From ae12c84f1ab9fc337e7d0363cd203eca56ad7549 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 12:55:13 +0000
Subject: [PATCH 01/43] Update dependency maven to v3.9.8

---
 .mvn/wrapper/maven-wrapper.properties | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties
index 23c7e599..f95f1ee8 100644
--- a/.mvn/wrapper/maven-wrapper.properties
+++ b/.mvn/wrapper/maven-wrapper.properties
@@ -16,4 +16,4 @@
 # under the License.
 wrapperVersion=3.3.2
 distributionType=only-script
-distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.7/apache-maven-3.9.7-bin.zip
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.8/apache-maven-3.9.8-bin.zip

From e125cf449e0a70a539d90001ef45ba02a07c114c Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:26:50 +0000
Subject: [PATCH 02/43] Update docker/build-push-action action to v6

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index bfdc32c3..c1c9dd7a 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -57,7 +57,7 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Build and Export to Docker
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           tags: flare:latest
@@ -222,7 +222,7 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           platforms: linux/amd64,linux/arm64

From d01a114b80d8c767004965617e364ced4469b711 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:37:26 +0000
Subject: [PATCH 03/43] Update keycloak/keycloak Docker tag to v25

---
 .../integration-test/oauth/docker-compose.yml    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index dfd9d34e..eae28a4a 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -29,19 +29,19 @@ services:
       generate-cert:
         condition: service_completed_successfully
   keycloak:
-    image: "keycloak/keycloak:24.0.5"
+    image: "keycloak/keycloak:25.0.1"
     command: ["start", "--import-realm"]
     healthcheck:
-      test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/8080;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]
+      test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/9000;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "30s"
     networks:
       test-oauth:
     environment:
-      KC_HOSTNAME_URL: "https://secure-keycloak:8443"
-      KC_HOSTNAME_ADMIN_URL: "https://secure-keycloak:8443"
+      KC_HOSTNAME: "https://secure-keycloak:8443"
+      KC_HOSTNAME_ADMIN: "https://secure-keycloak:8443"
       KC_HTTP_RELATIVE_PATH: "/"
       KC_PROXY_HEADERS: "xforwarded"
       KC_HTTP_ENABLED: "true"
@@ -55,7 +55,7 @@ services:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "5s"
     networks:
       test-oauth:
@@ -77,7 +77,7 @@ services:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "60s"
     networks:
       test-oauth:
@@ -106,7 +106,7 @@ services:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/cache/stats"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "60s"
     networks:
       test-oauth:

From f3de3739b8f9afbf64425ec421573a74cacb82bd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Tue, 9 Jul 2024 09:34:44 +0200
Subject: [PATCH 04/43] Implement cohort extraction endpoint

---
 .../flare/rest/QueryController.java           | 25 +++++++++-
 .../flare/service/StructuredQueryService.java | 21 ++++++--
 .../flare/rest/QueryControllerTest.java       | 50 +++++++++++++++++--
 .../service/StructuredQueryServiceIT.java     | 12 ++---
 .../service/StructuredQueryServiceTest.java   | 28 +++++------
 5 files changed, 106 insertions(+), 30 deletions(-)

diff --git a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
index dd42b672..eb0304ec 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
@@ -39,14 +39,15 @@ public QueryController(StructuredQueryService queryService) {
     @Bean
     public RouterFunction<ServerResponse> queryRouter() {
         return route(POST("query/execute").and(accept(MEDIA_TYPE_SQ)), this::execute)
-                .andRoute(POST("query/translate").and(accept(MEDIA_TYPE_SQ)), this::translate);
+                .andRoute(POST("query/translate").and(accept(MEDIA_TYPE_SQ)), this::translate)
+                .andRoute(POST("query/execute-cohort").and(accept(MEDIA_TYPE_SQ)), this::executeCohort);
     }
 
     public Mono<ServerResponse> execute(ServerRequest request) {
         var startNanoTime = System.nanoTime();
         logger.debug("Execute query");
         return request.bodyToMono(StructuredQuery.class)
-                .flatMap(queryService::execute)
+                .flatMap(queryService::executeCohortSize)
                 .flatMap(count -> {
                     logger.debug("Finished query returning {} patients in {} seconds.", count,
                             "%.1f".formatted(Util.durationSecondsSince(startNanoTime)));
@@ -62,6 +63,26 @@ public Mono<ServerResponse> execute(ServerRequest request) {
                 });
     }
 
+    public Mono<ServerResponse> executeCohort(ServerRequest request) {
+        var startNanoTime = System.nanoTime();
+        logger.debug("Execute query");
+        return request.bodyToMono(StructuredQuery.class)
+                .flatMap(queryService::executeCohort)
+                .flatMap(population -> {
+                    logger.debug("Finished query returning {} patients in {} seconds.", population.size(),
+                            "%.1f".formatted(Util.durationSecondsSince(startNanoTime)));
+                    return ok().bodyValue(population);
+                })
+                .onErrorResume(MappingException.class, e -> {
+                    logger.warn("Mapping error: {}", e.getMessage());
+                    return badRequest().bodyValue(new Error(e.getMessage()));
+                })
+                .onErrorResume(WebClientRequestException.class, e -> {
+                    logger.error("Service not available because of downstream web client errors: {}", e.getMessage());
+                    return status(503).bodyValue(new Error(e.getMessage()));
+                });
+    }
+
     public Mono<ServerResponse> translate(ServerRequest request) {
         logger.debug("Translate query");
         return request.bodyToMono(StructuredQuery.class)
diff --git a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
index f5499c15..27d7e787 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
@@ -34,13 +34,14 @@ public StructuredQueryService(@Qualifier("memCachingFhirQueryService") FhirQuery
         this.translator = requireNonNull(translator);
     }
 
+
     /**
-     * Executes {@code query} and returns the number of Patients qualifying its criteria.
+     * Executes {@code query} and returns the Population of Patient IDs.
      *
      * @param query the query to execute
-     * @return the number of Patients qualifying the criteria
+     * @return the Patient IDs qualifying the criteria
      */
-    public Mono<Integer> execute(StructuredQuery query) {
+    public Mono<Population> executeCohort(StructuredQuery query) {
         var includedPatients = query.inclusionCriteria().executeAndIntersection(this::executeUnionGroup)
                 .defaultIfEmpty(Population.of());
         var excludedPatients = query.exclusionCriteria().map(c -> c.map(CriterionGroup::wrapCriteria)
@@ -48,8 +49,18 @@ public Mono<Integer> execute(StructuredQuery query) {
                         .defaultIfEmpty(Population.of()))
                 .orElse(Mono.just(Population.of()));
         return includedPatients
-                .flatMap(i -> excludedPatients.map(i::difference))
-                .map(Set::size);
+                .flatMap(i -> excludedPatients.map(i::difference));
+    }
+
+
+    /**
+     * Executes {@code query} and returns the number of Patients qualifying its criteria.
+     *
+     * @param query the query to execute
+     * @return the number of Patients qualifying the criteria
+     */
+    public Mono<Integer> executeCohortSize(StructuredQuery query) {
+        return this.executeCohort(query).map(Set::size);
     }
 
     private Mono<Population> executeUnionGroup(CriterionGroup<Criterion> group) {
diff --git a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
index 8ca25d53..0dbaa876 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
@@ -1,6 +1,7 @@
 package de.medizininformatikinitiative.flare.rest;
 
 import de.medizininformatikinitiative.flare.Either;
+import de.medizininformatikinitiative.flare.model.Population;
 import de.medizininformatikinitiative.flare.model.fhir.Query;
 import de.medizininformatikinitiative.flare.model.mapping.MappingNotFoundException;
 import de.medizininformatikinitiative.flare.model.sq.*;
@@ -15,13 +16,19 @@
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.springframework.http.MediaType;
 import org.springframework.test.web.reactive.server.WebTestClient;
+import org.testcontainers.shaded.com.fasterxml.jackson.core.JsonProcessingException;
+import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper;
 import reactor.core.publisher.Mono;
 
+import java.util.Arrays;
+
 import static org.mockito.Mockito.when;
 
 @ExtendWith(MockitoExtension.class)
 class QueryControllerTest {
 
+    static final String PATIENT_ID = "patient-id-211701";
+    static final String PATIENT_ID_1 = "patient-id-1-131300";
     static final MediaType MEDIA_TYPE_SQ = MediaType.valueOf("application/sq+json");
     static final TermCode FEVER = TermCode.of("http://snomed.info/sct", "386661006", "Fever (finding)");
     static final StructuredQuery STRUCTURED_QUERY = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(
@@ -42,8 +49,8 @@ void setUp() {
     }
 
     @Test
-    void execute() {
-        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(1));
+    void executeCohortSize() {
+        when(queryService.executeCohortSize(STRUCTURED_QUERY)).thenReturn(Mono.just(1));
 
         client.post()
                 .uri("/query/execute")
@@ -75,9 +82,46 @@ void execute() {
                 .expectBody().json("1");
     }
 
+
+    @Test
+    void executeCohort() throws JsonProcessingException {
+        when(queryService.executeCohort(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID,PATIENT_ID_1)));
+
+        ObjectMapper objectMapper = new ObjectMapper();
+
+        client.post()
+                .uri("/query/execute-cohort")
+                .contentType(MEDIA_TYPE_SQ)
+                .bodyValue("""
+                        {
+                          "inclusionCriteria": [
+                            [
+                              {
+                                "context": {
+                                  "system": "context-system",
+                                  "code": "context-code",
+                                  "display": "context-display"
+                                },
+                                "termCodes": [
+                                  {
+                                    "system": "http://snomed.info/sct",
+                                    "code": "386661006",
+                                    "display": "Fever (finding)"
+                                  }
+                                ]
+                              }
+                            ]
+                          ]
+                        }
+                        """)
+                .exchange()
+                .expectStatus().isOk()
+                .expectBody().json(objectMapper.writeValueAsString(Arrays.asList(PATIENT_ID, PATIENT_ID_1)));
+    }
+
     @Test
     void execute_error() {
-        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.error(new MappingNotFoundException(ContextualTermCode.of(TestUtil.CONTEXT, FEVER))));
+        when(queryService.executeCohortSize(STRUCTURED_QUERY)).thenReturn(Mono.error(new MappingNotFoundException(ContextualTermCode.of(TestUtil.CONTEXT, FEVER))));
 
         client.post()
                 .uri("/query/execute")
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
index 8410931a..84b4cc49 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
@@ -131,7 +131,7 @@ void setUp() throws URISyntaxException, IOException {
     void execute_Criterion() {
         var query = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(Criterion.of(ContextualConcept.of(DIAGNOSIS, Concept.of(I08))))));
 
-        var result = service.execute(query).block();
+        var result = service.executeCohortSize(query).block();
 
         assertThat(result).isOne();
     }
@@ -140,7 +140,7 @@ void execute_Criterion() {
     void execute_genderTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("2-gender.json")));
 
-        var result = service.execute(query).block();
+        var result = service.executeCohortSize(query).block();
 
         assertThat(result).isEqualTo(172);
     }
@@ -149,7 +149,7 @@ void execute_genderTestCase() throws URISyntaxException, IOException {
     void execute_consentTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("consent.json")));
 
-        var result = service.execute(query).block();
+        var result = service.executeCohortSize(query).block();
 
         assertThat(result).isOne();
     }
@@ -165,7 +165,7 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
 
         var query = parseSq(slurpStructuredQueryService("referencedCriteria/sq-test-specimen-diag.json"));
 
-        var result = service.execute(query).block();
+        var result = service.executeCohortSize(query).block();
 
         assertThat(result).isOne();
     }
@@ -173,7 +173,7 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
     @ParameterizedTest
     @MethodSource("getTestQueriesReturningOnePatient")
     void execute_casesReturningOne(StructuredQuery query) {
-        var result = service.execute(query).block();
+        var result = service.executeCohortSize(query).block();
 
         assertThat(result).isOne();
     }
@@ -221,7 +221,7 @@ void execute_BloodPressureTestCase() throws Exception {
                 }
                 """);
 
-        var result = service_BloodPressure.execute(query).block();
+        var result = service_BloodPressure.executeCohortSize(query).block();
 
         assertThat(result).isOne();
     }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index 74b960bb..f5f9c611 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -63,7 +63,7 @@ void setUp() {
 
             @Test
             void execute() {
-                var result = service.execute(query);
+                var result = service.executeCohortSize(query);
 
                 StepVerifier.create(result).expectError(MappingNotFoundException.class).verify();
             }
@@ -85,7 +85,7 @@ class SingleExpansion {
             void execute() {
                 var query = query(incl(PATIENT));
 
-                var result = service.execute(query).block();
+                var result = service.executeCohortSize(query).block();
 
                 assertThat(result).isOne();
             }
@@ -110,7 +110,7 @@ class MultipleExpansion {
             void execute_MultiplePatients() {
                 var query = query(inclExpand(PATIENT_1, PATIENT_2));
 
-                var result = service.execute(query).block();
+                var result = service.executeCohortSize(query).block();
 
                 assertThat(result).isEqualTo(2);
             }
@@ -120,7 +120,7 @@ void execute_MultiplePatients() {
             void execute_SamePatient() {
                 var query = query(inclExpand(PATIENT, PATIENT));
 
-                var result = service.execute(query).block();
+                var result = service.executeCohortSize(query).block();
 
                 assertThat(result).isOne();
             }
@@ -146,7 +146,7 @@ class ConjunctionInclusion {
         void execute_MultiplePatients() {
             var query = query(inclAnd(PATIENT_1, PATIENT_2));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isZero();
         }
@@ -156,7 +156,7 @@ void execute_MultiplePatients() {
         void execute_SamePatient() {
             var query = query(inclAnd(PATIENT, PATIENT));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isOne();
         }
@@ -181,7 +181,7 @@ class DisjunctionInclusion {
         void execute_MultiplePatients() {
             var query = query(inclOr(PATIENT_1, PATIENT_2));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isEqualTo(2);
         }
@@ -191,7 +191,7 @@ void execute_MultiplePatients() {
         void execute_SamePatient() {
             var query = query(inclOr(PATIENT, PATIENT));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isOne();
         }
@@ -216,7 +216,7 @@ class SingleInclusionAndExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), excl(PATIENT_1));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isOne();
         }
@@ -226,7 +226,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), excl(PATIENT));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isZero();
         }
@@ -252,7 +252,7 @@ class SingleInclusionAndDisjunctionExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), exclOr(PATIENT_1, PATIENT_2));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isOne();
         }
@@ -262,7 +262,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclOr(PATIENT, PATIENT_1));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isZero();
         }
@@ -289,7 +289,7 @@ class SingleInclusionAndConjunctionExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT_1));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isOne();
         }
@@ -299,7 +299,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT));
 
-            var result = service.execute(query).block();
+            var result = service.executeCohortSize(query).block();
 
             assertThat(result).isZero();
         }

From a543223c1556959eb94b6647c755f16cfc781a03 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Wed, 10 Jul 2024 10:49:51 +0200
Subject: [PATCH 05/43] Refactor to only one execute function in query service

---
 .../flare/rest/QueryController.java           | 13 +++----
 .../flare/service/StructuredQueryService.java | 12 +------
 .../flare/rest/QueryControllerTest.java       | 13 +++----
 .../service/StructuredQueryServiceIT.java     | 18 +++++-----
 .../service/StructuredQueryServiceTest.java   | 34 ++++++++++---------
 5 files changed, 43 insertions(+), 47 deletions(-)

diff --git a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
index eb0304ec..283e932b 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
@@ -17,6 +17,7 @@
 import reactor.core.publisher.Mono;
 
 import java.util.Objects;
+import java.util.Set;
 
 import static org.springframework.web.reactive.function.server.RequestPredicates.POST;
 import static org.springframework.web.reactive.function.server.RequestPredicates.accept;
@@ -45,11 +46,11 @@ public RouterFunction<ServerResponse> queryRouter() {
 
     public Mono<ServerResponse> execute(ServerRequest request) {
         var startNanoTime = System.nanoTime();
-        logger.debug("Execute query");
+        logger.debug("Execute feasibility query");
         return request.bodyToMono(StructuredQuery.class)
-                .flatMap(queryService::executeCohortSize)
+                .flatMap(queryService::execute).map(Set::size)
                 .flatMap(count -> {
-                    logger.debug("Finished query returning {} patients in {} seconds.", count,
+                    logger.debug("Finished feasibility query returning cohort size {} in {} seconds.", count,
                             "%.1f".formatted(Util.durationSecondsSince(startNanoTime)));
                     return ok().bodyValue(count);
                 })
@@ -65,11 +66,11 @@ public Mono<ServerResponse> execute(ServerRequest request) {
 
     public Mono<ServerResponse> executeCohort(ServerRequest request) {
         var startNanoTime = System.nanoTime();
-        logger.debug("Execute query");
+        logger.debug("Execute cohort query");
         return request.bodyToMono(StructuredQuery.class)
-                .flatMap(queryService::executeCohort)
+                .flatMap(queryService::execute)
                 .flatMap(population -> {
-                    logger.debug("Finished query returning {} patients in {} seconds.", population.size(),
+                    logger.debug("Finished cohort query returning cohort of {} patient IDs in {} seconds.", population.size(),
                             "%.1f".formatted(Util.durationSecondsSince(startNanoTime)));
                     return ok().bodyValue(population);
                 })
diff --git a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
index 27d7e787..237af6a1 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
@@ -41,7 +41,7 @@ public StructuredQueryService(@Qualifier("memCachingFhirQueryService") FhirQuery
      * @param query the query to execute
      * @return the Patient IDs qualifying the criteria
      */
-    public Mono<Population> executeCohort(StructuredQuery query) {
+    public Mono<Population> execute(StructuredQuery query) {
         var includedPatients = query.inclusionCriteria().executeAndIntersection(this::executeUnionGroup)
                 .defaultIfEmpty(Population.of());
         var excludedPatients = query.exclusionCriteria().map(c -> c.map(CriterionGroup::wrapCriteria)
@@ -53,16 +53,6 @@ public Mono<Population> executeCohort(StructuredQuery query) {
     }
 
