Added service loader pattern for deserialization

engine.fhir/pom.xml

@@ -41,10 +41,6 @@
             <artifactId>jakarta.xml.bind-api</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>ca.uhn.hapi.fhir</groupId>
-            <artifactId>hapi-fhir-client</artifactId>
-        </dependency>
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-structures-dstu2</artifactId>
@@ -86,7 +82,13 @@
             <artifactId>org.eclipse.persistence.moxy</artifactId>
             <scope>test</scope>
         </dependency>
-
+        <!-- Uses Jackson to load some libraries for testing -->
+        <dependency>
+            <groupId>org.opencds.cqf.cql</groupId>
+            <artifactId>engine.jackson</artifactId>
+            <version>2.0.0-SNAPSHOT</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>info.cqframework</groupId>
             <artifactId>cql-to-elm</artifactId>
@@ -112,6 +114,13 @@
             <artifactId>elm-jackson</artifactId>
             <scope>test</scope>
         </dependency>
+
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-client</artifactId>
+            <scope>test</scope>
+        </dependency>
+
     </dependencies>
 
     <build>

engine.fhir/src/test/java/org/hl7/fhirpath/TestLibraryLoader.java

@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.io.StringReader;
+import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -13,19 +14,9 @@
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.cqframework.cql.elm.execution.Library;
 import org.cqframework.cql.elm.execution.VersionedIdentifier;
-import org.hl7.cql_annotations.r1.CqlToElmBase;
-import org.opencds.cqf.cql.engine.elm.serialization.CqlToElmBaseMixIn;
-import org.opencds.cqf.cql.engine.execution.JsonCqlLibraryReader;
+import org.cqframework.cql.elm.serializing.ElmLibraryWriterFactory;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.MapperFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.databind.json.JsonMapper;
-import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
+import org.opencds.cqf.cql.engine.serializing.jackson.JsonCqlLibraryReader;
 
 public class TestLibraryLoader implements LibraryLoader {
 
@@ -73,25 +64,16 @@ private Library loadLibrary(VersionedIdentifier libraryIdentifier) {
         CompiledLibrary compiledLibrary = libraryManager.resolveLibrary(identifier, CqlTranslatorOptions.defaultOptions(), errors);
         String json;
         try {
-            ObjectMapper mapper = JsonMapper.builder()
-                .defaultMergeable(true)
-                .enable(SerializationFeature.WRAP_ROOT_VALUE)
-                .enable(SerializationFeature.INDENT_OUTPUT)
-                .enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
-                .enable(MapperFeature.USE_BASE_TYPE_AS_DEFAULT_IMPL)
-                .defaultPropertyInclusion(JsonInclude.Value.construct(JsonInclude.Include.NON_NULL, JsonInclude.Include.NON_NULL))
-                .addModule(new JaxbAnnotationModule())
-                .addMixIn(CqlToElmBase.class, CqlToElmBaseMixIn.class)
-                .build();
-
-            json = mapper.writeValueAsString(compiledLibrary.getLibrary());
-        } catch (JsonProcessingException e) {
+            StringWriter writer = new StringWriter();
+            ElmLibraryWriterFactory.getWriter("application/elm+json").write(compiledLibrary.getLibrary(), writer);
+            json = writer.getBuffer().toString();
+        } catch (IOException e) {
             throw new RuntimeException(String.format("Errors encountered while loading library %s: %s", libraryIdentifier.getId(), e.getMessage()));
         }
 
         Library library = null;
         try {
-            library = JsonCqlLibraryReader.read(new StringReader(json));
+            library = new JsonCqlLibraryReader().read(new StringReader(json));
         } catch (IOException e) {
             throw new RuntimeException(String.format("Errors encountered while loading library %s: %s", libraryIdentifier.getId(), e.getMessage()));
         }

engine.fhir/src/test/java/org/hl7/fhirpath/TranslatorHelper.java

@@ -7,7 +7,7 @@
 import org.fhir.ucum.UcumEssenceService;
 import org.fhir.ucum.UcumException;
 import org.fhir.ucum.UcumService;
-import org.opencds.cqf.cql.engine.execution.JsonCqlLibraryReader;
+import org.opencds.cqf.cql.engine.serializing.jackson.JsonCqlLibraryReader;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 
 import java.io.IOException;
@@ -60,7 +60,7 @@ public Library translate(String cql) throws UcumException {
         String json = translator.toJson();
 
         try {
-            return JsonCqlLibraryReader.read(new StringReader(json));
+            return new JsonCqlLibraryReader().read(new StringReader(json));
         } catch (IOException e) {
             // TODO Auto-generated catch block
             e.printStackTrace();

engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/data/FhirExecutionTestBase.java

