Merge branch 'release/v0.30.0'

ehrbase · Aug 16, 2023 · 7070caa · 7070caa
2 parents 88ad672 + c1395b5
commit 7070caa
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres
 to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.30.0]
+ ### Added
+ ### Changed 
+ - Upgrade openEHR_SDK to version 2.2.0 see https://github.com/ehrbase/openEHR_SDK/blob/develop/CHANGELOG.md 
+ ### Fixed 
+ - Fix storing attributes of Locatable.name ([#1161](https://github.com/ehrbase/ehrbase/pull/1161))
+
 ## [0.29.0]
  ### Added
  ### Changed 
@@ -677,3 +684,4 @@ the next release this file will provide a proper overview.
 [0.27.4]: https://github.com/ehrbase/ehrbase/compare/v0.27.3...v0.27.4
 [0.28.0]: https://github.com/ehrbase/ehrbase/compare/v0.27.4...v0.28.0
 [0.29.0]: https://github.com/ehrbase/ehrbase/compare/v0.28.0...v0.29.0
+[0.30.0]: https://github.com/ehrbase/ehrbase/compare/v0.29.0...v0.30.0
diff --git a/UPDATING.md b/UPDATING.md
@@ -108,3 +108,14 @@ If exception occurs during the migration script execution (`V85__enforce_unique_
 
 Action Required:
 Ensure that the **ehr.template_store.id** and **ehr.template_store.template_id** columns have unique values within the tenant.
+
+## EHRbase 0.30.0
+
+### Fix storage of Locatable.name
+An error in the encoding for Locatable.name was fixed. 
+With the fixed encoding Locatable.name.mappings and Locatable.name.defining_code are now stored correctly in the DB and Locatable.name.defining_code can also be queried using AQL.
+There is a manual migration script available at `base/db-setup/fix-dv_coded_text-locatable-names.sql` which will fix the existing compositions.
+This migration is only needed if Locatable.name.defining_code is used in any composition. 
+Be aware that this migration might take a while, as it will affect every composition in the database. 
+It will replace the Strings `"codeString":` and `"terminologyId":` with `"code_string":` and `"terminology_id":`. 
+This replacement is done over the whole JSON stored in the database, so there is a small chance that not only the broken JSON keys are affected.
diff --git a/api/pom.xml b/api/pom.xml
@@ -26,7 +26,7 @@
     <parent>
         <groupId>org.ehrbase.openehr</groupId>
         <artifactId>server</artifactId>
-        <version>0.29.0</version>
+        <version>0.30.0</version>
     </parent>
 
     <artifactId>api</artifactId>

diff --git a/application/pom.xml b/application/pom.xml
@@ -26,7 +26,7 @@
     <parent>
         <groupId>org.ehrbase.openehr</groupId>
         <artifactId>server</artifactId>
-        <version>0.29.0</version>
+        <version>0.30.0</version>
     </parent>
 
     <artifactId>application</artifactId>

diff --git a/base/db-setup/fix-dv_coded_text-locatable-names.sql b/base/db-setup/fix-dv_coded_text-locatable-names.sql
@@ -0,0 +1,69 @@
+/*
+ * Copyright (c) 2023 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
+ *
+ *     https://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.
+ */
+
+ALTER TABLE ehr.entry
+    DISABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.entry_history
+    DISABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.event_context
+    DISABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.event_context_history
+    DISABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.status
+    DISABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.status_history
+    DISABLE ROW LEVEL SECURITY;
+
+--composition content
+UPDATE ehr.entry
+SET entry=REPLACE(REPLACE(entry::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb;
+
+UPDATE ehr.entry_history
+SET entry=REPLACE(REPLACE(entry::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb
+WHERE entry IS NOT NULL;
+
+--event_context.other_context
+UPDATE ehr.event_context
+SET other_context=REPLACE(REPLACE(other_context::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb
+WHERE other_context IS NOT NULL;
+
+UPDATE ehr.event_context_history
+SET other_context=REPLACE(REPLACE(other_context::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb
+WHERE other_context IS NOT NULL;
+
+--status.other_details
+UPDATE ehr.status
+SET other_details=REPLACE(REPLACE(other_details::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb
+WHERE other_details IS NOT NULL;
+
+UPDATE ehr.status_history
+SET other_details=REPLACE(REPLACE(other_details::text,'"codeString":', '"code_string":'),'"terminologyId":', '"terminology_id":')::jsonb
+WHERE other_details IS NOT NULL;
+
+ALTER TABLE ehr.entry
+    ENABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.entry_history
+    ENABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.event_context
+    ENABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.event_context_history
+    ENABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.status
+    ENABLE ROW LEVEL SECURITY;
+ALTER TABLE ehr.status_history
+    ENABLE ROW LEVEL SECURITY;
diff --git a/base/pom.xml b/base/pom.xml
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.ehrbase.openehr</groupId>
         <artifactId>server</artifactId>
-        <version>0.29.0</version>
+        <version>0.30.0</version>
     </parent>
 
