Feat/additional folder options (#6802)

* Added reusable feature set from hapifhir/hapi-fhir-jpaserver-starter#784

* Added a few sanity tests

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallationSpec.java

Co-authored-by: tadgh <[email protected]>

* Addressed most comments

* Reduced package size and added exception

* Added changelog

---------

Co-authored-by: tadgh <[email protected]>

Author: jkiddo

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_2_0/6861-support-parsing-additional-folder-resources.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 6861
+title: "Added support for parsing additional folder resources in IG packages as utility function.
+  This allows an easier way API-wise of adding e.g. test resources."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/AdditionalResourcesParser.java

@@ -0,0 +1,69 @@
+package ca.uhn.fhir.jpa.packages;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.BundleBuilder;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.jetbrains.annotations.NotNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.util.stream.Collectors;
+import java.util.*;
+
+public class AdditionalResourcesParser {
+
+	public static IBaseBundle bundleAdditionalResources(
+			Set<String> additionalResources, PackageInstallationSpec packageInstallationSpec, FhirContext fhirContext) {
+		NpmPackage npmPackage;
+		try {
+			npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(packageInstallationSpec.getPackageContents()));
+		} catch (IOException e) {
+			throw new InternalErrorException(e);
+		}
+		List<IBaseResource> resources = getAdditionalResources(additionalResources, npmPackage, fhirContext);
+
+		BundleBuilder bundleBuilder = new BundleBuilder(fhirContext);
+		resources.forEach(bundleBuilder::addTransactionUpdateEntry);
+		return bundleBuilder.getBundle();
+	}
+
+	@NotNull
+	public static List<IBaseResource> getAdditionalResources(
+			Set<String> folderNames, NpmPackage npmPackage, FhirContext fhirContext) {
+
+		List<NpmPackage.NpmPackageFolder> npmFolders = folderNames.stream()
+				.map(name -> npmPackage.getFolders().get(name))
+				.filter(Objects::nonNull)
+				.collect(Collectors.toList());
+
+		List<IBaseResource> resources = new LinkedList<>();
+		IParser parser = fhirContext.newJsonParser().setSuppressNarratives(true);
+
+		for (NpmPackage.NpmPackageFolder folder : npmFolders) {
+			List<String> fileNames;
+			try {
+				fileNames = folder.getTypes().values().stream()
+						.flatMap(Collection::stream)
+						.collect(Collectors.toList());
+			} catch (IOException e) {
+				throw new InternalErrorException(e.getMessage(), e);
+			}
+
+			resources.addAll(fileNames.stream()
+					.map(fileName -> {
+						try {
+							return new String(folder.fetchFile(fileName));
+						} catch (IOException e) {
+							throw new InternalErrorException(e.getMessage(), e);
+						}
+					})
+					.map(parser::parseResource)
+					.collect(Collectors.toList()));
+		}
+		return resources;
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallationSpec.java

@@ -29,6 +29,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 import java.util.function.Supplier;
 
 @Schema(name = "PackageInstallationSpec", description = "Defines a set of instructions for package installation")
@@ -39,7 +40,8 @@
 	"installMode",
 	"installResourceTypes",
 	"validationMode",
-	"reloadExisting"
+	"reloadExisting",
+	"additionalResourceFolders"
 })
 @ExampleSupplier({PackageInstallationSpec.ExampleSupplier.class, PackageInstallationSpec.ExampleSupplier2.class})
 @JsonInclude(JsonInclude.Include.NON_NULL)
@@ -90,6 +92,12 @@ public class PackageInstallationSpec {
 					"Any values provided here will be interpreted as a regex. Dependencies with an ID matching any regex will be skipped.")
 	private List<String> myDependencyExcludes;
 
+	@Schema(
+			description =
+					"List of folders in the package to extract additional resources from. Each folder listed will be scanned for resources which will be installed as part of package installation.")
+	@JsonProperty("additionalResourceFolders")
+	private Set<String> myAdditionalResourceFolders;
+
 	@JsonIgnore
 	private byte[] myPackageContents;
 
