Fixes exception while unmarshalling ELEMENT node with children DV_COD…

…ED_TEXT and DV_TEXT

CHANGELOG.md

@@ -15,7 +15,8 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
 - Fix NullPointerException when event has an empty state (https://github.com/ehrbase/openEHR_SDK/pull/294)
 - Fix issue when template does not contain list of values for DV_ORDINAL (https://github.com/ehrbase/openEHR_SDK/pull/295)
 - Fix issue in AQL regarding LIMIT and OFFSET (https://github.com/ehrbase/openEHR_SDK/pull/296)
-
+- Fix issue while unmarshalling FLAT composition that contains ELEMENT with children DV_CODED_TEXT and DV_TEXT (https://github.com/ehrbase/openEHR_SDK/pull/300)
+- 
 ## 1.16.0
 
 ### Added

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/std/marshal/StdFromCompositionWalker.java

@@ -19,7 +19,13 @@
 
 package org.ehrbase.serialisation.flatencoding.std.marshal;
 
+import static org.ehrbase.serialisation.flatencoding.std.umarshal.StdToCompositionWalker.handleDVTextInternal;
+
 import com.nedap.archie.rm.RMObject;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
 import org.ehrbase.serialisation.flatencoding.std.marshal.config.DefaultStdConfig;
 import org.ehrbase.serialisation.flatencoding.std.marshal.config.StdConfig;
 import org.ehrbase.serialisation.flatencoding.std.marshal.postprocessor.MarshalPostprocessor;
@@ -28,14 +34,7 @@
 import org.ehrbase.serialisation.walker.FromCompositionWalker;
 import org.ehrbase.util.reflection.ReflectionHelper;
 import org.ehrbase.webtemplate.model.WebTemplateNode;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import static org.ehrbase.serialisation.flatencoding.std.umarshal.StdToCompositionWalker.handleDVTextInternal;
+import org.ehrbase.webtemplate.util.WebTemplateUtils;
 
 public class StdFromCompositionWalker extends FromCompositionWalker<Map<String, Object>> {
 
@@ -112,24 +111,9 @@ public static <T extends RMObject> List<MarshalPostprocessor<T>> findPostprocess
 
   @Override
   protected void handleDVText(WebTemplateNode currentNode) {
-    if (currentNode.getRmType().equals("ELEMENT")) {
-      List<WebTemplateNode> trueChildren =
-          currentNode.getChildren().stream()
-              .filter(
-                  n ->
-                      !List.of("null_flavour", "feeder_audit").contains(n.getName())
-                          || !n.isNullable())
-              .collect(Collectors.toList());
-      if (trueChildren.stream()
-              .map(WebTemplateNode::getId)
-              .collect(Collectors.toList())
-              .containsAll(List.of("coded_text_value", "text_value"))
-          && currentNode.getChoicesInChildren().size() > 0
-          && trueChildren.size() == 2) {
-        handleDVTextInternal(currentNode);
-      } else {
-        super.handleDVText(currentNode);
-      }
+    if (currentNode.getRmType().equals("ELEMENT")
+        && WebTemplateUtils.hasDvCodedTextAndDvText(currentNode)) {
+      handleDVTextInternal(currentNode);
     } else {
       super.handleDVText(currentNode);
     }

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/std/umarshal/StdToCompositionWalker.java

@@ -19,6 +19,10 @@
 
 package org.ehrbase.serialisation.flatencoding.std.umarshal;
 
+import static org.ehrbase.util.rmconstants.RmConstants.DV_CODED_TEXT;
+import static org.ehrbase.util.rmconstants.RmConstants.DV_TEXT;
+import static org.ehrbase.util.rmconstants.RmConstants.ELEMENT;
+
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.nedap.archie.rm.RMObject;
@@ -30,6 +34,15 @@
 import com.nedap.archie.rm.datavalues.DvText;
 import com.nedap.archie.rm.generic.PartyRelated;
 import com.nedap.archie.rm.support.identification.TerminologyId;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
@@ -50,11 +63,7 @@
 import org.ehrbase.webtemplate.model.WebTemplateInput;
 import org.ehrbase.webtemplate.model.WebTemplateNode;
 import org.ehrbase.webtemplate.path.flat.FlatPathDto;
-
-import java.util.*;
-import java.util.stream.Collectors;
-
-import static org.ehrbase.util.rmconstants.RmConstants.*;
+import org.ehrbase.webtemplate.util.WebTemplateUtils;
 
 public class StdToCompositionWalker extends ToCompositionWalker<Map<FlatPathDto, String>> {
 
