Merge pull request #153 from ehrbase/feature/ehrbase/project_manageme…

…nt/issues/424_new_dto_flattener_aproch

Feature/ehrbase/project management/issues/424 new dto flattener aproch

README.md

@@ -1,31 +1,50 @@
-# EHRBase SDK  
+# EHRBase SDK
+
 ## client (mostly Beta)
+
 Generic openEHR Client and Objekt-mapper:
+
 * Define entity classes for openEHR-Templates (v1.4) in a jpa like way
 * Map entity <-> Archie RM objekts.
-* RestClient for openEHR Rest-API 
+* RestClient for openEHR Rest-API
 * AQL-Query generator (Alpha)
+
 ## generator (Beta)
-* Autogenerate  entity classes from template
+
+* Autogenerate entity classes from template
+
 ## opt-1.4 (Beta)
+
 * Opt 1.4 xmlbeans
+
 ## response-dto (Beta)
+
 * DTO's representing the response for the ehrsacpe and openEHR Rest API
+
 ## terminologie (Beta)
+
 * Mini openEHR terminologie implementation
+
 ## validation (Beta)
+
 * Validation of Compositions against templates
+
 ## test-data (Beta)
+
 * Example templates and Composition for tests
+
 ## serialisation (Beta)
+
 * map Compositions from and to JSON;XML
 
 ## Release Notes (v0.3.6)
+
 * CircleCI pipeline w/ Jacoco code coverage and sonarcloud.io analysis
 * semi automated version updating via [major] / [minor] / [patch] flags in merge commit title of Github PR
 * updated test dependencies to use Junit5
 
 ## Release Notes (v0.3.0)
+
 * RestClient for DIRECTORY endpoint
 * Improved clean-up of empty elements
 * Improved generation of EVENT classes
@@ -36,36 +55,57 @@ Generic openEHR Client and Objekt-mapper:
 ## Installation
 
 ### Build
+
 ```bash
 mvn clean install
 ```
 
 ## Usage
-###  Entity generation
+
+### Entity generation
+
 To generate an entity class from a template use
+
 ```bash
  java  -jar generator-version.jar
  -h               show help
  -opt <arg>       path to opt file
  -out <arg>       path to output directory
  -package <arg>   package name
+ -config <arg>    optional Path to config file
 ```
+
+In the optional config file you can define
+
+Parameter        | Default                         | Description
+ -----------     | ---------                       | ------------- 
+optimizerSetting | SECTION                         | Defines if nodes which belong to are archetype but are single valued generate a new class: <ul><li>NONE: Always generate a class for nodes which belong to a archetype</li><li>SECTION: Do not generate a class for nodes which have rm-type section and are single valued</li><li>ALL: Do not generate a class for nodes which are single valued</li></ul>
+addNullFlavor    | true                            | Whether or not to generate null flavor fields for Elements.
+replaceChars     | German and Norwegian Characters | Map to define Characters in the Node name to be replaced. 
+
+see generator/src/main/resources/DefaultConfig.yaml
+
 ### Use The SDK in your projekt
+
 You can include the SDK via [jitpack.io](https://jitpack.io/#ehrbase/openEHR_SDK)
-####  Map entity <-> Archie RM objekts
+
+#### Map entity <-> Archie RM objekts
 
 see FlattenerTest and UnflattenerTest
 
-#### RestClient for openEHR Rest-API 
+#### RestClient for openEHR Rest-API
 
 - ehr : see DefaultRestEhrEndpointIT
 - composition: see DefaultRestCompositionEndpointIT
 - template : see DefaultRestTemplateEndpointIT
 - directory : see DefaultRestDirectoryEndpointIT
+
 ## Contributing
+
 Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
 
 Please make sure to update tests as appropriate.
 
