#508,#552: Added support for profile validation in the retrieve

.travis.yml

@@ -13,7 +13,7 @@ script:
 before_cache:
 - rm -rf $HOME/.m2/repository/org/opencds/cqf/cql
 after_success:
-- test $TRAVIS_BRANCH = "master" && test $TRAVIS_PULL_REQUEST = "false" && ./scripts/deploy.sh
+- test ($TRAVIS_BRANCH = "master" || $TRAVIS_BRANCH = "v15") && test $TRAVIS_PULL_REQUEST = "false" && ./scripts/deploy.sh
 deploy:
   provider: releases
   api_key:

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

@@ -415,6 +415,16 @@ protected Object resolveProperty(Object target, String path) {
             return null;
         }
 
+        // If the instance is a primitive (including (or even especially an enumeration), and it has no value, return null
+        if (child instanceof RuntimeChildPrimitiveDatatypeDefinition) {
+            IBase value = values.get(0);
+            if (value instanceof IPrimitiveType) {
+                if (!((IPrimitiveType<?>)value).hasValue()) {
+                    return null;
+                }
+            }
+        }
+
         if (child instanceof RuntimeChildChoiceDefinition && !child.getElementName().equalsIgnoreCase(path)) {
             if (!values.get(0).getClass().getSimpleName()
                     .equalsIgnoreCase(child.getChildByName(path).getImplementingClass().getSimpleName())) {
@@ -630,6 +640,10 @@ public TemporalPrecisionEnum toTemporalPrecisionEnum(Precision precision) {
      */
 
     public Object toJavaPrimitive(Object result, Object source) {
+        if (source instanceof IPrimitiveType<?> && !((IPrimitiveType<?>)source).hasValue()) {
+            return null;
+        }
+
         String simpleName = source.getClass().getSimpleName();
         switch (simpleName) {
             case "InstantType":

engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/retrieve/FhirBundleCursor.java

@@ -1,10 +1,12 @@
 package org.opencds.cqf.cql.engine.fhir.retrieve;
 
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.opencds.cqf.cql.engine.fhir.exception.UnknownElement;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
@@ -14,19 +16,25 @@ public class FhirBundleCursor implements Iterable<Object> {
 
     public FhirBundleCursor(IGenericClient fhirClient, IBaseBundle results)
     {
-        this(fhirClient, results, null);
+        this(fhirClient, results, null, null);
     }
 
+    public FhirBundleCursor(IGenericClient fhirClient, IBaseBundle results, String dataType) { this(fhirClient, results, null, null); }
+
     // This constructor filters the bundle based on dataType
-    public FhirBundleCursor(IGenericClient fhirClient, IBaseBundle results, String dataType) {
+    // If templateId is provided, this is a trusted cursor, meaning that it will only return results
+    // for resources that declare they conform to the given profile
+    public FhirBundleCursor(IGenericClient fhirClient, IBaseBundle results, String dataType, String templateId) {
         this.fhirClient = fhirClient;
         this.results = results;
         this.dataType = dataType;
+        this.templateId = templateId;
     }
 
     private IGenericClient fhirClient;
     private IBaseBundle results;
     private String dataType;
+    private String templateId;
 
 
     /**
@@ -35,15 +43,21 @@ public FhirBundleCursor(IGenericClient fhirClient, IBaseBundle results, String d
      * @return an Iterator.
      */
     public Iterator<Object> iterator() {
-        return new FhirBundleIterator(fhirClient, results, dataType);
+        return new FhirBundleIterator(fhirClient, results, dataType, templateId);
     }
 
     private class FhirBundleIterator implements Iterator<Object> {
-        public FhirBundleIterator(IGenericClient fhirClient, IBaseBundle results, String dataType) {
+        public FhirBundleIterator(IGenericClient fhirClient, IBaseBundle results, String dataType, String templateId) {
             this.fhirClient = fhirClient;
             this.results =  results;
             this.current = -1;
             this.dataType = dataType;
+            this.templateId = templateId;
+
+            // Do not test templateId for base resource "profiles"
+            if (this.templateId != null && this.templateId.startsWith(String.format("http://hl7.org/fhir/StructureDefinition/%s", dataType))) {
+                this.templateId = null;
+            }
 
             if (dataType != null) {
                 this.dataTypeClass = this.fhirClient.getFhirContext().getResourceDefinition(this.dataType).getImplementingClass();
@@ -56,6 +70,7 @@ public FhirBundleIterator(IGenericClient fhirClient, IBaseBundle results, String
         private IBaseBundle results;
         private int current;
         private String dataType;
+        private String templateId;
         private Class<? extends IBaseResource> dataTypeClass;
         private List<? extends IBaseResource> currentEntry;
 