@@ -11,10 +11,10 @@
 import org.fhir.ucum.UcumException;
 import org.fhir.ucum.UcumService;
 import org.opencds.cqf.cql.engine.data.CompositeDataProvider;
-import org.opencds.cqf.cql.engine.execution.JsonCqlLibraryReader;
 import org.opencds.cqf.cql.engine.fhir.model.*;
 import org.opencds.cqf.cql.engine.fhir.retrieve.RestFhirRetrieveProvider;
 import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
+import org.opencds.cqf.cql.engine.serializing.jackson.JsonCqlLibraryReader;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 
@@ -106,14 +106,14 @@ public void beforeEachTestMethod() throws JAXBException, IOException, UcumExcept
                 for (Map.Entry<String, CompiledLibrary> entry : libraryManager.getCompiledLibraries().entrySet()) {
                     String jsonContent = CqlTranslator.convertToJson(entry.getValue().getLibrary());
                     StringReader sr = new StringReader(jsonContent);
-                    libraries.put(entry.getKey(), JsonCqlLibraryReader.read(sr));
+                    libraries.put(entry.getKey(), new JsonCqlLibraryReader().read(sr));
                     if (entry.getKey().equals(fileName)) {
                         library = libraries.get(entry.getKey());
                     }
                 }
 
                 if (library == null) {
-                    library = JsonCqlLibraryReader.read(new StringReader(translator.toJson()));
+                    library = new JsonCqlLibraryReader().read(new StringReader(translator.toJson()));
                     libraries.put(fileName, library);
                 }
             } catch (IOException e) {

engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/data/TestLibraryLoader.java

@@ -1,11 +1,11 @@
 package org.opencds.cqf.cql.engine.fhir.data;
 
+import java.util.Map;
+
 import org.cqframework.cql.elm.execution.Library;
 import org.cqframework.cql.elm.execution.VersionedIdentifier;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 
-import java.util.Map;
-
 public class TestLibraryLoader implements LibraryLoader {
     private Map<String, Library> libraries;
 

engine.jackson/pom.xml

@@ -0,0 +1,118 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.opencds.cqf.cql</groupId>
+        <artifactId>engine.shared</artifactId>
+        <version>2.0.0-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>engine.jackson</artifactId>
+    <packaging>jar</packaging>
+
+    <name>engine.jackson</name>
+    <description>CQL Engine Jackson Readers</description>
+    <url>https://github.com/DBCG/cql_engine/tree/master/engine.jaxb</url>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.opencds.cqf.cql</groupId>
+            <artifactId>engine</artifactId>
+            <version>2.0.0-SNAPSHOT</version>
+        </dependency>
+
+        <!-- Jackson dependencies -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>${jackson-databind.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.module</groupId>
+            <artifactId>jackson-module-jaxb-annotations</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-xml</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
+
+        <!-- This depedency adds to the javax.xml.namespace package which is not valid in Java 9+-->
+        <dependency>
+            <groupId>xpp3</groupId>
+            <artifactId>xpp3</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>xpp3</groupId>
+            <artifactId>xpp3_xpath</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>cql-to-elm</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>model-jackson</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>elm-jackson</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+    <build>
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.jacoco</groupId>
+                    <artifactId>jacoco-maven-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>jacoco-check</id>
+                            <phase>verify</phase>
+                            <goals>
+                                <goal>check</goal>
+                            </goals>
+                        </execution>
+                    </executions>
+                    <configuration>
+                        <!-- generated code -->
+                        <excludes>
+                            <exclude>**/org/cqframework/**</exclude>
+                        </excludes>
+                        <rules>
+                            <rule>
+                                <element>BUNDLE</element>
+                                <limits>
+                                    <limit>
+                                        <counter>LINE</counter>
+                                        <value>COVEREDRATIO</value>
+                                        <minimum>0.40</minimum>
+                                    </limit>
+                                </limits>
+                            </rule>
+                        </rules>
+                    </configuration>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+    </build>
+</project>

engine.jackson/src/main/java/org/opencds/cqf/cql/engine/serializing/jackson/CqlLibraryReaderProvider.java

@@ -0,0 +1,18 @@
+package org.opencds.cqf.cql.engine.serializing.jackson;
+
+import org.opencds.cqf.cql.engine.serializing.CqlLibraryReader;
+
+public class CqlLibraryReaderProvider implements org.opencds.cqf.cql.engine.serializing.CqlLibraryReaderProvider {
+    @Override
+    public CqlLibraryReader create(String contentType) {
+        if (contentType == null) {
+            contentType = "application/elm+json";
+        }
+
+        switch (contentType) {
+            case "application/elm+xml": return new XmlCqlLibraryReader();
+            case "application/elm+json":
+            default: return new JsonCqlLibraryReader();
+        }
+    }
+}

engine.jackson/src/main/java/org/opencds/cqf/cql/engine/serializing/jackson/JsonCqlLibraryReader.java

@@ -0,0 +1,41 @@
+package org.opencds.cqf.cql.engine.serializing.jackson;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Reader;
+import java.net.URI;
+import java.net.URL;
+
+import org.cqframework.cql.elm.execution.Library;
+import org.opencds.cqf.cql.engine.serializing.CqlLibraryReader;
+
+public class JsonCqlLibraryReader implements CqlLibraryReader {
+
+    public JsonCqlLibraryReader() {
+    }
+
+    public Library read(File file) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(file, Library.class);
+    }
+
+    public Library read(URL url) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(url, Library.class);
+    }
+
+    public Library read(URI uri) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(uri.toURL(), Library.class);
+    }
+
+    public Library read(String string) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(string, Library.class);
+    }
+
+    public Library read(InputStream inputStream) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(inputStream, Library.class);
+    }
+
+    public Library read(Reader reader) throws IOException {
+        return JsonCqlMapper.getMapper().readValue(reader, Library.class);
+    }
+}