#576: CQL 2.0.0 upgrade

.gitignore

@@ -16,3 +16,4 @@ core.*
 heapdump.*
 javacore.*
 Snap.*
+**/test-output

engine.fhir/pom.xml

@@ -9,7 +9,6 @@
         <version>1.5.10-SNAPSHOT</version>
     </parent>
 
-    <groupId>org.opencds.cqf.cql</groupId>
     <artifactId>engine.fhir</artifactId>
     <version>1.5.10-SNAPSHOT</version>
     <packaging>jar</packaging>
@@ -24,6 +23,24 @@
             <artifactId>engine</artifactId>
             <version>1.5.10-SNAPSHOT</version>
         </dependency>
+
+        <!-- StringUtils, ExceptionUtils and Pair classes. -->
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-text</artifactId>
+        </dependency>
+
+        <!-- Support for generated methods for toString(), equals() and hashCode() using jakarta-commons-lang -->
+        <dependency>
+            <groupId>org.jvnet.jaxb2_commons</groupId>
+            <artifactId>jaxb2-basics-runtime</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-client</artifactId>
@@ -48,6 +65,7 @@
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-structures-r5</artifactId>
         </dependency>
+
         <dependency>
             <groupId>xpp3</groupId>
             <artifactId>xpp3</artifactId>
@@ -63,6 +81,37 @@
             <artifactId>wiremock-jre8</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.eclipse.persistence</groupId>
+            <artifactId>org.eclipse.persistence.moxy</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>fhir-r4</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>quick</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>
@@ -103,7 +152,7 @@
                             <plugin>
                                 <groupId>org.jvnet.jaxb2_commons</groupId>
                                 <artifactId>jaxb2-basics</artifactId>
-                                <version>0.12.0</version>
+                                <version>0.13.1</version>
                             </plugin>
                             <plugin>
                                 <groupId>org.jvnet.jaxb2_commons</groupId>

engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/model/Dstu2FhirModelResolver.java

@@ -47,7 +47,7 @@ public Dstu2FhirModelResolver() {
 		this(FhirContext.forDstu2());
 	}
 
-	private Dstu2FhirModelResolver(FhirContext fhirContext) {
+    protected Dstu2FhirModelResolver(FhirContext fhirContext) {
         super(fhirContext);
         this.setPackageNames(Arrays.asList("ca.uhn.fhir.model.dstu2", "org.hl7.fhir.dstu2.model", "ca.uhn.fhir.model.primitive"));
         if (fhirContext.getVersion().getVersion() != FhirVersionEnum.DSTU2) {

engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/model/Dstu3FhirModelResolver.java

@@ -48,7 +48,7 @@ public Dstu3FhirModelResolver() {
         this(FhirContext.forDstu3());
     }
 
-    private Dstu3FhirModelResolver(FhirContext fhirContext) {
+    protected Dstu3FhirModelResolver(FhirContext fhirContext) {
         super(fhirContext);
         this.setPackageNames(Arrays.asList("org.hl7.fhir.dstu3.model"));
         if (fhirContext.getVersion().getVersion() != FhirVersionEnum.DSTU3) {

engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/model/R4FhirModelResolver.java

@@ -49,7 +49,7 @@ public R4FhirModelResolver() {
         this(FhirContext.forR4());
 	}
 
-	private R4FhirModelResolver(FhirContext fhirContext) {
+    protected R4FhirModelResolver(FhirContext fhirContext) {
         super(fhirContext);
         this.setPackageNames(Arrays.asList("org.hl7.fhir.r4.model"));
         if (fhirContext.getVersion().getVersion() != FhirVersionEnum.R4) {

