Bump CQL dependencies

.github/workflows/ci-build-test.yml

@@ -45,26 +45,26 @@ jobs:
           SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
 
 
-  check_java8:
+  check_java11:
     runs-on: ubuntu-latest
-    name: Java 8
+    name: Java 11
 
     steps:
       - uses: actions/checkout@v2
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
-          java-version: 8
+          java-version: 11
 
       - name: Gradle cache
         uses: actions/cache@v2
         with:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-jdk8-${{ hashFiles('**/*.gradle*') }}
+          key: ${{ runner.os }}-gradle-jdk11-${{ hashFiles('**/*.gradle*') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-jdk8
+            ${{ runner.os }}-gradle-jdk11
 
       - name: Compile with Gradle
         run: ./gradlew assemble
@@ -80,8 +80,8 @@ jobs:
         if: env.SLACK_WEBHOOK_URL
         with:
           status: custom
-          job_name: Java 8
-          author_name: Java 8 Build/Test
+          job_name: Java 11
+          author_name: Java 11 Build/Test
           fields: workflow,commit,repo,author,took
           # see https://action-slack.netlify.app/usecase/02-custom for custom payload info
           custom_payload: |

.github/workflows/deploy.yml

@@ -12,17 +12,17 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
-          java-version: 8
+          java-version: 11
 
       - name: Gradle cache
         uses: actions/cache@v2
         with:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-jdk8-${{ hashFiles('**/*.gradle*') }}
+          key: ${{ runner.os }}-gradle-jdk11-${{ hashFiles('**/*.gradle*') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-jdk8
+            ${{ runner.os }}-gradle-jdk11
 
       - name: Create Artifacts
         run: |

build.gradle

@@ -6,8 +6,7 @@
 // Apply the java plugin to add support for Java
 apply plugin: 'java'
 
-sourceCompatibility = '1.8'
-targetCompatibility = '1.8'
+sourceCompatibility = '11'
 
 apply plugin: 'application'
 apply plugin: 'eclipse'
@@ -41,42 +40,45 @@ jacoco {
 
 dependencies {
   // This dependency is found on compile classpath of this component and consumers.
-  implementation 'com.google.code.gson:gson:2.8.7'
-  implementation 'com.jayway.jsonpath:json-path:2.4.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:5.7.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:5.7.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:5.7.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:5.7.0'
-  implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:5.7.0'
+  implementation 'com.google.code.gson:gson:2.9.0'
+  implementation 'com.jayway.jsonpath:json-path:2.7.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-base:6.1.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:6.1.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:6.1.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.1.0'
+  implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:6.1.0'
   // C-CDA export uses Apache FreeMarker templates
-  implementation 'org.freemarker:freemarker:2.3.26-incubating'
+  implementation 'org.freemarker:freemarker:2.3.31'
 
   // google guava for some data structures
-  implementation 'com.google.guava:guava:30.0-jre'
+  implementation 'com.google.guava:guava:31.1-jre'
   implementation 'guru.nidi:graphviz-java:0.2.4'
   // CSV Stuff
-  implementation 'org.apache.commons:commons-csv:1.5'
-  implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-csv:2.8.8'
-  implementation 'org.yaml:snakeyaml:1.27'
+  implementation 'org.apache.commons:commons-csv:1.9.0'
+  implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-csv:2.13.4'
+  implementation 'org.yaml:snakeyaml:1.32'
   implementation 'org.apache.commons:commons-math3:3.6.1'
-  implementation 'org.apache.commons:commons-text:1.2'
-  implementation 'commons-validator:commons-validator:1.4.0'
+  implementation 'org.apache.commons:commons-text:1.9'
+  implementation 'commons-validator:commons-validator:1.7'
 