 
-    /**
-     * Executes {@code query} and returns the number of Patients qualifying its criteria.
-     *
-     * @param query the query to execute
-     * @return the number of Patients qualifying the criteria
-     */
-    public Mono<Integer> executeCohortSize(StructuredQuery query) {
-        return this.executeCohort(query).map(Set::size);
-    }
-
     private Mono<Population> executeUnionGroup(CriterionGroup<Criterion> group) {
         return group.executeAndUnion(this::executeSingle);
     }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
index 0dbaa876..e9fc0412 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
@@ -21,6 +21,7 @@
 import reactor.core.publisher.Mono;
 
 import java.util.Arrays;
+import java.util.List;
 
 import static org.mockito.Mockito.when;
 
@@ -49,8 +50,8 @@ void setUp() {
     }
 
     @Test
-    void executeCohortSize() {
-        when(queryService.executeCohortSize(STRUCTURED_QUERY)).thenReturn(Mono.just(1));
+    void executeCohort() {
+        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID)));
 
         client.post()
                 .uri("/query/execute")
@@ -84,8 +85,8 @@ void executeCohortSize() {
 
 
     @Test
-    void executeCohort() throws JsonProcessingException {
-        when(queryService.executeCohort(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID,PATIENT_ID_1)));
+    void execute() throws JsonProcessingException {
+        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID,PATIENT_ID_1)));
 
         ObjectMapper objectMapper = new ObjectMapper();
 
@@ -116,12 +117,12 @@ void executeCohort() throws JsonProcessingException {
                         """)
                 .exchange()
                 .expectStatus().isOk()
-                .expectBody().json(objectMapper.writeValueAsString(Arrays.asList(PATIENT_ID, PATIENT_ID_1)));
+                .expectBody().json(objectMapper.writeValueAsString(List.of(PATIENT_ID, PATIENT_ID_1)));
     }
 
     @Test
     void execute_error() {
-        when(queryService.executeCohortSize(STRUCTURED_QUERY)).thenReturn(Mono.error(new MappingNotFoundException(ContextualTermCode.of(TestUtil.CONTEXT, FEVER))));
+        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.error(new MappingNotFoundException(ContextualTermCode.of(TestUtil.CONTEXT, FEVER))));
 
         client.post()
                 .uri("/query/execute")
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
index 84b4cc49..9ebe17d1 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
@@ -96,6 +96,10 @@ private static Path resourcePathFlareApplication(String name) throws URISyntaxEx
         return Paths.get(Objects.requireNonNull(FlareApplication.class.getResource(name)).toURI());
     }
 
+    private int getExecutionResult(StructuredQuery query){
+        return service.execute(query).block().size();
+    }
+
     public static List<StructuredQuery> getTestQueriesReturningOnePatient() throws URISyntaxException, IOException {
         Path directoryPath = Paths.get(resourcePathFlareApplication("testCases").resolve("returningOnePatient").toString());
 
@@ -131,7 +135,7 @@ void setUp() throws URISyntaxException, IOException {
     void execute_Criterion() {
         var query = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(Criterion.of(ContextualConcept.of(DIAGNOSIS, Concept.of(I08))))));
 
-        var result = service.executeCohortSize(query).block();
+        var result = getExecutionResult(query);
 
         assertThat(result).isOne();
     }
@@ -139,8 +143,7 @@ void execute_Criterion() {
     @Test
     void execute_genderTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("2-gender.json")));
-
-        var result = service.executeCohortSize(query).block();
+        var result = getExecutionResult(query);
 
         assertThat(result).isEqualTo(172);
     }
@@ -148,8 +151,7 @@ void execute_genderTestCase() throws URISyntaxException, IOException {
     @Test
     void execute_consentTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("consent.json")));
-
-        var result = service.executeCohortSize(query).block();
+        var result = getExecutionResult(query);
 
         assertThat(result).isOne();
     }
@@ -165,7 +167,7 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
 
         var query = parseSq(slurpStructuredQueryService("referencedCriteria/sq-test-specimen-diag.json"));
 
-        var result = service.executeCohortSize(query).block();
+        var result = getExecutionResult(query);
 
         assertThat(result).isOne();
     }
@@ -173,7 +175,7 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
     @ParameterizedTest
     @MethodSource("getTestQueriesReturningOnePatient")
     void execute_casesReturningOne(StructuredQuery query) {
-        var result = service.executeCohortSize(query).block();
+        var result = getExecutionResult(query);
 
         assertThat(result).isOne();
     }
@@ -221,7 +223,7 @@ void execute_BloodPressureTestCase() throws Exception {
                 }
                 """);
 
-        var result = service_BloodPressure.executeCohortSize(query).block();
+        var result = service_BloodPressure.execute(query).block().size();
 
         assertThat(result).isOne();
     }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index f5f9c611..1d06f3ce 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -47,6 +47,10 @@ class StructuredQueryServiceTest {
     @InjectMocks
     private StructuredQueryService service;
 
+    private int getExecutionResult(StructuredQuery query){
+        return service.execute(query).block().size();
+    }
+
     @Nested
     class SingleInclusion {
 
@@ -63,7 +67,7 @@ void setUp() {
 
             @Test
             void execute() {
-                var result = service.executeCohortSize(query);
+                var result = service.execute(query);
 
                 StepVerifier.create(result).expectError(MappingNotFoundException.class).verify();
             }
@@ -85,7 +89,7 @@ class SingleExpansion {
             void execute() {
                 var query = query(incl(PATIENT));
 
-                var result = service.executeCohortSize(query).block();
+                var result = getExecutionResult(query);
 
                 assertThat(result).isOne();
             }
@@ -110,7 +114,7 @@ class MultipleExpansion {
             void execute_MultiplePatients() {
                 var query = query(inclExpand(PATIENT_1, PATIENT_2));
 
-                var result = service.executeCohortSize(query).block();
+                var result = getExecutionResult(query);
 
                 assertThat(result).isEqualTo(2);
             }
@@ -120,7 +124,7 @@ void execute_MultiplePatients() {
             void execute_SamePatient() {
                 var query = query(inclExpand(PATIENT, PATIENT));
 
-                var result = service.executeCohortSize(query).block();
+                var result = getExecutionResult(query);
 
                 assertThat(result).isOne();
             }
@@ -146,7 +150,7 @@ class ConjunctionInclusion {
         void execute_MultiplePatients() {
             var query = query(inclAnd(PATIENT_1, PATIENT_2));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isZero();
         }
@@ -156,7 +160,7 @@ void execute_MultiplePatients() {
         void execute_SamePatient() {
             var query = query(inclAnd(PATIENT, PATIENT));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isOne();
         }
@@ -181,7 +185,7 @@ class DisjunctionInclusion {
         void execute_MultiplePatients() {
             var query = query(inclOr(PATIENT_1, PATIENT_2));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isEqualTo(2);
         }
@@ -191,7 +195,7 @@ void execute_MultiplePatients() {
         void execute_SamePatient() {
             var query = query(inclOr(PATIENT, PATIENT));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isOne();
         }
@@ -215,9 +219,7 @@ class SingleInclusionAndExclusion {
         @DisplayName("execute: PATIENT is not excluded → returns 1")
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), excl(PATIENT_1));
-
-            var result = service.executeCohortSize(query).block();
-
+            var result = getExecutionResult(query);
             assertThat(result).isOne();
         }
 
@@ -226,7 +228,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), excl(PATIENT));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isZero();
         }
@@ -252,7 +254,7 @@ class SingleInclusionAndDisjunctionExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), exclOr(PATIENT_1, PATIENT_2));
 
-            var result = service.executeCohortSize(query).block();
+            var result = getExecutionResult(query);
 
             assertThat(result).isOne();
         }
@@ -262,7 +264,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclOr(PATIENT, PATIENT_1));
 
-            var result = service.executeCohortSize(query).block();
+            var result = service.execute(query).block().size();
 
             assertThat(result).isZero();
         }
@@ -289,7 +291,7 @@ class SingleInclusionAndConjunctionExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT_1));
 
-            var result = service.executeCohortSize(query).block();
+            var result = service.execute(query).block().size();
 
             assertThat(result).isOne();
         }
@@ -299,7 +301,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT));
 
-            var result = service.executeCohortSize(query).block();
+            var result = service.execute(query).block().size();
 
             assertThat(result).isZero();
         }

From f7b1717d04083a7fe8b9811bb155d2e1d976b974 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Wed, 10 Jul 2024 10:58:02 +0200
Subject: [PATCH 06/43] replace remaining .size() calls

---
 .../flare/service/StructuredQueryServiceTest.java           | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index 1d06f3ce..7b19274b 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -264,7 +264,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclOr(PATIENT, PATIENT_1));
 
-            var result = service.execute(query).block().size();
+            var result = getExecutionResult(query);
 
             assertThat(result).isZero();
         }
@@ -291,7 +291,7 @@ class SingleInclusionAndConjunctionExclusion {
         void execute_PatientNotExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT_1));
 
-            var result = service.execute(query).block().size();
+            var result = getExecutionResult(query);
 
             assertThat(result).isOne();
         }
@@ -301,7 +301,7 @@ void execute_PatientNotExcluded() {
         void execute_PatientExcluded() {
             var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT));
 
-            var result = service.execute(query).block().size();
+            var result = getExecutionResult(query);
 
             assertThat(result).isZero();
         }

From 27517af09b1d9982fe07018a51cd9c767611408a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Wed, 10 Jul 2024 16:47:32 +0200
Subject: [PATCH 07/43] Refactor tests, Change tets to test for specific
 patient IDs instead of the size of the Population

---
 .../flare/rest/QueryControllerTest.java       |   4 +-
 .../service/StructuredQueryServiceIT.java     |  22 ++--
 .../service/StructuredQueryServiceTest.java   | 113 +++++++++---------
 .../flare/GeneratedBundle.json                |  20 ++--
 .../specimen-diag-testbundle.json             |  12 +-
 5 files changed, 89 insertions(+), 82 deletions(-)

diff --git a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
index e9fc0412..6ccedb75 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
@@ -50,7 +50,7 @@ void setUp() {
     }
 
     @Test
-    void executeCohort() {
+    void execute() {
         when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID)));
 
         client.post()
@@ -85,7 +85,7 @@ void executeCohort() {
 
 
     @Test
-    void execute() throws JsonProcessingException {
+    void executeCohort() throws JsonProcessingException {
         when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID,PATIENT_ID_1)));
 
         ObjectMapper objectMapper = new ObjectMapper();
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
index 9ebe17d1..d7d83385 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.medizininformatikinitiative.flare.FlareApplication;
 import de.medizininformatikinitiative.flare.Util;
+import de.medizininformatikinitiative.flare.model.Population;
 import de.medizininformatikinitiative.flare.model.mapping.Mapping;
 import de.medizininformatikinitiative.flare.model.mapping.MappingContext;
 import de.medizininformatikinitiative.flare.model.mapping.TermCodeNode;
@@ -26,6 +27,7 @@
 import org.testcontainers.images.PullPolicy;
 import org.testcontainers.junit.jupiter.Container;
 import org.testcontainers.junit.jupiter.Testcontainers;
+import reactor.test.StepVerifier;
 
 import java.io.IOException;
 import java.net.URISyntaxException;
@@ -135,9 +137,8 @@ void setUp() throws URISyntaxException, IOException {
     void execute_Criterion() {
         var query = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(Criterion.of(ContextualConcept.of(DIAGNOSIS, Concept.of(I08))))));
 
-        var result = getExecutionResult(query);
-
-        assertThat(result).isOne();
+        var result = service.execute(query);
+        StepVerifier.create(result).expectNext(Population.of("id-pat-diag-I08.0")).verifyComplete();
     }
 
     @Test
@@ -151,9 +152,10 @@ void execute_genderTestCase() throws URISyntaxException, IOException {
     @Test
     void execute_consentTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("consent.json")));
-        var result = getExecutionResult(query);
 
-        assertThat(result).isOne();
+        var result = service.execute(query);
+
+        StepVerifier.create(result).expectNext(Population.of("id-pat-consent-test")).verifyComplete();
     }
 
     @Test
@@ -167,9 +169,10 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
 
         var query = parseSq(slurpStructuredQueryService("referencedCriteria/sq-test-specimen-diag.json"));
 
-        var result = getExecutionResult(query);
+        var result = service.execute(query);
+
+        StepVerifier.create(result).expectNext(Population.of("id-pat-diab-test-1")).verifyComplete();
 
-        assertThat(result).isOne();
     }
 
     @ParameterizedTest
@@ -223,9 +226,10 @@ void execute_BloodPressureTestCase() throws Exception {
                 }
                 """);
 
-        var result = service_BloodPressure.execute(query).block().size();
+        var result = service_BloodPressure.execute(query);
+
+        StepVerifier.create(result).expectNext(Population.of("id-pat-bloodpressure-test")).verifyComplete();
 
-        assertThat(result).isOne();
     }
 
     @Configuration
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index 7b19274b..cfca0fb7 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -34,9 +34,10 @@ class StructuredQueryServiceTest {
 
     static final String BFARM = "http://fhir.de/CodeSystem/bfarm/icd-10-gm";
     static final Criterion CONCEPT_CRITERION = Criterion.of(cc(1));
-    static final Population PATIENT = Population.of("patient-id-140857");
-    static final Population PATIENT_1 = Population.of("patient-id-144725");
-    static final Population PATIENT_2 = Population.of("patient-id-144727");
+    static final Population EMPTY_POP = Population.of();
+    static final Population PATIENT_POP = Population.of("patient-id-140857");
+    static final Population PATIENT_1_POP = Population.of("patient-id-144725");
+    static final Population PATIENT_2_POP = Population.of("patient-id-144727");
 
     @Mock
     private FhirQueryService fhirQueryService;
@@ -47,10 +48,6 @@ class StructuredQueryServiceTest {
     @InjectMocks
     private StructuredQueryService service;
 
-    private int getExecutionResult(StructuredQuery query){
-        return service.execute(query).block().size();
-    }
-
     @Nested
     class SingleInclusion {
 
@@ -87,11 +84,12 @@ class SingleExpansion {
             @Test
             @DisplayName("execute: returns 1")
             void execute() {
-                var query = query(incl(PATIENT));
+                var query = query(incl(PATIENT_POP));
+
+                var result = service.execute(query);
 
-                var result = getExecutionResult(query);
+                StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
 
-                assertThat(result).isOne();
             }
 
             @Test
@@ -112,21 +110,23 @@ class MultipleExpansion {
             @Test
             @DisplayName("execute: multiple patients → returns 2")
             void execute_MultiplePatients() {
-                var query = query(inclExpand(PATIENT_1, PATIENT_2));
+                var query = query(inclExpand(PATIENT_1_POP, PATIENT_2_POP));
 
-                var result = getExecutionResult(query);
+                var result = service.execute(query);
 
-                assertThat(result).isEqualTo(2);
+                StepVerifier.create(result).expectNext(PATIENT_1_POP.union(PATIENT_2_POP)).verifyComplete();
             }
 
             @Test
             @DisplayName("execute: same patient → returns 1")
             void execute_SamePatient() {
-                var query = query(inclExpand(PATIENT, PATIENT));
+                var query = query(inclExpand(PATIENT_POP, PATIENT_POP));
+
+                var result = service.execute(query);
+
+                StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
 
-                var result = getExecutionResult(query);
 
-                assertThat(result).isOne();
             }
 
             @Test
@@ -146,23 +146,23 @@ void translate() {
     class ConjunctionInclusion {
 
         @Test
-        @DisplayName("execute: multiple patients → returns 0")
+        @DisplayName("execute: multiple patients → returns empty population")
         void execute_MultiplePatients() {
-            var query = query(inclAnd(PATIENT_1, PATIENT_2));
+            var query = query(inclAnd(PATIENT_1_POP, PATIENT_2_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isZero();
+            StepVerifier.create(result).expectNext(EMPTY_POP).verifyComplete();
         }
 
