Remove annotations of objects that are removed in Flattened archetype (…

…#615)

* remove annotations when objects are removed because of zero occurrences

* Also remove annotations for objects that are prohibited, but are not removed

* Add test

* add test

* add tests for coverage

tools/src/main/java/com/nedap/archie/flattener/Flattener.java

@@ -253,12 +253,14 @@ private void prohibitZeroOccurrencesConstraints(Archetype archetype) {
             CObject object = workList.pop();
             for(CAttribute attribute:object.getAttributes()) {
                 if(attribute.getExistence() != null && attribute.getExistence().getUpper() == 0 && !attribute.getExistence().isUpperUnbounded()) {
-                    //remove children, but do not remove attribute itself to make sure it stays prohibited
+                    // Remove children, but do not remove attribute itself to make sure it stays prohibited
+                    FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, attribute.getChildren());
                     attribute.setChildren(new ArrayList<>());
                 } else {
                     List<CObject> objectsToRemove = new ArrayList<>();
                     for (CObject child : attribute.getChildren()) {
                         if (!child.isAllowed()) {
+                            FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, List.of(child));
                             if(child instanceof CComplexObject) {
                                 ((CComplexObject) child).setAttributes(new ArrayList<>());
                             }
@@ -271,9 +273,7 @@ private void prohibitZeroOccurrencesConstraints(Archetype archetype) {
                     }
                     attribute.getChildren().removeAll(objectsToRemove);
                 }
-
             }
-
         }
     }
 

tools/src/main/java/com/nedap/archie/flattener/FlattenerUtil.java

@@ -1,14 +1,15 @@
 package com.nedap.archie.flattener;
 
-import com.nedap.archie.aom.CObject;
+import com.nedap.archie.aom.Archetype;
+import com.nedap.archie.aom.ArchetypeConstraint;
 import com.nedap.archie.rules.Assertion;
 
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
 
 public class FlattenerUtil {
 
-
-
     public static List<Assertion> getPossiblyOverridenListValue(List<Assertion> parent, List<Assertion> child) {
         if(child != null && !child.isEmpty()) {
             return child;
@@ -22,4 +23,30 @@ public static <T> T getPossiblyOverridenValue(T parent, T specialized) {
         }
         return parent;
     }
+
+    /**
+     * Removes annotations for the objects given, also removes annotations for children underneath the objects.
+     */
+    public static void removeAnnotationsForArchetypeConstraints(Archetype result, List<? extends ArchetypeConstraint> archetypeConstraints) {
+        if (result.getAnnotations() == null ||
+                result.getAnnotations().getDocumentation() == null ||
+                result.getAnnotations().getDocumentation().isEmpty() ||
+                archetypeConstraints.isEmpty()
+        ) {
+            return;
+        }
+
+        removeAnnotationsForPaths(result.getAnnotations().getDocumentation(), archetypeConstraints.stream().map(ArchetypeConstraint::getPath).collect(Collectors.toList()));
+    }
+
+    private static void removeAnnotationsForPaths(Map<String, Map<String, Map<String, String>>> annotations, List<String> pathsToRemove) {
+        for (String pathToRemove : pathsToRemove) {
+            for (String languageKeys : annotations.keySet()) {
+                Map<String, Map<String, String>> languageAnnotations = annotations.get(languageKeys);
+                List<String> toRemove = languageAnnotations.keySet().stream().filter(path -> path.startsWith(pathToRemove)).collect(Collectors.toList());
+                toRemove.forEach(languageAnnotations::remove);
+            }
+
+        }
+    }
 }

tools/src/main/java/com/nedap/archie/flattener/OperationalTemplateCreator.java

@@ -84,10 +84,12 @@ public void removeZeroOccurrencesConstraints(Archetype archetype) {
                         }
                         workList.push(child);
                     }
+                    FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, objectsToRemove);
                     attribute.getChildren().removeAll(objectsToRemove);
                 }
 
             }
+            FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, attributesToRemove);
             object.getAttributes().removeAll(attributesToRemove);
         }
     }
@@ -262,8 +264,4 @@ private void fillArchetypeRoot(CArchetypeRoot root, OperationalTemplate result)
     private FlattenerConfiguration getConfig() {
         return flattener.getConfiguration();
     }
-
-
-
-
 }

tools/src/test/java/com/nedap/archie/flattener/AnnotationsFlattenerTest.java

@@ -1,14 +1,17 @@
 package com.nedap.archie.flattener;
 
 import com.nedap.archie.adlparser.ADLParser;
+import com.nedap.archie.aom.Archetype;
 import com.nedap.archie.aom.ResourceAnnotations;
 import com.nedap.archie.rminfo.ReferenceModels;
-import com.nedap.archie.aom.Archetype;
 import org.junit.Before;
 import org.junit.Test;
 import org.openehr.referencemodels.BuiltinReferenceModels;
 
