Merge pull request #106 from ehrbase/feature/ehrbase/openEHR_SDK/issu…

…es/91_native_contanment tested on my side
ehrbase · Oct 14, 2020 · 7818514 · 7818514
2 parents 7214973 + f07eb4f
commit 7818514
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Showing 5 changed files with 116 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes.
 ### Added
 - Basic support for flat formats (see https://github.com/ehrbase/openEHR_SDK/pull/67) 
 - Web-Templates (see https://github.com/ehrbase/openEHR_SDK/pull/81)
+- Allow Native Parts in Entity Queries  (see https://github.com/ehrbase/openEHR_SDK/pull/106)
 ### Fixed
 - Error when extracting name from a template where name has more than one child (see https://github.com/ehrbase/openEHR_SDK/pull/79)
 - Enums where not correctly generated for value-sets (see https://github.com/ehrbase/openEHR_SDK/pull/92)  

diff --git a/client/src/main/java/org/ehrbase/client/aql/containment/Containment.java b/client/src/main/java/org/ehrbase/client/aql/containment/Containment.java
@@ -43,11 +43,14 @@ public class Containment implements ContainmentExpression {
      * @param archetype The Archetype HRID. Sie <a href="https://specifications.openehr.org/releases/AM/latest/Overview.html#_identification_and_the_virtual_archetype_space">Identification and the Virtual Archetype Space</a>
      */
     public Containment(String archetype) {
-        this.archetype = archetype;
+
         typeName = StringUtils.substringBetween(archetype, "openEHR-EHR-", ".");
         if (StringUtils.isBlank(typeName)) {
             typeName = archetype;
+            archetype = null;
         }
+        this.archetype = archetype;
+
         if ("EHR".equals(typeName)) {
             type = null;
         } else {
@@ -61,8 +64,10 @@ public String buildAQL() {
         sb
                 .append(typeName.toUpperCase())
                 .append(" ")
-                .append(getVariableName())
-                .append("[").append(archetype).append("]");
+                .append(getVariableName());
+        if (archetype != null) {
+            sb.append("[").append(archetype).append("]");
+        }
         if (contains != null) {
             sb
                     .append(" contains ")

diff --git a/client/src/main/java/org/ehrbase/client/aql/field/NativeSelectAqlField.java b/client/src/main/java/org/ehrbase/client/aql/field/NativeSelectAqlField.java
@@ -0,0 +1,29 @@
+/*
+ *
+ *  *  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.aql.field;
+
+import org.ehrbase.client.aql.containment.Containment;
+
+public class NativeSelectAqlField<T> extends AqlFieldImp<T> {
+
+    public NativeSelectAqlField(Containment containment, String path, Class<T> valueClass) {
+        super(null, path, null, valueClass, false, containment);
+    }
+}
diff --git a/client/src/test/java/org/ehrbase/client/aql/query/EntityQueryTest.java b/client/src/test/java/org/ehrbase/client/aql/query/EntityQueryTest.java
@@ -20,15 +20,21 @@
 package org.ehrbase.client.aql.query;
 
 import org.ehrbase.client.aql.condition.Condition;
+import org.ehrbase.client.aql.containment.Containment;
+import org.ehrbase.client.aql.containment.ContainmentExpression;
 import org.ehrbase.client.aql.containment.ContainmentPath;
 import org.ehrbase.client.aql.field.EhrFields;
+import org.ehrbase.client.aql.field.NativeSelectAqlField;
 import org.ehrbase.client.aql.orderby.OrderByExpression;
 import org.ehrbase.client.aql.parameter.Parameter;
 import org.ehrbase.client.aql.record.Record3;
 import org.ehrbase.client.classgenerator.examples.ehrbasebloodpressuresimpledev0composition.EhrbaseBloodPressureSimpleDeV0CompositionContainment;
 import org.ehrbase.client.classgenerator.examples.ehrbasebloodpressuresimpledev0composition.definition.BloodPressureTrainingSampleObservation;
 import org.ehrbase.client.classgenerator.examples.ehrbasebloodpressuresimpledev0composition.definition.BloodPressureTrainingSampleObservationContainment;
 import org.ehrbase.client.classgenerator.examples.ehrbasebloodpressuresimpledev0composition.definition.CuffSizeDefiningcode;
+import org.ehrbase.client.classgenerator.examples.virologischerbefundcomposition.definition.BefundObservationContainment;
+import org.ehrbase.client.classgenerator.examples.virologischerbefundcomposition.definition.ProVirusClusterContainment;
+import org.ehrbase.client.classgenerator.examples.virologischerbefundcomposition.definition.ProbeClusterContainment;
 import org.junit.Test;
 
 import java.time.temporal.TemporalAccessor;
@@ -66,4 +72,33 @@ public void buildAql() {
                 "order by c0/context/start_time/value ASCENDING, o1/data[at0001]/events[at0002]/time/value DESCENDING");
 
