Feature/pem 96 support structured

CHANGELOG.md

@@ -8,6 +8,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
 
 - Added WebTemplate based RmSkeleton builder. (see https://github.com/ehrbase/openEHR_SDK/pull/241)
 - validate that all flat parts are consumed. (see https://github.com/ehrbase/openEHR_SDK/pull/264 )
+- support Structured format. (see https://github.com/ehrbase/openEHR_SDK/pull/273)
 
 ### Fixed
 

client/src/test/java/org/ehrbase/client/classgenerator/OldDtoModelTest.java

@@ -31,12 +31,11 @@
 import org.ehrbase.client.classgenerator.olddtoexamples.coronaanamnesecomposition.definition.VorhandenDefiningcode;
 import org.ehrbase.client.classgenerator.olddtoexamples.testalltypesenv1composition.TestAllTypesEnV1Composition;
 import org.ehrbase.client.flattener.Flattener;
-import org.ehrbase.client.flattener.RoundTripTest;
 import org.ehrbase.client.flattener.Unflattener;
 import org.ehrbase.client.templateprovider.TestDataTemplateProvider;
+import org.ehrbase.serialisation.RMDataFormat;
 import org.ehrbase.serialisation.flatencoding.FlatFormat;
 import org.ehrbase.serialisation.flatencoding.FlatJasonProvider;
-import org.ehrbase.serialisation.flatencoding.FlatJson;
 import org.ehrbase.serialisation.jsonencoding.CanonicalJson;
 import org.ehrbase.serialisation.jsonencoding.JacksonUtil;
 import org.ehrbase.test_data.composition.CompositionTestDataCanonicalJson;
@@ -161,7 +160,7 @@ public void testUnflattenCorona() throws IOException {
   public void checkTestCase(TestCase testCase, SoftAssertions softly) throws IOException {
 
     String value = IOUtils.toString(testCase.simSDTJson.getStream(), UTF_8);
-    FlatJson flatJson =
+    RMDataFormat flatJson =
         new FlatJasonProvider(new TestDataTemplateProvider())
             .buildFlatJson(FlatFormat.SIM_SDT, testCase.templateId);
 

client/src/test/java/org/ehrbase/client/flattener/RoundTripTest.java

@@ -19,30 +19,31 @@
 
 package org.ehrbase.client.flattener;
 
-import static java.nio.charset.StandardCharsets.UTF_8;
-
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.nedap.archie.rm.RMObject;
 import com.nedap.archie.rm.composition.Composition;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
 import org.apache.commons.io.IOUtils;
 import org.assertj.core.api.SoftAssertions;
 import org.ehrbase.client.classgenerator.examples.alternativeeventscomposition.AlternativeEventsComposition;
 import org.ehrbase.client.classgenerator.examples.coronaanamnesecomposition.CoronaAnamneseComposition;
 import org.ehrbase.client.classgenerator.examples.ehrbasemultioccurrencedev1composition.EhrbaseMultiOccurrenceDeV1Composition;
 import org.ehrbase.client.classgenerator.examples.testalltypesenv1composition.TestAllTypesEnV1Composition;
 import org.ehrbase.client.templateprovider.TestDataTemplateProvider;
+import org.ehrbase.serialisation.RMDataFormat;
 import org.ehrbase.serialisation.flatencoding.FlatFormat;
 import org.ehrbase.serialisation.flatencoding.FlatJasonProvider;
-import org.ehrbase.serialisation.flatencoding.FlatJson;
 import org.ehrbase.serialisation.jsonencoding.JacksonUtil;
 import org.ehrbase.test_data.composition.CompositionTestDataSimSDTJson;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 public class RoundTripTest {
 
   class TestCase {
@@ -170,7 +171,7 @@ public void testRoundTrip() throws IOException {
   public void checkTestCase(TestCase testCase, SoftAssertions softly) throws IOException {
 
     String value = IOUtils.toString(testCase.simSDTJson.getStream(), UTF_8);
-    FlatJson flatJson =
+    RMDataFormat flatJson =
         new FlatJasonProvider(new TestDataTemplateProvider())
             .buildFlatJson(FlatFormat.SIM_SDT, testCase.templateId);
 

pom.xml

@@ -543,6 +543,12 @@
                 <version>3.3.0</version>
                 <scope>test</scope>
             </dependency>
+            <dependency>
+                <groupId>org.skyscreamer</groupId>
+                <artifactId>jsonassert</artifactId>
+                <version>1.5.0</version>
+                <scope>test</scope>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

serialisation/pom.xml

@@ -108,6 +108,10 @@
             <groupId>com.github.ehrbase.openEHR_SDK</groupId>
             <artifactId>util</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.skyscreamer</groupId>
+            <artifactId>jsonassert</artifactId>
+        </dependency>
     </dependencies>
 