+import java.util.HashMap;
+
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
 
 public class AnnotationsFlattenerTest {
 
@@ -105,4 +108,68 @@ public void flattenUsedArchetypeWithAnnotations() throws Exception {
         assertEquals("this is a design note on intelerance", annotations.getDocumentation().get("en").get("/data[id2]/events[id3]/data[id4]/items[id6]").get("design note"));
         assertEquals("this is a design note for a cluster", annotations.getDocumentation().get("en").get("/data[id2]/events[id3]/data[id4]/items[id8]/items[id3]/value[id4]").get("design note"));
     }
+
+    @Test
+    public void flattenArchetypeWithZeroOccurrencesObject() throws Exception {
+        Archetype childWithExcluded = new ADLParser().parse(FlattenerTest.class.getResourceAsStream("openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls"));
+        repository.addArchetype(childWithExcluded);
+
+        flattener = new Flattener(repository, models).createOperationalTemplate(false);
+
+        Archetype flattened = flattener.flatten(childWithExcluded);
+        assertNull(flattened.getAnnotations().getDocumentation().get("en").get("/data[id2]/events[id3]/data[id4]/items[id6]"));
+    }
+
+    @Test
+    public void flattenArchetypeWithZeroOccurrencesObjectOPT() throws Exception {
+        Archetype childWithExcluded = new ADLParser().parse(FlattenerTest.class.getResourceAsStream("openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls"));
+        repository.addArchetype(childWithExcluded);
+
+        flattener = new Flattener(repository, models).createOperationalTemplate(true);
+
+        Archetype flattened = flattener.flatten(childWithExcluded);
+        assertNull(flattened.getAnnotations().getDocumentation().get("en").get("/data[id2]/events[id3]/data[id4]/items[id6]"));
+    }
+
+    @Test
+    public void flattenArchetypeWithNoAnnotations() throws Exception {
+        parent.setAnnotations(null);
+        repository.addArchetype(parent);
+        Archetype childWithExcluded = new ADLParser().parse(FlattenerTest.class.getResourceAsStream("openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls"));
+        childWithExcluded.setAnnotations(null);
+        repository.addArchetype(childWithExcluded);
+
+        flattener = new Flattener(repository, models).createOperationalTemplate(true);
+
+        Archetype flattened = flattener.flatten(childWithExcluded);
+        assertNull(flattened.getAnnotations());
+    }
+
+    @Test
+    public void flattenArchetypeWithNoDocumentation() throws Exception {
+        parent.setAnnotations(new ResourceAnnotations());
+        repository.addArchetype(parent);
+        Archetype childWithExcluded = new ADLParser().parse(FlattenerTest.class.getResourceAsStream("openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls"));
+        childWithExcluded.setAnnotations(new ResourceAnnotations());
+        repository.addArchetype(childWithExcluded);
+
+        flattener = new Flattener(repository, models).createOperationalTemplate(true);
+
+        Archetype flattened = flattener.flatten(childWithExcluded);
+        assertNull(flattened.getAnnotations().getDocumentation());
+    }
+
+    @Test
+    public void flattenArchetypeWithEmptyDocumentation() throws Exception {
+        parent.getAnnotations().setDocumentation(new HashMap<>());
+        repository.addArchetype(parent);
+        Archetype childWithExcluded = new ADLParser().parse(FlattenerTest.class.getResourceAsStream("openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls"));
+        childWithExcluded.getAnnotations().setDocumentation(new HashMap<>());
+        repository.addArchetype(childWithExcluded);
+
+        flattener = new Flattener(repository, models).createOperationalTemplate(true);
+
+        Archetype flattened = flattener.flatten(childWithExcluded);
+        assertEquals(0, flattened.getAnnotations().getDocumentation().size());
+    }
 }

tools/src/test/resources/com/nedap/archie/flattener/openEHR-EHR-OBSERVATION.to_flatten_child_with_annotations_exclude_object.v1.adls

@@ -0,0 +1,71 @@
+archetype (adl_version=2.0.5; rm_release=1.0.2; generated)
+	openEHR-EHR-OBSERVATION.to_flatten_child.v1.0.0
+
+specialize
+	openEHR-EHR-OBSERVATION.to_flatten_parent.v1
+
+language
+	original_language = <[ISO_639-1::en]>
+	translations = <
+		["ar-sy"] = <
+			language = <[ISO_639-1::ar-sy]>
+			author = <
+				["name"] = <"Mona Saleh">
+			>
+		>
+	>
+
+description
+	lifecycle_state = <"unmanaged">
+	original_author = <
+		["name"] = <"Heather Leslie">
+		["organisation"] = <"Ocean Informatics">
+		["email"] = <"[email protected]">
+		["date"] = <"2012-12-11">
+	>
+	copyright = <"none">
+	details = <
+		["en"] = <
+			language = <[ISO_639-1::en]>
+			purpose = <"specialized rules test">
+			use = <"testing specialized rules">
+			keywords = <"test">
+			misuse = <"">
+		>
+	>
+
+definition
+	OBSERVATION[id1.1] matches {	-- blood pressure
+      /data[id2]/events[id3]/data[id4]/items matches {
+        ELEMENT[id6] occurrences matches {0}
+    }
+  }
+
+terminology
+	term_definitions = <
+		["en"] = <
+			["id1.1"] = <
+				text = <"blood pressure observation">
+				description = <"blood pressure observation">
+			>
+		>
+	>
+
+annotations
+	documentation = <
+		["en"] = <
+			["/subject"] = <
+				["design note"] = <"xxxxxx">
+			>
+			["/data[id2]/events[id3]/data[id4]/items[id5]"] = <
+				["design note"] = <"this is a design note on allergic reaction, with some extra information">
+				["requirements note"] = <"this is a requirements note on allergic reaction">
+				["medline ref"] = <"this is a medline ref on allergic reaction">
+			>
+			["/data[id2]/events[id3]/data[id4]/items[id7]"] = <
+				["design note"] = <"this is also a design note on intelerance">
+				["requirements note"] = <"this is a requirements note on intolerance">
+				["national data dictionary"] = <"NDD ref for intolerance">
+			>
+		>
+	>