Jackson Serialization Issue with Library Refresh Operation (#527)

Removed jackson elm serialization deps

- Replaced Jackson ELM serialization with JAXB
- Added shouldApplySoftwareSystemStamp to Library refresh parameters
- Added tests
- Removed tooling-cli directory from tooling module (seemed like that was committed by mistake(?))

pom.xml

@@ -13,7 +13,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <maven.compiler.release>11</maven.compiler.release>
-        <cql.version>3.9.0</cql.version>
+        <cql.version>3.10.0-SNAPSHOT</cql.version>
         <hapi.version>7.0.2</hapi.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
         <slf4j.version>2.0.5</slf4j.version>
@@ -170,18 +170,6 @@
                 <version>${cql.version}</version>
             </dependency>
 
-            <dependency>
-                <groupId>info.cqframework</groupId>
-                <artifactId>elm-jackson</artifactId>
-                <version>${cql.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>info.cqframework</groupId>
-                <artifactId>model-jackson</artifactId>
-                <version>${cql.version}</version>
-            </dependency>
-
             <dependency>
                 <groupId>info.cqframework</groupId>
                 <artifactId>elm-jaxb</artifactId>

tooling-cli/pom.xml

@@ -30,12 +30,12 @@
 
         <dependency>
             <groupId>info.cqframework</groupId>
-            <artifactId>elm-jackson</artifactId>
+            <artifactId>elm-jaxb</artifactId>
         </dependency>
 
         <dependency>
             <groupId>info.cqframework</groupId>
-            <artifactId>model-jackson</artifactId>
+            <artifactId>model-jaxb</artifactId>
         </dependency>
 
         <dependency>

tooling/pom.xml

@@ -261,13 +261,13 @@
 
         <dependency>
             <groupId>info.cqframework</groupId>
-            <artifactId>elm-jackson</artifactId>
+            <artifactId>elm-jaxb</artifactId>
             <scope>test</scope>
         </dependency>
 
         <dependency>
             <groupId>info.cqframework</groupId>
-            <artifactId>model-jackson</artifactId>
+            <artifactId>model-jaxb</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

tooling/src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshLibraryArgumentProcessor.java

@@ -24,6 +24,7 @@ public class RefreshLibraryArgumentProcessor {
     public static final String[] FHIR_VERSION_OPTIONS = {"fv", "fhir-version"};
     public static final String[] OUTPUT_ENCODING = {"e", "encoding"};
     public static final String[] VERSIONED_OPTIONS = {"v", "versioned"};
+    public static final String[] SOFTWARE_STAMP = { "ss", "stamp" };
 
     @SuppressWarnings("unused")
     public OptionParser build() {
@@ -36,6 +37,7 @@ public OptionParser build() {
         OptionSpecBuilder libraryOutputDirectoryBuilder = parser.acceptsAll(asList(Library_Output_DIRECTORY_OPTIONS),"If omitted, the libraries will overwrite any existing libraries");
         OptionSpecBuilder fhirVersionBuilder = parser.acceptsAll(asList(FHIR_VERSION_OPTIONS),"Limited to a single version of FHIR.");
         OptionSpecBuilder outputEncodingBuilder = parser.acceptsAll(asList(OUTPUT_ENCODING), "If omitted, output will be generated using JSON encoding.");
+        OptionSpecBuilder shouldApplySoftwareSystemStampBuilder = parser.acceptsAll(asList(SOFTWARE_STAMP),"Indicates whether refreshed Library resources should be stamped with the 'cqf-tooling' stamp via the cqfm-softwaresystem Extension.");
 
         OptionSpec<String> ini = iniBuilder.withOptionalArg().describedAs("IG ini file");
         OptionSpec<String> igCanonicalBasePath = igCanonicalBaseBuilder.withOptionalArg().describedAs("resource canonical base");
@@ -44,6 +46,7 @@ public OptionParser build() {
         OptionSpec<String> libraryOutputDirectoryPath = libraryOutputDirectoryBuilder.withOptionalArg().describedAs("path to the output directory for updated libraries");
         OptionSpec<String> fhirVersion = fhirVersionBuilder.withOptionalArg().describedAs("fhir version");
         OptionSpec<String> outputEncoding = outputEncodingBuilder.withOptionalArg().describedAs("desired output encoding for resources");
+        OptionSpec<String> shouldApplySoftwareSystemStamp = shouldApplySoftwareSystemStampBuilder.withOptionalArg().describedAs("Indicates whether refreshed Library resources should be stamped with the 'cqf-tooling' stamp via the cqfm-softwaresystem Extension");
 
         parser.acceptsAll(asList(OPERATION_OPTIONS),"The operation to run.");
         parser.acceptsAll(asList(VERSIONED_OPTIONS),"If omitted resources must be uniquely named.");
@@ -64,6 +67,7 @@ public RefreshLibraryParameters parseAndConvert(String[] args) {
         String cqlPath = (String)options.valueOf(CQL_PATH_OPTIONS[0]);
         String fhirVersion = (String)options.valueOf(FHIR_VERSION_OPTIONS[0]);
         String encoding = (String)options.valueOf(OUTPUT_ENCODING[0]);
+        String softwareStamp = (String)options.valueOf(SOFTWARE_STAMP[0]);
         String libraryPath = (String)options.valueOf(Library_PATH_OPTIONS[0]);
         if (libraryPath == null) {
             libraryPath = "";
@@ -77,6 +81,10 @@ public RefreshLibraryParameters parseAndConvert(String[] args) {
             outputEncodingEnum = Encoding.parse(encoding.toLowerCase());
         }
         Boolean versioned = options.has(VERSIONED_OPTIONS[0]);
+        Boolean shouldApplySoftwareSystemStamp = true;
+        if ((softwareStamp != null) && softwareStamp.equalsIgnoreCase("false")) {
+            shouldApplySoftwareSystemStamp = false;
+        }
 