         @Test
-        @DisplayName("execute: same patient → returns 1")
+        @DisplayName("execute: same patient → returns the Patient once")
         void execute_SamePatient() {
-            var query = query(inclAnd(PATIENT, PATIENT));
+            var query = query(inclAnd(PATIENT_POP, PATIENT_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isOne();
+            StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
         }
 
         @Test
@@ -181,23 +181,23 @@ void translate() {
     class DisjunctionInclusion {
 
         @Test
-        @DisplayName("execute: multiple patients → returns 2")
+        @DisplayName("execute: multiple patients → returns the two patients")
         void execute_MultiplePatients() {
-            var query = query(inclOr(PATIENT_1, PATIENT_2));
+            var query = query(inclOr(PATIENT_1_POP, PATIENT_2_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isEqualTo(2);
+            StepVerifier.create(result).expectNext(PATIENT_1_POP.union(PATIENT_2_POP)).verifyComplete();
         }
 
         @Test
         @DisplayName("execute: same patient → returns 1")
         void execute_SamePatient() {
-            var query = query(inclOr(PATIENT, PATIENT));
+            var query = query(inclOr(PATIENT_POP, PATIENT_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isOne();
+            StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
         }
 
         @Test
@@ -216,21 +216,23 @@ void translate() {
     class SingleInclusionAndExclusion {
 
         @Test
-        @DisplayName("execute: PATIENT is not excluded → returns 1")
+        @DisplayName("execute: PATIENT is not excluded → returns patient")
         void execute_PatientNotExcluded() {
-            var query = query(incl(PATIENT), excl(PATIENT_1));
-            var result = getExecutionResult(query);
-            assertThat(result).isOne();
+            var query = query(incl(PATIENT_POP), excl(PATIENT_1_POP));
+
+            var result = service.execute(query);
+
+            StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
         }
 
         @Test
-        @DisplayName("execute: PATIENT is excluded → returns 0")
+        @DisplayName("execute: PATIENT is excluded → returns empty Population")
         void execute_PatientExcluded() {
-            var query = query(incl(PATIENT), excl(PATIENT));
+            var query = query(incl(PATIENT_POP), excl(PATIENT_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isZero();
+            StepVerifier.create(result).expectNext(EMPTY_POP).verifyComplete();
         }
 
         @Test
@@ -250,23 +252,24 @@ void translate() {
     class SingleInclusionAndDisjunctionExclusion {
 
         @Test
-        @DisplayName("execute: PATIENT is not excluded → returns 1")
+        @DisplayName("execute: PATIENT is not excluded → returns PATIENT")
         void execute_PatientNotExcluded() {
-            var query = query(incl(PATIENT), exclOr(PATIENT_1, PATIENT_2));
+            var query = query(incl(PATIENT_POP), exclOr(PATIENT_1_POP, PATIENT_2_POP));
+
+            var result = service.execute(query);
 
-            var result = getExecutionResult(query);
+            StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
 
-            assertThat(result).isOne();
         }
 
         @Test
-        @DisplayName("execute: PATIENT is excluded → returns 0")
+        @DisplayName("execute: PATIENT is excluded → returns empty Population")
         void execute_PatientExcluded() {
-            var query = query(incl(PATIENT), exclOr(PATIENT, PATIENT_1));
+            var query = query(incl(PATIENT_POP), exclOr(PATIENT_POP, PATIENT_1_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isZero();
+            StepVerifier.create(result).expectNext(EMPTY_POP).verifyComplete();
         }
 
         @Test
@@ -287,23 +290,23 @@ void translate() {
     class SingleInclusionAndConjunctionExclusion {
 
         @Test
-        @DisplayName("execute: PATIENT is not excluded → returns 1")
+        @DisplayName("execute: PATIENT is not excluded → returns PATIENT")
         void execute_PatientNotExcluded() {
-            var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT_1));
+            var query = query(incl(PATIENT_POP), exclAnd(PATIENT_POP, PATIENT_1_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isOne();
+            StepVerifier.create(result).expectNext(PATIENT_POP).verifyComplete();
         }
 
         @Test
-        @DisplayName("execute: PATIENT is excluded → returns 0")
+        @DisplayName("execute: PATIENT is excluded → returns empty Population")
         void execute_PatientExcluded() {
-            var query = query(incl(PATIENT), exclAnd(PATIENT, PATIENT));
+            var query = query(incl(PATIENT_POP), exclAnd(PATIENT_POP, PATIENT_POP));
 
-            var result = getExecutionResult(query);
+            var result = service.execute(query);
 
-            assertThat(result).isZero();
+            StepVerifier.create(result).expectNext(EMPTY_POP).verifyComplete();
         }
 
         @Test
diff --git a/src/test/resources/de/medizininformatikinitiative/flare/GeneratedBundle.json b/src/test/resources/de/medizininformatikinitiative/flare/GeneratedBundle.json
index fac19a2d..be6e47b3 100644
--- a/src/test/resources/de/medizininformatikinitiative/flare/GeneratedBundle.json
+++ b/src/test/resources/de/medizininformatikinitiative/flare/GeneratedBundle.json
@@ -47,7 +47,7 @@
             ]
         },
         "subject": {
-            "reference": "Patient/062d64e5-e4e5-4c89-8fa7-a47ae3b2b95c",
+            "reference": "Patient/id-pat-bloodpressure-test",
             "display": "Alexia Wachtel"
         },
         "effectiveDateTime": "2010-08-05T07:16:58+02:00",
@@ -176,7 +176,7 @@
   }, {
     "resource": {
       "resourceType": "Patient",
-      "id": "7ca6f273-82f1-4fd5-9b0d-e9e4f957fe42",
+      "id": "id-pat-diag-I08.0",
       "meta": {
         "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient" ]
       },
@@ -211,7 +211,7 @@
     },
     "request": {
       "method": "PUT",
-      "url": "Patient/7ca6f273-82f1-4fd5-9b0d-e9e4f957fe42"
+      "url": "Patient/id-pat-diag-I08.0"
     }
   }, {
     "resource": {
@@ -228,7 +228,7 @@
         } ]
       },
       "subject": {
-        "reference": "Patient/7ca6f273-82f1-4fd5-9b0d-e9e4f957fe42",
+        "reference": "Patient/id-pat-diag-I08.0",
         "display": "Baran Stolle"
       },
       "recordedDate": "2012-12-11T00:26:30+01:00"
@@ -255,7 +255,7 @@
   }, {
     "resource": {
       "resourceType": "Patient",
-      "id": "8da7a09c-c2b4-4b8f-9144-0ecf407f2ed1",
+      "id": "id-pat-consent-test",
       "meta": {
         "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient" ]
       },
@@ -290,7 +290,7 @@
     },
     "request": {
       "method": "PUT",
-      "url": "Patient/8da7a09c-c2b4-4b8f-9144-0ecf407f2ed1"
+      "url": "Patient/id-pat-consent-test"
     }
   }, {
     "resource": {
@@ -313,7 +313,7 @@
         } ]
       } ],
       "patient": {
-        "reference": "Patient/8da7a09c-c2b4-4b8f-9144-0ecf407f2ed1",
+        "reference": "Patient/id-pat-consent-test",
         "display": "Ina Bielert"
       },
       "dateTime": "2003-07-09T00:45:44+02:00",
@@ -663,7 +663,7 @@
   }, {
     "resource": {
       "resourceType": "Patient",
-      "id": "062d64e5-e4e5-4c89-8fa7-a47ae3b2b95c",
+      "id": "id-pat-bloodpressure-test",
       "meta": {
         "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient" ]
       },
@@ -698,7 +698,7 @@
     },
     "request": {
       "method": "PUT",
-      "url": "Patient/062d64e5-e4e5-4c89-8fa7-a47ae3b2b95c"
+      "url": "Patient/id-pat-bloodpressure-test"
     }
   }, {
     "resource": {
@@ -750,7 +750,7 @@
         } ]
       },
       "subject": {
-        "reference": "Patient/062d64e5-e4e5-4c89-8fa7-a47ae3b2b95c",
+        "reference": "Patient/id-pat-bloodpressure-test",
         "display": "Alexia Wachtel"
       },
       "effectiveDateTime": "2010-08-05T07:16:58+02:00",
diff --git a/src/test/resources/de/medizininformatikinitiative/flare/service/referencedCriteria/specimen-diag-testbundle.json b/src/test/resources/de/medizininformatikinitiative/flare/service/referencedCriteria/specimen-diag-testbundle.json
index 0ce4d36a..864eaaa0 100644
--- a/src/test/resources/de/medizininformatikinitiative/flare/service/referencedCriteria/specimen-diag-testbundle.json
+++ b/src/test/resources/de/medizininformatikinitiative/flare/service/referencedCriteria/specimen-diag-testbundle.json
@@ -3,10 +3,10 @@
   "type": "transaction",
   "entry": [
     {
-      "fullUrl": "Patient/SPEC-DIAB-TEST-P-1",
+      "fullUrl": "Patient/id-pat-diab-test-1",
       "resource": {
         "resourceType": "Patient",
-        "id": "SPEC-DIAB-TEST-P-1",
+        "id": "id-pat-diab-test-1",
         "meta": {
           "profile": [
             "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient"
@@ -24,7 +24,7 @@
               ]
             },
             "system": "https://test/pid",
-            "value": "SPEC-DIAB-TEST-P-1"
+            "value": "id-pat-diab-test-1"
           }
         ],
         "gender": "male",
@@ -32,7 +32,7 @@
       },
       "request": {
         "method": "PUT",
-        "url": "Patient/SPEC-DIAB-TEST-P-1"
+        "url": "Patient/id-pat-diab-test-1"
       }
     },
     {
@@ -61,7 +61,7 @@
           "text": "Idiopathische Hypotonie"
         },
         "subject": {
-          "reference": "Patient/SPEC-DIAB-TEST-P-1"
+          "reference": "Patient/id-pat-diab-test-1"
         },
         "recordedDate": "2021-01-01T00:00:00+01:00"
       },
@@ -99,7 +99,7 @@
           "text": "Serum Specimen"
         },
         "subject": {
-          "reference": "Patient/SPEC-DIAB-TEST-P-1"
+          "reference": "Patient/id-pat-diab-test-1"
         }
       },
       "request": {

From 371ef1f61e00d1e533884c8ce4f8a2e4acda5217 Mon Sep 17 00:00:00 2001
From: Bastian Schaffer <bastianschaffer.it@gmail.com>
Date: Mon, 2 Sep 2024 15:16:58 +0200
Subject: [PATCH 08/43] Update Mapping Tree

Fixes: #191
---
 .../synthea-test-mapping/mapping.zip          | Bin 1994 -> 1768 bytes
 .gitignore                                    |   1 +
 pom.xml                                       |   5 +-
 .../flare/Util.java                           |  13 +-
 .../flare/model/mapping/MappingContext.java   |   8 +-
 .../flare/model/mapping/MappingTreeBase.java  |  22 ++
 .../model/mapping/MappingTreeModuleEntry.java |  16 +
 .../model/mapping/MappingTreeModuleRoot.java  |  34 +++
 .../flare/model/mapping/TermCodeNode.java     |  99 ------
 .../flare/service/StructuredQueryService.java |   2 -
 .../model/mapping/MappingContextTest.java     |  34 ++-
 .../model/mapping/MappingTreeBaseTest.java    | 289 ++++++++++++++++++
 .../flare/model/mapping/TermCodeNodeTest.java | 192 ------------
 .../flare/rest/QueryControllerTest.java       |   3 +-
 .../service/StructuredQueryServiceIT.java     |   9 +-
 .../service/StructuredQueryServiceTest.java   |   1 -
 .../tree-bloodPressure.json                   |  27 +-
 .../testCases/returningOnePatient/1-age.json  |  33 +-
 18 files changed, 452 insertions(+), 336 deletions(-)
 create mode 100644 src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
 create mode 100644 src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleEntry.java
 create mode 100644 src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
 delete mode 100644 src/main/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNode.java
 create mode 100644 src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
 delete mode 100644 src/test/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNodeTest.java

diff --git a/.github/integration-test/synthea-test-mapping/mapping.zip b/.github/integration-test/synthea-test-mapping/mapping.zip
index fdeb51490e3acd21181010748448d1adb690bacb..415497d9ffa57ba640ed76d0756ee0c5d3a97f3c 100644
GIT binary patch
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diff --git a/.gitignore b/.gitignore
index 505763e4..62a060e8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 .mvn
+.idea/
 cache
 target
 /ontology/mapping.zip
diff --git a/pom.xml b/pom.xml
index 16f36097..c78ce822 100644
--- a/pom.xml
+++ b/pom.xml
@@ -21,7 +21,7 @@
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.19.8</testcontainers.version>
-    <ontology.version>2.2.0</ontology.version>
+    <ontology.version>3.0.0-test.1</ontology.version>
   </properties>
 
   <dependencies>
@@ -206,9 +206,10 @@
               <goal>wget</goal>
             </goals>
             <configuration>
-              <url>https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v${ontology.version}/example/mii_core_data_set/ontology/mapping.zip</url>
+              <url>https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/v${ontology.version}/example/fdpg-ontology/mapping.zip</url>
               <outputFileName>mapping.zip</outputFileName>
               <outputDirectory>ontology/</outputDirectory>
+              <skipCache>true</skipCache>
             </configuration>
           </execution>
         </executions>
diff --git a/src/main/java/de/medizininformatikinitiative/flare/Util.java b/src/main/java/de/medizininformatikinitiative/flare/Util.java
index 6ca035c1..a1551424 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/Util.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/Util.java
@@ -3,7 +3,8 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.medizininformatikinitiative.flare.model.mapping.Mapping;
 import de.medizininformatikinitiative.flare.model.mapping.MappingContext;
-import de.medizininformatikinitiative.flare.model.mapping.TermCodeNode;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeBase;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeModuleRoot;
 import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
 
 import java.io.BufferedInputStream;
@@ -79,11 +80,11 @@ static double durationSecondsSince(long startNanoTime) {
     static MappingContext flareMappingContext(Clock clock) throws Exception {
         var mapper = new ObjectMapper();
         String ontologyZipFile = "ontology/mapping.zip";
-        String mappingFile = "ontology/mapping/mapping_fhir.json";
-        String conceptTreeFile = "ontology/mapping/mapping_tree.json";
+        String mappingFile = "mapping/fhir/mapping_fhir.json";
+        String conceptTreeFile = "mapping/mapping_tree.json";
 
         Map<ContextualTermCode, Mapping> mappings = null;
-        TermCodeNode conceptTree = null;
+        MappingTreeBase conceptTree = null;
 
         try (FileInputStream fis = new FileInputStream(ontologyZipFile);
              BufferedInputStream bis = new BufferedInputStream(fis);
@@ -94,8 +95,8 @@ static MappingContext flareMappingContext(Clock clock) throws Exception {
                     mappings = Arrays.stream(mapper.readValue(readZipEntryContent(zis), Mapping[].class))
                             .collect(Collectors.toMap(Mapping::key, identity()));
                 } else if (ze.getName().equals(conceptTreeFile)) {
-                    String treeString = readZipEntryContent(zis);
-                    conceptTree = mapper.readValue(treeString, TermCodeNode.class);
+                    conceptTree = new MappingTreeBase(
+                            Arrays.stream(mapper.readValue(readZipEntryContent(zis), MappingTreeModuleRoot[].class)).toList());
                 }
             }
         }
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingContext.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingContext.java
index 7da06eb1..a9299429 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingContext.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingContext.java
@@ -21,10 +21,10 @@
 public class MappingContext {
 
     private final Map<ContextualTermCode, Mapping> mappings;
-    private final TermCodeNode conceptTree;
+    private final MappingTreeBase conceptTree;
     private final Clock clock;
 
-    private MappingContext(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree, Clock clock) {
+    private MappingContext(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree, Clock clock) {
         this.mappings = Map.copyOf(mappings);
         this.conceptTree = requireNonNull(conceptTree);
         this.clock = requireNonNull(clock);
@@ -37,7 +37,7 @@ private MappingContext(Map<ContextualTermCode, Mapping> mappings, TermCodeNode c
      * @param conceptTree a tree of concepts to expand (can be null)
      * @return the mapping context
      */
-    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree) {
+    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree) {
         return new MappingContext(mappings, conceptTree, Clock.systemDefaultZone());
     }
 
@@ -49,7 +49,7 @@ public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermC
      * @param clock       a clock that is used for time-related calculations
      * @return the mapping context
      */
-    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, TermCodeNode conceptTree, Clock clock) {
+    public static MappingContext of(Map<ContextualTermCode, Mapping> mappings, MappingTreeBase conceptTree, Clock clock) {
         return new MappingContext(mappings, conceptTree, clock);
     }
 