-  implementation 'org.opencds.cqf:cql-engine:1.3.12'
-  implementation 'info.cqframework:cql:1.3.17'
-  implementation 'info.cqframework:model:1.3.17'
-  implementation 'info.cqframework:cql-to-elm:1.3.17'
+  implementation 'org.opencds.cqf.cql:engine.jackson:2.0.0'
+  implementation 'org.opencds.cqf.cql:engine:2.0.0'
+  implementation 'info.cqframework:cql:2.1.0'
+  implementation 'info.cqframework:model:2.1.0'
+  implementation 'info.cqframework:cql-to-elm:2.1.0'
+  implementation 'info.cqframework:model-jackson:2.1.0'
+  implementation 'info.cqframework:elm-jackson:2.1.0'
 
-  implementation 'org.springframework:spring-web:5.2.7.RELEASE'
+  implementation 'com.squareup.okhttp3:okhttp:4.10.0'
 
   // Java 9 no longer includes these APIs by default
   implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
-  implementation 'org.glassfish.jaxb:jaxb-runtime:2.3.2'
+  implementation 'org.glassfish.jaxb:jaxb-runtime:4.0.0'
   implementation 'javax.activation:javax.activation-api:1.2.0'
 
   // get rid of SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
   // if we switch to a real logging framework we may want to switch this
-  implementation "org.slf4j:slf4j-api:1.7.9"
+  implementation "org.slf4j:slf4j-api:2.0.0"
   //implementation "org.slf4j:slf4j-nop:1.7.9" // SLF4J seems to already be provided by org.apache.logging.log4j
 
   // ensure transitive dependencies do not use vulnerable log4j
@@ -88,28 +90,29 @@ dependencies {
 
   // Physiology simulation dependencies
   implementation files('lib/sbscl/SimulationCoreLibrary_v1.5_slim.jar')
-  implementation 'org.sbml.jsbml:jsbml:1.5', {
+  implementation 'org.sbml.jsbml:jsbml:1.6.1', {
       exclude group:'org.apache.logging.log4j', module: 'log4j-slf4j-impl'
   }
   implementation 'org.apache.commons:commons-math:2.2'
 
   // JfreeChart for drawing physiology charts
-  implementation 'org.jfree:jfreechart:1.5.0'
+  implementation 'org.jfree:jfreechart:1.5.3'
 
   // Use JUnit test framework
-  testImplementation 'junit:junit:4.12'
+  testImplementation 'junit:junit:4.13.2'
   testImplementation fileTree(dir: 'lib/mdhtruntime/mdht', include: '*.jar')
   testImplementation fileTree(dir: 'lib/mdhtruntime/non-mdht', include: '*.jar')
-  testImplementation 'org.mockito:mockito-core:2.19.0'
-  testImplementation 'org.powermock:powermock-module-junit4:1.7.1'
-  testImplementation 'org.powermock:powermock-api-mockito2:1.7.1'
-  testImplementation 'com.github.tomakehurst:wiremock-jre8:2.26.3'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:5.7.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:5.7.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:5.7.0'
-  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:5.7.0'
+  testImplementation 'org.mockito:mockito-core:4.7.0'
+  testImplementation 'org.powermock:powermock-module-junit4:2.0.9'
+  testImplementation 'org.powermock:powermock-api-mockito2:2.0.9'
+  testImplementation 'com.github.tomakehurst:wiremock-jre8:2.33.2'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:6.1.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:6.1.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:6.1.0'
+  testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:6.1.0'
   testImplementation 'com.helger:ph-schematron:5.6.5'
-  testImplementation 'com.helger:ph-commons:9.5.4'
+  testImplementation 'com.helger:ph-commons:9.5.5'
+  testImplementation 'com.squareup.okhttp3:mockwebserver:4.10.0'
 }
 
 // Provide more descriptive test failure output

src/main/java/org/mitre/synthea/helpers/ExpressionProcessor.java

@@ -22,7 +22,6 @@
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import javax.xml.bind.JAXBException;
 
