mirror of
https://github.com/hapifhir/hapi-fhir.git
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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>
This commit is contained in:
KGJ-software
GitHub
parent
d1f988f98a
commit
4d16a109de
@ -25,7 +25,7 @@ public final class Msg {
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/**
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* IMPORTANT: Please update the following comment after you add a new code
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* Last used code value: 2140
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* Last used code value: 2141
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*/
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private Msg() {}
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@ -27,6 +27,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.SingleValidationMessage;
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import ca.uhn.fhir.validation.ValidationOptions;
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import ca.uhn.fhir.validation.ValidationResult;
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import com.google.common.base.Charsets;
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import com.helger.commons.io.file.FileHelper;
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@ -40,7 +41,6 @@ import org.fusesource.jansi.Ansi.Color;
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import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
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import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import java.io.File;
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import java.io.FileInputStream;
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@ -136,40 +136,27 @@ public class ValidateCommand extends BaseCommand {
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FhirContext ctx = getFhirContext();
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FhirValidator val = ctx.newValidator();
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IBaseResource localProfileResource = null;
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ValidationOptions options = new ValidationOptions();
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if (theCommandLine.hasOption("l")) {
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String localProfile = theCommandLine.getOptionValue("l");
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ourLog.info("Loading profile: {}", localProfile);
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String input = loadFile(localProfile);
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localProfileResource = ca.uhn.fhir.rest.api.EncodingEnum.detectEncodingNoDefault(input).newParser(ctx).parseResource(input);
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options.addProfile(localProfile);
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}
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if (theCommandLine.hasOption("p")) {
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switch (ctx.getVersion().getVersion()) {
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case DSTU2: {
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ValidationSupportChain validationSupport = new ValidationSupportChain(
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new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
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if (theCommandLine.hasOption("r")) {
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validationSupport.addValidationSupport((IValidationSupport) new LoadingValidationSupportDstu2());
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}
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FhirInstanceValidator instanceValidator;
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instanceValidator = new FhirInstanceValidator(validationSupport);
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ValidationSupportChain validationSupportChain = ValidationSupportChainCreator.getValidationSupportChainDstu2(ctx, theCommandLine);
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instanceValidator = new FhirInstanceValidator(validationSupportChain);
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val.registerValidatorModule(instanceValidator);
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break;
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}
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case DSTU3:
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case R4: {
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FhirInstanceValidator instanceValidator = new FhirInstanceValidator(ctx);
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val.registerValidatorModule(instanceValidator);
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ValidationSupportChain validationSupport = new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
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if (theCommandLine.hasOption("r")) {
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validationSupport.addValidationSupport((IValidationSupport) new LoadingValidationSupportDstu3());
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}
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instanceValidator.setValidationSupport(validationSupport);
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ValidationSupportChain validationSupportChain = ValidationSupportChainCreator.getValidationSupportChainR4(ctx, theCommandLine);
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instanceValidator.setValidationSupport(validationSupportChain);
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break;
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}
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default:
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@ -182,7 +169,7 @@ public class ValidateCommand extends BaseCommand {
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ValidationResult results;
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try {
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results = val.validateWithResult(contents);
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results = val.validateWithResult(contents, options);
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} catch (DataFormatException e) {
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throw new CommandFailureException(Msg.code(1621) + e.getMessage());
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}
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@ -0,0 +1,51 @@
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package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
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import ca.uhn.fhir.i18n.Msg;
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import org.apache.commons.cli.CommandLine;
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import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.LocalFileValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
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import java.io.IOException;
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public class ValidationSupportChainCreator {
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public static ValidationSupportChain getValidationSupportChainR4(FhirContext ctx, CommandLine commandLine) {
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ValidationSupportChain chain = new ValidationSupportChain(
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new DefaultProfileValidationSupport(ctx),
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new InMemoryTerminologyServerValidationSupport(ctx));
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if (commandLine.hasOption("l")) {
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try {
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String localProfile = commandLine.getOptionValue("l");
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LocalFileValidationSupport localFileValidationSupport = new LocalFileValidationSupport(ctx);
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localFileValidationSupport.loadFile(localProfile);
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chain.addValidationSupport(localFileValidationSupport);
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chain.addValidationSupport(new SnapshotGeneratingValidationSupport(ctx));
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} catch (IOException e) {
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throw new RuntimeException(Msg.code(2141) + "Failed to load local profile.", e);
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}
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}
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if (commandLine.hasOption("r")) {
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chain.addValidationSupport(new LoadingValidationSupportDstu3());
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}
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return chain;