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
new file mode 100644
index 00000000..a96ac4d6
--- /dev/null
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
@@ -0,0 +1,22 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
+
+import java.util.List;
+import java.util.stream.Stream;
+
+public record MappingTreeBase(List<MappingTreeModuleRoot> moduleRoots) {
+
+    public Stream<ContextualTermCode> expand(ContextualTermCode termCode) {
+        var key = termCode.termCode().code();
+
+        return moduleRoots.stream().flatMap(moduleRoot ->
+                isModuleMatching(termCode, moduleRoot) ? moduleRoot.expand(key) : Stream.empty());
+    }
+
+    private boolean isModuleMatching(ContextualTermCode termCode, MappingTreeModuleRoot moduleRoot) {
+        return termCode.context().equals(moduleRoot.context()) &&
+                moduleRoot.system().equals(termCode.termCode().system()) &&
+                moduleRoot.entries().containsKey(termCode.termCode().code());
+    }
+}
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleEntry.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleEntry.java
new file mode 100644
index 00000000..465a9d14
--- /dev/null
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleEntry.java
@@ -0,0 +1,16 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.List;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+record MappingTreeModuleEntry(String key, List<String> children) {
+    @JsonCreator
+    static MappingTreeModuleEntry fromJson(@JsonProperty("key") String key,
+                                           @JsonProperty("children") List<String> children) {
+        return new MappingTreeModuleEntry(key, children);
+    }
+}
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
new file mode 100644
index 00000000..68a6c6aa
--- /dev/null
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
@@ -0,0 +1,34 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
+import de.medizininformatikinitiative.flare.model.sq.TermCode;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static java.util.function.Function.identity;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public record MappingTreeModuleRoot(TermCode context, String system, Map<String, MappingTreeModuleEntry> entries) {
+    @JsonCreator
+    static MappingTreeModuleRoot fromJson(@JsonProperty("context") TermCode context,
+                                          @JsonProperty("system") String system,
+                                          @JsonProperty("entries") List<MappingTreeModuleEntry> entries) {
+        return new MappingTreeModuleRoot(
+                context,
+                system,
+                entries.stream().collect(Collectors.toMap(MappingTreeModuleEntry::key, identity())));
+    }
+
+    public Stream<ContextualTermCode> expand(String key) {
+        var newTermCode = new ContextualTermCode(context, new TermCode(system, key, ""));
+
+        return Stream.concat(Stream.of(newTermCode), entries.get(key).children().stream().flatMap(this::expand));
+    }
+}
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNode.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNode.java
deleted file mode 100644
index bd8bfd3a..00000000
--- a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNode.java
+++ /dev/null
@@ -1,99 +0,0 @@
-package de.medizininformatikinitiative.flare.model.mapping;
-
-import com.fasterxml.jackson.annotation.JsonCreator;
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
-import de.medizininformatikinitiative.flare.model.sq.TermCode;
-
-import java.util.List;
-import java.util.stream.Stream;
-
-import static java.util.Objects.requireNonNull;
-
-/**
- * @author Alexander Kiel
- */
-@JsonIgnoreProperties(ignoreUnknown = true)
-public sealed interface TermCodeNode permits TermCodeNode.Abstract, TermCodeNode.Normal {
-
-    static TermCodeNode createAbstract(ContextualTermCode termCode, TermCodeNode... children) {
-        return new TermCodeNode.Abstract(termCode, children == null ? List.of() : List.of(children));
-    }
-
-    static TermCodeNode createNormal(ContextualTermCode termCode, TermCodeNode... children) {
-        return new TermCodeNode.Normal(termCode, children == null ? List.of() : List.of(children));
-    }
-
-    @JsonCreator
-    static TermCodeNode fromJson(@JsonProperty("context") TermCode context,
-                                 @JsonProperty("termCode") TermCode termCode,
-                                 @JsonProperty("abstract") boolean abstractJson,
-                                 @JsonProperty("children") TermCodeNode... children) {
-        var contextualTermCode = ContextualTermCode.of(requireNonNull(context, "missing JSON property: context"),
-                requireNonNull(termCode, "missing JSON property: termCode"));
-        return abstractJson
-                ? new Abstract(contextualTermCode, children == null ? List.of() : List.of(children))
-                : new Normal(contextualTermCode, children == null ? List.of() : List.of(children));
-    }
-
-    Stream<ContextualTermCode> expand(ContextualTermCode termCode);
-
-    Stream<ContextualTermCode> leafConcepts();
-
-    ContextualTermCode contextualTermCode();
-
-    List<TermCodeNode> children();
-
-    record Abstract(ContextualTermCode contextualTermCode, List<TermCodeNode> children) implements TermCodeNode {
-
-        public Abstract {
-            requireNonNull(contextualTermCode);
-            children = List.copyOf(children);
-        }
-
-        @Override
-        public Stream<ContextualTermCode> expand(ContextualTermCode termCode) {
-            if (requireNonNull(termCode).equals(this.contextualTermCode)) {
-                return leafConcepts();
-            } else if (children.isEmpty()) {
-                return Stream.of();
-            } else {
-                return children.stream().flatMap(n -> n.expand(termCode));
-            }
-        }
-
-        @Override
-        public Stream<ContextualTermCode> leafConcepts() {
-            return children.isEmpty() ? Stream.of() : children.stream().flatMap(TermCodeNode::leafConcepts);
-        }
-    }
-
-    record Normal(ContextualTermCode contextualTermCode, List<TermCodeNode> children) implements TermCodeNode {
-
-        public Normal {
-            requireNonNull(contextualTermCode);
-            children = List.copyOf(children);
-        }
-
-        @Override
-        public Stream<ContextualTermCode> expand(ContextualTermCode termCode) {
-            if (requireNonNull(termCode).equals(this.contextualTermCode)) {
-                return leafConcepts();
-            } else if (children.isEmpty()) {
-                return Stream.of();
-            } else {
-                return children.stream().flatMap(n -> n.expand(termCode));
-            }
-        }
-
-        @Override
-        public Stream<ContextualTermCode> leafConcepts() {
-            if (children.isEmpty()) {
-                return Stream.of(contextualTermCode);
-            } else {
-                return Stream.concat(Stream.of(contextualTermCode), children.stream().flatMap(TermCodeNode::leafConcepts));
-            }
-        }
-    }
-}
diff --git a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
index 237af6a1..035c6235 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/service/StructuredQueryService.java
@@ -15,8 +15,6 @@
 import reactor.core.publisher.Flux;
 import reactor.core.publisher.Mono;
 
-import java.util.Set;
-
 import static de.medizininformatikinitiative.flare.model.translate.Operator.Name.UNION;
 import static java.util.Objects.requireNonNull;
 
diff --git a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
index c858f8c3..745111c7 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
@@ -5,6 +5,7 @@
 import de.medizininformatikinitiative.flare.model.sq.TermCode;
 import org.junit.jupiter.api.Test;
 
+import java.util.List;
 import java.util.Map;
 
 import static de.medizininformatikinitiative.flare.Assertions.assertThat;
@@ -13,36 +14,45 @@
 class MappingContextTest {
 
     static final TermCode CONTEXT = TermCode.of("context", "context", "context");
+    static final String SYSTEM = "sys";
     static final ContextualTermCode ROOT = ContextualTermCode.of(CONTEXT, TermCode.of("root", "root", "root"));
-    static final ContextualTermCode C1 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c1", "c1"));
-    static final ContextualTermCode C11 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c11", "c11"));
-    static final ContextualTermCode C12 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c12", "c12"));
+    static final String C1 = "c1";
+    static final String C2 = "c2";
+
+    private ContextualTermCode contextualTermCodeOf(String code) {
+        return new ContextualTermCode(MappingContextTest.CONTEXT, new TermCode(MappingContextTest.SYSTEM, code, "display"));
+    }
 
     @Test
     void expandConcept_ConceptNotExpandable() {
-        var context = MappingContext.of(Map.of(), TermCodeNode.createNormal(ROOT));
+        var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of()))));
 
-        var result = context.expandConcept(ContextualConcept.of(C1));
+        var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
         assertThat(result).isLeftInstanceOf(ContextualConceptNotExpandableException.class);
     }
 
     @Test
     void expandConcept_OneConcept() {
-        var context = MappingContext.of(Map.of(), TermCodeNode.createNormal(ROOT, TermCodeNode.createNormal(C1)));
+        var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of(C1, new MappingTreeModuleEntry(C1, List.of()))))));
 
-        var result = context.expandConcept(ContextualConcept.of(C1));
+        var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
-        assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(C1));
+        assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(contextualTermCodeOf(C1)));
     }
 
     @Test
     void expandConcept_TwoConcepts() {
-        var context = MappingContext.of(Map.of(), TermCodeNode.createAbstract(C1, TermCodeNode.createNormal(C11),
-                TermCodeNode.createNormal(C12)));
+        var context = MappingContext.of(Map.of(), new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT, SYSTEM, Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2)),
+                        C2, new MappingTreeModuleEntry(C2, List.of()))))));
 
-        var result = context.expandConcept(ContextualConcept.of(C1));
+        var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
-        assertThat(result).isRightSatisfying(r -> assertThat(r).containsExactly(C11, C12));
+        assertThat(result).isRightSatisfying(r -> {
+            assertThat(r.get(0)).isEqualTo(contextualTermCodeOf(C1));
+            assertThat(r.get(1)).isEqualTo(contextualTermCodeOf(C2));
+        });
     }
 }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
new file mode 100644
index 00000000..b47c0b2d
--- /dev/null
+++ b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
@@ -0,0 +1,289 @@
+package de.medizininformatikinitiative.flare.model.mapping;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
+import de.medizininformatikinitiative.flare.model.sq.TermCode;
+import org.junit.jupiter.api.Test;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
+
+class MappingTreeBaseTest {
+
+    static final TermCode CONTEXT_1 = TermCode.of("context1", "context1", "context1");
+    static final TermCode CONTEXT_2 = TermCode.of("context2", "context2", "context2");
+    static final String SYSTEM_1 = "sys1";
+    static final String SYSTEM_2 = "sys2";
+    static final String C1 = "c1";
+    static final String C2 = "c2";
+    static final String C3 = "c3";
+    static final String C4 = "c4";
+    static final String C5 = "c5";
+
+
+    private ContextualTermCode contextualTermCodeOf(TermCode context, String system, String code) {
+        return new ContextualTermCode(context, new TermCode(system, code, "display"));
+    }
+
+    @Test
+    void expand_empty() {
+        var base = new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1, Map.of())));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).isEmpty();
+    }
+
+    @Test
+    void expand_noMatch_differentCode() {
+        var base = new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                Map.of(C1, new MappingTreeModuleEntry(C1, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2)).toList();
+
+        assertThat(result).isEmpty();
+    }
+
+    @Test
+    void expand_noMatch_differentContext() {
+        var base = new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                Map.of(C1, new MappingTreeModuleEntry(C1, List.of())))));
+
+        var result = base.expand(
+                        contextualTermCodeOf(new TermCode("", "different-context", ""), SYSTEM_1, C2))
+                .toList();
+
+        assertThat(result).isEmpty();
+    }
+
+    @Test
+    void expand_noMatch_differentSystem() {
+        var base = new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                Map.of(C1, new MappingTreeModuleEntry(C1, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, "system2", C2)).toList();
+
+        assertThat(result).isEmpty();
+    }
+
+    @Test
+    void expand_oneModule_twoEntries_withoutChildren() {
+        var base = new MappingTreeBase(List.of(new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                Map.of(C1, new MappingTreeModuleEntry(C1, List.of()),
+                        C2, new MappingTreeModuleEntry(C2, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1));
+    }
+
+    @Test
+    void expand_twoModules_sameContext_differentSystem_withoutChildren() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of()),
+                                C2, new MappingTreeModuleEntry(C2, List.of()))),
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_2,
+                        Map.of(C3, new MappingTreeModuleEntry(C3, List.of()),
+                                C4, new MappingTreeModuleEntry(C4, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2));
+    }
+
+    @Test
+    void expand_twoModules_sameSystem_differentContext_withoutChildren() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of()),
+                                C2, new MappingTreeModuleEntry(C2, List.of()))),
+                new MappingTreeModuleRoot(CONTEXT_2, SYSTEM_1,
+                        Map.of(C3, new MappingTreeModuleEntry(C3, List.of()),
+                                C4, new MappingTreeModuleEntry(C4, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2));
+    }
+
+    @Test
+    void expand_oneChild_withNoReference() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2))))));
+
+        assertThatThrownBy(() -> base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList())
+                .isInstanceOf(NullPointerException.class);
+    }
+
+    @Test
+    void expand_oneChild_onFirstLayer() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2)),
+                                C2, new MappingTreeModuleEntry(C2, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2));
+    }
+
+    @Test
+    void expand_twoChildren_onFirstLayer() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2, C3)),
+                                C2, new MappingTreeModuleEntry(C2, List.of()),
+                                C3, new MappingTreeModuleEntry(C3, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C3));
+    }
+
+    @Test
+    void expand_twoChildren_onFirstAndSecondLayer() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2, C3)),
+                                C2, new MappingTreeModuleEntry(C2, List.of(C4)),
+                                C3, new MappingTreeModuleEntry(C3, List.of(C5)),
+                                C4, new MappingTreeModuleEntry(C4, List.of()),
+                                C5, new MappingTreeModuleEntry(C5, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C3),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C4),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C5));
+    }
+
+    @Test
+    void expand_oneChild_onThreeLayers() {
+        var base = new MappingTreeBase(List.of(
+                new MappingTreeModuleRoot(CONTEXT_1, SYSTEM_1,
+                        Map.of(C1, new MappingTreeModuleEntry(C1, List.of(C2)),
+                                C2, new MappingTreeModuleEntry(C2, List.of(C3)),
+                                C3, new MappingTreeModuleEntry(C3, List.of(C4, C5)),
+                                C4, new MappingTreeModuleEntry(C4, List.of()),
+                                C5, new MappingTreeModuleEntry(C5, List.of())))));
+
+        var result = base.expand(contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1)).toList();
+
+        assertThat(result).containsExactlyInAnyOrder(
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C1),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C2),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C3),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C4),
+                contextualTermCodeOf(CONTEXT_1, SYSTEM_1, C5));
+    }
+
+    @Test
+    void fromJson() throws Exception {
+        var base = parse("""
+                [
+                  {
+                    "entries": [
+                      {
+                        "key": "C1",
+                        "parents": [],
+                        "children": []
+                      }
+                    ],
+                    "context": {
+                      "system": "sys1",
+                      "code": "code1",
+                      "display": "display"
+                    },
+                    "system": "module-system"
+                  }
+                ]
+                """);
+
+        assertThat(base.moduleRoots().get(0).context())
+                .isEqualTo(new TermCode("sys1", "code1", "display"));
+        assertThat(base.moduleRoots().get(0).system()).isEqualTo("module-system");
+        assertThat(base.moduleRoots().get(0).entries().get("C1")).isNotNull();
+    }
+
+    @Test
+    void fromJson_AdditionalPropertyIsIgnored() throws Exception {
+        var base = parse("""
+                [
+                  {
+                    "foo-133831": "bar-133841",
+                    "entries": [
+                      {
+                        "key": "C1",
+                        "parents": [],
+                        "children": []
+                      }
+                    ],
+                    "context": {
+                      "system": "sys1",
+                      "code": "code1",
+                      "display": "display"
+                    },
+                    "system": "module-system"
+                  }
+                ]
+                """);
+
+        assertThat(base.moduleRoots().get(0).context())
+                .isEqualTo(new TermCode("sys1", "code1", "display"));
+        assertThat(base.moduleRoots().get(0).system()).isEqualTo("module-system");
+        assertThat(base.moduleRoots().get(0).entries().get("C1")).isNotNull();
+    }
+
+    @Test
+    void fromJson_withChildren() throws Exception {
+        var base = parse("""
+                [
+                  {
+                    "entries": [
+                      {
+                        "key": "C1",
+                        "parents": [],
+                        "children": ["C2"]
+                      },
+                      {
+                        "key": "C2",
+                        "parents": [],
+                        "children": []
+                      }
+                    ],
+                    "context": {
+                      "system": "sys1",
+                      "code": "code1",
+                      "display": "display"
+                    },
+                    "system": "module-system"
+                  }
+                ]
+                """);
+
+        assertThat(base.moduleRoots().get(0).context())
+                .isEqualTo(new TermCode("sys1", "code1", "display"));
+        assertThat(base.moduleRoots().get(0).system()).isEqualTo("module-system");
+        assertThat(base.moduleRoots().get(0).entries().get("C1").children()).containsExactly("C2");
+        assertThat(base.moduleRoots().get(0).entries().get("C2")).isNotNull();
+    }
+
+    static MappingTreeBase parse(String s) throws JsonProcessingException {
+        return new MappingTreeBase(Arrays.stream(new ObjectMapper().readValue(s, MappingTreeModuleRoot[].class)).toList());
+    }
+}
diff --git a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNodeTest.java b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNodeTest.java
deleted file mode 100644
index 389eab9e..00000000
--- a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/TermCodeNodeTest.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package de.medizininformatikinitiative.flare.model.mapping;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import de.medizininformatikinitiative.flare.model.sq.ContextualTermCode;
-import de.medizininformatikinitiative.flare.model.sq.TermCode;
-import org.junit.jupiter.api.Test;
-
-import static org.assertj.core.api.Assertions.assertThat;
-
-class TermCodeNodeTest {
-
-    static final TermCode CONTEXT = TermCode.of("context", "context", "context");
-    static final ContextualTermCode ROOT = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "root", "root"));
-    static final ContextualTermCode C1 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c1", "c1"));
-    static final ContextualTermCode C2 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c2", "c2"));
-    static final ContextualTermCode C11 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c11", "c11"));
-    static final ContextualTermCode C12 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c12", "c12"));
-    static final ContextualTermCode C111 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c111", "c111"));
-    static final ContextualTermCode C112 = ContextualTermCode.of(CONTEXT, TermCode.of("foo", "c112", "c112"));
-
-    @Test
-    void noChildren() {
-        var node = TermCodeNode.createNormal(ROOT);
-
-        assertThat(node.children()).isEmpty();
-    }
-
-    @Test
-    void expand_notFound() {
-        var node = TermCodeNode.createNormal(ROOT);
-
-        var result = node.expand(C1).toList();
-
-        assertThat(result).isEmpty();
-    }
-
-    @Test
-    void expand_itSelf_asLeaf() {
-        var node = TermCodeNode.createNormal(ROOT);
-
-        var result = node.expand(ROOT).toList();
-
-        assertThat(result).containsExactly(ROOT);
-    }
-
-    @Test
-    void expand_itSelf_withChildren_abstract() {
-        var node = TermCodeNode.createAbstract(ROOT, TermCodeNode.createNormal(C1), TermCodeNode.createNormal(C2));
-
-        var result = node.expand(ROOT).toList();
-
-        assertThat(result).containsExactly(C1, C2);
-    }
-
-    @Test
-    void expand_itSelf_withChildren_normal() {
-        var node = TermCodeNode.createNormal(ROOT, TermCodeNode.createNormal(C1), TermCodeNode.createNormal(C2));
-
-        var result = node.expand(ROOT).toList();
-
-        assertThat(result).containsExactly(ROOT, C1, C2);
-    }
-
-    @Test
-    void expand_child_withChildren() {
-        var c1 = TermCodeNode.createNormal(C1, TermCodeNode.createNormal(C11), TermCodeNode.createNormal(C12));
-        var node = TermCodeNode.createNormal(ROOT, c1, TermCodeNode.createNormal(C2));
-
-        var result = node.expand(C1).toList();
-
-        assertThat(result).containsExactly(C1, C11, C12);
-    }
-
-    @Test
-    void expand_child_deep() {
-        var c11 = TermCodeNode.createNormal(C11, TermCodeNode.createNormal(C111), TermCodeNode.createNormal(C112));
-        var c1 = TermCodeNode.createNormal(C1, c11, TermCodeNode.createNormal(C12));
-        var node = TermCodeNode.createNormal(ROOT, c1, TermCodeNode.createNormal(C2));
-
-        var result = node.expand(C1).toList();
-
-        assertThat(result).containsOnly(C1, C11, C12, C111, C112);
-    }
-
-    @Test
-    void fromJson() throws Exception {
-        var conceptNode = parse("""
-                {
-                  "context": {
-                    "system": "context-system-142748",
-                    "code": "context-code-142803",
-                    "display": "context-display-142810"
-                  },
-                  "termCode": {
-                    "system": "system-143705",
-                    "code": "code-143708",
-                    "display": "display-143716"
-                  },
-                  "children": []
-                }
-                """);
-
-        assertThat(conceptNode.contextualTermCode())
-                .isEqualTo(ContextualTermCode.of(
-                        TermCode.of("context-system-142748", "context-code-142803", "context-display-142810"),
-                        TermCode.of("system-143705", "code-143708", "display-143716")));
-    }
-
-    @Test
-    void fromJson_AdditionalPropertyIsIgnored() throws Exception {
-        var conceptNode = parse("""
-                {
-                  "foo-152133": "bar-152136",
-                  "context": {
-                    "system": "context-system-142748",
-                    "code": "context-code-142803",
-                    "display": "context-display-142810"
-                  },
-                  "termCode": {
-                    "system": "system-143705",
-                    "code": "code-143708",
-                    "display": "display-143716"
-                  },
-                  "children": []
-                }
-                """);
-
-        assertThat(conceptNode.contextualTermCode().context().system()).isEqualTo("context-system-142748");
-    }
-
-    @Test
-    void fromJson_WithChildren() throws Exception {
-        var conceptNode = parse("""
-                {
-                   "context": {
-                     "system": "parent-context-system",
-                     "code": "parent-context-code",
-                     "display": "parent-context-display"
-                   },
-                   "termCode": {
-                     "system": "parent-system",
-                     "code": "parent-code",
-                     "display": "parent-display"
-                   },
-                   "children": [
-                     {
-                       "context": {
-                         "system": "child-1-context-system",
-                         "code": "child-1-context-code",
-                         "display": "child-1-context-display"
-                       },
-                       "termCode": {
-                         "system": "child-1-system",
-                         "code": "child-1-code",
-                         "display": "child-1-display"
-                       }
-                     },
-                     {
-                       "context": {
-                         "system": "child-2-context-system",
-                         "code": "child-2-context-code",
-                         "display": "child-2-context-display"
-                       },
-                       "termCode": {
-                         "system": "child-2-system",
-                         "code": "child-2-code",
-                         "display": "child-2-display"
-                       }
-                     }
-                   ]
-                 }
-                """);
-
-        assertThat(conceptNode.contextualTermCode())
-                .isEqualTo(ContextualTermCode.of(
-                        TermCode.of("parent-context-system", "parent-context-code", "parent-context-display"),
-                        TermCode.of("parent-system", "parent-code", "parent-display")));
-        assertThat(conceptNode.children().get(0).contextualTermCode())
-                .isEqualTo(ContextualTermCode.of(
-                        TermCode.of("child-1-context-system", "child-1-context-code", "child-1-context-display"),
-                        TermCode.of("child-1-system", "child-1-code", "child-1-display")));
-        assertThat(conceptNode.children().get(1).contextualTermCode())
-                .isEqualTo(ContextualTermCode.of(
-                        TermCode.of("child-2-context-system", "child-2-context-code", "child-2-context-display"),
-                        TermCode.of("child-2-system", "child-2-code", "child-2-display")));
-    }
-
-    static TermCodeNode parse(String s) throws JsonProcessingException {
-        return new ObjectMapper().readValue(s, TermCodeNode.class);
-    }
-}
diff --git a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
index 6ccedb75..1268ea7c 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
@@ -20,7 +20,6 @@
 import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper;
 import reactor.core.publisher.Mono;
 