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.LibraryManager;
@@ -31,8 +30,9 @@
 import org.cqframework.cql.elm.execution.Library;
 import org.mitre.synthea.world.agents.Person;
 import org.mitre.synthea.world.concepts.VitalSign;
-import org.opencds.cqf.cql.execution.Context;
-import org.opencds.cqf.cql.execution.CqlLibraryReader;
+import org.opencds.cqf.cql.engine.execution.Context;
+import org.opencds.cqf.cql.engine.serializing.CqlLibraryReader;
+import org.opencds.cqf.cql.engine.serializing.jackson.XmlCqlLibraryReader;
 import org.simulator.math.odes.MultiTable;
 import org.simulator.math.odes.MultiTable.Block.Column;
 
@@ -106,9 +106,10 @@ public ExpressionProcessor(String expression, Map<String,String> paramTypeMap) {
     this.elm = cqlToElm(wrappedExpression);
     synchronized (ExpressionProcessor.class) {
       try {
-        this.library = CqlLibraryReader.read(new ByteArrayInputStream(
+        CqlLibraryReader reader = new XmlCqlLibraryReader();
+        this.library = reader.read(new ByteArrayInputStream(
             elm.getBytes(StandardCharsets.UTF_8)));
-      } catch (IOException | JAXBException ex) {
+      } catch (IOException ex) {
         throw new RuntimeException(ex);
       }
     }
@@ -378,7 +379,7 @@ private String convertParameterizedExpressionToCql(String expression) {
         .append(paramTypeMap.getOrDefault(paramEntry.getKey(), "Decimal"));
     }
 
-    wrappedExpression.append("\n\ncontext Patient\n\n");
+    wrappedExpression.append("\n\ncontext Unfiltered\n\n");
 
     String[] statements = expression.split("\n");
 

src/main/java/org/mitre/synthea/helpers/RandomCodeGenerator.java

@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
+
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -11,19 +13,16 @@
 import java.util.Random;
 
 import javax.annotation.Nonnull;
+
+import okhttp3.OkHttpClient;
+import okhttp3.Request;
+import okhttp3.Response;
+import okhttp3.ResponseBody;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.validator.routines.UrlValidator;
 import org.mitre.synthea.world.concepts.HealthRecord.Code;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.http.HttpEntity;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpMethod;
-
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.client.RestClientException;
-import org.springframework.web.client.RestTemplate;
 
 /**
  * Generates random codes based upon ValueSet URIs, with the help of a FHIR
@@ -40,9 +39,8 @@ public abstract class RandomCodeGenerator {
   private static final Logger logger = LoggerFactory.getLogger(RandomCodeGenerator.class);
   public static Map<String, List<Object>> codeListCache = new HashMap<>();
   public static List<Code> selectedCodes = new ArrayList<>();
-  private static UrlValidator urlValidator = new UrlValidator();
-
-  public static RestTemplate restTemplate = new RestTemplate();
+  private static UrlValidator urlValidator = new UrlValidator(UrlValidator.ALLOW_2_SLASHES);
+  private static OkHttpClient client = new OkHttpClient();
 
   /**
    * Gets a random code from the expansion of a ValueSet.
@@ -71,22 +69,26 @@ public static Code getCode(String valueSetUri, long seed, Code code) {
   @SuppressWarnings("unchecked")
   private static synchronized void expandValueSet(String valueSetUri) {
     if (!codeListCache.containsKey(valueSetUri)) {
-      HttpHeaders headers = new HttpHeaders();
-      headers.setContentType(MediaType.APPLICATION_JSON);
-      HttpEntity<String> request = new HttpEntity<>(headers);
+      Request request = new Request.Builder()
+              .url(expandBaseUrl + valueSetUri)
+              .header("Content-Type", "application/json")
+              .build();
       Map<String, Object> valueSet = null;
       try {
-        ResponseEntity<String> response = restTemplate.exchange(expandBaseUrl + valueSetUri,
-            HttpMethod.GET, request,
-            String.class);
+        Response response = client.newCall(request).execute();
         ObjectMapper objectMapper = new ObjectMapper();
-        valueSet = objectMapper.readValue(response.getBody(),
-            new TypeReference<Map<String, Object>>() {
+        ResponseBody body = response.body();
+        if (body != null) {
+          valueSet = objectMapper.readValue(body.byteStream(),
+                  new TypeReference<Map<String, Object>>() {
             });
+        } else {
+          throw new RuntimeException("Value Set Expansion contained no body");
+        }
       } catch (JsonProcessingException e) {
         throw new RuntimeException("JsonProcessingException while parsing valueSet response");
-      } catch (RestClientException e) {
-        throw new RestClientException("RestClientException while fetching valueSet response");
+      } catch (IOException e) {
+        throw new RuntimeException("Issue when expanding the value set", e);
       }
 