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}
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public static ValidationSupportChain getValidationSupportChainDstu2(FhirContext ctx, CommandLine commandLine) {
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ValidationSupportChain chain = new ValidationSupportChain(
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new DefaultProfileValidationSupport(ctx), new InMemoryTerminologyServerValidationSupport(ctx));
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if (commandLine.hasOption("r")) {
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chain.addValidationSupport(new LoadingValidationSupportDstu2());
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}
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return chain;
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}
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}
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@ -1,22 +1,57 @@
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package ca.uhn.fhir.cli;
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import ch.qos.logback.classic.Level;
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import ch.qos.logback.classic.Logger;
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import ch.qos.logback.classic.LoggerContext;
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import ch.qos.logback.classic.joran.JoranConfigurator;
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import ch.qos.logback.classic.spi.ILoggingEvent;
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import ch.qos.logback.core.joran.spi.JoranException;
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import ch.qos.logback.core.read.ListAppender;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.DefaultParser;
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import org.apache.commons.cli.ParseException;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.slf4j.LoggerFactory;
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import java.util.List;
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import java.util.stream.Collectors;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.fail;
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public class ValidateCommandTest {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateCommandTest.class);
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private final Logger ourLog = (Logger) LoggerFactory.getLogger(ValidateCommand.class);
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private ValidateCommand myValidateCommand = new ValidateCommand();
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private ListAppender<ILoggingEvent> myListAppender = new ListAppender<>();
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@BeforeEach
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public void beforeEach() {
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ourLog.setLevel(Level.ALL);
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myListAppender = new ListAppender<>();
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myListAppender.start();
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ourLog.addAppender(myListAppender);
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}
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@AfterEach
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public void afterEach() {
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myListAppender.stop();
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}
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@BeforeEach
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public void before() {
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System.setProperty("test", "true");
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}
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@Test
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public void testValidateLocalProfileDstu3() {
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String resourcePath = ValidateCommandTest.class.getResource("/patient-uslab-example1.xml").getFile();
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ourLog.info(resourcePath);
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App.main(new String[] {
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App.main(new String[]{
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"validate",
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"-v", "dstu3",
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"-p",
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@ -28,10 +63,23 @@ public class ValidateCommandTest {
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String resourcePath = ValidateCommandTest.class.getResource("/patient-uslab-example1.xml").getFile();
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ourLog.info(resourcePath);
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App.main(new String[] {
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App.main(new String[]{
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"validate",
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"-v", "R4",
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"-p",
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"-n", resourcePath});
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}
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@Test
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public void validate_withLocalProfileR4_shouldPass_whenResourceCompliesWithProfile() {
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String patientJson = ValidateCommandTest.class.getResource("/validate/Patient.json").getFile();
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String patientProfile = ValidateCommandTest.class.getResource("/validate/PatientIn-Profile.json").getFile();
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App.main(new String[]{
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"validate",
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"--fhir-version", "r4",
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"--profile",
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"--file", patientJson,
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"-l", patientProfile});
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}
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}
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@ -0,0 +1,39 @@
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package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.DefaultParser;
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import org.apache.commons.cli.ParseException;
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import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.junit.jupiter.api.Test;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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public class ValidationSupportChainCreatorTest {
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private static FhirContext myContextDstu2 = FhirContext.forDstu2();
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private static FhirContext myContextR4 = FhirContext.forR4();
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private ValidateCommand myValidateCommand = new ValidateCommand();
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@Test
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public void getR4Chain_shouldProvideExpectedValidationSupport() throws ParseException {
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String patientJson = ValidateCommandTest.class.getResource("/validate/Patient-no-identifier.json").getFile();
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String patientProfile = ValidateCommandTest.class.getResource("/validate/PatientIn-Profile.json").getFile();
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String[] args = new String[]{
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"validate",
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"--fhir-version", "r4",
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"--profile",
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"--file", patientJson,
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"-l", patientProfile
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};
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CommandLine commandLine = new DefaultParser().parse(myValidateCommand.getOptions(), args);
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ValidationSupportChain chain = ValidationSupportChainCreator.getValidationSupportChainR4(myContextR4, commandLine);
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StructureDefinition structureDefinition = (StructureDefinition) chain.fetchStructureDefinition("https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient");
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assertEquals(structureDefinition.getName(), "Profile_MII_Patient_PatientIn");