-import java.util.Arrays;
 import java.util.List;
 
 import static org.mockito.Mockito.when;
@@ -86,7 +85,7 @@ void execute() {
 
     @Test
     void executeCohort() throws JsonProcessingException {
-        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID,PATIENT_ID_1)));
+        when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID, PATIENT_ID_1)));
 
         ObjectMapper objectMapper = new ObjectMapper();
 
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
index d7d83385..5347e3e9 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
@@ -7,7 +7,8 @@
 import de.medizininformatikinitiative.flare.model.Population;
 import de.medizininformatikinitiative.flare.model.mapping.Mapping;
 import de.medizininformatikinitiative.flare.model.mapping.MappingContext;
-import de.medizininformatikinitiative.flare.model.mapping.TermCodeNode;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeBase;
+import de.medizininformatikinitiative.flare.model.mapping.MappingTreeModuleRoot;
 import de.medizininformatikinitiative.flare.model.sq.*;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -43,7 +44,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static java.util.function.Function.identity;
+import static java.util.function.UnaryOperator.identity;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.springframework.http.MediaType.APPLICATION_JSON;
 
@@ -98,7 +99,7 @@ private static Path resourcePathFlareApplication(String name) throws URISyntaxEx
         return Paths.get(Objects.requireNonNull(FlareApplication.class.getResource(name)).toURI());
     }
 
-    private int getExecutionResult(StructuredQuery query){
+    private int getExecutionResult(StructuredQuery query) {
         return service.execute(query).block().size();
     }
 
@@ -255,7 +256,7 @@ public MappingContext mappingContext_BloodPressure() throws Exception {
             var mapper = new ObjectMapper();
             var mappings = Arrays.stream(mapper.readValue(slurpStructuredQueryService("compositeSearchParams/mapping-bloodPressure.json"), Mapping[].class))
                     .collect(Collectors.toMap(Mapping::key, identity()));
-            var conceptTree = mapper.readValue(slurpStructuredQueryService("compositeSearchParams/tree-bloodPressure.json"), TermCodeNode.class);
+            var conceptTree = new MappingTreeBase(Arrays.stream(mapper.readValue(slurpStructuredQueryService("compositeSearchParams/tree-bloodPressure.json"), MappingTreeModuleRoot[].class)).toList());
             return MappingContext.of(mappings, conceptTree, CLOCK_2000);
         }
 
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index cfca0fb7..e3fa3e45 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -25,7 +25,6 @@
 import static de.medizininformatikinitiative.flare.Assertions.assertThat;
 import static de.medizininformatikinitiative.flare.model.fhir.QueryParams.conceptValue;
 import static de.medizininformatikinitiative.flare.model.sq.TestUtil.*;
-import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.when;
 
 @SuppressWarnings("SameParameterValue")
diff --git a/src/test/resources/de/medizininformatikinitiative/flare/service/compositeSearchParams/tree-bloodPressure.json b/src/test/resources/de/medizininformatikinitiative/flare/service/compositeSearchParams/tree-bloodPressure.json
index f377bcdc..284cda92 100644
--- a/src/test/resources/de/medizininformatikinitiative/flare/service/compositeSearchParams/tree-bloodPressure.json
+++ b/src/test/resources/de/medizininformatikinitiative/flare/service/compositeSearchParams/tree-bloodPressure.json
@@ -1,13 +1,18 @@
-{
-  "context": {
-    "code": "Laboruntersuchung",
-    "display": "Laboruntersuchung",
-    "system": "fdpg.mii.cds",
-    "version": "1.0.0"
-  },
-  "termCode": {
-    "code": "85354-9",
-    "display": "Blood pressure panel with all children optional",
+[
+  {
+    "entries": [
+      {
+        "key": "85354-9",
+        "parents": [],
+        "children": []
+      }
+    ],
+    "context": {
+      "code": "Laboruntersuchung",
+      "display": "Laboruntersuchung",
+      "system": "fdpg.mii.cds",
+      "version": "1.0.0"
+    },
     "system": "http://loinc.org"
   }
-}
+]
diff --git a/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json b/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
index 6f0a3e20..a00889b2 100644
--- a/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
+++ b/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
@@ -1 +1,32 @@
-{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "424144002", "display": "Current chronological age (observable entity)", "system": "http://snomed.info/sct"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "a", "display": "a"}, "value": 9}, "context": {"code": "Patient", "display": "Patient", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}
+{
+  "inclusionCriteria": [
+    [
+      {
+        "attributeFilters": [],
+        "termCodes": [
+          {
+            "code": "424144002",
+            "display": "Current chronological age (observable entity)",
+            "system": "http://snomed.info/sct"
+          }
+        ],
+        "valueFilter": {
+          "comparator": "eq",
+          "type": "quantity-comparator",
+          "unit": {
+            "code": "a",
+            "display": "a"
+          },
+          "value": 9
+        },
+        "context": {
+          "code": "Patient",
+          "display": "Patient",
+          "system": "fdpg.mii.cds",
+          "version": "1.0.0"
+        }
+      }
+    ]
+  ],
+  "version": "http://to_be_decided.com/draft-1/schema#"
+}

From 8c295af057ac1eea7ddad0bf786046001aadf95b Mon Sep 17 00:00:00 2001
From: Alexander Kiel <alexanderkiel@gmx.net>
Date: Tue, 3 Sep 2024 13:31:34 +0200
Subject: [PATCH 09/43] Minor Improvements of Update Mapping Tree

* moved isModuleMatching method into MappingTreeModuleRoot class
* improve assert in MappingContextTest.expandConcept_TwoConcepts
* made some method static
* updated Blaze to v0.29
* use StepVerifier instead of blocking on Mono
* reverted formatting on 1-age.json
---
 .../basic-auth/docker-compose.yml             |  2 +-
 .../no-auth/docker-compose.yml                |  2 +-
 .../integration-test/oauth/docker-compose.yml |  2 +-
 docker-compose.yml                            |  2 +-
 .../flare/model/mapping/MappingTreeBase.java  |  8 +----
 .../model/mapping/MappingTreeModuleRoot.java  |  6 ++++
 .../model/mapping/MappingContextTest.java     |  9 ++---
 .../model/mapping/MappingTreeBaseTest.java    |  3 +-
 .../flare/service/DataStoreIT.java            |  2 +-
 .../service/StructuredQueryServiceIT.java     | 22 +++++--------
 .../testCases/returningOnePatient/1-age.json  | 33 +------------------
 11 files changed, 25 insertions(+), 66 deletions(-)

diff --git a/.github/integration-test/basic-auth/docker-compose.yml b/.github/integration-test/basic-auth/docker-compose.yml
index 2a9b7eaf..85b441f1 100644
--- a/.github/integration-test/basic-auth/docker-compose.yml
+++ b/.github/integration-test/basic-auth/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.29"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/.github/integration-test/no-auth/docker-compose.yml b/.github/integration-test/no-auth/docker-compose.yml
index 0ed3af12..d6495841 100644
--- a/.github/integration-test/no-auth/docker-compose.yml
+++ b/.github/integration-test/no-auth/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.29"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index eae28a4a..0fe92965 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -72,7 +72,7 @@ services:
       keycloak:
         condition: service_healthy
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.29"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/docker-compose.yml b/docker-compose.yml
index 32dbf096..90ebf5f3 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.29"
     environment:
       BASE_URL: "http://localhost:8082"
       JAVA_TOOL_OPTIONS: "-Xmx1g"
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
index a96ac4d6..bc4ecd7d 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBase.java
@@ -11,12 +11,6 @@ public Stream<ContextualTermCode> expand(ContextualTermCode termCode) {
         var key = termCode.termCode().code();
 
         return moduleRoots.stream().flatMap(moduleRoot ->
-                isModuleMatching(termCode, moduleRoot) ? moduleRoot.expand(key) : Stream.empty());
-    }
-
-    private boolean isModuleMatching(ContextualTermCode termCode, MappingTreeModuleRoot moduleRoot) {
-        return termCode.context().equals(moduleRoot.context()) &&
-                moduleRoot.system().equals(termCode.termCode().system()) &&
-                moduleRoot.entries().containsKey(termCode.termCode().code());
+                moduleRoot.isModuleMatching(termCode) ? moduleRoot.expand(key) : Stream.empty());
     }
 }
diff --git a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
index 68a6c6aa..5ce27256 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeModuleRoot.java
@@ -31,4 +31,10 @@ public Stream<ContextualTermCode> expand(String key) {
 
         return Stream.concat(Stream.of(newTermCode), entries.get(key).children().stream().flatMap(this::expand));
     }
+
+    boolean isModuleMatching(ContextualTermCode contextualTermCode) {
+        return context.equals(contextualTermCode.context()) &&
+                system.equals(contextualTermCode.termCode().system()) &&
+                entries.containsKey(contextualTermCode.termCode().code());
+    }
 }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
index 745111c7..304aceee 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingContextTest.java
@@ -15,11 +15,10 @@ class MappingContextTest {
 
     static final TermCode CONTEXT = TermCode.of("context", "context", "context");
     static final String SYSTEM = "sys";
-    static final ContextualTermCode ROOT = ContextualTermCode.of(CONTEXT, TermCode.of("root", "root", "root"));
     static final String C1 = "c1";
     static final String C2 = "c2";
 
-    private ContextualTermCode contextualTermCodeOf(String code) {
+    private static ContextualTermCode contextualTermCodeOf(String code) {
         return new ContextualTermCode(MappingContextTest.CONTEXT, new TermCode(MappingContextTest.SYSTEM, code, "display"));
     }
 
@@ -50,9 +49,7 @@ void expandConcept_TwoConcepts() {
 
         var result = context.expandConcept(ContextualConcept.of(contextualTermCodeOf(C1)));
 
-        assertThat(result).isRightSatisfying(r -> {
-            assertThat(r.get(0)).isEqualTo(contextualTermCodeOf(C1));
-            assertThat(r.get(1)).isEqualTo(contextualTermCodeOf(C2));
-        });
+        assertThat(result).isRightSatisfying(r ->
+                assertThat(r).containsExactly(contextualTermCodeOf(C1), contextualTermCodeOf(C2)));
     }
 }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
index b47c0b2d..0c58c3ca 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/model/mapping/MappingTreeBaseTest.java
@@ -25,8 +25,7 @@ class MappingTreeBaseTest {
     static final String C4 = "c4";
     static final String C5 = "c5";
 
-
-    private ContextualTermCode contextualTermCodeOf(TermCode context, String system, String code) {
+    private static ContextualTermCode contextualTermCodeOf(TermCode context, String system, String code) {
         return new ContextualTermCode(context, new TermCode(system, code, "display"));
     }
 
