Add a test for nested dependencies.

Src/java/cqf-fhir-npm/build.gradle

@@ -3,4 +3,5 @@
 dependencies {
  implementation project(':cql-to-elm')
  implementation group: 'com.google.code.gson', name: 'gson', version: '2.9.1'
+ implementation group:'org.apache.commons', name: 'commons-compress', version: '1.20'
 }

Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmPackageManager.java

@@ -15,18 +15,20 @@
 import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.formats.FormatUtilities;
+import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.model.Constants;
-import org.hl7.fhir.r5.model.ImplementationGuide;
+import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideDependsOnComponent;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.json.JsonTrackingParser;
+import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.npm.ToolsVersion;
 
 public class NpmPackageManager implements IWorkerContext.ILoggingService {
- private FilesystemPackageCacheManager pcm;
+ private BasePackageCacheManager pcm;
  private List<NpmPackage> npmList = new ArrayList<>();
  public List<NpmPackage> getNpmList() {
  return npmList;
@@ -58,7 +60,7 @@ public static NpmPackageManager fromStream(InputStream is, String version) throw
  return new NpmPackageManager((ImplementationGuide) versionConvertor_40_50.convertResource(FormatUtilities.loadFile(is)), version);
  }
 
- public NpmPackageManager(ImplementationGuide sourceIg, String version) throws IOException {
+ NpmPackageManager(ImplementationGuide sourceIg, String version, BasePackageCacheManager pcm) throws IOException {
  if (version == null || version.equals("")) {
  throw new IllegalArgumentException("version is required");
  }
@@ -71,15 +73,7 @@ public NpmPackageManager(ImplementationGuide sourceIg, String version) throws IO
 
  this.sourceIg = sourceIg;
 
- try {
- // userMode indicates whether the packageCache is within the working directory or in the user home
- pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
- }
- catch(IOException e) {
- String message = "error creating the FilesystemPackageCacheManager";
- logMessage(message);
- throw new NpmPackageManagerException(message, e);
- }
+ this.pcm = pcm;
 
  loadCorePackage();
 
@@ -90,20 +84,36 @@ public NpmPackageManager(ImplementationGuide sourceIg, String version) throws IO
  }
  }
 
+
+ public NpmPackageManager(ImplementationGuide sourceIg, String version) throws IOException {
+ this(sourceIg, version, createPackageManager());
+ }
+
+ private static FilesystemPackageCacheManager createPackageManager() {
+ try {
+ // userMode indicates whether the packageCache is within the working directory or in the user home
+ return new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+ }
+ catch(IOException e) {
+ String message = "error creating the FilesystemPackageCacheManager";
+ throw new NpmPackageManagerException(message, e);
+ }
+ }
+
  private void loadCorePackage() {
  NpmPackage pi = null;
 
  String v = version.equals(Constants.VERSION) ? "current" : version;
 
  logMessage("Core Package "+ VersionUtilities.packageForVersion(v)+"#"+v);
  try {
- pi = pcm.loadPackage(VersionUtilities.packageForVersion(v), v); 
+ pi = pcm.loadPackage(VersionUtilities.packageForVersion(v), v);
  }
  catch(Exception e) {
  try {
  // Appears to be race condition in FHIR core where they are
  // loading a custom cert provider.
- pi = pcm.loadPackage(VersionUtilities.packageForVersion(v), v); 
+ pi = pcm.loadPackage(VersionUtilities.packageForVersion(v), v);
  }
  catch (Exception ex) {
  throw new NpmPackageManagerException("Error loading core package", e);
@@ -160,6 +170,12 @@ private void loadIg(ImplementationGuide.ImplementationGuideDependsOnComponent de
  logMessage("The correct canonical URL for this dependency is "+cu);
  }
  }
+ // for (String dependency: pi.dependencies()) {
+ // String[] depParts = dependency.split("#");
+ // String depName = depParts[0];
+ // String depVersion = depParts[1];
+ // loadIg(new ImplementationGuideDependsOnComponent().setPackageId(depName).setVersion(depVersion), -1);
+ // }
  }
 
  private String determineCanonical(String url, String path) throws FHIRException {

Src/java/cqf-fhir-npm/src/test/java/org/cqframework/fhir/npm/NpmPackageManagerTests.java

@@ -1,15 +1,29 @@
 package org.cqframework.fhir.npm;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
 import java.io.IOException;
 import java.io.InputStream;
 
+import java.util.Arrays;
+import java.util.List;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import javax.annotation.Nullable;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
+import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r5.model.ImplementationGuide;
+import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideDependsOnComponent;
+import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.PackageGenerator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.testng.annotations.Ignore;
@@ -95,6 +109,58 @@ public void TestModelInfoProvider() throws IOException {
  assertTrue(mi.getName().equals("QICore"));
  }
 
+ @Test
+ public void TestNestedDependencies() throws IOException {
+ ImplementationGuide ig = new ImplementationGuide()
+ .setPackageId("test.source")
+ .addDependsOn(new ImplementationGuideDependsOnComponent()
+ .setPackageId("test.dep1").setVersion("1.0.0"))
+ .addDependsOn(new ImplementationGuideDependsOnComponent()
+ .setPackageId("test.dep2").setVersion("1.0.0"));
+
+ NpmPackageManager pm = new NpmPackageManager(ig, "4.0.1", new FakePackageManager());
+
+ List<String> packageNames = pm.getNpmList().stream().map(NpmPackage::name)
+ .collect(Collectors.toList());
+ List<String> expectedDependencies = Arrays.asList("hl7.fhir.r4.core", "test.dep1", "test.dep3",
+ "test.dep2", "test.dep4");
+ assertEquals(packageNames.toString(), expectedDependencies.toString());
+
+ }
+
+ private static class FakePackageManager extends BasePackageCacheManager {
+
+ @Override
+ public NpmPackage loadPackageFromCacheOnly(String id, @Nullable String version)
+ throws IOException {
+ return loadPackage(id, version);
+ }
+
+ @Override
+ public NpmPackage addPackageToCache(String id, String version,
+ InputStream packageTgzInputStream, String sourceDesc) throws IOException {
+ return loadPackage(id, version);
+ }
+
+ @Override
+ public NpmPackage loadPackage(String id, String version) throws FHIRException, IOException {
+ PackageGenerator packageGenerator = new PackageGenerator().name(id).version(version);
+ switch (id) {
+ case "test.dep1":
+ return NpmPackage.empty(packageGenerator.dependency("test.dep3", version));
+ case "test.dep2":
+ return NpmPackage.empty(packageGenerator.dependency("test.dep4", version));
+ default:
+ return NpmPackage.empty(packageGenerator);
+ }
+ }
+
+ @Override
+ public String getPackageUrl(String packageId) throws IOException {
+ return String.format("http:https://%s/ImplmentationGuide/", packageId);
+ }
+ }
+
  @Override
  public void logMessage(String msg) {
  logger.info(msg);

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/Cql2ElmVisitor.java

@@ -3497,6 +3497,7 @@ else if (classType.getPrimaryCodePath() != null) {
  return result;
  }
 
+ @SuppressWarnings("unchecked")
  private Retrieve buildRetrieve(cqlParser.RetrieveContext ctx, boolean useStrictRetrieveTyping, NamedType namedType,
  ClassType classType, String codePath, String codeComparator, Property property,
  DataType propertyType, Exception propertyException, Expression terminology) {