engine.fhir/src/test/java/org/hl7/fhirpath/CQLOperationsDstu3Test.java

@@ -0,0 +1,215 @@
+package org.hl7.fhirpath;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import com.google.common.collect.Sets;
+import org.fhir.ucum.UcumException;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhirpath.tests.Group;
+import org.opencds.cqf.cql.engine.data.CompositeDataProvider;
+import org.opencds.cqf.cql.engine.elm.execution.EqualEvaluator;
+import org.opencds.cqf.cql.engine.execution.Context;
+import org.opencds.cqf.cql.engine.fhir.model.CachedDstu3FhirModelResolver;
+import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
+import org.opencds.cqf.cql.engine.fhir.model.FhirModelResolver;
+import org.opencds.cqf.cql.engine.fhir.retrieve.RestFhirRetrieveProvider;
+import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
+import org.opencds.cqf.cql.engine.runtime.Code;
+import org.testng.ITest;
+import org.testng.SkipException;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Factory;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+public class CQLOperationsDstu3Test extends TestFhirPath implements ITest {
+    private static FhirContext fhirContext = FhirContext.forCached(FhirVersionEnum.DSTU3);
+    private static Dstu3FhirModelResolver fhirModelResolver = new CachedDstu3FhirModelResolver();
+    private static RestFhirRetrieveProvider retrieveProvider = new RestFhirRetrieveProvider(
+        new SearchParameterResolver(fhirContext),
+        fhirModelResolver,
+        fhirContext.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3")
+    );
+    private static CompositeDataProvider provider = new CompositeDataProvider(fhirModelResolver, retrieveProvider);
+
+    private final String file;
+    private final org.hl7.fhirpath.tests.Test test;
+    private final Group group;
+
+    @Factory(dataProvider = "dataMethod")
+    public CQLOperationsDstu3Test(String file, Group group, org.hl7.fhirpath.tests.Test test) {
+        this.file = file;
+        this.group = group;
+        this.test = test;
+    }
+
+    @DataProvider
+    public static Object[][] dataMethod() {
+        String[] listOfFiles = {
+            "stu3/tests-fhir-r3.xml"
+        };
+
+        List<Object[]> testsToRun = new ArrayList<>();
+        for (String file: listOfFiles) {
+            for (Group group : loadTestsFile(file).getGroup()) {
+                for (org.hl7.fhirpath.tests.Test test : group.getTest()) {
+                    if (!"2.1.0".equals(test.getVersion())) { // unsupported version
+                        testsToRun.add(new Object[] {
+                            file,
+                            group,
+                            test
+                        });
+                    }
+                }
+            }
+        }
+        return testsToRun.toArray(new Object[testsToRun.size()][]);
+    }
+
+    public static Set<String> SKIP = Sets.newHashSet(
+        "stu3/tests-fhir-r3/Dollar/testDollarOrderNotAllowed(Patient.children().skip(1))",
+        "stu3/tests-fhir-r3/Dollar/testDollarThis1(Patient.name.given.where(substring($this.length()-3) = 'out'))",
+        "stu3/tests-fhir-r3/Dollar/testDollarThis2(Patient.name.given.where(substring($this.length()-3) = 'ter'))",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate((0).not() = false)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate((1).not() = false)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate((1|2).not() = false)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @1974-12-25T12:34:00)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @1974-12-25T12:34:00+10:00)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @1974-12-25T12:34:00-10:00)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @1974-12-25T12:34:00Z)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @T12:14)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDate(Patient.birthDate != @T12:14:15)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDecimal(Observation.value.value < 190)",
+        "stu3/tests-fhir-r3/Literals/testLiteralDecimal(Observation.value.value > 0)",
+        "stu3/tests-fhir-r3/Literals/testLiteralString(Patient.name.given.first() = 'Peter')",
+        "stu3/tests-fhir-r3/Literals/testLiteralUnicode(Patient.name.given.first() = 'P\\u0065ter')",
+        "stu3/tests-fhir-r3/testAll(Patient.name.select(family.exists()).all())",