     <artifactId>base</artifactId>

diff --git a/bom/pom.xml b/bom/pom.xml
@@ -24,7 +24,7 @@
 
     <groupId>org.ehrbase.openehr</groupId>
     <artifactId>bom</artifactId>
-    <version>0.29.0</version>
+    <version>0.30.0</version>
     <packaging>pom</packaging>
 
     <name>EHRbase</name>
@@ -102,13 +102,13 @@
         <antlr4.version>4.11.1</antlr4.version>
         <archie.version>3.3.0</archie.version>
         <commons-io.version>2.13.0</commons-io.version>
-        <commons-lang3.version>3.12.0</commons-lang3.version>
-        <ehrbase.sdk.version>2.1.0</ehrbase.sdk.version>
+        <commons-lang3.version>3.13.0</commons-lang3.version>
+        <ehrbase.sdk.version>2.2.0</ehrbase.sdk.version>
         <flyway.version>8.5.13</flyway.version>
         <jackson-bom.version>2.15.0</jackson-bom.version>
-        <javamelody.version>1.94.0</javamelody.version>
+        <javamelody.version>1.95.0</javamelody.version>
         <joda.version>2.12.5</joda.version>
-        <jooq.version>3.18.5</jooq.version>
+        <jooq.version>3.18.6</jooq.version>
         <json-path.version>2.8.0</json-path.version>
         <junit.version>5.7.2</junit.version>
         <maven-dependency-plugin.version>3.6.0</maven-dependency-plugin.version>

diff --git a/jooq-pq/pom.xml b/jooq-pq/pom.xml
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.ehrbase.openehr</groupId>
         <artifactId>server</artifactId>
-        <version>0.29.0</version>
+        <version>0.30.0</version>
     </parent>
 
     <artifactId>jooq-pg</artifactId>

diff --git a/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/EncodeUtilArchie.java b/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/EncodeUtilArchie.java
@@ -22,6 +22,7 @@
 import com.nedap.archie.rm.datatypes.CodePhrase;
 import com.nedap.archie.rm.datavalues.DvCodedText;
 import com.nedap.archie.rm.datavalues.DvText;
+import com.nedap.archie.rm.datavalues.TermMapping;
 import com.nedap.archie.rm.datavalues.quantity.datetime.DvDate;
 import com.nedap.archie.rm.datavalues.quantity.datetime.DvDateTime;
 import com.nedap.archie.rm.datavalues.quantity.datetime.DvDuration;
@@ -41,6 +42,7 @@
 import org.ehrbase.jooq.dbencoding.wrappers.json.writer.ParticipationAdapter;
 import org.ehrbase.jooq.dbencoding.wrappers.json.writer.PartyIdentifiedAdapter;
 import org.ehrbase.jooq.dbencoding.wrappers.json.writer.PartyRefAdapter;
+import org.ehrbase.jooq.dbencoding.wrappers.json.writer.TermMappingAdapter;
 import org.ehrbase.jooq.dbencoding.wrappers.json.writer.translator_db2raw.ArrayListAdapter;
 import org.ehrbase.jooq.dbencoding.wrappers.json.writer.translator_db2raw.LinkedTreeMapAdapter;
 
@@ -67,7 +69,8 @@ public static GsonBuilder getGsonBuilderInstance() {
                 .registerTypeAdapter(CodePhrase.class, new CodePhraseAdapter())
                 .registerTypeAdapter(Participation.class, new ParticipationAdapter())
                 .registerTypeAdapter(PartyIdentified.class, new PartyIdentifiedAdapter())
-                .registerTypeAdapter(PartyRef.class, new PartyRefAdapter());
+                .registerTypeAdapter(PartyRef.class, new PartyRefAdapter())
+                .registerTypeAdapter(TermMapping.class, new TermMappingAdapter(AdapterType.PG_JSONB));
     }
 
     public static GsonBuilder getGsonBuilderInstance(AdapterType dbjson2rawjson) {

diff --git a/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/NameAsDvText.java b/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/NameAsDvText.java
@@ -42,6 +42,9 @@ public Map<String, Object> toMap() {
         }
         if (aName != null) {
             nameMap.put("value", aName.getValue());
+            if (aName.getMappings() != null) {
+                nameMap.put("mappings", aName.getMappings());
+            }
         }
         nameMap.put(I_DvTypeAdapter.AT_TYPE, new SnakeCase(DvText.class.getSimpleName()).camelToUpperSnake());
         return nameMap;

diff --git a/...-pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/CodePhraseAdapter.java b/...-pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/CodePhraseAdapter.java
@@ -17,34 +17,31 @@
  */
 package org.ehrbase.jooq.dbencoding.wrappers.json.writer;
 
