Cr read resource from npm package

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/packages/NpmJpaValidationSupportIT.java

@@ -0,0 +1,95 @@
+package ca.uhn.fhir.jpa.packages;
+
+import ca.uhn.fhir.implementationguide.ImplementationGuideCreator;
+import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
+import ca.uhn.test.util.LogbackTestExtension;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.Questionnaire;
+import org.hl7.fhir.r4.model.SearchParameter;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+import org.junit.jupiter.api.io.TempDir;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class NpmJpaValidationSupportIT extends BaseJpaR4Test {
+	@Autowired
+	private NpmJpaValidationSupport mySvc;
+
+	@Autowired
+	private IPackageInstallerSvc myPackageInstallerSvc;
+
+	@RegisterExtension
+	public final LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension(NpmJpaValidationSupport.class);
+
+	@Test
+	public void loadIGAndFetchSpecificResource(@TempDir Path theTempDirPath) throws IOException {
+		// create an IG
+		ImplementationGuideCreator igCreator = new ImplementationGuideCreator(myFhirContext);
+		igCreator.setDirectory(theTempDirPath);
+
+		// create some resources
+		String spUrl = "http://localhost/ig-test-dir/sp";
+		String qUrl = "http://localhost/ig-test-dir/q";
+		for (int i = 0; i < 2; i++) {
+			SearchParameter sp = new SearchParameter();
+			sp.setUrl(spUrl + i);
+			sp.setCode("helloWorld" + i);
+			sp.setName(sp.getCode());
+			sp.setDescription("description");
+			sp.setType(Enumerations.SearchParamType.STRING);
+			sp.addBase("Patient");
+			sp.setExpression("Patient.name.given");
+			sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			igCreator.addResourceToIG(sp.getName(), sp);
+
+			Questionnaire questionnaire = new Questionnaire();
+			questionnaire.setUrl(qUrl + i);
+			questionnaire.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			questionnaire.setName("questionnaire" + i);
+			igCreator.addResourceToIG(questionnaire.getName(), questionnaire);
+
+			// others?
+		}
+
+		PackageInstallationSpec installationSpec = createAndInstallPackageSpec(igCreator, PackageInstallationSpec.InstallModeEnum.STORE_ONLY);
+
+		IBaseResource sp = mySvc.fetchResource("SearchParameter", spUrl + "1");
+		assertNotNull(sp);
+		assertTrue(sp instanceof SearchParameter);
+		assertEquals(spUrl + "1", ((SearchParameter)sp).getUrl());
+		IBaseResource q = mySvc.fetchResource("Questionnaire", qUrl + "1");
+		assertNotNull(q);
+		assertTrue(q instanceof Questionnaire);
+		assertEquals(qUrl + "1", ((Questionnaire)q).getUrl());
+	}
+
+	private PackageInstallationSpec createAndInstallPackageSpec(ImplementationGuideCreator theIgCreator,
+																PackageInstallationSpec.InstallModeEnum theInstallModeEnum) throws IOException {
+		// create a source directory
+		Path outputFileName = theIgCreator.createTestIG();
+
+		// add some NPM package
+		PackageInstallationSpec spec = new PackageInstallationSpec()
+			.setName(theIgCreator.getPackageName())
+			.setVersion(theIgCreator.getPackageVersion())
+			.setInstallMode(theInstallModeEnum)
+			.setPackageContents(Files.readAllBytes(outputFileName))
+		;
+		PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
+
+		assertNotNull(outcome);
+		assertTrue(outcome.getMessage()
+				.stream().anyMatch(m -> m.contains("Successfully added package")),
+			String.join(", ", outcome.getMessage()));
+		return spec;
+	}
+}

hapi-fhir-test-utilities/pom.xml

@@ -209,6 +209,13 @@
 			<groupId>org.assertj</groupId>
 			<artifactId>assertj-core</artifactId>
 		</dependency>
+		<!-- Apache compres: https://commons.apache.org/proper/commons-compress/ -->
+		<!-- Apache license -->
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-compress</artifactId>
+			<version>1.28.0</version>
+		</dependency>
 </dependencies>
 
