Feature support negation profiles 20 (#618)

* #508,#552: Added support for profile validation in the retrieve #520: Fixed incorrect handling of null enumerations and primitives for FHIR-based models # Conflicts: # engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu2ModelResolver.java # engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu3ModelResolver.java # engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestR4ModelResolver.java # pom.xml * Add v15 branch to release scripting * Merge master (#627) * update v2.1.0 (#617) * update v2.1.0 * update reference for FhirLibrarySourceProvider * remove xpp3 exclusion * update readme * Rework xpp3 dependencies due to test failures Co-authored-by: Jonathan Percival <[email protected]> * snapshot v2.2.0 (#619) * ModelResolver Task to Patient path returns `for` instead of `requester` (#624) * Adding Android compliance check on the engine, engine.fhir and engine.jackson * Correctly using plugin management * Fixing Test case * Using Assert equals and not assertTrue(equals(x)) * Fixing #621 Co-authored-by: mdnazmulkarim <[email protected]> Co-authored-by: Jonathan Percival <[email protected]> Co-authored-by: Vitor Pamplona <[email protected]> Co-authored-by: mdnazmulkarim <[email protected]> Co-authored-by: Jonathan Percival <[email protected]> Co-authored-by: Vitor Pamplona <[email protected]>
cqframework · Oct 20, 2022 · d245db1 · d245db1
1 parent e13c23d
commit d245db1
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Showing 8 changed files with 82 additions and 8 deletions.
diff --git a/.travis.yml b/.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:

diff --git a/engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/model/FhirModelResolver.java b/engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/model/FhirModelResolver.java
@@ -648,6 +648,10 @@ 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":

diff --git a/engine.fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/retrieve/FhirBundleCursor.java b/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.");
         }
     }

diff --git a/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu2ModelResolver.java b/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu2ModelResolver.java
@@ -249,4 +249,14 @@ public void resolveNullEnumerationReturnsNull() {
         Object result = resolver.resolvePath(sq, "comparator");
         assertNull(result);
     }
+
+    //@Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new Dstu2FhirModelResolver(FhirContext.forCached(FhirVersionEnum.DSTU2));
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }
diff --git a/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu3ModelResolver.java b/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestDstu3ModelResolver.java
@@ -281,4 +281,14 @@ public void resolveNullEnumerationReturnsNull() {
         Object result = resolver.resolvePath(sq, "comparator");
         assertNull(result);
     }
+
+    @Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new Dstu3FhirModelResolver(FhirContext.forCached(FhirVersionEnum.DSTU3));
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }
diff --git a/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestR4ModelResolver.java b/engine.fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/model/TestR4ModelResolver.java
@@ -394,4 +394,14 @@ public void resolveNullEnumerationReturnsNull() {
         Object result = resolver.resolvePath(sq, "comparator");
         assertNull(result);
     }
+
+    @Test
+    public void resolveNullPrimitiveReturnsNull() {
+        FhirModelResolver<Base,BaseDateTimeType,?,?,?,?,?,?> resolver = new R4FhirModelResolver(FhirContext.forCached(FhirVersionEnum.R4));
+
+        DateTimeType dt = new DateTimeType();
+
+        Object result = resolver.resolvePath(dt, "value");
+        assertNull(result);
+    }
 }
diff --git a/engine/src/main/java/org/opencds/cqf/cql/engine/data/SystemDataProvider.java b/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()));
         }
     }

diff --git a/scripts/deploy.sh b/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