 ## License
+
 [APACHE 2.0](https://www.apache.org/licenses/LICENSE-2.0)

UPDATING.md

@@ -0,0 +1,23 @@
+# Updating the SDK
+
+This file documents any backwards-incompatible changes in SDK and
+assists users migrating to a new version.
+
+## SDK 1.0.0
+### Using the sdk with old generated classes
+Classes generated with the old SDK can be used with the new version
+### Migrating from old generated classes to new ones
+It is recommended to update the generated classes. To do this:
+* Update the sdk version
+* Rename any Name with *defningcode to *defningCode
+* replace the EnumValueSet in your local shareddefinition folder with the new from the sdk:
+  * Language -> org.ehrbase.client.classgenerator.shareddefinition.Language
+  * CategoryDefiningcode -> org.ehrbase.client.classgenerator.shareddefinition.Category
+  * MathFunctionDefiningcode -> org.ehrbase.client.classgenerator.shareddefinition.MathFunction
+  * SettingDefiningcode -> org.ehrbase.client.classgenerator.shareddefinition.Setting
+  * Territory -> org.ehrbase.client.classgenerator.shareddefinition.Territory
+  * TransitionDefiningcode ->  org.ehrbase.client.classgenerator.shareddefinition.Transition
+
+* Generate your classes new with the generator using generator/src/main/resources/LegacyConfig.yaml as config
+* Delete you old classes and replaces them with the new one
+* There may be some more changes regrading the naming or the class structure which you have to change in your code.

building/src/main/java/org/ehrbase/building/OptSkeletonBuilder.java

@@ -398,7 +398,8 @@ private void addNodeId(CCOMPLEXOBJECT ccobj, Map<String, String> termDef, Map<St
             } else {
                 log.debug("set archetype_node_id={}", nodeId);
                 valueMap.put("archetype_node_id", nodeId);
-                String termName = termDef.get(nodeId);
+                Optional<String> name = OptNameHelper.extractName(ccobj);
+                String termName = name.orElse(termDef.get(nodeId));
                 if (termName != null) {
                     txtName = new DvText(termName);
                     valueMap.put("name", txtName);

client/pom.xml

@@ -34,14 +34,14 @@
 
 
     <dependencies>
-        <dependency>
-            <groupId>org.jooq</groupId>
-            <artifactId>joor</artifactId>
-        </dependency>
         <dependency>
             <groupId>javax.cache</groupId>
             <artifactId>cache-api</artifactId>
         </dependency>
+        <dependency>
+            <groupId>javax.annotation</groupId>
+            <artifactId>javax.annotation-api</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.github.ehrbase.openEHR_SDK</groupId>
             <artifactId>opt-1.4</artifactId>

client/src/main/java/org/ehrbase/client/aql/query/Query.java

@@ -3,7 +3,28 @@
 import org.ehrbase.client.aql.containment.ContainmentExpression;
 import org.ehrbase.client.aql.field.AqlField;
 import org.ehrbase.client.aql.field.SelectAqlField;
-import org.ehrbase.client.aql.record.*;
+import org.ehrbase.client.aql.record.Record;
+import org.ehrbase.client.aql.record.Record1;
+import org.ehrbase.client.aql.record.Record10;
+import org.ehrbase.client.aql.record.Record11;
+import org.ehrbase.client.aql.record.Record12;
+import org.ehrbase.client.aql.record.Record13;
+import org.ehrbase.client.aql.record.Record14;
+import org.ehrbase.client.aql.record.Record15;
+import org.ehrbase.client.aql.record.Record16;
+import org.ehrbase.client.aql.record.Record17;
+import org.ehrbase.client.aql.record.Record18;
+import org.ehrbase.client.aql.record.Record19;
+import org.ehrbase.client.aql.record.Record2;
+import org.ehrbase.client.aql.record.Record20;
+import org.ehrbase.client.aql.record.Record21;
+import org.ehrbase.client.aql.record.Record3;
+import org.ehrbase.client.aql.record.Record4;
+import org.ehrbase.client.aql.record.Record5;
+import org.ehrbase.client.aql.record.Record6;
+import org.ehrbase.client.aql.record.Record7;
+import org.ehrbase.client.aql.record.Record8;
+import org.ehrbase.client.aql.record.Record9;
 
 import java.util.Arrays;
 

client/src/main/java/org/ehrbase/client/classgenerator/interfaces/CompositionEntity.java