 <build>

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/implementationguide/GZipCreatorUtil.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.implementationguide;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
+import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
+
+import java.io.BufferedOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+public class GZipCreatorUtil {
+
+	/**
+	 * Create a tarball of the provided input and saves it to the provided output.
+	 *
+	 * @param theSource - the input path to the directory containing all source files to be zipped
+	 * @param theOutput - the output path to the gzip file.
+	 */
+	public static void createTarGz(Path theSource, Path theOutput) throws IOException {
+		try (OutputStream fos = Files.newOutputStream(theOutput);
+				BufferedOutputStream bos = new BufferedOutputStream(fos);
+				GzipCompressorOutputStream gzos = new GzipCompressorOutputStream(bos);
+				TarArchiveOutputStream taos = new TarArchiveOutputStream(gzos)) {
+			addFilesToTarGz(theSource, "", taos);
+		}
+	}
+
+	private static void addFilesToTarGz(Path thePath, String theParent, TarArchiveOutputStream theTarballOutputStream)
+			throws IOException {
+		String entryName = theParent + thePath.getFileName().toString();
+		TarArchiveEntry entry = new TarArchiveEntry(thePath.toFile(), entryName);
+		theTarballOutputStream.putArchiveEntry(entry);
+
+		if (Files.isRegularFile(thePath)) {
+			// add file
+			try (InputStream fis = Files.newInputStream(thePath)) {
+				byte[] buffer = new byte[1024];
+				int len;
+				while ((len = fis.read(buffer)) > 0) {
+					theTarballOutputStream.write(buffer, 0, len);
+				}
+			}
+			theTarballOutputStream.closeArchiveEntry();
+		} else {
+			theTarballOutputStream.closeArchiveEntry();
+			// walk directory
+			try (DirectoryStream<Path> stream = Files.newDirectoryStream(thePath)) {
+				for (Path child : stream) {
+					addFilesToTarGz(child, entryName + "/", theTarballOutputStream);
+				}
+			}
+		}
+	}
+}

hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/implementationguide/ImplementationGuideCreator.java