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreIT.java
index ed58cd70..98f2e1aa 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreIT.java
@@ -35,7 +35,7 @@ class DataStoreIT {
 
     @Container
     @SuppressWarnings("resource")
-    private final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.28")
+    private final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.29")
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withExposedPorts(8080)
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
index 5347e3e9..c5b0ead9 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java
@@ -44,8 +44,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static java.util.function.UnaryOperator.identity;
-import static org.assertj.core.api.Assertions.assertThat;
+import static java.util.function.Function.identity;
 import static org.springframework.http.MediaType.APPLICATION_JSON;
 
 @Testcontainers
@@ -54,16 +53,13 @@ class StructuredQueryServiceIT {
 
     private static final Clock CLOCK_2000 = Clock.fixed(LocalDate.of(2000, 1, 1).atStartOfDay().toInstant(ZoneOffset.UTC), ZoneOffset.UTC);
     private static final TermCode I08 = TermCode.of("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "I08", "");
-    private static final TermCode COVID = TermCode.of("http://loinc.org", "94500-6", "");
-    private static final TermCode INVALID = TermCode.of("http://loinc.org", "LA15841-2", "Invalid");
     private static final TermCode DIAGNOSIS = TermCode.of("fdpg.mii.cds", "Diagnose", "Diagnose");
-    private static final TermCode OBSERVATION = TermCode.of("fdpg.mii.cds", "Laboruntersuchung", "Laboruntersuchung");
 
     private static final Logger logger = LoggerFactory.getLogger(StructuredQueryServiceIT.class);
 
     @Container
     @SuppressWarnings("resource")
-    private static final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.28")
+    private static final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.29")
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withEnv("DB_SEARCH_PARAM_BUNDLE", "/app/custom-search-parameters.json")
@@ -99,10 +95,6 @@ private static Path resourcePathFlareApplication(String name) throws URISyntaxEx
         return Paths.get(Objects.requireNonNull(FlareApplication.class.getResource(name)).toURI());
     }
 
-    private int getExecutionResult(StructuredQuery query) {
-        return service.execute(query).block().size();
-    }
-
     public static List<StructuredQuery> getTestQueriesReturningOnePatient() throws URISyntaxException, IOException {
         Path directoryPath = Paths.get(resourcePathFlareApplication("testCases").resolve("returningOnePatient").toString());
 
@@ -139,15 +131,17 @@ void execute_Criterion() {
         var query = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(Criterion.of(ContextualConcept.of(DIAGNOSIS, Concept.of(I08))))));
 
         var result = service.execute(query);
+
         StepVerifier.create(result).expectNext(Population.of("id-pat-diag-I08.0")).verifyComplete();
     }
 
     @Test
     void execute_genderTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("2-gender.json")));
-        var result = getExecutionResult(query);
 
-        assertThat(result).isEqualTo(172);
+        var result = service.execute(query);
+
+        StepVerifier.create(result).expectNextMatches(p -> p.size() == 172).verifyComplete();
     }
 
     @Test
@@ -179,9 +173,9 @@ void execute_specimenTestCase() throws IOException, URISyntaxException {
     @ParameterizedTest
     @MethodSource("getTestQueriesReturningOnePatient")
     void execute_casesReturningOne(StructuredQuery query) {
-        var result = getExecutionResult(query);
+        var result = service.execute(query);
 
-        assertThat(result).isOne();
+        StepVerifier.create(result).expectNextMatches(p -> p.size() == 1).verifyComplete();
     }
 
     @Test
diff --git a/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json b/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
index a00889b2..6f0a3e20 100644
--- a/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
+++ b/src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json
@@ -1,32 +1 @@
-{
-  "inclusionCriteria": [
-    [
-      {
-        "attributeFilters": [],
-        "termCodes": [
-          {
-            "code": "424144002",
-            "display": "Current chronological age (observable entity)",
-            "system": "http://snomed.info/sct"
-          }
-        ],
-        "valueFilter": {
-          "comparator": "eq",
-          "type": "quantity-comparator",
-          "unit": {
-            "code": "a",
-            "display": "a"
-          },
-          "value": 9
-        },
-        "context": {
-          "code": "Patient",
-          "display": "Patient",
-          "system": "fdpg.mii.cds",
-          "version": "1.0.0"
-        }
-      }
-    ]
-  ],
-  "version": "http://to_be_decided.com/draft-1/schema#"
-}
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "424144002", "display": "Current chronological age (observable entity)", "system": "http://snomed.info/sct"}], "valueFilter": {"comparator": "eq", "type": "quantity-comparator", "unit": {"code": "a", "display": "a"}, "value": 9}, "context": {"code": "Patient", "display": "Patient", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

From 2227ef2201376e822b4308969fc7eca7ba636786 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 11:56:29 +0000
Subject: [PATCH 10/43] Update testcontainers-java monorepo to v1.20.1

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index c78ce822..cbba99f1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,7 +20,7 @@
 
   <properties>
     <java.version>17</java.version>
-    <testcontainers.version>1.19.8</testcontainers.version>
+    <testcontainers.version>1.20.1</testcontainers.version>
     <ontology.version>3.0.0-test.1</ontology.version>
   </properties>
 

From 4e496041043d9adf1b745db08f7fe97428c415ef Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 13:00:50 +0000
Subject: [PATCH 11/43] Update keycloak/keycloak Docker tag to v25.0.4

---
 .github/integration-test/oauth/docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index 0fe92965..dbbe5db4 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -29,7 +29,7 @@ services:
       generate-cert:
         condition: service_completed_successfully
   keycloak:
-    image: "keycloak/keycloak:25.0.1"
+    image: "keycloak/keycloak:25.0.4"
     command: ["start", "--import-realm"]
     healthcheck:
       test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/9000;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]

From b0418e8a25948a3cb136821cc80353902505a1f4 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 13:16:19 +0000
Subject: [PATCH 12/43] Update dependency org.rocksdb:rocksdbjni to v9.5.2

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index cbba99f1..048243ef 100644
--- a/pom.xml
+++ b/pom.xml
@@ -61,7 +61,7 @@
     <dependency>
       <groupId>org.rocksdb</groupId>
       <artifactId>rocksdbjni</artifactId>
-      <version>9.2.1</version>
+      <version>9.5.2</version>
     </dependency>
 
     <dependency>

From fe7d5877de8d2956c33ee039da30701016e78966 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 13:28:21 +0000
Subject: [PATCH 13/43] Update dependency
 org.springframework.boot:spring-boot-starter-parent to v3.3.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 048243ef..feac6a9a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.1</version>
+    <version>3.3.3</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 

From 4aa255fdab901e751f15e33378eb72cea69c67c4 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 13:41:28 +0000
Subject: [PATCH 14/43] Update dependency maven to v3.9.9

---
 .mvn/wrapper/maven-wrapper.properties | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties
index f95f1ee8..d58dfb70 100644
--- a/.mvn/wrapper/maven-wrapper.properties
+++ b/.mvn/wrapper/maven-wrapper.properties
@@ -16,4 +16,4 @@
 # under the License.
 wrapperVersion=3.3.2
 distributionType=only-script
-distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.8/apache-maven-3.9.8-bin.zip
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.9/apache-maven-3.9.9-bin.zip

From 6b93f2031edd048435d0a73d7f85adf62bb70a32 Mon Sep 17 00:00:00 2001
From: Bastian Schaffer <bastianschaffer.it@gmail.com>
Date: Tue, 3 Sep 2024 15:13:39 +0200
Subject: [PATCH 15/43] Change Docker Compose

Fixes: #184

Also updated README
---
 README.md          | 46 ++++++++++++++++++++++++----------------------
 docker-compose.yml | 36 +++++++++++++++++++++++++++---------
 2 files changed, 51 insertions(+), 31 deletions(-)

diff --git a/README.md b/README.md
index 43d3dfa2..825fdfa3 100644
--- a/README.md
+++ b/README.md
@@ -34,28 +34,30 @@ docker run -p 8080:8080 ghcr.io/medizininformatik-initiative/flare:2.3
 
 ## Environment Variables
 
-| Name                              | Default                               | Description                                                                                      |
-|:----------------------------------|:--------------------------------------|:-------------------------------------------------------------------------------------------------|
-| FLARE_FHIR_SERVER                 | http://localhost:8082/fhir            | The base URL of the FHIR server to use.                                                          |
-| FLARE_FHIR_USER                   |                                       | The username to use for HTTP Basic Authentication.                                               |
-| FLARE_FHIR_PASSWORD               |                                       | The password to use for HTTP Basic Authentication.                                               |
-| FLARE_FHIR_OAUTH_ISSUER_URI       |                                       | The issuer URI of the OpenID Connect provider.                                                   |
-| FLARE_FHIR_OAUTH_CLIENT_ID        |                                       | The client ID to use for authentication with OpenID Connect provider.                            |
-| FLARE_FHIR_OAUTH_CLIENT_SECRET    |                                       | The client secret to use for authentication with OpenID Connect provider.                        |
-| FLARE_FHIR_MAX_CONNECTIONS        | 4                                     | The maximum number of connections Flare opens towards the FHIR server.                           |
-| FLARE_FHIR_MAX_QUEUE_SIZE         | 500                                   | The maximum number FHIR server requests Flare queues before returning an error.                  |
-| FLARE_FHIR_PAGE_COUNT             | 1000                                  | The number of resources per page to request from the FHIR server.                                |
-| FLARE_CACHE_MEM_SIZE_MB           | 1024                                  | The size of the in-memory cache in mebibytes.                                                    |
-| FLARE_CACHE_MEM_EXPIRE            | PT48H                                 | The duration after which in-memory cache entries should expire in [ISO 8601 durations][1].       |
-| FLARE_CACHE_MEM_REFRESH           | PT24H                                 | The duration after which in-memory cache entries should be refreshed in [ISO 8601 durations][1]. |
-| FLARE_CACHE_DISK_PATH             | cache                                 | The name of the directory in which the on-disk cache should be written.                          |
-| FLARE_CACHE_DISK_EXPIRE           | P7D                                   | The duration after which on-disk cache entries should expire in [ISO 8601 durations][1].         |
-| FLARE_CACHE_DISK_THREADS          | 4                                     | The number of threads the disk cache should use for reading and writing entries.                 |
-| FLARE_MAPPING_MAPPING_FILE        | ontology/codex-term-code-mapping.json | The mappings to use.                                                                             |
-| FLARE_MAPPING_CONCEPT_TREE_FILE   | ontology/codex-code-tree.json         | The code tree to use.                                                                            |
-| SERVER_PORT                       | 8080                                  | The port at which Flare provides its REST API.                                                   |
-| JAVA_TOOL_OPTIONS                 | -Xmx4g                                | JVM options \(Docker only\)                                                                      |
-| LOG_LEVEL                         | info                                  | one of trace, debug, info, warn or error                                                         |
+| Name                            | Default                               | Depr ¹ | Description                                                                                      |
+|:--------------------------------|:--------------------------------------|--------|:-------------------------------------------------------------------------------------------------|
+| FLARE_FHIR_SERVER               | http://localhost:8082/fhir            |        | The base URL of the FHIR server to use.                                                          |
+| FLARE_FHIR_USER                 |                                       |        | The username to use for HTTP Basic Authentication.                                               |
+| FLARE_FHIR_PASSWORD             |                                       |        | The password to use for HTTP Basic Authentication.                                               |
+| FLARE_FHIR_OAUTH_ISSUER_URI     |                                       |        | The issuer URI of the OpenID Connect provider.                                                   |
+| FLARE_FHIR_OAUTH_CLIENT_ID      |                                       |        | The client ID to use for authentication with OpenID Connect provider.                            |
+| FLARE_FHIR_OAUTH_CLIENT_SECRET  |                                       |        | The client secret to use for authentication with OpenID Connect provider.                        |
+| FLARE_FHIR_MAX_CONNECTIONS      | 4                                     |        | The maximum number of connections Flare opens towards the FHIR server.                           |
+| FLARE_FHIR_MAX_QUEUE_SIZE       | 500                                   |        | The maximum number FHIR server requests Flare queues before returning an error.                  |
+| FLARE_FHIR_PAGE_COUNT           | 1000                                  |        | The number of resources per page to request from the FHIR server.                                |
+| FLARE_CACHE_MEM_SIZE_MB         | 1024                                  |        | The size of the in-memory cache in mebibytes.                                                    |
+| FLARE_CACHE_MEM_EXPIRE          | PT48H                                 |        | The duration after which in-memory cache entries should expire in [ISO 8601 durations][1].       |
+| FLARE_CACHE_MEM_REFRESH         | PT24H                                 |        | The duration after which in-memory cache entries should be refreshed in [ISO 8601 durations][1]. |
+| FLARE_CACHE_DISK_PATH           | cache                                 |        | The name of the directory in which the on-disk cache should be written.                          |
+| FLARE_CACHE_DISK_EXPIRE         | P7D                                   |        | The duration after which on-disk cache entries should expire in [ISO 8601 durations][1].         |
+| FLARE_CACHE_DISK_THREADS        | 4                                     |        | The number of threads the disk cache should use for reading and writing entries.                 |
+| FLARE_MAPPING_MAPPING_FILE      | ontology/codex-term-code-mapping.json | v2.4.0 | The mappings to use.                                                                             |
+| FLARE_MAPPING_CONCEPT_TREE_FILE | ontology/codex-code-tree.json         | v2.4.0 | The code tree to use.                                                                            |
+| SERVER_PORT                     | 8080                                  |        | The port at which Flare provides its REST API.                                                   |
+| JAVA_TOOL_OPTIONS               | -Xmx4g                                |        | JVM options \(Docker only\)                                                                      |
+| LOG_LEVEL                       | info                                  |        | one of trace, debug, info, warn or error                                                         |
+
+¹ Deprecated since
 
 ## Default Configuration
 
diff --git a/docker-compose.yml b/docker-compose.yml
index 90ebf5f3..e48e9082 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,13 +1,31 @@
 services:
-  data-store:
-    image: "samply/blaze:0.29"
-    environment:
-      BASE_URL: "http://localhost:8082"
-      JAVA_TOOL_OPTIONS: "-Xmx1g"
-      LOG_LEVEL: "debug"
+  flare:
+    image: ghcr.io/medizininformatik-initiative/flare:2.3.0
     ports:
-    - "8082:8080"
+      - 8080:8080
+    environment:
+      FLARE_FHIR_SERVER: ${FLARE_FHIR_SERVER_URL:-http://fhir-server:8080/fhir/}
+      FLARE_FHIR_USER: ${FLARE_FHIR_USER:-}
+      FLARE_FHIR_PASSWORD: ${FLARE_FHIR_PW:-}
+      FLARE_FHIR_OAUTH_ISSUER_URI: ${FLARE_FHIR_OAUTH_ISSUER_URI}
+      FLARE_FHIR_OAUTH_CLIENT_ID: ${FLARE_FHIR_OAUTH_CLIENT_ID}
+      FLARE_FHIR_OAUTH_CLIENT_SECRET: ${FLARE_FHIR_OAUTH_CLIENT_SECRET}
+      FLARE_FHIR_MAX_CONNECTIONS: ${FLARE_FHIR_MAX_CONNECTIONS:-32}
+      FLARE_FHIR_MAX_QUEUE_SIZE: ${FLARE_FHIR_MAX_QUEUE_SIZE:-500}
+      FLARE_FHIR_PAGE_COUNT: ${FLARE_FHIR_PAGE_COUNT:-500}
+      FLARE_CACHE_MEM_SIZE_MB: ${FLARE_CACHE_MEM_SIZE_MB:-1024}
+      FLARE_CACHE_MEM_EXPIRE: ${FLARE_CACHE_MEM_EXPIRE:-PT48H}
+      FLARE_CACHE_MEM_REFRESH: ${FLARE_CACHE_MEM_REFRESH:-PT24H}
+      FLARE_CACHE_DISK_PATH: ${FLARE_CACHE_DISK_PATH:-cache}
+      FLARE_CACHE_DISK_EXPIRE: ${FLARE_CACHE_DISK_EXPIRE:-P7D}
+      FLARE_CACHE_DISK_THREADS: ${FLARE_CACHE_DISK_THREADS:-4}
+      JAVA_TOOL_OPTIONS: ${FLARE_JAVA_TOOL_OPTIONS:--Xmx4g}
+      LOG_LEVEL: ${FLARE_LOG_LEVEL:-info}
     volumes:
-    - "data-store-data:/app/data"
+      - type: volume
+        source: flare-cache
+        target: /app/cache
+
 volumes:
-  data-store-data:
+  flare-cache:
+    name: "flare-cache"

From 1f2e856371af55879f32c5ec5baa1230bd2aa1c1 Mon Sep 17 00:00:00 2001
From: Bastian Schaffer <bastianschaffer.it@gmail.com>
Date: Tue, 3 Sep 2024 16:33:01 +0200
Subject: [PATCH 16/43] Remove Old Test Environment

---
 README.md           | 18 +++---------------
 docker-compose.yml  | 23 +----------------------
 import-test-data.sh |  7 -------
 3 files changed, 4 insertions(+), 44 deletions(-)
 delete mode 100755 import-test-data.sh

diff --git a/README.md b/README.md
index 825fdfa3..2ee62c63 100644
--- a/README.md
+++ b/README.md
@@ -6,20 +6,6 @@
 
 The goal of this project is to provide a service that allows for execution of feasibility queries on a FHIR-server.
 