@@ -144,12 +153,12 @@ protected ImmutablePair<Map<FlatPathDto, String>, RMObject> extractPair(
       Integer i) {
 
     if (
-    // Nodes with children need to be put on the stack even if there are skip since the might have
-    // children. If there are empty there will be removed in ToCompositionWalker::normalise
-    (CollectionUtils.isEmpty(childNode.getChildren())
+      // Nodes with children need to be put on the stack even if there are skip since the might have
+      // children. If there are empty there will be removed in ToCompositionWalker::normalise
+        (CollectionUtils.isEmpty(childNode.getChildren())
             && context.getFlatHelper().skip(childNode, currentNode))
-        //  NonMandatoryRmAttribute are handled in the UnmarshalPostprocessor
-        || (currentNode != null
+            //  NonMandatoryRmAttribute are handled in the UnmarshalPostprocessor
+            || (currentNode != null
             && context.getFlatHelper().isNonMandatoryRmAttribute(childNode, currentNode))) {
       return new ImmutablePair<>(null, null);
     }
@@ -208,7 +217,7 @@ protected void preHandle(Context<Map<FlatPathDto, String>> context) {
 
       if (context.getRmObjectDeque().peek().getClass().isAssignableFrom(DvCodedText.class)
           && context.getObjectDeque().peek().keySet().stream()
-              .anyMatch(k -> "other".equals(k.getLast().getAttributeName()))) {
+          .anyMatch(k -> "other".equals(k.getLast().getAttributeName()))) {
         replaceRmObject(context, new DvText());
       }
 
@@ -285,8 +294,8 @@ private boolean isRaw(Context<Map<FlatPathDto, String>> context) {
     return Objects.equals(current.getKey().getLast().getAttributeName(), "raw")
         // last flat path segment matches node_id ( starting '_' marks optional flat path )
         && Objects.equals(
-            StringUtils.removeStart(context.getNodeDeque().peek().getId(false), "_"),
-            StringUtils.removeStart(current.getKey().getLast().getName(), "_"));
+        StringUtils.removeStart(context.getNodeDeque().peek().getId(false), "_"),
+        StringUtils.removeStart(current.getKey().getLast().getName(), "_"));
   }
 
   @Override
@@ -310,7 +319,8 @@ protected void postHandle(Context<Map<FlatPathDto, String>> context) {
               if (context.getFlatHelper().skip(childNode, currentNode)) {
 
                 context.getNodeDeque().push(childNode);
-                context.getRmObjectDeque().push(new RMObject() {});
+                context.getRmObjectDeque().push(new RMObject() {
+                });
 
                 String path = context.getFlatHelper().buildNamePath(context, true);
                 Map<FlatPathDto, String> subValues =
@@ -385,54 +395,20 @@ public static <T extends RMObject> List<UnmarshalPostprocessor<T>> findUnmarshal
 
   @Override
   protected void handleDVText(WebTemplateNode currentNode) {
-    if (currentNode.getRmType().equals(ELEMENT)) {
-      List<WebTemplateNode> trueChildren =
-          currentNode.getChildren().stream()
-              .filter(n -> !"name".equals(n.getId()))
-              .filter(
-                  n ->
-                      !List.of("null_flavour", "feeder_audit").contains(n.getId())
-                          || !n.isNullable())
-              .collect(Collectors.toList());
-      if (trueChildren.stream()
-              .map(WebTemplateNode::getRmType)
-              .collect(Collectors.toList())
-              .containsAll(List.of(DV_TEXT, DV_CODED_TEXT))
-          && currentNode.getChoicesInChildren().size() > 0
-          && trueChildren.size() == 2) {
-        handleDVTextInternal(currentNode);
-      } else {
-        super.handleDVText(currentNode);
-      }
+    if (currentNode.getRmType().equals("ELEMENT")
+        && WebTemplateUtils.hasDvCodedTextAndDvText(currentNode)) {
+      handleDVTextInternal(currentNode);
     } else {
       super.handleDVText(currentNode);
     }
   }
 
   public static void handleDVTextInternal(WebTemplateNode node) {
-
-    if (node.getRmType().equals(ELEMENT)) {
-      List<WebTemplateNode> trueChildren =
-          node.getChildren().stream()
-              .filter(n -> !"name".equals(n.getId()))
-              .filter(
-                  n ->
-                      !List.of("null_flavour", "feeder_audit").contains(n.getId())
-                          || !n.isNullable())
-              .collect(Collectors.toList());
-      if (trueChildren.stream()
-              .map(WebTemplateNode::getId)
-              .collect(Collectors.toList())
-              .containsAll(List.of("coded_text_value", "text_value"))
-          && node.getChoicesInChildren().size() > 0
-          && trueChildren.size() == 2) {
-        WebTemplateNode merged = Filter.mergeDVText(node);
-
-        node.getChildren()
-            .removeIf(n -> List.of("coded_text_value", "text_value").contains(n.getId()));
-        node.getChildren().add(merged);
-      }
-    }
+    WebTemplateNode merged = Filter.mergeDVText(node);
+    node.getChildren()
+        .removeIf(
+            childNode -> List.of("coded_text_value", "text_value").contains(childNode.getId()));
+    node.getChildren().add(merged);
   }
 
