From ff83a903815a73dc1f7edd21decb25567b0db793 Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Tue, 12 Mar 2024 07:59:22 -0400
Subject: [PATCH] Support for Translator 3.7.1 (#40)

* Support for Translator 3.7.1

* clean up comment
---
 pom.xml                                       | 16 +++++++++--
 .../FormatFailureException.java               |  6 ++--
 .../FormatterResource.java                    | 22 +++++++--------
 .../bonnie/cqlTranslationServer/Main.java     |  4 +--
 .../TranslationFailureException.java          |  6 ++--
 .../TranslationResource.java                  | 28 +++++++++----------
 .../FormatterResourceTest.java                | 14 +++++-----
 .../TranslationResourceTest.java              | 28 +++++++++++--------
 8 files changed, 69 insertions(+), 55 deletions(-)

diff --git a/pom.xml b/pom.xml
index 968a8da..b6ddcaa 100644
--- a/pom.xml
+++ b/pom.xml
@@ -53,7 +53,7 @@
     <dependency>
       <groupId>org.glassfish.jaxb</groupId>
       <artifactId>jaxb-runtime</artifactId>
-      <version>2.4.0-b180830.0438</version>
+      <version>3.1.0-M1</version>
       <scope>runtime</scope>
     </dependency>
     <dependency>
@@ -121,6 +121,16 @@
       <artifactId>xpp3</artifactId>
       <version>1.1.6</version>
     </dependency>
+    <dependency>
+      <groupId>jakarta.validation</groupId>
+      <artifactId>jakarta.validation-api</artifactId>
+      <version>3.1.0-M1</version>
+    </dependency>
+    <dependency>
+      <groupId>jakarta.xml.bind</groupId>
+      <artifactId>jakarta.xml.bind-api</artifactId>
+      <version>3.0.1</version>
+    </dependency>
   </dependencies>
 
   <build>
@@ -184,8 +194,8 @@
   </build>
 
   <properties>
-    <cql.version>3.3.2</cql.version>
-    <jersey.version>2.41</jersey.version>
+    <cql.version>3.7.1</cql.version>
+    <jersey.version>3.0.12</jersey.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
   </properties>
 </project>
diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatFailureException.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatFailureException.java
index 2ffd668..f7da435 100644
--- a/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatFailureException.java
+++ b/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatFailureException.java
@@ -1,9 +1,9 @@
 package org.mitre.bonnie.cqlTranslationServer;
 
 import java.util.List;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
 
 public class FormatFailureException extends WebApplicationException {
 
diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatterResource.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatterResource.java
index a363049..0326977 100644
--- a/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatterResource.java
+++ b/src/main/java/org/mitre/bonnie/cqlTranslationServer/FormatterResource.java
@@ -3,17 +3,17 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.HeaderParam;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.ResponseBuilder;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.HeaderParam;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.ResponseBuilder;
+import jakarta.ws.rs.core.UriInfo;
 import org.cqframework.cql.tools.formatter.CqlFormatterVisitor;
 import org.cqframework.cql.tools.formatter.CqlFormatterVisitor.FormatResult;
 import org.glassfish.jersey.media.multipart.FormDataBodyPart;
diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/Main.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/Main.java
index f4a681a..f2a1335 100644
--- a/src/main/java/org/mitre/bonnie/cqlTranslationServer/Main.java
+++ b/src/main/java/org/mitre/bonnie/cqlTranslationServer/Main.java
@@ -3,8 +3,8 @@
 import java.io.IOException;
 import java.net.URI;
 
-import javax.ws.rs.core.Feature;
-import javax.ws.rs.core.FeatureContext;
+import jakarta.ws.rs.core.Feature;
+import jakarta.ws.rs.core.FeatureContext;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationFailureException.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationFailureException.java
index 7ece83f..15008e1 100644
--- a/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationFailureException.java
+++ b/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationFailureException.java
@@ -5,9 +5,9 @@
  */
 package org.mitre.bonnie.cqlTranslationServer;
 
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
 
 /**
  *
diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java
index 90a2e73..091aaab 100644
--- a/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java
+++ b/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java
@@ -5,20 +5,20 @@
 import java.util.Arrays;
 import java.io.File;
 import java.io.IOException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.HeaderParam;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.MultivaluedHashMap;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.ResponseBuilder;
-import javax.ws.rs.core.Response.Status;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.HeaderParam;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MultivaluedHashMap;
+import jakarta.ws.rs.core.MultivaluedMap;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.ResponseBuilder;
+import jakarta.ws.rs.core.Response.Status;
+import jakarta.ws.rs.core.UriInfo;
 
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.CqlTranslator;
diff --git a/src/test/java/org/mitre/bonnie/cqlTranslationServer/FormatterResourceTest.java b/src/test/java/org/mitre/bonnie/cqlTranslationServer/FormatterResourceTest.java
index a760bba..723ddad 100644
--- a/src/test/java/org/mitre/bonnie/cqlTranslationServer/FormatterResourceTest.java
+++ b/src/test/java/org/mitre/bonnie/cqlTranslationServer/FormatterResourceTest.java
@@ -3,13 +3,13 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
-import javax.ws.rs.client.Client;
-import javax.ws.rs.client.ClientBuilder;
-import javax.ws.rs.client.Entity;
-import javax.ws.rs.client.WebTarget;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ws.rs.client.Client;
+import jakarta.ws.rs.client.ClientBuilder;
+import jakarta.ws.rs.client.Entity;
+import jakarta.ws.rs.client.WebTarget;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
 
 import org.glassfish.grizzly.http.server.HttpServer;
 import org.glassfish.jersey.media.multipart.FormDataMultiPart;
diff --git a/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java b/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java
index 8b298a5..6ed7c70 100644
--- a/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java
+++ b/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java
@@ -13,17 +13,17 @@
 import java.util.Iterator;
 import java.util.Map;
 
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.ws.rs.client.Client;
-import javax.ws.rs.client.ClientBuilder;
-import javax.ws.rs.client.Entity;
-import javax.ws.rs.client.WebTarget;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.ws.rs.client.Client;
+import jakarta.ws.rs.client.ClientBuilder;
+import jakarta.ws.rs.client.Entity;
+import jakarta.ws.rs.client.WebTarget;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
 import javax.xml.namespace.NamespaceContext;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -216,7 +216,11 @@ public void testValidLibraryAsJson() {
     JsonArray defs = library.getJsonObject("statements").getJsonArray("def");
     assertEquals(2, defs.size());
     assertFalse(defs.getJsonObject(1).containsKey("resultTypeName"));
-    assertFalse(defs.getJsonObject(1).containsKey("annotation"));
+    // assertFalse(defs.getJsonObject(1).containsKey("annotation"));
+    // As of translator 3.7.1 the annotation property is present but empty
+    assertTrue(defs.getJsonObject(1).containsKey("annotation"));
+    JsonArray subannotations = defs.getJsonObject(1).getJsonArray("annotation");
+    assertTrue(subannotations.isEmpty());
   }
 
   @Test