-## Setting up the test-environment
-
-Set up FHIR test server
-
-```sh
-docker compose up
-```
-
-Load example data into FHIR server
-
-```sh
-import-test-data.sh
-```
-
 ## Build
 
 ```sh
@@ -29,9 +15,11 @@ mvn clean install
 ## Run
 
 ```sh
-docker run -p 8080:8080 ghcr.io/medizininformatik-initiative/flare:2.3
+docker-compose up
 ```
 
+In order for flare to work, a FHIR server such as [blaze](https://github.com/samply/blaze) must be running.
+
 ## Environment Variables
 
 | Name                            | Default                               | Depr ¹ | Description                                                                                      |
diff --git a/docker-compose.yml b/docker-compose.yml
index e48e9082..36fc942b 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -3,29 +3,8 @@ services:
     image: ghcr.io/medizininformatik-initiative/flare:2.3.0
     ports:
       - 8080:8080
-    environment:
-      FLARE_FHIR_SERVER: ${FLARE_FHIR_SERVER_URL:-http://fhir-server:8080/fhir/}
-      FLARE_FHIR_USER: ${FLARE_FHIR_USER:-}
-      FLARE_FHIR_PASSWORD: ${FLARE_FHIR_PW:-}
-      FLARE_FHIR_OAUTH_ISSUER_URI: ${FLARE_FHIR_OAUTH_ISSUER_URI}
-      FLARE_FHIR_OAUTH_CLIENT_ID: ${FLARE_FHIR_OAUTH_CLIENT_ID}
-      FLARE_FHIR_OAUTH_CLIENT_SECRET: ${FLARE_FHIR_OAUTH_CLIENT_SECRET}
-      FLARE_FHIR_MAX_CONNECTIONS: ${FLARE_FHIR_MAX_CONNECTIONS:-32}
-      FLARE_FHIR_MAX_QUEUE_SIZE: ${FLARE_FHIR_MAX_QUEUE_SIZE:-500}
-      FLARE_FHIR_PAGE_COUNT: ${FLARE_FHIR_PAGE_COUNT:-500}
-      FLARE_CACHE_MEM_SIZE_MB: ${FLARE_CACHE_MEM_SIZE_MB:-1024}
-      FLARE_CACHE_MEM_EXPIRE: ${FLARE_CACHE_MEM_EXPIRE:-PT48H}
-      FLARE_CACHE_MEM_REFRESH: ${FLARE_CACHE_MEM_REFRESH:-PT24H}
-      FLARE_CACHE_DISK_PATH: ${FLARE_CACHE_DISK_PATH:-cache}
-      FLARE_CACHE_DISK_EXPIRE: ${FLARE_CACHE_DISK_EXPIRE:-P7D}
-      FLARE_CACHE_DISK_THREADS: ${FLARE_CACHE_DISK_THREADS:-4}
-      JAVA_TOOL_OPTIONS: ${FLARE_JAVA_TOOL_OPTIONS:--Xmx4g}
-      LOG_LEVEL: ${FLARE_LOG_LEVEL:-info}
     volumes:
-      - type: volume
-        source: flare-cache
-        target: /app/cache
+      - flare-cache:/app/cache
 
 volumes:
   flare-cache:
-    name: "flare-cache"
diff --git a/import-test-data.sh b/import-test-data.sh
deleted file mode 100755
index d601ebb7..00000000
--- a/import-test-data.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash -e
-
-curl -sH 'Content-Type: application/fhir+json' \
-  -d @src/test/resources/de/medizininformatikinitiative/flare/GeneratedBundle.json \
-  -o /dev/null \
-  -w 'Result: %{response_code}\n' \
-  http://localhost:8082/fhir

From 362b84076f76ddd0379eef14d0449192305ed2a8 Mon Sep 17 00:00:00 2001
From: Bastian Schaffer <bastianschaffer.it@gmail.com>
Date: Tue, 3 Sep 2024 17:05:16 +0200
Subject: [PATCH 17/43] Update README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2ee62c63..82b4e83f 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@ mvn clean install
 docker-compose up
 ```
 
-In order for flare to work, a FHIR server such as [blaze](https://github.com/samply/blaze) must be running.
+In order for flare to work, a FHIR server such as [Blaze](https://github.com/samply/blaze) must be running on port 8082 by default.
 
 ## Environment Variables
 

From ac8f04d3cf8da324f03f16d4b27a813331a2519c Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 15:16:58 +0000
Subject: [PATCH 18/43] Update dependency org.yaml:snakeyaml to v2.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index feac6a9a..00a6c27c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.yaml</groupId>
       <artifactId>snakeyaml</artifactId>
-      <version>2.2</version>
+      <version>2.3</version>
     </dependency>
 
     <dependency>

From 7bb4d529bf3b112e6c25ee7e1c5d2ed697d618e8 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Wed, 4 Sep 2024 08:25:12 +0000
Subject: [PATCH 19/43] Update nginx Docker tag to v1.27.1

---
 .github/integration-test/basic-auth/docker-compose.yml | 2 +-
 .github/integration-test/oauth/docker-compose.yml      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/integration-test/basic-auth/docker-compose.yml b/.github/integration-test/basic-auth/docker-compose.yml
index 85b441f1..0b332f26 100644
--- a/.github/integration-test/basic-auth/docker-compose.yml
+++ b/.github/integration-test/basic-auth/docker-compose.yml
@@ -37,7 +37,7 @@ services:
     depends_on:
       - data-store
   proxy:
-    image: "nginx:1.27.0"
+    image: "nginx:1.27.1"
     volumes:
       - "./nginx.conf:/etc/nginx/nginx.conf"
       - "./proxy.htpasswd:/etc/auth/.htpasswd"
diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index dbbe5db4..99b609b0 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -50,7 +50,7 @@ services:
     volumes:
       - "./realm-test.json:/opt/keycloak/data/import/realm-test.json"
   proxy:
-    image: "nginx:1.27.0"
+    image: "nginx:1.27.1"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080"]
       interval: "5s"

From 68dc945303f698465e38053fb7a4b0dc872c55a6 Mon Sep 17 00:00:00 2001
From: Alexander Kiel <alexanderkiel@gmx.net>
Date: Wed, 4 Sep 2024 14:44:23 +0200
Subject: [PATCH 20/43] Release v2.4.0-alpha.1

---
 CHANGELOG.md | 8 ++++++++
 pom.xml      | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e5b2dec..8f6908e5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## v2.4.0-alpha.1
+
+### Enhancements
+
+* Update mapping_tree creation ([#191](https://github.com/medizininformatik-initiative/flare/issues/191))
+* Add cohort extraction endpoint ([#178](https://github.com/medizininformatik-initiative/flare/issues/178))
+* docker-compose.yml should be for flare instead of blaze ([#184](https://github.com/medizininformatik-initiative/flare/issues/184))
+
 ## v2.3.0
 
 ### Enhancements
diff --git a/pom.xml b/pom.xml
index 00a6c27c..3624df61 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>flare</artifactId>
-  <version>2.3.0</version>
+  <version>2.4.0-alpha.1</version>
 
   <name>Flare</name>
   <description>Flare</description>

From 933903a11bbd1f214cd3c6eb02154f7b9cc1dfb4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Sep 2024 08:19:03 +0000
Subject: [PATCH 21/43] Bump
 org.springframework.boot:spring-boot-starter-parent

Bumps [org.springframework.boot:spring-boot-starter-parent](https://github.com/spring-projects/spring-boot) from 3.3.3 to 3.3.4.
- [Release notes](https://github.com/spring-projects/spring-boot/releases)
- [Commits](https://github.com/spring-projects/spring-boot/compare/v3.3.3...v3.3.4)

---
updated-dependencies:
- dependency-name: org.springframework.boot:spring-boot-starter-parent
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 3624df61..a7f5a5c1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.3</version>
+    <version>3.3.4</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 

From 78c5e6c2992db0bafb3cd3b401e00590c0f237ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Wed, 2 Oct 2024 17:39:30 +0200
Subject: [PATCH 22/43] bump ontology version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a7f5a5c1..39c8a36a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -21,7 +21,7 @@
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.20.1</testcontainers.version>
-    <ontology.version>3.0.0-test.1</ontology.version>
+    <ontology.version>3.0.0-test.9</ontology.version>
   </properties>
 
   <dependencies>

From afcf51fc99a12a3e243e17e5f713f0b09134d312 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Mon, 21 Oct 2024 00:10:23 +0200
Subject: [PATCH 23/43] add trivy fix and update ontology version to
 v3.0.0-alpha

---
 .github/workflows/build.yml | 3 +++
 pom.xml                     | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index c1c9dd7a..039b1d16 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -94,6 +94,9 @@ jobs:
           output: trivy-results.sarif
           severity: 'CRITICAL,HIGH'
           timeout: '15m0s'
+        env:
+          TRIVY_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-db:2
+          TRIVY_JAVA_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-java-db:1
 
       - name: Upload Trivy Scan Results to GitHub Security Tab
         uses: github/codeql-action/upload-sarif@v3
diff --git a/pom.xml b/pom.xml
index 39c8a36a..acddcdea 100644
--- a/pom.xml
+++ b/pom.xml
@@ -21,7 +21,7 @@
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.20.1</testcontainers.version>
-    <ontology.version>3.0.0-test.9</ontology.version>
+    <ontology.version>3.0.0-alpha</ontology.version>
   </properties>
 
   <dependencies>

From 6be61cfb9c3555f9ea842085ec8a9552f30a6043 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Mon, 21 Oct 2024 00:30:29 +0200
Subject: [PATCH 24/43] Release v2.4.0-alpha.2

---
 CHANGELOG.md       | 4 ++++
 docker-compose.yml | 2 +-
 pom.xml            | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8f6908e5..2a27b3f6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## v2.4.0-alpha.2
+
+* Updated ontology to v3.0.0-alpha
+
 ## v2.4.0-alpha.1
 
 ### Enhancements
diff --git a/docker-compose.yml b/docker-compose.yml
index 36fc942b..30622073 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.3.0
+    image: ghcr.io/medizininformatik-initiative/flare:2.3.0-alpha.2
     ports:
       - 8080:8080
     volumes:
diff --git a/pom.xml b/pom.xml
index acddcdea..dab95319 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>flare</artifactId>
-  <version>2.4.0-alpha.1</version>
+  <version>2.4.0-alpha.2</version>
 
   <name>Flare</name>
   <description>Flare</description>

From 7cf4169b78e7c4c555396dc37d60cb186c1b2626 Mon Sep 17 00:00:00 2001
From: Alexander Kiel <alexanderkiel@gmx.net>
Date: Wed, 6 Nov 2024 15:12:05 +0100
Subject: [PATCH 25/43] Refactor StepVerifier Verify Calls

---
 .../medizininformatikinitiative/flare/service/DataStore.java  | 1 +
 src/test/java/de/medizininformatikinitiative/MonosTest.java   | 2 +-
 .../flare/service/DataStoreTest.java                          | 4 ++--
 .../flare/service/StructuredQueryServiceTest.java             | 2 +-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/java/de/medizininformatikinitiative/flare/service/DataStore.java b/src/main/java/de/medizininformatikinitiative/flare/service/DataStore.java
index 5f6405da..653ec1a7 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/service/DataStore.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/service/DataStore.java
@@ -76,6 +76,7 @@ private static boolean shouldRetry(HttpStatusCode code) {
     }
 
     private Mono<Bundle> fetchPage(String url) {
+
         logger.trace("fetch page {}", url);
         return client.get()
                 .uri(url)
diff --git a/src/test/java/de/medizininformatikinitiative/MonosTest.java b/src/test/java/de/medizininformatikinitiative/MonosTest.java
index e57da28e..faeec000 100644
--- a/src/test/java/de/medizininformatikinitiative/MonosTest.java
+++ b/src/test/java/de/medizininformatikinitiative/MonosTest.java
@@ -20,7 +20,7 @@ class OfEither {
         void ofLeft() {
             var result = Monos.ofEither(Either.left(new Exception(MESSAGE)));
 
-            StepVerifier.create(result).expectErrorMessage(MESSAGE).verify();
+            StepVerifier.create(result).verifyErrorMessage(MESSAGE);
         }
 
         @Test
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreTest.java
index 839a6e27..ea4e43fb 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/DataStoreTest.java
@@ -66,7 +66,7 @@ void execute_retry_fails() {
 
         var result = dataStore.execute(Query.ofType("Observation"));
 
-        StepVerifier.create(result).expectErrorMessage("Retries exhausted: 3/3").verify();
+        StepVerifier.create(result).verifyErrorMessage("Retries exhausted: 3/3");
     }
 
     @Test
@@ -76,6 +76,6 @@ void execute_retry_400() {
 
         var result = dataStore.execute(Query.ofType("Observation"));
 
-        StepVerifier.create(result).expectError(WebClientResponseException.BadRequest.class).verify();
+        StepVerifier.create(result).verifyError(WebClientResponseException.BadRequest.class);
     }
 }
diff --git a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
index e3fa3e45..5ce6a4cc 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceTest.java
@@ -65,7 +65,7 @@ void setUp() {
             void execute() {
                 var result = service.execute(query);
 
-                StepVerifier.create(result).expectError(MappingNotFoundException.class).verify();
+                StepVerifier.create(result).verifyError(MappingNotFoundException.class);
             }
 
             @Test

From 66db740f42adf50b4de7ed721024fbccac9ad85d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 17:26:36 +0100
Subject: [PATCH 26/43] Add toggle to enable cohort endpoint