@@ -0,0 +1,79 @@
+/*
+ *
+ *  *  Copyright (c) 2020  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.client.classgenerator.interfaces;
+
+import com.nedap.archie.rm.generic.Participation;
+import com.nedap.archie.rm.generic.PartyIdentified;
+import com.nedap.archie.rm.generic.PartyProxy;
+import org.ehrbase.client.classgenerator.shareddefinition.Category;
+import org.ehrbase.client.classgenerator.shareddefinition.Language;
+import org.ehrbase.client.classgenerator.shareddefinition.Setting;
+import org.ehrbase.client.classgenerator.shareddefinition.Territory;
+import org.ehrbase.client.openehrclient.VersionUid;
+
+import java.time.temporal.TemporalAccessor;
+import java.util.List;
+
+public interface CompositionEntity extends LocatableEntity {
+
+    void setParticipations(List<Participation> participations);
+
+    List<Participation> getParticipations();
+
+    void setHealthCareFacility(PartyIdentified healthCareFacility);
+
+    PartyIdentified getHealthCareFacility();
+
+    void setComposer(PartyProxy composer);
+
+    PartyProxy getComposer();
+
+    void setLanguage(Language language);
+
+    Language getLanguage();
+
+    void setCategoryDefiningCode(Category categoryDefiningCode);
+
+    Category getCategoryDefiningCode();
+
+    void setTerritory(Territory territory);
+
+    Territory getTerritory();
+
+    VersionUid getVersionUid();
+
+    void setVersionUid(VersionUid versionUid);
+
+    void setStartTimeValue(TemporalAccessor startTimeValue);
+
+    TemporalAccessor getStartTimeValue();
+
+    void setEndTimeValue(TemporalAccessor endTimeValue);
+
+    TemporalAccessor getEndTimeValue();
+
+    void setLocation(String location);
+
+    String getLocation();
+
+    void setSettingDefiningCode(Setting settingDefiningCode);
+
+    Setting getSettingDefiningCode();
+}

client/src/main/java/org/ehrbase/client/classgenerator/interfaces/EntryEntity.java

@@ -0,0 +1,34 @@
+/*
+ *
+ *  *  Copyright (c) 2020  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.client.classgenerator.interfaces;
+
+import com.nedap.archie.rm.generic.PartyProxy;
+import org.ehrbase.client.classgenerator.interfaces.LocatableEntity;
+import org.ehrbase.client.classgenerator.shareddefinition.Language;
+
+public interface EntryEntity extends LocatableEntity {
+    void setSubject(PartyProxy subject);
+
+    PartyProxy getSubject();
+
+    void setLanguage(Language language);
+
+    Language getLanguage();
+}

client/src/main/java/org/ehrbase/client/classgenerator/interfaces/EventEntity.java

@@ -0,0 +1,28 @@
+/*
+ *
+ *  *  Copyright (c) 2020  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.client.classgenerator.interfaces;
+
+import java.time.temporal.TemporalAccessor;
+
+public interface EventEntity {
+    void setTimeValue(TemporalAccessor timeValue);
+
+    TemporalAccessor getTimeValue();
+}

client/src/main/java/org/ehrbase/client/classgenerator/interfaces/IntervalEventEntity.java

@@ -0,0 +1,40 @@
+/*
+ *
+ *  *  Copyright (c) 2020  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.client.classgenerator.interfaces;
+
+import org.ehrbase.client.classgenerator.shareddefinition.MathFunction;
+
+import java.time.temporal.TemporalAccessor;
+import java.time.temporal.TemporalAmount;
+
+public interface IntervalEventEntity extends LocatableEntity, EventEntity {
+
+    void setWidthValue(TemporalAmount widthValue);
+
+    TemporalAmount getWidthValue();
+
+    void setMathFunctionDefiningCode(MathFunction mathFunctionDefiningCode);
+
+    MathFunction getMathFunctionDefiningCode();
+
+    void setSampleCount(Long sampleCount);
+
+    Long getSampleCount();
+}