   @Override

serialisation/src/test/java/org/ehrbase/serialisation/flatencoding/std/marshal/FlatJsonMarshallerTest.java

@@ -184,6 +184,63 @@ public void toFlatJsonAllTypes() throws IOException, XmlException {
         });
   }
 
+  @Test
+  public void toFlatJsonIps() throws Exception {
+    OPERATIONALTEMPLATE template =
+        TemplateDocument.Factory.parse(OperationalTemplateTestData.IPS.getStream())
+            .getTemplate();
+
+    Composition composition =
+        new CanonicalJson()
+            .unmarshal(
+                IOUtils.toString(
+                    CompositionTestDataCanonicalJson.IPS.getStream(), StandardCharsets.UTF_8),
+                Composition.class);
+
+    FlatJsonMarshaller marshaller = new FlatJsonMarshaller();
+
+    String actual = marshaller.toFlatJson(composition, new OPTParser(template).parse());
+    assertThat(actual).isNotNull();
+
+    String expected =
+        IOUtils.toString(
+            CompositionTestDataSimSDTJson.IPS.getStream(), StandardCharsets.UTF_8);
+
+    List<String> errors = compere(actual, expected);
+
+
+    checkErrors(errors,
+        new String[] {
+            "Missing path: international_patient_summary/medication_summary/medication_statement/order_id:0|id, value: 9a0e5173-07c8-443d-b414-24432b9d95ca",
+            "Missing path: international_patient_summary/medical_devices/device_use_statement/device_details:0/medical_device/unique_device_identifier_udi|id, value: 73b166ae-1c28-4ce0-8c08-a9587d8fd95a",
+            "Missing path: international_patient_summary/medical_devices/device_use_statement/device_details:0/medical_device/other_identifier:0|id, value: 60287ff3-ec0f-4cd5-9000-2c05af2e6a84",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/requester_order_identifier|id, value: 38a6687c-5136-4e75-9f1c-126e8f0e112b",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/receiver_order_identifier|id, value: 9fc6db02-81de-4ec9-afe4-f365c42019e1",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/report_identifier|id, value: a147525c-4763-4070-ba22-26e6b33348f4",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/reported_image:0/image_identifier|id, value: 5462ef5c-2275-47c2-8fb5-f9f1d7a19613",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/reported_image:0/dicom_series_identifier|id, value: 55dd86d7-52ff-4064-8dc7-f8d9b2bc22e7",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/comparison_image:0/image_identifier|id, value: a6c20273-7b53-4c04-9b2c-2d4c218893b2",
+            "Missing path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/comparison_image:0/dicom_series_identifier|id, value: 1ba8eff7-8f3f-4625-9432-05aa01726073",
+            "Missing path: international_patient_summary/vital_signs/pulse_oximetry/any_event:0/spo, value: 0.8920999999999999",
+            "Missing path: international_patient_summary/plan_of_care/care_plan/care_plan_id|id, value: 0942fb74-27f8-48c6-869e-10192740c371",
+            "Missing path: international_patient_summary/plan_of_care/service_request/current_activity:0/action_archetype_id, value: /.*/"
+        },
+        new String[] {
+            "Extra path: international_patient_summary/medication_summary/medication_statement/order_id:0, value: 9a0e5173-07c8-443d-b414-24432b9d95ca",
+            "Extra path: international_patient_summary/medical_devices/device_use_statement/device_details:0/medical_device/unique_device_identifier_udi, value: 73b166ae-1c28-4ce0-8c08-a9587d8fd95a",
+            "Extra path: international_patient_summary/medical_devices/device_use_statement/device_details:0/medical_device/other_identifier:0, value: 60287ff3-ec0f-4cd5-9000-2c05af2e6a84",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/requester_order_identifier, value: 38a6687c-5136-4e75-9f1c-126e8f0e112b",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/receiver_order_identifier, value: 9fc6db02-81de-4ec9-afe4-f365c42019e1",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/report_identifier, value: a147525c-4763-4070-ba22-26e6b33348f4",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/reported_image:0/image_identifier, value: 5462ef5c-2275-47c2-8fb5-f9f1d7a19613",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/reported_image:0/dicom_series_identifier, value: 55dd86d7-52ff-4064-8dc7-f8d9b2bc22e7",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/comparison_image:0/image_identifier, value: a6c20273-7b53-4c04-9b2c-2d4c218893b2",
+            "Extra path: international_patient_summary/diagnostic_results/imaging_examination_result/examination_request_details:0/comparison_image:0/dicom_series_identifier, value: 1ba8eff7-8f3f-4625-9432-05aa01726073",
+            "Extra path: international_patient_summary/vital_signs/pulse_oximetry/any_event:0/spo, value: 0.8921",
+            "Extra path: international_patient_summary/plan_of_care/care_plan/care_plan_id, value: 0942fb74-27f8-48c6-869e-10192740c371"
+        });
+  }
+
   public void checkErrors(List<String> errors, String[] missing, String[] extra) {
 