@@ -0,0 +1,202 @@
+package ca.uhn.fhir.implementationguide;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.util.FhirTerser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import jakarta.annotation.Nonnull;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.intellij.lang.annotations.Language;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class ImplementationGuideCreator {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ImplementationGuideCreator.class);
+
+	@Language("JSON")
+	private static final String PACKAGE_JSON_BASE =
+			"""
+	{
+	"name": "test.fhir.ca.com",
+	"version": "1.2.3",
+	"tools-version": 3,
+	"type": "fhir.ig",
+	"date": "20200831134427",
+	"license": "not-open-source",
+	"canonical": "http://test-ig.com/fhir/us/providerdataexchange",
+	"url": "file://C:\\\\dev\\\\test-exchange\\\\fsh\\\\build\\\\output",
+	"title": "Test Implementation Guide",
+	"description": "Test Implementation Guide",
+	"fhirVersions": [
+		"4.0.1"
+	],
+	"dependencies": {
+	},
+	"author": "SmileCDR",
+	"maintainers": [
+		{
+		"name": "Smile",
+		"email": "[email protected]",
+		"url": "https://www.smilecdr.com"
+		}
+	],
+	"directories": {
+		"lib": "package",
+		"example": "example"
+	}
+	}
+""";
+
+	private Path myDir;
+	private final FhirContext myFhirContext;
+
+	private final FhirTerser myTerser;
+	private final IParser myParser;
+
+	private final String myPackageJson;
+
+	private final String myPackageName;
+	private final String myPackageVersion;
+
+	private final Map<String, IBaseResource> myResourcesToInclude = new HashMap<>();
+
+	public ImplementationGuideCreator(@Nonnull FhirContext theFhirContext) throws JsonProcessingException {
+		this(theFhirContext, "test.fhir.ca.com", "1.2.3");
+	}
+
+	public ImplementationGuideCreator(
+			@Nonnull FhirContext theFhirContext, String thePackageName, String thePackageVersion)
+			throws JsonProcessingException {
+		this(
+				theFhirContext,
+				theFhirContext.getVersion().getVersion().getFhirVersionString(),
+				thePackageName,
+				thePackageVersion);
+	}
+
+	/**
+	 * Constructor
+	 * @param theFhirContext - FhirContext to use
+	 * @param theFhirVersion - fhir version to use (provided to allow setting a custom value different form the FhirContext)
+	 * @param theName - name to set in package.json's name field
+	 * @param theVersion - version to set in package.json's version field
+	 */
+	@SuppressWarnings("unchecked")
+	public ImplementationGuideCreator(
+			@Nonnull FhirContext theFhirContext, String theFhirVersion, String theName, String theVersion)
+			throws JsonProcessingException {
+		myFhirContext = theFhirContext;
+		myTerser = myFhirContext.newTerser();
+		myParser = myFhirContext.newJsonParser();
+		myPackageName = theName;
+		myPackageVersion = theVersion;
+
+		ObjectMapper mapper = new ObjectMapper();
+		mapper.enable(SerializationFeature.INDENT_OUTPUT);
+
+		Map<String, Object> mapJson = mapper.readValue(PACKAGE_JSON_BASE, Map.class);
+
+		// update provided values
+		List<String> versions = (List<String>) mapJson.get("fhirVersions");
+		versions.clear();
+		versions.add(theFhirVersion);
+		mapJson.replace("name", myPackageName);
+		mapJson.replace("version", myPackageVersion);
+
+		myPackageJson = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(mapJson);
+
+		ourLog.info(myPackageJson);
+	}
+
+	/**
+	 * Sets the directory where files will be created.
+	 * Should be a temp dir for tests.
+	 */
+	public ImplementationGuideCreator setDirectory(Path thePath) {
+		myDir = thePath;
+		return this;
+	}
+
+	public String getPackageName() {
+		return myPackageName;
+	}
+
+	public String getPackageVersion() {
+		return myPackageVersion;
+	}
+
+	/**
+	 * Adds a Resource to the ImplementationGuide.
+	 * No validation is done
+	 */
+	public void addResourceToIG(String theFileName, IBaseResource theResource) {
+		myResourcesToInclude.put(theFileName, theResource);
+	}
+
+	private void verifyDir() {
+		String msg = "Directory must be set first.";
+
+		assertNotNull(myDir, msg);
+		assertTrue(isNotBlank(myDir.toString()), msg);
+	}
+
+	/**
+	 * Creates an the IG from all the provided SearchParameters,
+	 * zips them up, and provides the path to the newly created gzip file.
+	 */
+	public Path createTestIG() throws IOException {
+		verifyDir();
+
+		Path sourceDir = Files.createDirectory(Path.of(myDir.toString(), "package"));
+
+		// add the package.json
+		addFileToDir(myPackageJson, "package.json", sourceDir);
+
+		// add search parameters
+		int index = 0;
+		for (Map.Entry<String, IBaseResource> nameAndResource : myResourcesToInclude.entrySet()) {
+			addFileToDir(
+					myParser.encodeResourceToString(nameAndResource.getValue()),
+					nameAndResource.getKey() + ".json",
+					sourceDir);
+			index++;
+		}
+
+		// we can add other resources here (not req'd for now)
+
+		Path outputFileName = Files.createFile(Path.of(myDir.toString(), myPackageName + ".gz.tar"));
+		GZipCreatorUtil.createTarGz(sourceDir, outputFileName);
+		return outputFileName;
+	}
+
+	private void addFileToDir(String theContent, String theFileName, Path theOutputPath) throws IOException {
+		byte[] bytes = new byte[1024];
+		int length = 0;
+
+		try (FileOutputStream outputStream = new FileOutputStream(theOutputPath.toString() + "/" + theFileName)) {
+			try (InputStream stream = new ByteArrayInputStream(theContent.getBytes(StandardCharsets.UTF_8))) {
+				while ((length = stream.read(bytes)) >= 0) {
+					outputStream.write(bytes, 0, length);
+				}
+			}
+		}
+	}
+}