@@ -177,6 +185,14 @@ public void setReloadExisting(boolean reloadExisting) {
 		this.myReloadExisting = reloadExisting;
 	}
 
+	public Set<String> getAdditionalResourceFolders() {
+		return myAdditionalResourceFolders;
+	}
+
+	public void setAdditionalResourceFolders(Set<String> additionalResourceFolders) {
+		this.myAdditionalResourceFolders = additionalResourceFolders;
+	}
+
 	public PackageInstallationSpec addDependencyExclude(String theExclude) {
 		getDependencyExcludes().add(theExclude);
 		return this;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/AdditionalResourcesParserTest.java

@@ -0,0 +1,84 @@
+package ca.uhn.fhir.jpa.packages;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.ClasspathUtil;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.util.Set;
+
+import static ca.uhn.fhir.jpa.packages.AdditionalResourcesParser.bundleAdditionalResources;
+import static ca.uhn.fhir.jpa.packages.AdditionalResourcesParser.getAdditionalResources;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertThrowsExactly;
+
+public class AdditionalResourcesParserTest {
+
+	@Test
+	public void testBundleAdditionalResourcesSingleFolder() throws IOException {
+
+		// Arrange
+		var packageAsBytes = ClasspathUtil.loadResourceAsStream("/cqf-ccc.tgz").readAllBytes();
+		var packageInstallationSpec = new PackageInstallationSpec().setPackageContents(packageAsBytes).setName("fhir.cqf.ccc").setVersion("0.1.0");
+
+		// Act
+		var bundle = (Bundle) bundleAdditionalResources(Set.of("tests"), packageInstallationSpec, FhirContext.forR4Cached());
+
+		// Assert
+		assertEquals(3, bundle.getEntry().size());
+	}
+
+	@Test
+	public void testBundleAdditionalResourcesMultipleFolders() throws IOException {
+
+		// Arrange
+		var packageAsBytes = ClasspathUtil.loadResourceAsStream("/cqf-ccc.tgz").readAllBytes();
+		var packageInstallationSpec = new PackageInstallationSpec().setPackageContents(packageAsBytes).setName("fhir.cqf.ccc").setVersion("0.1.0");
+
+		// Act
+		var bundle = (Bundle) bundleAdditionalResources(Set.of("tests", "package"), packageInstallationSpec, FhirContext.forR4Cached());
+
+		// Assert
+		assertEquals(7, bundle.getEntry().size());
+	}
+
+	@Test
+	public void testBundleAdditionalResourcesUnknownFolder() throws IOException {
+
+		// Arrange
+		var packageAsBytes = ClasspathUtil.loadResourceAsStream("/cqf-ccc.tgz").readAllBytes();
+		var packageInstallationSpec = new PackageInstallationSpec().setPackageContents(packageAsBytes).setName("fhir.cqf.ccc").setVersion("0.1.0");
+
+		// Act
+		var bundle = (Bundle) bundleAdditionalResources(Set.of("testsUnknown/", "testsUnknown"), packageInstallationSpec, FhirContext.forR4Cached());
+
+		// Assert
+		assertEquals(0, bundle.getEntry().size());
+	}
+
+	@Test
+	public void testGetAdditionalResources() throws IOException {
+		// Arrange
+		var npmPackage = NpmPackage.fromPackage(ClasspathUtil.loadResourceAsStream("/cqf-ccc.tgz"));
+
+		// Act
+		var resourceList = getAdditionalResources(Set.of("tests"), npmPackage, FhirContext.forR4Cached());
+
+		// Assert
+		assertEquals(3, resourceList.size());
+	}
+
+	@Test
+	public void testVerifyExceptionHandlingInvalidPackages() {
+		// Arrange
+		Exception exception = assertThrows(InternalErrorException.class, () -> NpmPackage.fromPackage(ClasspathUtil.loadResourceAsStream("/invalid.tgz")));
+
+		// Assert
+		assertThat(exception.getMessage()).contains("HAPI-1758: Unable to find classpath resource: /invalid.tgz");
+	}
+}