Cr uplift merged (#335)

* WIP * further cleanup * WIP * WIP * WIP * WIP * WIP * Holy coly, that's a lot of movement * WIP * Pom cleanup * Remove thunder tests... there's no server here? * WIP IGRepositoryImplementation * WIP * add logger * remove some commented code * First pass at search in IG repo * fix build * PlanDef tests * More tests passing * Fix questionnaire cql location * Fix parameters * move tests * Add search params library name and version * Fix search by name and version * cleanup pom * Add data provider for additional bundle * Add support for NpmProcessor in Engines * Disable Cli tests * Add FederatedDataProvider * Fix test data * Delete builder and library * cleanup * Fix poms * Fix loop * Fix questionnaire benchmark --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
cqframework · Aug 31, 2023 · ce49600 · ce49600
1 parent 82db6d6
commit ce49600
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -10,6 +10,7 @@
     "cdshooks",
     "clinicalreasoning",
     "Codeable",
+    "CODEABLECONCEPT",
     "codesystems",
     "Configurer",
     "connectathon",
@@ -27,6 +28,7 @@
     "Fhir",
     "fhirpath",
     "Gson",
+    "hamcrest",
     "helloworld",
     "INITIALPOPULATION",
     "INPROGRESS",
@@ -48,6 +50,7 @@
     "opioidcds",
     "PATIENTLIST",
     "plandefinition",
+    "Pointcut",
     "ppca",
     "prepopulate",
     "proxying",
@@ -127,7 +130,7 @@
   },
   "editor.formatOnSave": true,
   "editor.codeActionsOnSave": {
-    "source.organizeImports": true
+    // "source.organizeImports": true
   },
   "editor.detectIndentation": false,
   "editor.foldingImportsByDefault": true,

diff --git a/cqf-fhir-benchmark/pom.xml b/cqf-fhir-benchmark/pom.xml
@@ -23,8 +23,8 @@
     </dependency>
 
     <dependency>
-      <groupId>org.opencds.cqf.cql</groupId>
-      <artifactId>evaluator.jackson-deps</artifactId>
+      <groupId>org.opencds.cqf.fhir</groupId>
+      <artifactId>cqf-fhir-jackson</artifactId>
       <version>3.0.0-PRE6-SNAPSHOT</version>
       <type>pom</type>
     </dependency>
@@ -33,7 +33,11 @@
       <artifactId>cqf-fhir-utility</artifactId>
       <version>3.0.0-PRE6-SNAPSHOT</version>
     </dependency>
-
+    <dependency>
+      <groupId>org.opencds.cqf.fhir</groupId>
+      <artifactId>cqf-fhir-test</artifactId>
+      <version>3.0.0-PRE6-SNAPSHOT</version>
+    </dependency>
     <dependency>
       <groupId>org.opencds.cqf.cql</groupId>
       <artifactId>evaluator.measure-hapi</artifactId>
@@ -73,7 +77,6 @@
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
-
     <dependency>
       <groupId>org.skyscreamer</groupId>
       <artifactId>jsonassert</artifactId>
@@ -87,30 +90,11 @@
       <optional>true</optional>
       <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>info.cqframework</groupId>
-      <artifactId>model-jackson</artifactId>
-      <version>${cql.version}</version>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>info.cqframework</groupId>
-      <artifactId>elm-jackson</artifactId>
-      <version>${cql.version}</version>
-      <scope>test</scope>
-    </dependency>
   </dependencies>
 
   <build>
     <pluginManagement>
       <plugins>
-        <plugin>
-          <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.0.0-M1</version>
-          <configuration>
-            <skip>true</skip>
-          </configuration>
-        </plugin>
         <plugin>
           <groupId>org.sonatype.plugins</groupId>
           <artifactId>nexus-staging-maven-plugin</artifactId>

diff --git a/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/BenchmarksIT.java b/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/BenchmarksIT.java
@@ -1,13 +1,14 @@
 package org.opencds.cqf.fhir.benchmark;
 
 import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.text.DecimalFormat;
 import java.util.Collection;
 import java.util.Map;
 
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.openjdk.jmh.results.RunResult;
 import org.openjdk.jmh.runner.Runner;

diff --git a/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/PlanDefinitions.java b/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/PlanDefinitions.java
@@ -1,16 +1,16 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import static org.opencds.cqf.cql.evaluator.fhir.util.r4.Parameters.parameters;
-import static org.opencds.cqf.cql.evaluator.fhir.util.r4.Parameters.part;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
 
 import java.util.Collection;
 import java.util.concurrent.TimeUnit;
 
 import org.hl7.fhir.r4.model.IdType;
-import org.opencds.cqf.cql.evaluator.fhir.test.TestRepositoryFactory;
 import org.opencds.cqf.cql.evaluator.plandefinition.r4.PlanDefinition;
 import org.opencds.cqf.cql.evaluator.plandefinition.r4.PlanDefinition.Apply;
 import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.test.TestRepositoryFactory;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;
@@ -33,7 +33,7 @@
 public class PlanDefinitions {
   private static final FhirContext FHIR_CONTEXT = FhirContext.forR4Cached();
   private static final Repository REPOSITORY = TestRepositoryFactory.createRepository(FHIR_CONTEXT,
-      PlanDefinition.Assert.class, "anc-dak");
+      PlanDefinition.Assert.class, PlanDefinition.CLASS_PATH + "/anc-dak");
 
   private Apply apply;
 

diff --git a/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/Questionnaires.java b/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/Questionnaires.java
@@ -1,17 +1,17 @@
 package org.opencds.cqf.fhir.benchmark;
 