 </project>

serialisation/src/main/java/org/ehrbase/serialisation/RMDataFormat.java

@@ -19,12 +19,17 @@
 package org.ehrbase.serialisation;
 
 import com.nedap.archie.rm.RMObject;
+import com.nedap.archie.rm.composition.Composition;
 
 public interface RMDataFormat {
 
     String marshal(RMObject rmObject);
 
     <T extends RMObject> T unmarshal(String value, Class<T> clazz);
 
+    default Composition unmarshal(String value){
+
+        return unmarshal(value,Composition.class);
+    }
 
 }

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/FlatFormat.java

@@ -22,11 +22,13 @@
 /**
  * The supported flat jason formats
  *
- * @see <a href="https://specifications.openehr.org/releases/ITS-REST/latest/simplified_data_template.html">Simplified Data Template (SDT)</a>
+ * @see <a
+ *     href="https://specifications.openehr.org/releases/ITS-REST/latest/simplified_data_template.html">Simplified
+ *     Data Template (SDT)</a>
  */
 public enum FlatFormat {
-    /**
-     * Simplified IM Simplified Data template.
-     */
-    SIM_SDT;
+  /** Simplified IM Simplified Data template. */
+  SIM_SDT,
+  /** STRUCTURED */
+  STRUCTURED;
 }

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/FlatJasonProvider.java

@@ -19,7 +19,7 @@
 
 package org.ehrbase.serialisation.flatencoding;
 
-
+import org.ehrbase.serialisation.RMDataFormat;
 import org.ehrbase.util.exception.SdkException;
 import org.ehrbase.webtemplate.templateprovider.TemplateProvider;
 
@@ -28,32 +28,33 @@
  */
 public class FlatJasonProvider {
 
-    private final TemplateProvider templateProvider;
-
-    public FlatJasonProvider(TemplateProvider templateProvider) {
-        this.templateProvider = templateProvider;
-    }
-
-    /**
-     * Builds a {@link FlatJson} for the template with {@code templateId} and {@link FlatFormat} {@code format}
-     *
-     * @param format
-     * @param templateId
-     * @return
-     */
-    public FlatJson buildFlatJson(FlatFormat format, String templateId) {
-
-        switch (format) {
-            case SIM_SDT:
-                return new FlatJson(this, templateId);
-            default:
-                throw new SdkException(String.format("Format %s not supported", format));
-        }
-
-
+  private final TemplateProvider templateProvider;
+
+  public FlatJasonProvider(TemplateProvider templateProvider) {
+    this.templateProvider = templateProvider;
+  }
+
+  /**
+   * Builds a {@link FlatJson} for the template with {@code templateId} and {@link FlatFormat}
+   * {@code format}
+   *
+   * @param format
+   * @param templateId
+   * @return
+   */
+  public RMDataFormat buildFlatJson(FlatFormat format, String templateId) {
+
+    switch (format) {
+      case SIM_SDT:
+        return new FlatJson(this, templateId);
+      case STRUCTURED:
+        return new StructuredJson(this, templateId);
+      default:
+        throw new SdkException(String.format("Format %s not supported", format));
     }
+  }
 
-    TemplateProvider getTemplateProvider() {
-        return templateProvider;
-    }
+  TemplateProvider getTemplateProvider() {
+    return templateProvider;
+  }
 }

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/FlatJson.java

@@ -27,24 +27,14 @@
 import org.ehrbase.serialisation.flatencoding.std.umarshal.FlatJsonUnmarshaller;
 import org.ehrbase.util.exception.SdkException;
 import org.ehrbase.webtemplate.model.WebTemplate;
-import org.openehr.schemas.v1.OPERATIONALTEMPLATE;
 
 public class FlatJson implements RMDataFormat {
 
-  private final OPERATIONALTEMPLATE operationaltemplate;
   private final WebTemplate templateIntrospect;
   private final FlatJsonMarshaller flatJsonMarshaller;
 
   FlatJson(FlatJasonProvider flatJasonProvider, String templateId) {
 
-    operationaltemplate =
-        flatJasonProvider
-            .getTemplateProvider()
-            .find(templateId)
-            .orElseThrow(
-                () -> new SdkException(String.format("Template %s not found", templateId)));
-
-
     templateIntrospect =
         flatJasonProvider
             .getTemplateProvider()
@@ -75,6 +65,7 @@ public <T extends RMObject> T unmarshal(String value, Class<T> clazz) {
     }
   }
 
+  @Override
   public Composition unmarshal(String value) {
     return new FlatJsonUnmarshaller().unmarshal(value, templateIntrospect);
   }