         RefreshLibraryParameters lp = new RefreshLibraryParameters();
         lp.ini = ini;
@@ -87,6 +95,7 @@ public RefreshLibraryParameters parseAndConvert(String[] args) {
         lp.versioned = versioned;
         lp.libraryPath = libraryPath;
         lp.libraryOutputDirectory = libraryOutputDirectory;
+        lp.shouldApplySoftwareSystemStamp = shouldApplySoftwareSystemStamp;
 
         return lp;
     }

tooling/src/test/java/org/opencds/cqf/tooling/RefreshTest.java

@@ -1,6 +1,7 @@
 package org.opencds.cqf.tooling;
 
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
 
 import java.io.File;
 import java.io.IOException;
@@ -62,6 +63,17 @@ protected void validateCqfmSoftwareSystemExtension(String domainResourcePath) {
         }
     }
 
+    protected void validateNoCqfmSoftwareSystemExtension(String domainResourcePath) {
+        IBaseResource resource = IOUtils.readResource(domainResourcePath, getFhirContext());
+        if (resource == null || !(resource instanceof Library)) {
+            // log error
+        } else {
+            DomainResource domainResource = (DomainResource)resource;
+            Extension softwareSystemExtension = domainResource.getExtensionByUrl(cqfmSoftwareSystemExtensionUrl);
+            assertNull(softwareSystemExtension);
+        }
+    }
+
     protected void copyResourcesToTargetDir(String targetDirectory, String resourceDirectoryPath) throws IOException {
         File outputDirectory = new File(targetDirectory);
         outputDirectory.mkdirs();

tooling/src/test/java/org/opencds/cqf/tooling/library/LibraryProcessorTest.java

@@ -46,4 +46,18 @@ protected void runRefresh(String targetDirectory, String libraryResourcePath, St
         params.shouldApplySoftwareSystemStamp = true;
         getLibraryProcessor().refreshLibraryContent(params);
     }
+
+    protected void runRefresh(String targetDirectory, String libraryResourcePath, String libraryOutputDirectoryPath,
+                              String cqlResourcePath, boolean versioned, boolean shouldApplySoftwareSystemStamp) {
+        RefreshLibraryParameters params = new RefreshLibraryParameters();
+        params.encoding = Encoding.JSON;
+        params.fhirContext = getFhirContext();
+        params.libraryPath = libraryResourcePath;
+        params.libraryOutputDirectory = libraryOutputDirectoryPath;
+        params.cqlContentPath = cqlResourcePath;
+        params.ini = targetDirectory + separator + "ig.ini";
+        params.versioned = versioned;
+        params.shouldApplySoftwareSystemStamp = shouldApplySoftwareSystemStamp;
+        getLibraryProcessor().refreshLibraryContent(params);
+    }
 }

tooling/src/test/java/org/opencds/cqf/tooling/library/r4/R4LibraryProcessorTest.java

@@ -33,7 +33,7 @@ public void setUp() throws Exception {
     }
 
     @Test
-    void testRefreshOverwriteLibraries() throws Exception {
+    void testRefreshOverwriteLibrariesWithCqfmSoftwareSystemExtension() throws Exception {
         String targetDirectory = "target" + separator + "refreshLibraries" + separator + this.resourceDirectory;
         copyResourcesToTargetDir(targetDirectory, this.resourceDirectory);
 
@@ -48,6 +48,22 @@ void testRefreshOverwriteLibraries() throws Exception {
         validateCqfmSoftwareSystemExtension(targetDirectory + libraryPath);
     }
 
+    @Test
+    void testRefreshOverwriteLibrariesWithoutCqfmSoftwareSystemExtension() throws Exception {
+        String targetDirectory = "target" + separator + "refreshLibraries" + separator + this.resourceDirectory;
+        copyResourcesToTargetDir(targetDirectory, this.resourceDirectory);
+
+        String libraryPath = separator + "input" + separator + "resources" + separator + "library" + separator + "library-EXM124_FHIR4-8.2.000.json";
+        runRefresh(
+                targetDirectory,
+                targetDirectory + libraryPath, null,
+                targetDirectory + separator + "input" + separator + "pagecontent" + separator + "cql" + separator + "EXM124_FHIR4-8.2.000.cql",
+                false, false
+        );
+
+        validateNoCqfmSoftwareSystemExtension(targetDirectory + libraryPath);
+    }
+
     @Test
     void testRefreshOutputDirectory() throws Exception {
         // create a output directory under target directory