+        "stu3/tests-fhir-r3/testAll(Patient.name.select(given.exists()).all())",
+        "stu3/tests-fhir-r3/testBooleanImplies((true implies {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanImplies(({} implies false) = true)",
+        "stu3/tests-fhir-r3/testBooleanImplies(({} implies {}) = true)",
+        "stu3/tests-fhir-r3/testBooleanLogicAnd((true and {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicAnd(({} and true) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicAnd(({} and {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicOr((false or {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicOr(({} or false) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicOr(({} or {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicXOr((false xor {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicXOr((true xor {}) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicXOr(({} xor false) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicXOr(({} xor true) = {})",
+        "stu3/tests-fhir-r3/testBooleanLogicXOr(({} xor {}) = {})",
+        "stu3/tests-fhir-r3/testConcatenate((1 | 2 | 3) & 'b' = '1,2,3b')",
+        "stu3/tests-fhir-r3/testConcatenate(1 & 'a' = '1a')",
+        "stu3/tests-fhir-r3/testConcatenate(1 & 1 = '11')",
+        "stu3/tests-fhir-r3/testContainsString('12345'.contains('') = false)",
+        "stu3/tests-fhir-r3/testDistinct((1 | 2 | 3).isDistinct())",
+        "stu3/tests-fhir-r3/testDistinct(Questionnaire.descendants().linkId.distinct())",
+        "stu3/tests-fhir-r3/testDistinct(Questionnaire.descendants().linkId.isDistinct())",
+        "stu3/tests-fhir-r3/testDistinct(Questionnaire.descendants().linkId.select(substring(0,1)).distinct())",
+        "stu3/tests-fhir-r3/testDistinct(Questionnaire.descendants().linkId.select(substring(0,1)).isDistinct().not())",
+        "stu3/tests-fhir-r3/testDivide(1.2 / 1.8 = 0.67)",
+        "stu3/tests-fhir-r3/testEndsWith('12345'.endsWith('') = false)",
+        "stu3/tests-fhir-r3/testEquality(0.0 = 0)",
+        "stu3/tests-fhir-r3/testEquality(1.10 = 1.1)",
+        "stu3/tests-fhir-r3/testEquality(name = name.first() | name.last())",
+        "stu3/tests-fhir-r3/testEquality(name = name.last() | name.first())",
+        "stu3/tests-fhir-r3/testEquivalent(@2012-04-15 ~ @2012-04-15T10:00:00)",
+        "stu3/tests-fhir-r3/testEquivalent(name.given ~ name.first().given | name.last().given)",
+        "stu3/tests-fhir-r3/testEquivalent(name.given ~ name.last().given | name.first().given)",
+        "stu3/tests-fhir-r3/testExtension(Patient.birthDate.extension(%\"ext-patient-birthTime\").exists())",
+        "stu3/tests-fhir-r3/testExtension(Patient.birthDate.extension('http://hl7.org/fhir/StructureDefinition/patient-birthTime').exists())",
+        "stu3/tests-fhir-r3/testExtension(Patient.birthDate.extension('http://hl7.org/fhir/StructureDefinition/patient-birthTime1').empty())",
+        "stu3/tests-fhir-r3/testFirstLast(Patient.name.first().given = 'Peter' | 'James')",
+        "stu3/tests-fhir-r3/testFirstLast(Patient.name.last().given = 'Jim')",
+        "stu3/tests-fhir-r3/testIif(iif(Patient.name.empty(), 'unnamed', 'named') = 'named')",
+        "stu3/tests-fhir-r3/testIif(iif(Patient.name.exists(), 'named', 'unnamed') = 'named')",
+        "stu3/tests-fhir-r3/testIndexer(Patient.name[0].given = 'Peter' | 'James')",
+        "stu3/tests-fhir-r3/testIndexer(Patient.name[1].given = 'Jim')",
+        "stu3/tests-fhir-r3/testNEquality(0.0 != 0)",
+        "stu3/tests-fhir-r3/testNEquality(1.10 != 1.1)",
+        "stu3/tests-fhir-r3/testNEquality(name != name.first() | name.last())",
+        "stu3/tests-fhir-r3/testNEquality(name != name.last() | name.first())",
+        "stu3/tests-fhir-r3/testNotEquivalent(@2012-04-15 !~ @2012-04-15T10:00:00)",
+        "stu3/tests-fhir-r3/testNotEquivalent(name.given !~ name.first().given | name.last().given)",
+        "stu3/tests-fhir-r3/testNotEquivalent(name.given !~ name.last().given | name.first().given)",
+        "stu3/tests-fhir-r3/testNow(now().toString().length() > 10)",
+        "stu3/tests-fhir-r3/testNow(Patient.birthDate < now())",
+        "stu3/tests-fhir-r3/testRepeat(Questionnaire.children().concept.count() = 2)",
+        "stu3/tests-fhir-r3/testRepeat(Questionnaire.descendants().concept.count() = 10)",
+        "stu3/tests-fhir-r3/testRepeat(Questionnaire.repeat(item).concept.count() = 10)",