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}
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}
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@ -0,0 +1,9 @@
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{
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"resourceType": "Patient",
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"id": "ExamplePatientPatientFull",
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"meta": {
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"profile": [
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"https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
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]
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}
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}
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@ -0,0 +1,24 @@
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{
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"resourceType": "Patient",
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"id": "ExamplePatientPatientFull",
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"meta": {
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"profile": [
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"https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
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]
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},
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"identifier": [
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{
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"use": "usual",
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"type": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
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"code": "MR"
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}
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]
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},
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"system": "https://www.example.org/fhir/sid/patienten",
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"value": "42285243"
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}
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]
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}
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@ -0,0 +1,34 @@
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{
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"resourceType": "StructureDefinition",
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"id": "Profile-MII-Patient-PatientIn",
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"url": "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient",
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"version": "2.0.0",
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"name": "Profile_MII_Patient_PatientIn",
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"title": "Profile - MI-I - Patient - PatientIn",
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"status": "active",
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"fhirVersion": "4.0.1",
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"kind": "resource",
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"abstract": false,
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"type": "Patient",
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"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Patient.identifier",
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"path": "Patient.identifier",
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"slicing": {
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"discriminator": [
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{
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"type": "pattern",
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"path": "$this"
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}
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],
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"rules": "open"
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},
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"min": 1,
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"mustSupport": true
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}
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]
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}
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}
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 4003
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jira: SMILE-3459
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title: "Added support for -l parameter for providing a local validation profile in the HAPI FHIR CLI."
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@ -0,0 +1,48 @@
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package org.hl7.fhir.common.hapi.validation.support;
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/*-
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* #%L
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* HAPI FHIR - Command Line Client - API
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* %%
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* Copyright (C) 2014 - 2022 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.context.FhirContext;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.InputStreamReader;
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public class LocalFileValidationSupport extends PrePopulatedValidationSupport {
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public LocalFileValidationSupport(FhirContext ctx) {
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super(ctx);
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}
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@Override
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public FhirContext getFhirContext() {
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return myCtx;
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}
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public void loadFile(String theFileName) throws IOException {
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String contents = IOUtils.toString(new InputStreamReader(new FileInputStream(theFileName), "UTF-8"));
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IBaseResource resource = myCtx.newJsonParser().parseResource(contents);
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this.addResource(resource);
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}
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}
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@ -229,7 +229,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
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.setBestPracticeWarningLevel(getBestPracticeWarningLevel())
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.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
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.setExtensionDomains(getExtensionDomains())
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.setValidatorResourceFetcher(validatorResourceFetcher)
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.setValidationPolicyAdvisor(validatorPolicyAdvisor)
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.setNoTerminologyChecks(isNoTerminologyChecks())
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.setNoExtensibleWarnings(isNoExtensibleWarnings())
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@ -0,0 +1,42 @@
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package org.hl7.fhir.r4.validation;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.common.hapi.validation.support.LocalFileValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.BufferedInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.nio.charset.StandardCharsets;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.fail;
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public class LocalFileValidationSupportTest {
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private FhirContext myFhirCtx = FhirContext.forR4();
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private static final Logger ourLog = LoggerFactory.getLogger(LocalFileValidationSupportTest.class);
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@Test
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public void getStructureDefinition_shouldReturnLocalFile_whenLocalFileProvided() throws IOException {
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String patientProfile = LocalFileValidationSupportTest.class.getResource("/PatientIn-Profile.json").getFile();
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LocalFileValidationSupport localFileValidationSupport = new LocalFileValidationSupport(myFhirCtx);
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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");
|
||||
}
|
||||
|
||||
}
|
||||
@ -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
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user