "ExamplePatientPatientFull",
+    "meta": {
+        "profile":  [
+            "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
+        ]
+    },
+    "identifier":  [
+        {
+            "use": "usual",
+            "type": {
+                "coding":  [
+                    {
+                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                        "code": "MR"
+                    }
+                ]
+            },
+            "system": "https://www.example.org/fhir/sid/patienten",
+            "value": "42285243"
+        }
+    ]
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/validate/PatientIn-Profile.json

@@ -0,0 +1,34 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "Profile-MII-Patient-PatientIn",
+  "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient",
+  "version": "2.0.0",
+  "name": "Profile_MII_Patient_PatientIn",
+  "title": "Profile - MI-I - Patient - PatientIn",
+  "status": "active",
+  "fhirVersion": "4.0.1",
+  "kind": "resource",
+  "abstract": false,
+  "type": "Patient",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
+  "derivation": "constraint",
+  "differential": {
+    "element": [
+      {
+        "id": "Patient.identifier",
+        "path": "Patient.identifier",
+        "slicing": {
+          "discriminator": [
+            {
+              "type": "pattern",
+              "path": "$this"
+            }
+          ],
+          "rules": "open"
+        },
+        "min": 1,
+        "mustSupport": true
+      }
+    ]
+  }
+}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4003-add-support-for-local-validation-profile-hapi-fhir-cli.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4003
+jira: SMILE-3459
+title: "Added support for -l parameter for providing a local validation profile in the HAPI FHIR CLI."

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/LocalFileValidationSupport.java

@@ -0,0 +1,48 @@
+package org.hl7.fhir.common.hapi.validation.support;
+
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - API
+ * %%
+ * Copyright (C) 2014 - 2022 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+public class LocalFileValidationSupport extends PrePopulatedValidationSupport {
+
+	public LocalFileValidationSupport(FhirContext ctx) {
+		super(ctx);
+	}
+
+	@Override
+	public FhirContext getFhirContext() {
+		return myCtx;
+	}
+
+	public void loadFile(String theFileName) throws IOException {
+		String contents = IOUtils.toString(new InputStreamReader(new FileInputStream(theFileName), "UTF-8"));
+		IBaseResource resource  = myCtx.newJsonParser().parseResource(contents);
+		this.addResource(resource);
+	}
+
+}

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java

@@ -229,7 +229,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
 			.setBestPracticeWarningLevel(getBestPracticeWarningLevel())
 			.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
 			.setExtensionDomains(getExtensionDomains())
-			.setValidatorResourceFetcher(validatorResourceFetcher)
 			.setValidationPolicyAdvisor(validatorPolicyAdvisor)
 			.setNoTerminologyChecks(isNoTerminologyChecks())
 			.setNoExtensibleWarnings(isNoExtensibleWarnings())

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

@@ -0,0 +1,42 @@
+package org.hl7.fhir.r4.validation;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
+import ca.uhn.fhir.context.support.ValidationSupportContext;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.common.hapi.validation.support.LocalFileValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.StructureDefinition;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
+public class LocalFileValidationSupportTest {
+
+	private FhirContext myFhirCtx = FhirContext.forR4();
+	private static final Logger ourLog = LoggerFactory.getLogger(LocalFileValidationSupportTest.class);
+
+	@Test
+	public void getStructureDefinition_shouldReturnLocalFile_whenLocalFileProvided() throws IOException {
+		String patientProfile = LocalFileValidationSupportTest.class.getResource("/PatientIn-Profile.json").getFile();
+
+		LocalFileValidationSupport localFileValidationSupport = new LocalFileValidationSupport(myFhirCtx);
+		localFileValidationSupport.loadFile(patientProfile);
+		StructureDefinition structureDefinition = (StructureDefinition) localFileValidationSupport.fetchStructureDefinition("https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient");
+
+		assertEquals(structureDefinition.getName(), "Profile_MII_Patient_PatientIn");
+	}
+
+}

hapi-fhir-validation/src/test/resources/PatientIn-Profile.json

@@ -0,0 +1,34 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "Profile-MII-Patient-PatientIn",
+  "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient",
+  "version": "2.0.0",
+  "name": "Profile_MII_Patient_PatientIn",
+  "title": "Profile - MI-I - Patient - PatientIn",
+  "status": "active",
+  "fhirVersion": "4.0.1",
+  "kind": "resource",
+  "abstract": false,
+  "type": "Patient",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
+  "derivation": "constraint",
+  "differential": {
+    "element": [
+      {
+        "id": "Patient.identifier",
+        "path": "Patient.identifier",
+        "slicing": {
+          "discriminator": [
+            {
+              "type": "pattern",
+              "path": "$this"
+            }
+          ],
+          "rules": "open"
+        },
+        "min": 1,
+        "mustSupport": true
+      }
+    ]
+  }
+}