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/StructuredJson.java

@@ -0,0 +1,75 @@
+/*
+ *  Copyright (c) 2021  Stefan Spiska (Vitasystems GmbH) and Hannover Medical School
+ *
+ *  This file is part of Project EHRbase
+ *   Licensed under the Apache License, Version 2.0 (the "License");
+ *   you may not use this file except in compliance with the License.
+ *   You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *   Unless required by applicable law or agreed to in writing, software
+ *   distributed under the License is distributed on an "AS IS" BASIS,
+ *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *   See the License for the specific language governing permissions and
+ *   limitations under the License.
+ *
+ */
+
+package org.ehrbase.serialisation.flatencoding;
+
+import com.nedap.archie.rm.RMObject;
+import com.nedap.archie.rm.composition.Composition;
+import org.ehrbase.serialisation.RMDataFormat;
+import org.ehrbase.serialisation.exception.MarshalException;
+import org.ehrbase.serialisation.flatencoding.std.marshal.FlatJsonMarshaller;
+import org.ehrbase.serialisation.flatencoding.std.umarshal.FlatJsonUnmarshaller;
+import org.ehrbase.serialisation.flatencoding.structured.StructuredHelper;
+import org.ehrbase.util.exception.SdkException;
+import org.ehrbase.webtemplate.model.WebTemplate;
+
+public class StructuredJson implements RMDataFormat {
+
+  private final WebTemplate templateIntrospect;
+  private final FlatJsonMarshaller flatJsonMarshaller;
+
+  StructuredJson(FlatJasonProvider flatJasonProvider, String templateId) {
+
+    templateIntrospect =
+        flatJasonProvider
+            .getTemplateProvider()
+            .buildIntrospect(templateId)
+            .orElseThrow(
+                () -> new SdkException(String.format("Template %s not found", templateId)));
+    flatJsonMarshaller = new FlatJsonMarshaller();
+  }
+
+  @Override
+  public String marshal(RMObject rmObject) {
+    if (rmObject instanceof Composition) {
+      String flatJson = flatJsonMarshaller.toFlatJson((Composition) rmObject, templateIntrospect);
+      return StructuredHelper.convertFlatToStructured(flatJson);
+    } else {
+      throw new MarshalException(
+          String.format(
+              "Class %s not supported in Structured format", rmObject.getClass().getSimpleName()));
+    }
+  }
+
+  @Override
+  public <T extends RMObject> T unmarshal(String value, Class<T> clazz) {
+    if (clazz.isAssignableFrom(Composition.class)) {
+      return (T) unmarshal(value);
+    } else {
+      throw new SdkException(
+          String.format("Class %s not supported in Structured format", clazz.getSimpleName()));
+    }
+  }
+
+  @Override
+  public Composition unmarshal(String value) {
+
+    return new FlatJsonUnmarshaller()
+        .unmarshal(StructuredHelper.convertStructuredToFlat(value), templateIntrospect);
+  }
+}

serialisation/src/main/java/org/ehrbase/serialisation/flatencoding/std/marshal/config/CodePhraseStdConfig.java

@@ -29,25 +29,24 @@
 
 public class CodePhraseStdConfig extends AbstractsStdConfig<CodePhrase> {
 
-    @Override
-    /**
-     * {@inheritDoc}
-     */
-    public Map<String, Object> buildChildValues(String currentTerm, CodePhrase rmObject, Context<Map<String, Object>> context) {
-        Map<String, Object> result = new HashMap<>();
-        addValue(result, currentTerm, "code", rmObject.getCodeString());
-        addValue(result, currentTerm, "terminology", Optional.of(rmObject.getTerminologyId()).map(ObjectId::getValue).orElse(null));
-
-        return result;
-    }
-
-    @Override
-    /**
-     * {@inheritDoc}
-     */
-    public Class<CodePhrase> getAssociatedClass() {
-        return CodePhrase.class;
-    }
-
-
+  @Override
+  /** {@inheritDoc} */
+  public Map<String, Object> buildChildValues(
+      String currentTerm, CodePhrase rmObject, Context<Map<String, Object>> context) {
+    Map<String, Object> result = new HashMap<>();
+    addValue(result, currentTerm, "code", rmObject.getCodeString());
+    addValue(
+        result,
+        currentTerm,
+        "terminology",
+        Optional.of(rmObject.getTerminologyId()).map(ObjectId::getValue).orElse(null));
+
+    return result;
+  }
+
+  @Override
+  /** {@inheritDoc} */
+  public Class<CodePhrase> getAssociatedClass() {
+    return CodePhrase.class;
+  }
 }