Br connectathon fixes (#584)

* Do not report dependencies on model info that is loaded from the translator, or from CQF Common

* Fix attachment URL preventing CQL source file information lookup

* Fixed measure packages not including Group resource

* Fixed test case

Author: brynrhodes

tooling/src/main/java/org/opencds/cqf/tooling/library/LibraryProcessor.java

@@ -236,6 +236,9 @@ protected Library refreshGeneratedContent(Library sourceLibrary) {
             var translatorOptions = getCqlProcessor().getCqlTranslatorOptions();
             var formats = translatorOptions.getFormats();
             CqlProcessor.CqlSourceFileInformation info = getCqlProcessor().getFileInformation(attachment.getUrl());
+            if (this.parentContext != null && this.parentContext.getCanonicalBase() != null) {
+                attachment.setUrl(this.parentContext.getCanonicalBase() + "/" + fileName);
+            }
             if (info != null) {
                 if (info.getElm() != null && emptyIfNull(formats).contains(Format.XML)) {
                     sourceLibrary.addContent().setContentType("application/elm+xml").setData(info.getElm());
@@ -379,9 +382,7 @@ private Attachment loadFile(String fn) throws IOException {
                 Attachment att = new Attachment();
                 att.setContentType("text/cql");
                 att.setData(TextFile.fileToBytes(f));
-                if (this.parentContext != null && this.parentContext.getCanonicalBase() != null) {
-                    att.setUrl(this.parentContext.getCanonicalBase() + "/Library-" + f.getName());
-                }
+                att.setUrl(f.getAbsolutePath());
                 return att;
             }
         }

tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureRefreshProcessor.java

@@ -38,6 +38,7 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
         clearRelatedArtifacts(measureToUse);
 
     	Library moduleDefinitionLibrary = getModuleDefinitionLibrary(measureToUse, libraryManager, compiledLibrary, options);
+        removeModelInfoDependencies(moduleDefinitionLibrary);
         measureToUse.setDate(new Date());
         // http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/measure-cqfm
         setMeta(measureToUse, moduleDefinitionLibrary);
@@ -51,6 +52,24 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
         return measureToUse;
     }
 
+    private void removeModelInfoDependencies(Library moduleDefinitionLibrary) {
+        // NOTE: see similar logic in CqlProcessor.translateFile
+        if (moduleDefinitionLibrary.hasRelatedArtifact()) {
+            for (int i = moduleDefinitionLibrary.getRelatedArtifact().size() - 1; i >= 0; i--) {
+                RelatedArtifact relatedArtifact = moduleDefinitionLibrary.getRelatedArtifact().get(i);
+                if (relatedArtifact != null && relatedArtifact.hasResource() && (
+                    relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/QICore-ModelInfo")
+                            || relatedArtifact.getResource().startsWith("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo")
+                            || relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/USCore-ModelInfo")
+                )) {
+                    // Do not report dependencies on model info loaded from the translator, or
+                    // from CQF Common (because these should be loaded from Using CQL now)
+                    moduleDefinitionLibrary.getRelatedArtifact().remove(i);
+                }
+            }
+        }
+    }
+
     private Library getModuleDefinitionLibrary(Measure measureToUse, LibraryManager libraryManager, CompiledLibrary compiledLibrary, CqlCompilerOptions options){
         Set<String> expressionList = getExpressions(measureToUse);
         DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();

tooling/src/main/java/org/opencds/cqf/tooling/packaging/r4/PackageMeasure.java

@@ -140,17 +140,18 @@ public void output() {
 
         if (isIncludeTests() && testPackage != null) {
             logger.info("Packaging {} Tests...", testPackage.getTests().size());
-            if (testPackage.getGroup() != null) {
-                IOUtils.writeResource(testPackage.getGroup(), measureFilesOutputPath, IOUtils.Encoding.JSON, getFhirContext(),
-                        true, "Group-" + testPackage.getGroup().getIdElement().getIdPart());
-            }
             testPackage.getTests().forEach(
                     test -> {
                         dependencies.addAll(BundleUtils.getR4ResourcesFromBundle((Bundle) test));
                         IOUtils.writeBundle(test, measureFilesOutputPath, IOUtils.Encoding.JSON,
                                 getFhirContext(), test.getIdElement().getIdPart());
                     }
             );
+            if (testPackage.getGroup() != null) {
+                dependencies.add(testPackage.getGroup());
+                IOUtils.writeResource(testPackage.getGroup(), measureFilesOutputPath, IOUtils.Encoding.JSON, getFhirContext(),
+                        true, "Group-" + testPackage.getGroup().getIdElement().getIdPart());
+            }
         }
 
         dependencies.add(mainArtifact);

tooling/src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java

@@ -432,7 +432,20 @@ private void translateFile(LibraryManager libraryManager, File file, CqlCompiler
                     //result.extension.addAll(requirementsLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"));
 
                     // Extract relatedArtifact data (models, libraries, code systems, and value sets)
-                    result.relatedArtifacts.addAll(requirementsLibrary.getRelatedArtifact());
+                    for (RelatedArtifact relatedArtifact : requirementsLibrary.getRelatedArtifact()) {
+                        // NOTE: see similar logic in MeasureRefreshProcessor.removeModelInfoDependencies
+                        if (relatedArtifact.hasResource() && (
+                                relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/QICore-ModelInfo")
+                                    || relatedArtifact.getResource().startsWith("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo")
+                                    || relatedArtifact.getResource().startsWith("http://hl7.org/fhir/Library/USCore-ModelInfo")
+                        )) {
+                            // Do not report dependencies on model info loaded from the translator, or
+                            // from CQF Common (because these should be loaded from Using CQL now)
+                            continue;
+                        }
+
+                        result.relatedArtifacts.add(relatedArtifact);
+                    }
 
                     // Extract parameter data and validate result types are supported types
                     result.parameters.addAll(requirementsLibrary.getParameter());

tooling/src/test/java/org/opencds/cqf/tooling/processor/IGProcessorTest.java

@@ -61,6 +61,7 @@ public class IGProcessorTest extends RefreshTest {
 	private final String BUNDLE_TYPE = "Bundle";
 	private final String LIB_TYPE = "Library";
 	private final String MEASURE_TYPE = "Measure";
+	private final String GROUP_TYPE = "Group";
 
 	private final String INI_LOC = "target" + separator + "refreshIG" + separator + "ig.ini";
 
@@ -136,10 +137,11 @@ void testRefreshIG() throws Exception {
 							// ensure "resourceType" exists
 							if (map.containsKey(RESOURCE_TYPE)) {
 								String parentResourceType = (String) map.get(RESOURCE_TYPE);
-								// if Library, resource will produce a "Measure" in main bundled file:
+								// if Library, resource will produce a "Measure" and a "Group" in main bundled file:
 								if (parentResourceType.equalsIgnoreCase(LIB_TYPE)) {
 									resourceTypeMap.put(MEASURE_TYPE + "_" + map.get(ID), MEASURE_TYPE);
 									resourceTypeMap.put(LIB_TYPE + "_" + map.get(ID), LIB_TYPE);
+									resourceTypeMap.put(GROUP_TYPE + "_" + map.get(ID), GROUP_TYPE);
 								} else if (parentResourceType.equalsIgnoreCase(BUNDLE_TYPE)) {
 									// file is a bundle type, loop through resources in entry list, build up map of
 									// <id, resourceType>: