Merge branch 'master' into feature-445-cqlOptions-support

pom.xml

@@ -5,19 +5,18 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-parent</artifactId>
-    <version>2.5.0-SNAPSHOT</version>
-
+    <version>2.6.0-SNAPSHOT</version>
 
     <packaging>pom</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cql-engine.version>2.9.0-SNAPSHOT</cql-engine.version>
+        <cql-engine.version>3.3.2</cql-engine.version>
         <cql-evaluator.version>2.6.0</cql-evaluator.version>
-        <cqframework.version>2.9.0-SNAPSHOT</cqframework.version>
-        <hapi.version>6.0.1</hapi.version>
-        <core.version>5.6.36</core.version>
+        <cqframework.version>3.3.2</cqframework.version>
+        <hapi.version>6.8.0</hapi.version>
+        <core.version>6.0.22</core.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
     </properties>
 
@@ -217,6 +216,11 @@
                 <artifactId>FastInfoset</artifactId>
                 <version>1.2.18</version>
             </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-core</artifactId>
+                <version>2.15.2</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 
@@ -351,6 +355,7 @@
                     <version>3.0.0-M5</version>
                     <configuration>
                         <argLine>-Xmx4096m</argLine>
+                        <classesDirectory>${project.build.outputDirectory}</classesDirectory>
                     </configuration>
                     <executions>
                         <execution>

tooling-cli/pom.xml

@@ -6,12 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>2.5.0-SNAPSHOT</version>
+        <version>2.6.0-SNAPSHOT</version>
     </parent>
 
-    <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-cli</artifactId>
-    <version>2.5.0-SNAPSHOT</version>
+    <version>2.6.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling CLI</description>
@@ -20,8 +19,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>2.5.0-SNAPSHOT</version>
-            <!-- <packaging>jar</packaging> -->
+            <version>2.6.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>
@@ -35,6 +33,19 @@
             <artifactId>org.eclipse.persistence.moxy</artifactId>
             <version>2.7.7</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.reflections</groupId>
+            <artifactId>reflections</artifactId>
+            <version>0.10.2</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>7.7.0</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/Main.java

@@ -123,13 +123,14 @@
             - This tooling decomposes a Bundle entry into separate resource files
             - Accepts Bundles with .json or .xml extensions
 
-        - MAT Bundle extraction
-        	- mvn exec:java -Dexec.args="[-ExtractMatBundle] [Bundle file path] (-v)
-        	- Example: mvn exec:java -Dexec.args="-ExtractMatBundle /Users/mholck/Development/ecqm-content-r4/bundles/mat/EXM124/EXM124.json -v=r4"
-        	- This tooling extracts out the resources and CQL from a MAT export bundle and puts them in the appropriate directories
-        	- Accepts Bundles with .json or .xml extensions
-        	- version = FHIR version { stu3, r4 }
-                Default version: r4
+- MAT Bundle extraction
+    - mvn exec:java -Dexec.args="[-ExtractMatBundle] [Bundle file path] (-v) (-dir)
+    - Example: mvn exec:java -Dexec.args="-ExtractMatBundle /Users/mholck/Development/ecqm-content-r4/bundles/mat/EXM124/EXM124.json -v=r4"
+    - This tooling extracts out the resources and CQL from a MAT export bundle and puts them in the appropriate directories
+    - Accepts Bundles with .json or .xml extensions
+    - version = FHIR version { stu3, r4 }
+        Default version: r4
+    - dir = Directory indicator. To process the input location as a directory of files, the input should point to a valid directory and the -dir flag should be present in the arguments list.
 
         - Generate StructureDefinitions from ModelInfo
             - command: mvn exec:java -Dexec.args="[-GenerateSDs] [path to modelinfo xml] (-outputpath | -op) (-encoding | -e)"
@@ -218,7 +219,58 @@
 
         */
 
+//import org.opencds.cqf.tooling.exception.InvalidOperationArgs;
+//import org.opencds.cqf.tooling.exception.InvalidOperationInitialization;
+//import org.opencds.cqf.tooling.exception.OperationNotFound;
+//import org.opencds.cqf.tooling.operations.ExecutableOperation;
+//import org.opencds.cqf.tooling.operations.Operation;
+//import org.reflections.Reflections;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+//import java.lang.reflect.InvocationTargetException;
+//import java.util.HashMap;
+//import java.util.Map;
+//import java.util.Set;
+
 public class Main {
+    private static final Logger logger = LoggerFactory.getLogger(Main.class);
+
+// TODO: Uncomment this block and imports once operation refactor is ready
+//    private static Map<String, Class<?>> operationClassMap;
+//
+//    public static void main(String[] args) {
+//        if (args == null || args.length == 0) {
+//            logger.error("cqf-tooling version: {}", Main.class.getPackage().getImplementationVersion());
+//            throw new OperationNotFound(
+//                    "Requests must include which operation to run as a command line argument. See docs for examples on how to use this project.");
+//        }
+//
+//        // NOTE: we may want to use the Spring Context Library to find the annotated classes
+//        if (operationClassMap == null) {
+//            operationClassMap = new HashMap<>();
+//            Reflections reflections = new Reflections("org.opencds.cqf.tooling.operations");
+//            Set<Class<?>> operationClasses = reflections
+//                    .getTypesAnnotatedWith(Operation.class);
+//            operationClasses.forEach(clazz -> operationClassMap.put(clazz.getAnnotation(Operation.class).name(), clazz));
+//        }
+//
+//        String operation = args[0];
+//        if (!operation.startsWith("-")) {
+//            throw new InvalidOperationArgs(
+//                    "Invalid operation syntax: " + operation + ". Operations must be declared with a \"-\" prefix");
+//        }
+//
+//        try {
+//            ExecutableOperation executableOperation = OperationFactory.createOperation(
+//                    operation, operationClassMap.get(operation.substring(1)), args);
+//            if (executableOperation != null) {
+//                executableOperation.execute();
+//            }
+//        } catch (InvocationTargetException | NoSuchMethodException | InstantiationException | IllegalAccessException e) {
+//            throw new InvalidOperationInitialization(e.getMessage(), e);
+//        }
+//    }
 
     public static void main(String[] args) {
         if (args.length == 0) {

tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java

@@ -1,8 +1,11 @@
 package org.opencds.cqf.tooling.cli;
 
-//import org.opencds.cqf.tooling.jsonschema.SchemaGenerator;
 import org.opencds.cqf.tooling.casereporting.transformer.ErsdTransformer;
 import org.opencds.cqf.tooling.dateroller.DataDateRollerOperation;
+import org.opencds.cqf.tooling.exception.InvalidOperationArgs;
+import org.opencds.cqf.tooling.exception.OperationNotFound;
+import org.opencds.cqf.tooling.operations.ExecutableOperation;
+import org.opencds.cqf.tooling.operations.OperationParam;
 import org.opencds.cqf.tooling.terminology.templateToValueSetGenerator.TemplateToValueSetGenerator;
 import org.apache.commons.lang3.NotImplementedException;
 import org.opencds.cqf.tooling.Operation;
@@ -40,9 +43,92 @@
 import org.opencds.cqf.tooling.terminology.VSACBatchValueSetGenerator;
 import org.opencds.cqf.tooling.terminology.VSACValueSetGenerator;
 import org.opencds.cqf.tooling.terminology.distributable.DistributableValueSetGenerator;
+import org.opencds.cqf.tooling.utilities.OperationUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.util.HashMap;
+import java.util.Map;
 
 
 class OperationFactory {
+    private static final Logger logger = LoggerFactory.getLogger(OperationFactory.class);
+    private static String operationName;
+    private static Map<String, String> paramMap;
+    private static boolean showHelpMenu = false;
+
+    private OperationFactory() {
+
+    }
+
+    private static void processArgs(String[] args) {
+        paramMap = new HashMap<>();
+        for (int i = 1; i < args.length; ++i) {
+            if (OperationUtils.isHelpArg(args[i])) {
+                showHelpMenu = true;
+                return;
+            }
+            String[] argAndValue = args[i].split("=", 2);
+            if (argAndValue.length == 2) {
+                paramMap.put(argAndValue[0].replace("-", ""), argAndValue[1]);
+            }
+            else {
+                throw new InvalidOperationArgs(String.format(
+                        "Invalid argument: %s found for operation: %s", args[i], operationName));
+            }
+        }
+    }
+
+    private static ExecutableOperation initialize(ExecutableOperation operation)
+            throws NoSuchMethodException, InvocationTargetException, IllegalAccessException {
+        for (Field field : operation.getClass().getDeclaredFields()) {
+            if (field.isAnnotationPresent(OperationParam.class)) {
+                boolean isInitialized = false;
+                for (String alias : field.getAnnotation(OperationParam.class).alias()) {
+                    if (paramMap.containsKey(alias)) {
+                        Class<?> paramType = OperationUtils.getParamType(operation,
+                                field.getAnnotation(OperationParam.class).setter());
+                        operation.getClass().getDeclaredMethod(
+                                field.getAnnotation(OperationParam.class).setter(), paramType
+                        ).invoke(operation, OperationUtils.mapParamType(paramMap.get(alias), paramType));
+                        isInitialized = true;
+                    }
+                }
+                if (!isInitialized) {
+                    if (field.getAnnotation(OperationParam.class).required()) {
+                        throw new InvalidOperationArgs("Missing required argument: " + field.getName());
+                    }
+                    else if (!field.getAnnotation(OperationParam.class).defaultValue().isEmpty()) {
+                        Class<?> paramType = OperationUtils.getParamType(operation,
+                                field.getAnnotation(OperationParam.class).setter());
+                        operation.getClass().getDeclaredMethod(
+                                field.getAnnotation(OperationParam.class).setter(), paramType
+                        ).invoke(operation, OperationUtils.mapParamType(
+                                field.getAnnotation(OperationParam.class).defaultValue(), paramType));
+                    }
+                }
+            }
+        }
+        return operation;
+    }
+
+    static ExecutableOperation createOperation(String operationName, Class<?> operationClass, String[] args)
+            throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
+        if (operationClass == null) {
+            throw new OperationNotFound("Unable to resolve operation: " + operationName);
+        }
+        OperationFactory.operationName = operationName;
+        processArgs(args);
+        if (showHelpMenu) {
+            logger.info(OperationUtils.getHelpMenu(
+                    (ExecutableOperation) operationClass.getDeclaredConstructor().newInstance()));
+            showHelpMenu = false;
+            return null;
+        }
+        return initialize((ExecutableOperation) operationClass.getDeclaredConstructor().newInstance());
+    }
 
     static Operation createOperation(String operationName) {
         switch (operationName) {

tooling-cli/src/test/java/org/opencds/cqf/tooling/cli/OperationInitializationIT.java

@@ -0,0 +1,37 @@
+package org.opencds.cqf.tooling.cli;
+
+import org.opencds.cqf.tooling.exception.InvalidOperationArgs;
+import org.opencds.cqf.tooling.exception.OperationNotFound;
+import org.testng.Assert;
+import org.testng.annotations.Ignore;
+import org.testng.annotations.Test;
+
+public class OperationInitializationIT {
+   @Test
+   @Ignore("Skipped until operation refactor is ready")
+   void missingOperationName() {
+      String[] args = new String[]{};
+      Assert.assertThrows(OperationNotFound.class, () -> Main.main(args));
+   }
+
+   @Test
+   @Ignore("Skipped until operation refactor is ready")
+   void invalidOperationName() {
+      String[] args = new String[]{ "-NonexistentOperationName" };
+      Assert.assertThrows(OperationNotFound.class, () -> Main.main(args));
+   }
+
+   @Test
+   @Ignore("Skipped until operation refactor is ready")
+   void InvalidOperationDeclaration() {
+      String[] args = new String[]{ "BundleResources", "-ptr=some/directory/path" };
+      Assert.assertThrows(InvalidOperationArgs.class, () -> Main.main(args));
+   }
+
+   @Test
+   @Ignore("Skipped until operation refactor is ready")
+   void missingRequiredOperationArgs() {
+      String[] args = new String[]{ "-BundleResources" };
+      Assert.assertThrows(InvalidOperationArgs.class, () -> Main.main(args));
+   }
+}