       Map<String, Object> expansion = (Map<String, Object>) valueSet.get("expansion");

src/test/java/org/mitre/synthea/engine/StateTest.java

@@ -7,7 +7,7 @@
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import static org.mockito.Mockito.verifyZeroInteractions;
+import static org.mockito.Mockito.verifyNoInteractions;
 import static org.mockito.Mockito.withSettings;
 
 import java.io.IOException;
@@ -178,7 +178,7 @@ public void condition_onset() throws Exception {
     // Should pass through this state immediately without calling the record
     assertTrue(condition.process(person, time));
 
-    verifyZeroInteractions(person.record);
+    verifyNoInteractions(person.record);
   }
 
   @Test
@@ -301,7 +301,7 @@ public void allergy_onset() throws Exception {
     // Should pass through this state immediately without calling the record
     assertTrue(allergy.process(person, time));
 
-    verifyZeroInteractions(person.record);
+    verifyNoInteractions(person.record);
   }
 
   @Test
@@ -545,7 +545,7 @@ public void gmfTwoVitalSign() throws Exception {
     assertTrue(person.getVitalSign(VitalSign.SYSTOLIC_BLOOD_PRESSURE, time) >= 110);
     assertTrue(person.getVitalSign(VitalSign.SYSTOLIC_BLOOD_PRESSURE, time) <= 130);
 
-    verifyZeroInteractions(person.record);
+    verifyNoInteractions(person.record);
   }
 
 
@@ -562,7 +562,7 @@ public void vitalsign() throws Exception {
 
     assertEquals(120.0, person.getVitalSign(VitalSign.SYSTOLIC_BLOOD_PRESSURE, time), 0.0);
 
-    verifyZeroInteractions(person.record);
+    verifyNoInteractions(person.record);
   }
 
   @Test

src/test/java/org/mitre/synthea/export/CodeResolveAndExportTest.java

@@ -59,7 +59,6 @@
 import org.mitre.synthea.world.concepts.HealthRecord.Encounter;
 import org.mitre.synthea.world.concepts.HealthRecord.EncounterType;
 import org.mitre.synthea.world.geography.Location;
-import org.springframework.web.client.RestTemplate;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -101,7 +100,6 @@ public void setUp() throws Exception {
     Config.set("exporter.fhir_stu3.export", "true");
     Config.set("exporter.fhir_dstu2.export", "true");
     Config.set("generate.terminology_service_url", mockTerminologyService.baseUrl() + "/fhir");
-    RandomCodeGenerator.restTemplate = new RestTemplate();
 
     person = new Person(12345L);
     time = new SimpleDateFormat("yyyy-MM-dd").parse("2013-06-10").getTime();
@@ -159,7 +157,7 @@ public void resolveAndExportEncounterCodes()
     String reasonCode = "417981005";
     String reasonDisplay = "Exposure to blood and/or body fluid";
     encounter.reason = new Code(SNOMED_URI, reasonCode, reasonDisplay);
-    encounter.reason.valueSet = SNOMED_URI + "?fhir_vs=ecl/<418307001";
+    encounter.reason.valueSet = SNOMED_URI + "?fhir_vs=ecl%2F%3C418307001";
     encounter.codes.add(encounter.reason);
 
     String observationDisplay = OBSERVATION_DISPLAY;