     SoftAssertions softAssertions = new SoftAssertions();

serialisation/src/test/java/org/ehrbase/serialisation/flatencoding/std/umarshal/FlatJsonUnmarshallerTest.java

@@ -192,4 +192,21 @@ public void unmarshallNestedComposition() throws Exception {
 
     assertDoesNotThrow(() -> new Validator(optTemplate).check(composition));
   }
+
+
+  @Test
+  public void unmarshallIpsComposition() throws Exception {
+    var optTemplate = TemplateDocument.Factory.parse(OperationalTemplateTestData.IPS.getStream())
+        .getTemplate();
+    var webTemplate = new OPTParser(optTemplate).parse();
+
+    var json = IOUtils.toString(CompositionTestDataSimSDTJson.IPS.getStream(),
+        StandardCharsets.UTF_8);
+
+    var composition = new FlatJsonUnmarshaller().unmarshal(json, webTemplate);
+
+    assertThat(composition).isNotNull();
+
+    assertDoesNotThrow(() -> new Validator(optTemplate).check(composition));
+  }
 }

test-data/src/main/java/org/ehrbase/test_data/composition/CompositionTestDataCanonicalJson.java

@@ -61,7 +61,8 @@ public enum CompositionTestDataCanonicalJson {
     MINIMAL_WITHOUT_OPTIONAL_ATTRIBUTE("dv multimedia without alternate_text", "minimal_without_optional_attribute.json"),
     GECCO_PERSONENDATEN("GECCO_Personendaten", "gecco_personendaten.json"),
     GECCO_LABORBEFUND("GECCO_Laborbefund", "gecco_laborbefund.json"),
-    PARTICIPATION_NO_CONTENT("to test various participation CR #710", "participation_no_content.json");
+    PARTICIPATION_NO_CONTENT("to test various participation CR #710", "participation_no_content.json"),
+    IPS("Internation Patient Summary", "ips_canonical.json");
 
 
     private final String filename;

test-data/src/main/java/org/ehrbase/test_data/composition/CompositionTestDataSimSDTJson.java

@@ -41,7 +41,8 @@ public enum CompositionTestDataSimSDTJson {
   MULTI_LIST("MULTI_LIST", "multi_list.json"),
   NCD("NCD", "NCD.json"),
   EREACT_COVID_MANAGEMENT("flat with action", "EREACT - Covid status monitoring - FLAT.json"),
-  NESTED("nested.en.v1", "nested.en.v1.json");
+  NESTED("nested.en.v1", "nested.en.v1.json"),
+  IPS("International Patient Summary", "ips_flat.json");
 
   private final String filename;
   private final String description;

test-data/src/main/java/org/ehrbase/test_data/operationaltemplate/OperationalTemplateTestData.java

@@ -104,7 +104,8 @@ public enum OperationalTemplateTestData {
   MINIMAL_ACTION("Minimal Action 3", "minimal_action3.opt", "minimal_action_3.en.v1"),
   NCD("ncd", "NCD.opt", "NCD"),
   MULTIMEDIA_TEST("MultimediaTest", "multimedia_test.en.v1.opt", "multimedia_test.en.v1"),
-  NESTED("nested.en.v1", "nested.en.v1.opt", "nested.en.v1");
+  NESTED("nested.en.v1", "nested.en.v1.opt", "nested.en.v1"),
+  IPS("International Patient Summary", "ips.v0.opt", "International Patient Summary");
 
   private final String filename;
   private final String templateId;