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 import com.google.gson.stream.JsonReader;
 import com.google.gson.stream.JsonWriter;
 import com.nedap.archie.rm.datatypes.CodePhrase;
-import com.nedap.archie.rm.support.identification.TerminologyId;
 import java.io.IOException;
+import java.util.Optional;
 import org.ehrbase.jooq.dbencoding.wrappers.json.I_DvTypeAdapter;
 import org.ehrbase.openehr.sdk.util.ObjectSnakeCase;
-import org.ehrbase.openehr.sdk.util.SnakeCase;
 
 /**
  * GSON adapter for DvDateTime
  * Required since JSON does not support natively a DateTime data type
  */
 public class CodePhraseAdapter extends DvTypeAdapter<CodePhrase> {
 
-    private Gson gson;
+    private TerminologyIDAdapter terminologyIDAdapter;
 
     public CodePhraseAdapter(AdapterType adapterType) {
         super(adapterType);
-        gson = new GsonBuilder()
-                .registerTypeAdapter(TerminologyId.class, new TerminologyIDAdapter(adapterType))
-                .setPrettyPrinting()
-                .create();
+        terminologyIDAdapter = new TerminologyIDAdapter(adapterType);
     }
 
-    public CodePhraseAdapter() {}
+    public CodePhraseAdapter() {
+        super();
+        terminologyIDAdapter = new TerminologyIDAdapter(adapterType);
+    }
 
     @Override
     public CodePhrase read(JsonReader arg0) throws IOException {
@@ -58,23 +55,17 @@ public void write(JsonWriter writer, CodePhrase codePhrase) throws IOException {
             writer.nullValue();
             return;
         }
-
-        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB) {
-            writer.beginObject();
-            writer.name("codeString").value(codePhrase.getCodeString());
-            writer.name(TAG_CLASS_RAW_JSON).value(new SnakeCase(CodePhrase.class.getSimpleName()).camelToUpperSnake());
-            writer.name("terminologyId");
-            writer.beginObject();
-            writer.name("value").value(codePhrase.getTerminologyId().getValue());
-            writer.name(TAG_CLASS_RAW_JSON)
-                    .value(new SnakeCase(TerminologyId.class.getSimpleName()).camelToUpperSnake());
-            writer.endObject();
-            writer.endObject();
-        } else if (adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
+        Optional<String> preferredTerm = Optional.of(codePhrase).map(CodePhrase::getPreferredTerm);
+        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB
+                || adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
             writer.beginObject();
             writer.name(TAG_CLASS_RAW_JSON).value(new ObjectSnakeCase(codePhrase).camelToUpperSnake());
             writer.name("code_string").value(codePhrase.getCodeString());
-            writer.name("terminology_id").value(gson.toJson(codePhrase.getTerminologyId()));
+            writer.name("terminology_id");
+            terminologyIDAdapter.write(writer, codePhrase.getTerminologyId());
+            if (preferredTerm.isPresent()) {
+                writer.name("preferred_term").value(preferredTerm.get());
+            }
             writer.endObject();
         }
     }

diff --git a/...pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/DvCodedTextAdapter.java b/...pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/DvCodedTextAdapter.java
@@ -17,36 +17,31 @@
  */
 package org.ehrbase.jooq.dbencoding.wrappers.json.writer;
 
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 import com.google.gson.stream.JsonReader;
 import com.google.gson.stream.JsonWriter;
 import com.nedap.archie.rm.datatypes.CodePhrase;
 import com.nedap.archie.rm.datavalues.DvCodedText;
-import com.nedap.archie.rm.support.identification.TerminologyId;
 import java.io.IOException;
 import java.util.Optional;
 import org.ehrbase.jooq.dbencoding.wrappers.json.I_DvTypeAdapter;
 import org.ehrbase.openehr.sdk.util.ObjectSnakeCase;
-import org.ehrbase.openehr.sdk.util.SnakeCase;
 
 /**
  * GSON adapter for DvDateTime
  * Required since JSON does not support natively a DateTime data type
  */
 public class DvCodedTextAdapter extends DvTypeAdapter<DvCodedText> {
-
-    private Gson gson;
+    private final CodePhraseAdapter codePhraseAdapter;
 
     public DvCodedTextAdapter(AdapterType adapterType) {
         super(adapterType);
-        gson = new GsonBuilder()
-                .registerTypeAdapter(CodePhrase.class, new CodePhraseAdapter(adapterType))
-                .setPrettyPrinting()
-                .create();
+        codePhraseAdapter = new CodePhraseAdapter(adapterType);
     }
 