+        "stu3/tests-fhir-r3/testRepeat(ValueSet.expansion.repeat(contains).count() = 10)",
+        "stu3/tests-fhir-r3/testSelect(Patient.name.select(given) = 'Peter' | 'James' | 'Jim')",
+        "stu3/tests-fhir-r3/testSelect(Patient.name.select(given | family) = 'Peter' | 'James' | 'Chalmers' | 'Jim')",
+        "stu3/tests-fhir-r3/testSkip((0 | 1 | 2).skip(1) = 1 | 2)",
+        "stu3/tests-fhir-r3/testSkip(Patient.name.skip(1).given = 'Jim')",
+        "stu3/tests-fhir-r3/testStartsWith('12345'.startsWith('') = false)",
+        "stu3/tests-fhir-r3/testSubSetOf(Patient.name.first().subsetOf($this.name))",
+        "stu3/tests-fhir-r3/testSubSetOf(Patient.name.subsetOf($this.name.first()).not())",
+        "stu3/tests-fhir-r3/testSuperSetOf(Patient.name.first().supersetOf($this.name).not())",
+        "stu3/tests-fhir-r3/testSuperSetOf(Patient.name.supersetOf($this.name.first()))",
+        "stu3/tests-fhir-r3/testTail((0 | 1 | 2).tail() = 1 | 2)",
+        "stu3/tests-fhir-r3/testTail(Patient.name.tail().given = 'Jim')",
+        "stu3/tests-fhir-r3/testTake((0 | 1 | 2).take(2) = 0 | 1)",
+        "stu3/tests-fhir-r3/testTake(Patient.name.take(1).given = 'Peter' | 'James')",
+        "stu3/tests-fhir-r3/testTake(Patient.name.take(2).given = 'Peter' | 'James' | 'Jim')",
+        "stu3/tests-fhir-r3/testTake(Patient.name.take(3).given = 'Peter' | 'James' | 'Jim')",
+        "stu3/tests-fhir-r3/testToday(Patient.birthDate < today())",
+        "stu3/tests-fhir-r3/testToday(today().toString().length() = 10)",
+        "stu3/tests-fhir-r3/testToInteger('0.0'.toInteger().empty())",
+        "stu3/tests-fhir-r3/testVariables(%\"vs-administrative-gender\" = 'http://hl7.org/fhir/ValueSet/administrative-gender')",
+        "stu3/tests-fhir-r3/testVariables(%loinc = 'http://loinc.org')",
+        "stu3/tests-fhir-r3/testVariables(%sct = 'http://snomed.info/sct')",
+        "stu3/tests-fhir-r3/testVariables(%ucum = 'http://unitsofmeasure.org')",
+        "stu3/tests-fhir-r3/testWhere(Patient.name.where($this.given = 'Jim').count() = 1)",
+        "stu3/tests-fhir-r3/testWhere(Patient.name.where(given = 'Jim').count() = 1)",
+        "stu3/tests-fhir-r3/testWhere(Patient.name.where(given = 'X').count() = 0)"
+    );
+
+    @Override
+    public String getTestName() {
+        return
+            file.replaceAll(".xml", "")
+                + "/"+ group.getName()
+                + (test.getName() != null ? "/"+ test.getName() : "")
+                + "("+ test.getExpression().getValue() +")";
+    }
+
+    @Test
+    public void test() throws UcumException {
+        if (SKIP.contains(getTestName())) {
+            throw new SkipException("Skipping " + getTestName());
+        }
+
+        runTest(test, "stu3/input/", fhirContext, provider, fhirModelResolver);
+    }
+
+    public Boolean compareResults(Object expectedResult, Object actualResult, Context context, FhirModelResolver<?, ?, ?, ?, ?, ?, ?, ?> resolver) {
+        // Perform FHIR system-defined type conversions
+        if (actualResult instanceof Enumeration) {
+            actualResult = ((Enumeration<?>) actualResult).getValueAsString();
+        } else if (actualResult instanceof BooleanType) {
+            actualResult = ((BooleanType) actualResult).getValue();
+        } else if (actualResult instanceof IntegerType) {
+            actualResult = ((IntegerType) actualResult).getValue();
+        } else if (actualResult instanceof DecimalType) {
+            actualResult = ((DecimalType) actualResult).getValue();
+        } else if (actualResult instanceof StringType) {
+            actualResult = ((StringType) actualResult).getValue();
+        } else if (actualResult instanceof BaseDateTimeType) {
+            actualResult = resolver.toJavaPrimitive(actualResult, actualResult);
+        } else if (actualResult instanceof Quantity) {
+            Quantity quantity = (Quantity) actualResult;
+            actualResult = new org.opencds.cqf.cql.engine.runtime.Quantity().withValue(quantity.getValue())
+                .withUnit(quantity.getUnit());
+        } else if (actualResult instanceof Coding) {
+            Coding coding = (Coding) actualResult;
+            actualResult = new Code().withCode(coding.getCode()).withDisplay(coding.getDisplay())
+                .withSystem(coding.getSystem()).withVersion(coding.getVersion());
+        }
+        return EqualEvaluator.equal(expectedResult, actualResult, context);
+    }
+}