     }
+
+    @Test
+    public void buildAqlWithNativePath() {
+        BefundObservationContainment befundObservationContainment = BefundObservationContainment.getInstance();
+        ProVirusClusterContainment proVirusClusterContainment = ProVirusClusterContainment.getInstance();
+        ProbeClusterContainment probeClusterContainment = ProbeClusterContainment.getInstance();
+
+        Containment compositionContainment = new Containment("COMPOSITION");
+        ContainmentExpression containment =
+                compositionContainment.contains(befundObservationContainment).contains(proVirusClusterContainment.and(probeClusterContainment));
+        EntityQuery<Record3<String, TemporalAccessor, UUID>> entityQuery = Query.buildEntityQuery(
+                containment,
+                proVirusClusterContainment.VIRUS_VALUE,
+                probeClusterContainment.ZEITPUNKT_DER_PROBENENTNAHME_VALUE,
+                new NativeSelectAqlField<>(compositionContainment, "/uid/value", UUID.class)
+        );
+
+        entityQuery
+                .where(Condition.equal(new NativeSelectAqlField<>(compositionContainment, "/name/value", String.class), "Mikrobiologischer Befund"));
+
+        assertThat(entityQuery.buildAql()).isEqualTo(
+                "Select c0/items[at0024]/value/value as F0, c1/items[at0015]/value/value as F1, c2/uid/value as F2 " +
+                        "from EHR e  " +
+                        "contains COMPOSITION c2 " +
+                        "contains OBSERVATION o3[openEHR-EHR-OBSERVATION.laboratory_test_result.v1] " +
+                        "contains (CLUSTER c0[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1] and CLUSTER c1[openEHR-EHR-CLUSTER.specimen.v1]) " +
+                        "where c2/name/value = 'Mikrobiologischer Befund'"
+        );
+    }
 }
diff --git a/client/src/test/java/org/ehrbase/client/openehrclient/defaultrestclient/AqlTestIT.java b/client/src/test/java/org/ehrbase/client/openehrclient/defaultrestclient/AqlTestIT.java
@@ -30,7 +30,13 @@
 import org.assertj.core.groups.Tuple;
 import org.ehrbase.client.Integration;
 import org.ehrbase.client.TestData;
+import org.ehrbase.client.aql.condition.Condition;
+import org.ehrbase.client.aql.containment.Containment;
+import org.ehrbase.client.aql.field.EhrFields;
+import org.ehrbase.client.aql.field.NativeSelectAqlField;
+import org.ehrbase.client.aql.parameter.Parameter;
 import org.ehrbase.client.aql.parameter.ParameterValue;
+import org.ehrbase.client.aql.query.EntityQuery;
 import org.ehrbase.client.aql.query.Query;
 import org.ehrbase.client.aql.record.Record2;
 import org.ehrbase.client.classgenerator.examples.coronaanamnesecomposition.CoronaAnamneseComposition;
@@ -394,4 +400,41 @@ public void testExecute11() throws IOException {
 
 
     }
+
+    @Test
+    public void testExecute12() {
+
+        UUID ehr = openEhrClient.ehrEndpoint().createEhr();
+
+        openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(TestData.buildEhrbaseBloodPressureSimpleDeV0());
+
+        EhrbaseBloodPressureSimpleDeV0Composition pressureSimple1 = TestData.buildEhrbaseBloodPressureSimpleDeV0();
+        pressureSimple1.getBloodPressureTrainingSample().get(0).setSystolicMagnitude(1.1);
+        openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(pressureSimple1);
+
+        EhrbaseBloodPressureSimpleDeV0Composition pressureSimple2 = TestData.buildEhrbaseBloodPressureSimpleDeV0();
+        pressureSimple2.getBloodPressureTrainingSample().get(0).setSystolicMagnitude(1.1);
+        openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(pressureSimple2);
+
+        Containment observationContainment = new Containment("OBSERVATION");
+
+        NativeSelectAqlField<Double> magnitudeField = new NativeSelectAqlField<>(observationContainment, "/data[at0001]/events[at0002]/data[at0003]/items[at0004]/value/magnitude", Double.class);
+        EntityQuery<Record2<UUID, Double>> entityQuery = Query.buildEntityQuery(
+                observationContainment,
+                EhrFields.EHR_ID(),
+                magnitudeField
+        );
+
+        Parameter<UUID> ehrIdParameter = entityQuery.buildParameter();
+        entityQuery.where(
+                Condition.equal(EhrFields.EHR_ID(), ehrIdParameter)
+                        .and(Condition.equal(magnitudeField, 1.1d))
+        );
+
+        List<Record2<UUID, Double>> result = openEhrClient.aqlEndpoint().execute(entityQuery, ehrIdParameter.setValue(ehr));
+        assertThat(result)
+                .isNotNull()
+                .size().isEqualTo(2);
+
+    }
 }