-    public DvCodedTextAdapter() {}
+    public DvCodedTextAdapter() {
+        super();
+        codePhraseAdapter = new CodePhraseAdapter(adapterType);
+    }
 
     @Override
     public DvCodedText read(JsonReader arg0) {
@@ -64,33 +59,21 @@ public void write(JsonWriter writer, DvCodedText dvalue) throws IOException {
             return;
         }
 
-        TermMappingAdapter termMappingAdapter = new TermMappingAdapter();
-
-        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB) {
-            writer.beginObject();
-            writer.name(VALUE).value(dvalue.getValue());
-            writer.name(TAG_CLASS_RAW_JSON).value(new SnakeCase(DvCodedText.class.getSimpleName()).camelToUpperSnake());
-            writer.name("definingCode");
-            writer.beginObject();
-            writer.name("codeString").value(dvalue.getDefiningCode().getCodeString());
-            writer.name("terminologyId");
-            writer.beginObject();
-            writer.name(VALUE).value(dvalue.getDefiningCode().getTerminologyId().getValue());
-            writer.name(TAG_CLASS_RAW_JSON)
-                    .value(new SnakeCase(TerminologyId.class.getSimpleName()).camelToUpperSnake());
-            writer.endObject();
-            writer.name(TAG_CLASS_RAW_JSON).value(new SnakeCase(CodePhrase.class.getSimpleName()).camelToUpperSnake());
-            writer.endObject();
-            termMappingAdapter.write(writer, dvalue.getMappings());
-            writer.endObject();
-        } else if (adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
-            writer.beginObject();
-            writer.name(TAG_CLASS_RAW_JSON).value(new ObjectSnakeCase(dvalue).camelToUpperSnake());
-            writer.name(VALUE).value(dvalue.getValue());
-            CodePhrase codePhrase = dvalue.getDefiningCode();
-            writer.name("defining_code").value(gson.toJson(codePhrase));
-            writer.name(TAG_CLASS_RAW_JSON).value(new SnakeCase(CodePhrase.class.getSimpleName()).camelToUpperSnake());
-            writer.endObject();
+        TermMappingAdapter termMappingAdapter = new TermMappingAdapter(adapterType);
+        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB
+                || adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
+            writeDvCodedText(writer, dvalue, termMappingAdapter);
         }
     }
+
+    private void writeDvCodedText(JsonWriter writer, DvCodedText dvalue, TermMappingAdapter termMappingAdapter)
+            throws IOException {
+        writer.beginObject();
+        writer.name(TAG_CLASS_RAW_JSON).value(new ObjectSnakeCase(dvalue).camelToUpperSnake());
+        writer.name(VALUE).value(dvalue.getValue());
+        writer.name("defining_code");
+        codePhraseAdapter.write(writer, dvalue.getDefiningCode());
+        termMappingAdapter.write(writer, dvalue.getMappings());
+        writer.endObject();
+    }
 }
diff --git a/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/DvTextAdapter.java b/jooq-pq/src/main/java/org/ehrbase/jooq/dbencoding/wrappers/json/writer/DvTextAdapter.java
@@ -23,7 +23,6 @@
 import java.io.IOException;
 import org.ehrbase.jooq.dbencoding.wrappers.json.I_DvTypeAdapter;
 import org.ehrbase.openehr.sdk.util.ObjectSnakeCase;
-import org.ehrbase.openehr.sdk.util.SnakeCase;
 
 /**
  * GSON adapter for DvDateTime
@@ -49,18 +48,13 @@ public void write(JsonWriter writer, DvText dvalue) throws IOException {
             return;
         }
 
-        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB) {
-            TermMappingAdapter termMappingAdapter = new TermMappingAdapter();
+        TermMappingAdapter termMappingAdapter = new TermMappingAdapter(adapterType);
+        if (adapterType == I_DvTypeAdapter.AdapterType.PG_JSONB
+                || adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
             writer.beginObject();
             writer.name("value").value(dvalue.getValue());
-            writer.name(I_DvTypeAdapter.TAG_CLASS_RAW_JSON)
-                    .value(new SnakeCase(DvText.class.getSimpleName()).camelToUpperSnake());
-            termMappingAdapter.write(writer, dvalue.getMappings());
-            writer.endObject();
-        } else if (adapterType == I_DvTypeAdapter.AdapterType.RAW_JSON) {
-            writer.beginObject();
             writer.name(I_DvTypeAdapter.TAG_CLASS_RAW_JSON).value(new ObjectSnakeCase(dvalue).camelToUpperSnake());
-            writer.name("value").value(dvalue.getValue());
+            termMappingAdapter.write(writer, dvalue.getMappings());
             writer.endObject();
         }
     }