@@ -74,13 +89,33 @@ public boolean hasNext() {
         private List<? extends IBaseResource> getEntry() {
             if (this.dataTypeClass != null)
             {
-                return BundleUtil.toListOfResourcesOfType(this.fhirClient.getFhirContext(), this.results, this.dataTypeClass);
+                List<? extends IBaseResource> entries = BundleUtil.toListOfResourcesOfType(this.fhirClient.getFhirContext(), this.results, this.dataTypeClass);
+                if (templateId != null) {
+                    return getTrustedEntries(entries, templateId);
+                }
+                else {
+                    return entries;
+                }
             }
             else {
                 return BundleUtil.toListOfResources(this.fhirClient.getFhirContext(), this.results);
             }
         }
 
+        private List<? extends IBaseResource> getTrustedEntries(List<? extends IBaseResource> entries, String templateId) {
+            List<IBaseResource> trustedEntries = new ArrayList<IBaseResource>();
+            for (IBaseResource entry : entries) {
+                if (entry.getMeta() != null && entry.getMeta().getProfile() != null) {
+                    for (IPrimitiveType<?> profile : entry.getMeta().getProfile()) {
+                        if (profile.hasValue() && profile.getValueAsString().equals(templateId)) {
+                            trustedEntries.add(entry);
+                        }
+                    }
+                }
+            }
+            return trustedEntries;
+        }
+
         private String getLink() {
             return BundleUtil.getLinkUrlOfType(this.fhirClient.getFhirContext(), this.results, IBaseBundle.LINK_NEXT);
         }
@@ -105,6 +140,7 @@ public Object next() {
             }
 
             // TODO: It would be possible to get here if the next link was present, but the returned page had 0 entries...
+            // NOTE: This is especially true if the page has only data that is not conformant to the given profile
             throw new UnknownElement("The iteration has no more elements.");
         }
     }

engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu2ModelResolver.java

@@ -5,16 +5,18 @@
 import static org.testng.Assert.assertTrue;
 
 import java.lang.reflect.Field;
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
 
+
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.cql2elm.model.Model;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ClassInfo;
 import org.hl7.elm_modelinfo.r1.TypeInfo;
-import org.hl7.fhir.dstu2.model.EnumFactory;
-import org.hl7.fhir.dstu2.model.Enumeration;
+
+import org.hl7.fhir.dstu2.model.*;
 import org.hl7.fhir.dstu2.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu2.model.Enumerations.AgeUnits;
 import org.hl7.fhir.dstu2.model.Enumerations.BindingStrength;
@@ -29,7 +31,6 @@
 import org.hl7.fhir.dstu2.model.Enumerations.ResourceType;
 import org.hl7.fhir.dstu2.model.Enumerations.SearchParamType;
 import org.hl7.fhir.dstu2.model.Enumerations.SpecialValues;
-import org.hl7.fhir.dstu2.model.Patient;
 import org.opencds.cqf.cql.engine.fhir.exception.UnknownType;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.testng.annotations.Test;
@@ -232,4 +233,28 @@ public void resolveMissingPropertyReturnsNull() {
         Object result = resolver.resolvePath(p, "not-a-path");
         assertNull(result);
     }
+
+
+    //@Test
+    public void resolveNullEnumerationReturnsNull() {
+        FhirModelResolver<Base,?,?,SimpleQuantity,?,?,?,?> resolver = new Dstu2FhirModelResolver();
+
+        Quantity q = new Quantity();
+        q.setValue(new BigDecimal("10.0"));
+        q.setUnit("1");
+        SimpleQuantity sq = resolver.castToSimpleQuantity(q);
+
+        Object result = resolver.resolvePath(sq, "comparator");
+        assertNull(result);
+    }
+
+    //@Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new Dstu2FhirModelResolver();
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }

engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu3ModelResolver.java

@@ -4,6 +4,7 @@
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -12,7 +13,7 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ClassInfo;
 import org.hl7.elm_modelinfo.r1.TypeInfo;
-import org.hl7.fhir.dstu3.model.Enumeration;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Enumerations.AbstractType;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Enumerations.AgeUnits;
@@ -30,7 +31,6 @@
 import org.hl7.fhir.dstu3.model.Enumerations.ResourceType;
 import org.hl7.fhir.dstu3.model.Enumerations.SearchParamType;
 import org.hl7.fhir.dstu3.model.Enumerations.SpecialValues;
-import org.hl7.fhir.dstu3.model.Patient;
 import org.opencds.cqf.cql.engine.fhir.exception.UnknownType;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.testng.annotations.Test;
@@ -262,4 +262,27 @@ public void resolveMissingPropertyReturnsNull() {
         Object result = resolver.resolvePath(p, "not-a-path");
         assertNull(result);
     }
+
+    @Test
+    public void resolveNullEnumerationReturnsNull() {
+        FhirModelResolver<Base,?,?,SimpleQuantity,?,?,?,?> resolver = new Dstu3FhirModelResolver();
+
+        Quantity q = new Quantity();
+        q.setValue(new BigDecimal("10.0"));
+        q.setUnit("1");
+        SimpleQuantity sq = resolver.castToSimpleQuantity(q);
+
+        Object result = resolver.resolvePath(sq, "comparator");
+        assertNull(result);
+    }
+
+    @Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new Dstu3FhirModelResolver();
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }

engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestR4ModelResolver.java

@@ -6,6 +6,7 @@
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.GregorianCalendar;
@@ -16,8 +17,7 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ClassInfo;
 import org.hl7.elm_modelinfo.r1.TypeInfo;
-import org.hl7.fhir.r4.model.DateTimeType;
-import org.hl7.fhir.r4.model.Enumeration;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Enumerations.AbstractType;
 import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Enumerations.AgeUnits;
@@ -40,9 +40,6 @@
 import org.hl7.fhir.r4.model.Enumerations.ResourceType;
 import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
 import org.hl7.fhir.r4.model.Enumerations.SpecialValues;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.VisionPrescription;
 import org.opencds.cqf.cql.engine.fhir.exception.UnknownType;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.testng.annotations.Test;
@@ -164,7 +161,7 @@ public void modelInfoSpecialCaseTests() {
     public void modelInfo400Tests() {
         ModelResolver resolver = new R4FhirModelResolver();
         ModelManager mm = new ModelManager();
-        Model m = mm.resolveModel(new VersionedIdentifier().withId("FHIR").withVersion("4.0.0"));
+        Model m = mm.resolveModel(new VersionedIdentifier().withId("FHIR").withVersion("4.0.1"));
 
         List<TypeInfo> typeInfos = m.getModelInfo().getTypeInfo();
 
@@ -378,4 +375,27 @@ public void resolveDateTimeProviderReturnsDate() {
         assertNotNull(result);
         assertThat(result, is(dateTimeType));
     }
+
+    @Test
+    public void resolveNullEnumerationReturnsNull() {
+        FhirModelResolver<Base,?,?,SimpleQuantity,?,?,?,?> resolver = new R4FhirModelResolver();
+
+        Quantity q = new Quantity();
+        q.setValue(new BigDecimal("10.0"));
+        q.setUnit("1");
+        SimpleQuantity sq = resolver.castToSimpleQuantity(q);
+
+        Object result = resolver.resolvePath(sq, "comparator");
+        assertNull(result);
+    }
+
+    @Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new R4FhirModelResolver();
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }

engine/src/main/java/org/opencds/cqf/cql/engine/data/SystemDataProvider.java

@@ -41,6 +41,10 @@ private Field getProperty(Class<?> clazz, String path) {
             Field field = clazz.getDeclaredField(path);
             return field;
         } catch (NoSuchFieldException e) {
+            if (clazz.getSuperclass() != null) {
+                Field field = getProperty(clazz.getSuperclass(), path);
+                return field;
+            }
             throw new IllegalArgumentException(String.format("Could not determine field for path %s of type %s", path, clazz.getSimpleName()));
         }
     }

pom.xml

@@ -50,7 +50,7 @@
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <jackson.version>2.13.2</jackson.version>
         <jackson-databind.version>2.13.2.1</jackson-databind.version>
-        <cqframework.version>1.5.11</cqframework.version>
+        <cqframework.version>1.5.12-SNAPSHOT</cqframework.version>
         <hapi.version>5.6.3</hapi.version>
         <slf4j.version>1.7.29</slf4j.version>
     </properties>

scripts/deploy.sh

@@ -4,9 +4,9 @@
 set -euxo pipefail
 bash -n "$0"
 
-if [[ "$TRAVIS_BRANCH" != "master" && -z "$TRAVIS_TAG" ]]
+if [[ "$TRAVIS_BRANCH" != "master" && "$TRAVIS_BRANCH" != "v15" && -z "$TRAVIS_TAG" ]]
 then
-  echo "Not on the master branch or a git tag. Skipping deploy."
+  echo "Not on the master or v15 branches or a git tag. Skipping deploy."
   exit 0
 fi