-import static org.opencds.cqf.cql.evaluator.fhir.util.r4.Parameters.parameters;
-import static org.opencds.cqf.cql.evaluator.fhir.util.r4.Parameters.stringPart;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
 
 import java.util.Collection;
 import java.util.concurrent.TimeUnit;
 
 import org.hl7.fhir.r4.model.IdType;
-import org.opencds.cqf.cql.evaluator.fhir.test.TestRepositoryFactory;
 import org.opencds.cqf.cql.evaluator.questionnaire.r4.QuestionnaireProcessorTests;
 import org.opencds.cqf.cql.evaluator.questionnaire.r4.helpers.TestQuestionnaire;
 import org.opencds.cqf.cql.evaluator.questionnaire.r4.helpers.TestQuestionnaire.QuestionnaireResult;
 import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.test.TestRepositoryFactory;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;
@@ -33,17 +33,18 @@
 public class Questionnaires {
   private static final FhirContext FHIR_CONTEXT = FhirContext.forR4Cached();
   private static final Repository REPOSITORY = TestRepositoryFactory.createRepository(FHIR_CONTEXT,
-      QuestionnaireProcessorTests.class, "pa-aslp");
+      QuestionnaireProcessorTests.class, TestQuestionnaire.CLASS_PATH + "/pa-aslp");
 
   private QuestionnaireResult result;
 
   @Setup(Level.Iteration)
   public void setupIteration() throws Exception {
-    this.result = TestQuestionnaire.Assert.that(new IdType("Questionnaire", "ASLPA1"), "positive")
-        .withRepository(REPOSITORY)
-        .withParameters(parameters(stringPart("Service Request Id", "SleepStudy"),
-            stringPart("Service Request Id", "SleepStudy2"),
-            stringPart("Coverage Id", "Coverage-positive")));
+    this.result =
+        TestQuestionnaire.Assert.that(new IdType("Questionnaire", "ASLPA1"), "positive")
+            .withRepository(REPOSITORY)
+            .withParameters(parameters(stringPart("Service Request Id", "SleepStudy"),
+                stringPart("Service Request Id", "SleepStudy2"),
+                stringPart("Coverage Id", "Coverage-positive")));
   }
 
   @Benchmark

diff --git a/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/TerminologyProviders.java b/cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/TerminologyProviders.java
@@ -5,9 +5,9 @@
 
 import org.opencds.cqf.cql.engine.runtime.Code;
 import org.opencds.cqf.cql.engine.terminology.ValueSetInfo;
-import org.opencds.cqf.cql.evaluator.engine.terminology.RepositoryTerminologyProvider;
-import org.opencds.cqf.cql.evaluator.fhir.test.TestRepositoryFactory;
 import org.opencds.cqf.cql.evaluator.measure.r4.MeasureProcessorEvaluateTest;
+import org.opencds.cqf.fhir.cql.engine.terminology.RepositoryTerminologyProvider;
+import org.opencds.cqf.fhir.test.TestRepositoryFactory;
 import org.openjdk.jmh.annotations.Benchmark;
 import org.openjdk.jmh.annotations.Fork;
 import org.openjdk.jmh.annotations.Level;

diff --git a/cqf-fhir-bom/pom.xml b/cqf-fhir-bom/pom.xml
@@ -39,26 +39,6 @@
         <artifactId>cqf-fhir-cql</artifactId>
         <version>${project.version}</version>
       </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-cql-dstu3</artifactId>
-        <version>${project.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-cql-r4</artifactId>
-        <version>${project.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-cql-r5</artifactId>
-        <version>${project.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-elm</artifactId>
-        <version>${project.version}</version>
-      </dependency>
       <dependency>
         <groupId>org.opencds.cqf.fhir</groupId>
         <artifactId>cqf-fhir-jackson</artifactId>
@@ -76,11 +56,6 @@
         <artifactId>cqf-fhir-cr</artifactId>
         <version>${project.version}</version>
       </dependency>
-      <dependency>
-        <groupId>org.opencds.cqf.fhir</groupId>
-        <artifactId>cqf-fhir-cdshooks</artifactId>
-        <version>${project.version}</version>
-      </dependency>
     </dependencies>
   </dependencyManagement>
 </project>
diff --git a/cqf-fhir-cdshooks/pom.xml b/cqf-fhir-cdshooks/pom.xml
diff --git a/cqf-fhir-cdshooks/src/main/java/org/opencds/cqf/fhir/cdshooks/CdsHooksMapper.java b/cqf-fhir-cdshooks/src/main/java/org/opencds/cqf/fhir/cdshooks/CdsHooksMapper.java
diff --git a/cqf-fhir-cql-dstu3/pom.xml b/cqf-fhir-cql-dstu3/pom.xml
diff --git a/cqf-fhir-cql-dstu3/src/main/java/org/opencds/cqf/fhir/cql/dstu3/ModelInfo.java b/cqf-fhir-cql-dstu3/src/main/java/org/opencds/cqf/fhir/cql/dstu3/ModelInfo.java
diff --git a/cqf-fhir-cql-r4/pom.xml b/cqf-fhir-cql-r4/pom.xml
diff --git a/cqf-fhir-cql-r4/src/main/java/org/opencds/cqf/fhir/cql/r4/ModelInfo.java b/cqf-fhir-cql-r4/src/main/java/org/opencds/cqf/fhir/cql/r4/ModelInfo.java
diff --git a/cqf-fhir-cql-r5/pom.xml b/cqf-fhir-cql-r5/pom.xml