---
 README.md                                     |  1 +
 docs/api.md                                   | 62 +++++++++++++++++++
 .../flare/rest/QueryController.java           | 15 +++--
 src/main/resources/application.yml            |  2 +
 .../flare/rest/QueryControllerTest.java       | 40 +++++++++++-
 5 files changed, 114 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 82b4e83f..271c460f 100644
--- a/README.md
+++ b/README.md
@@ -41,6 +41,7 @@ In order for flare to work, a FHIR server such as [Blaze](https://github.com/sam
 | FLARE_CACHE_DISK_THREADS        | 4                                     |        | The number of threads the disk cache should use for reading and writing entries.                 |
 | FLARE_MAPPING_MAPPING_FILE      | ontology/codex-term-code-mapping.json | v2.4.0 | The mappings to use.                                                                             |
 | FLARE_MAPPING_CONCEPT_TREE_FILE | ontology/codex-code-tree.json         | v2.4.0 | The code tree to use.                                                                            |
+| FLARE_COHORT_ENABLED            | false                                 |        | Toggle - enables the cohort extraction endpoint, which returns the actual patient ids            |
 | SERVER_PORT                     | 8080                                  |        | The port at which Flare provides its REST API.                                                   |
 | JAVA_TOOL_OPTIONS               | -Xmx4g                                |        | JVM options \(Docker only\)                                                                      |
 | LOG_LEVEL                       | info                                  |        | one of trace, debug, info, warn or error                                                         |
diff --git a/docs/api.md b/docs/api.md
index f57245a0..912df69c 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -45,6 +45,68 @@ The result of that query could be:
 31910
 ```
 
+## Execute Cohort (Cohort Extraction)
+
+> [!CAUTION]
+> This feature is disabled by default. Be aware that it returns the actual patient IDs (techinal IDs of the FHIR server) for the patients.
+> To enable set the env var FLARE_COHORT_ENABLED=true
+
+The ExecuteCohort-Endpoint returns a list of patient ids for patients fitting the criteria of the structured query that is passed in the body of a POST-Request. Also, the POST-Request must contain `application/sq+json` as Content-Type. It can be called like this:
+
+```sh
+curl -s http://localhost:8080/query/execute-cohort -H "Content-Type: application/sq+json" -d '<query>'
+```
+
+An example `<query>` is:
+```json
+{
+  "version": "https://medizininformatik-initiative.de/fdpg/StructuredQuery/v3/schema",
+  "display": "",
+  "inclusionCriteria": [
+    [
+      {
+        "termCodes": [
+          {
+            "code": "263495000",
+            "system": "http://snomed.info/sct",
+            "display": "Geschlecht"
+          }
+        ],
+        "valueFilter": {
+          "selectedConcepts": [
+            {
+              "code": "female",
+              "system": "http://hl7.org/fhir/administrative-gender",
+              "display": "Female"
+            }
+          ],
+          "type": "concept"
+        }
+      }
+    ]
+  ]
+}
+```
+
+The result of that query could be:
+```json
+[
+  "VHF02060",
+  "VHF02061",
+  "VHF02062",
+  "VHF02066",
+  "VHF02067",
+  "VHF02069",
+  "VHF02072",
+  "VHF02073",
+  "VHF02075",
+  "VHF02076",
+  "VHF02082",
+  "VHF02083"
+]
+```
+
+
 ## Translate
 
 Flare also provides a Translate-Endpoint, which returns the separate FHIR Search queries wrapped in a json format that shows each set operation that is necessary to fit the original inclusion/ exclusion structure.
diff --git a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
index 283e932b..538926ef 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
@@ -7,6 +7,7 @@
 import de.medizininformatikinitiative.flare.service.StructuredQueryService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.http.MediaType;
 import org.springframework.stereotype.Component;
@@ -38,10 +39,16 @@ public QueryController(StructuredQueryService queryService) {
     }
 
     @Bean
-    public RouterFunction<ServerResponse> queryRouter() {
-        return route(POST("query/execute").and(accept(MEDIA_TYPE_SQ)), this::execute)
-                .andRoute(POST("query/translate").and(accept(MEDIA_TYPE_SQ)), this::translate)
-                .andRoute(POST("query/execute-cohort").and(accept(MEDIA_TYPE_SQ)), this::executeCohort);
+    public RouterFunction<ServerResponse> queryRouter(@Value("${flare.cohort.enabled}") boolean cohortEnabled) {
+
+        var route = route(POST("query/execute").and(accept(MEDIA_TYPE_SQ)), this::execute)
+                .andRoute(POST("query/translate").and(accept(MEDIA_TYPE_SQ)), this::translate);
+
+        if (cohortEnabled){
+            route = route.andRoute(POST("query/execute-cohort").and(accept(MEDIA_TYPE_SQ)), this::executeCohort);
+        }
+
+        return route;
     }
 
     public Mono<ServerResponse> execute(ServerRequest request) {
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index dbf1b040..326d80da 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -1,4 +1,6 @@
 flare:
+  cohort:
+    enabled: false
   fhir:
     server: 'http://localhost:8082/fhir'
     user: ''
diff --git a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
index 1268ea7c..8ba19d52 100644
--- a/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
+++ b/src/test/java/de/medizininformatikinitiative/flare/rest/QueryControllerTest.java
@@ -15,6 +15,9 @@
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.springframework.http.MediaType;
+import org.springframework.test.context.event.annotation.BeforeTestExecution;
+import org.springframework.test.context.event.annotation.BeforeTestMethod;
+import org.springframework.test.context.transaction.BeforeTransaction;
 import org.springframework.test.web.reactive.server.WebTestClient;
 import org.testcontainers.shaded.com.fasterxml.jackson.core.JsonProcessingException;
 import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper;
@@ -45,7 +48,7 @@ class QueryControllerTest {
 
     @BeforeEach
     void setUp() {
-        client = WebTestClient.bindToRouterFunction(controller.queryRouter()).build();
+        client = WebTestClient.bindToRouterFunction(controller.queryRouter(true)).build();
     }
 
     @Test
@@ -82,7 +85,6 @@ void execute() {
                 .expectBody().json("1");
     }
 
-
     @Test
     void executeCohort() throws JsonProcessingException {
         when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.just(Population.of(PATIENT_ID, PATIENT_ID_1)));
@@ -119,6 +121,40 @@ void executeCohort() throws JsonProcessingException {
                 .expectBody().json(objectMapper.writeValueAsString(List.of(PATIENT_ID, PATIENT_ID_1)));
     }
 
+    @Test
+    void executeCohortDisabled() {
+
+        client = WebTestClient.bindToRouterFunction(controller.queryRouter(false)).build();
+
+        client.post()
+                .uri("/query/execute-cohort")
+                .contentType(MEDIA_TYPE_SQ)
+                .bodyValue("""
+                        {
+                          "inclusionCriteria": [
+                            [
+                              {
+                                "context": {
+                                  "system": "context-system",
+                                  "code": "context-code",
+                                  "display": "context-display"
+                                },
+                                "termCodes": [
+                                  {
+                                    "system": "http://snomed.info/sct",
+                                    "code": "386661006",
+                                    "display": "Fever (finding)"
+                                  }
+                                ]
+                              }
+                            ]
+                          ]
+                        }
+                        """)
+                .exchange()
+                .expectStatus().isNotFound();
+    }
+
     @Test
     void execute_error() {
         when(queryService.execute(STRUCTURED_QUERY)).thenReturn(Mono.error(new MappingNotFoundException(ContextualTermCode.of(TestUtil.CONTEXT, FEVER))));

From 0135c2e600a698d94a0e0f1324e1dcfb9f7c99c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 19:46:29 +0100
Subject: [PATCH 27/43] Add integration test for cohort endpoint

---
 .../no-auth-cohort-enabled/docker-compose.yml | 40 +++++++++++++++++++
 .../no-auth-cohort-enabled/load-data.sh       |  5 +++
 .../scripts/execute-cohort-query-enabled.sh   | 39 ++++++++++++++++++
 .../execute-cohort-query-not-enabled.sh       | 12 ++++++
 .github/scripts/util.sh                       | 28 +++++++++++++
 .github/workflows/build.yml                   | 21 +++++++---
 README.md                                     |  2 +-
 .../flare/rest/QueryController.java           |  2 +-
 src/main/resources/application.yml            |  2 +-
 9 files changed, 142 insertions(+), 9 deletions(-)
 create mode 100644 .github/integration-test/no-auth-cohort-enabled/docker-compose.yml
 create mode 100755 .github/integration-test/no-auth-cohort-enabled/load-data.sh
 create mode 100755 .github/scripts/execute-cohort-query-enabled.sh
 create mode 100755 .github/scripts/execute-cohort-query-not-enabled.sh

diff --git a/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml b/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml
new file mode 100644
index 00000000..d8e9cd14
--- /dev/null
+++ b/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml
@@ -0,0 +1,40 @@
+services:
+  data-store:
+    image: "samply/blaze:0.29"
+    healthcheck:
+      test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
+      interval: "5s"
+      timeout: "5s"
+      retries: "3"
+      start_period: "60s"
+    environment:
+      BASE_URL: "http://data-store:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      LOG_LEVEL: "debug"
+    ports:
+      - "8082:8080"
+    volumes:
+      - "data-store-data:/app/data"
+  flare:
+    image: "flare:latest"
+    healthcheck:
+      test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/cache/stats"]
+      interval: "5s"
+      timeout: "5s"
+      retries: "3"
+      start_period: "60s"
+    environment:
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      FLARE_FHIR_SERVER: "http://data-store:8080/fhir"
+      LOG_LEVEL: "debug"
+      FLARE_ENABLE_COHORT_ENDPOINT: true
+    ports:
+      - "8080:8080"
+    volumes:
+      - "flare-cache:/app/cache"
+      - "../synthea-test-mapping:/app/ontology"
+    depends_on:
+      - data-store
+volumes:
+  data-store-data:
+  flare-cache:
diff --git a/.github/integration-test/no-auth-cohort-enabled/load-data.sh b/.github/integration-test/no-auth-cohort-enabled/load-data.sh
new file mode 100755
index 00000000..57e469aa
--- /dev/null
+++ b/.github/integration-test/no-auth-cohort-enabled/load-data.sh
@@ -0,0 +1,5 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+
+blazectl --no-progress --server http://localhost:8082/fhir upload "$SCRIPT_DIR/../../test-data/synthea"
diff --git a/.github/scripts/execute-cohort-query-enabled.sh b/.github/scripts/execute-cohort-query-enabled.sh
new file mode 100755
index 00000000..9e02c145
--- /dev/null
+++ b/.github/scripts/execute-cohort-query-enabled.sh
@@ -0,0 +1,39 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "util.sh"
+
+
+BASE="http://localhost:8080"
+curl_response=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
+
+ACTUAL_PAT_ID_ARRAY=()
+
+while IFS= read -r line; do
+    ACTUAL_PAT_ID_ARRAY+=("$line")
+done < <(echo "$curl_response" | jq -r '.[]')
+
+
+EXPECTED_PAT_ID_ARRAY=(
+                          "DEZLXBBZCMJRHIWP" "DEZLXBBZGCL4O6LJ" "DEZLXBC7JY7I7VTM" "DEZLXBCWHPIDEXQP"
+                          "DEZLXBD2ZFD7ICE5" "DEZLXBD6YMHCAI5B" "DEZLXBDDTY5KODRB" "DEZLXBDGKPNNPOLS"
+                          "DEZLXBDLW2IYJNEV" "DEZLXBDQSTBEEKD3" "DEZLXBDVCCO6KA5K" "DEZLXBDYX5VLFMDF"
+                          "DEZLXBEGC5T2PBAM" "DEZLXBEJDWUZP7A5" "DEZLXBEKK3HVHOCL" "DEZLXBESEJYLN2RV"
+                          "DEZLXBEZ5C5V77WP" "DEZLXBF4MNTUBRUT" "DEZLXBFBLJUS3IS6" "DEZLXBFE2ON4CWLO"
+                          "DEZLXBG3MKK6PUVX" "DEZLXBG7NVKBU3JG" "DEZLXBGKPFVZ7AI3" "DEZLXBGKU74A44Z7"
+                          "DEZLXBGQ44BQHYDL" "DEZLXBGQDKOZHFU6" "DEZLXBGTXJS2VHEG" "DEZLXBGVQRWEBUGV"
+                          "DEZLXBH6JTYKLN37" "DEZLXBHP4DGCTTRN" "DEZLXBHQG2CBAKXS" "DEZLXBI4I24ZCM3H"
+                          "DEZLXBI5A2TSPB5S" "DEZLXBIIP6ZUTPIA" "DEZLXBIMZPVN64B3" "DEZLXBIT7CK3VRVH"
+                          "DEZLXBIUGA4R4KTC" "DEZLXBJJWNJTPMYC" "DEZLXBK3LRLPGP2U" "DEZLXBK4R55CSR2X"
+                          "DEZLXBKAF4GKMAQD" "DEZLXBKFWGK4TDK5" "DEZLXBKIQNZAHQJV" "DEZLXBL7YHECLK7W"
+                          "DEZLXBLD72E7CEJT" "DEZLXBLFX7YBP6HI" "DEZLXBLNYKQLJS5T" "DEZLXBLQGE5EKJGE"
+                          "DEZLXBM7F2I6MGPG" "DEZLXBMJLDY5OXHS" "DEZLXBMOJAE635MI" "DEZLXBMQR4FTZKEP"
+                          "DEZLXBN5O5IJB2OM" "DEZLXBN7PFFZDAYM" "DEZLXBNCGIA6Y2P7" "DEZLXBNIU42GXBTO"
+                          "DEZLXBNM37HOP6GW" "DEZLXBNU37U7ZIFR" "DEZLXBNY4SPRN7MD" "DEZLXBOS3OMTQZ42"
+                          "DEZLXBPJTYSY4PUU" "DEZLXBPJZEVQ6JYY" "DEZLXBPNIOO7JG4O" "DEZLXBPSXO5T4ZIO"
+                          "DEZLXBQI5WPVLRR4" "DEZLXBQWR5KHBB44" "DEZLXBR4IC6RUSTD" "DEZLXBRJ4TA7BJYV"
+                          "DEZLXBS5QKVCQCTT"
+                      )
+
+
+test_array "cohort test" ACTUAL_PAT_ID_ARRAY EXPECTED_PAT_ID_ARRAY
diff --git a/.github/scripts/execute-cohort-query-not-enabled.sh b/.github/scripts/execute-cohort-query-not-enabled.sh
new file mode 100755
index 00000000..5b1d8aac
--- /dev/null
+++ b/.github/scripts/execute-cohort-query-not-enabled.sh
@@ -0,0 +1,12 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "util.sh"
+
+
+BASE="http://localhost:8080"
+curl_response=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
+
+status_code=$(curl -s -o /dev/null -w "%{http_code}" "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
+
+test "cohort endpoint status code" $status_code 404
diff --git a/.github/scripts/util.sh b/.github/scripts/util.sh
index 93519cd2..5bc3ad8c 100644
--- a/.github/scripts/util.sh
+++ b/.github/scripts/util.sh
@@ -8,3 +8,31 @@ test() {
     exit 1
   fi
 }
+
+test_array() {
+  local name="$1"
+  local array1_name="$2"
+  local array2_name="$3"
+
+  # Get the length of both arrays
+  local len1=$(eval "echo \${#$array1_name[@]}")
+  local len2=$(eval "echo \${#$array2_name[@]}")
+
+  # Check if the arrays have the same length
+  if [ "$len1" -ne "$len2" ]; then
+    echo "Fail: the $name arrays have different lengths ($len1 vs $len2)"
+    exit 1
+  fi
+
+  # Compare each element
+  for i in $(seq 0 $((len1 - 1))); do
+    local val1=$(eval "echo \${$array1_name[$i]}")
+    local val2=$(eval "echo \${$array2_name[$i]}")
+    if [ "$val1" != "$val2" ]; then
+      echo "Fail: the $name arrays differ at index $i: $val1 != $val2"
+      exit 1
+    fi
+  done
+
+  echo "OK: the $name arrays are equal"
+}
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 039b1d16..aaf28c74 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -3,16 +3,16 @@ name: Build
 on:
   push:
     branches:
-    - main
-    - develop
+      - main
+      - develop
     tags:
-    - 'v*.*.*'
+      - 'v*.*.*'
   pull_request:
     branches:
-    - main
-    - develop
+      - main
+      - develop
   schedule:
-  - cron: '0 1 * * *'
+    - cron: '0 1 * * *'
 
 jobs:
   build:
@@ -134,6 +134,7 @@ jobs:
           - no-auth
           - basic-auth
           - oauth
+          - no-auth-cohort-enabled
     runs-on: ubuntu-22.04
 
     steps:
@@ -161,6 +162,14 @@ jobs:
       - name: Query for Viral sinusitis (disorder)
         run: .github/scripts/execute-query.sh 444814009 69
 
+      - name: Query for Viral sinusitis (disorder) cohort not enabled
+        if: ${{ matrix.test != 'no-auth-cohort-enabled' }}
+        run: .github/scripts/execute-cohort-query-not-enabled.sh 444814009
+
+      - name: Query for Viral sinusitis (disorder) cohort enabled
+        if: ${{ matrix.test == 'no-auth-cohort-enabled' }}
+        run: .github/scripts/execute-cohort-query-enabled.sh 444814009
+
   push-image:
     needs:
       - build
diff --git a/README.md b/README.md
index 271c460f..09db85eb 100644
--- a/README.md
+++ b/README.md
@@ -41,7 +41,7 @@ In order for flare to work, a FHIR server such as [Blaze](https://github.com/sam
 | FLARE_CACHE_DISK_THREADS        | 4                                     |        | The number of threads the disk cache should use for reading and writing entries.                 |
 | FLARE_MAPPING_MAPPING_FILE      | ontology/codex-term-code-mapping.json | v2.4.0 | The mappings to use.                                                                             |
 | FLARE_MAPPING_CONCEPT_TREE_FILE | ontology/codex-code-tree.json         | v2.4.0 | The code tree to use.                                                                            |
-| FLARE_COHORT_ENABLED            | false                                 |        | Toggle - enables the cohort extraction endpoint, which returns the actual patient ids            |
+| FLARE_ENABLE_COHORT_ENDPOINT    | false                                 |        | Set to `true` to enable the cohort extraction endpoint, which returns the actual patient IDs.    |
 | SERVER_PORT                     | 8080                                  |        | The port at which Flare provides its REST API.                                                   |
 | JAVA_TOOL_OPTIONS               | -Xmx4g                                |        | JVM options \(Docker only\)                                                                      |
 | LOG_LEVEL                       | info                                  |        | one of trace, debug, info, warn or error                                                         |
diff --git a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
index 538926ef..e2d26cb6 100644
--- a/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
+++ b/src/main/java/de/medizininformatikinitiative/flare/rest/QueryController.java
@@ -44,7 +44,7 @@ public RouterFunction<ServerResponse> queryRouter(@Value("${flare.cohort.enabled
         var route = route(POST("query/execute").and(accept(MEDIA_TYPE_SQ)), this::execute)
                 .andRoute(POST("query/translate").and(accept(MEDIA_TYPE_SQ)), this::translate);
 
-        if (cohortEnabled){
+        if (cohortEnabled) {
             route = route.andRoute(POST("query/execute-cohort").and(accept(MEDIA_TYPE_SQ)), this::executeCohort);
         }
 
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 326d80da..bc7e4e57 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -1,6 +1,6 @@
 flare:
   cohort:
-    enabled: false
+    enabled: ${FLARE_ENABLE_COHORT_ENDPOINT:false}
   fhir:
     server: 'http://localhost:8082/fhir'
     user: ''

From f09edc21189acd2ec8027403d41d292b4897162f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 19:59:48 +0100
Subject: [PATCH 28/43] fix script dirs for new test scripts

---
 .github/scripts/execute-cohort-query-enabled.sh     |  9 +++------
 .github/scripts/execute-cohort-query-not-enabled.sh | 10 ++++------
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/.github/scripts/execute-cohort-query-enabled.sh b/.github/scripts/execute-cohort-query-enabled.sh
index 9e02c145..fbc8a547 100755
--- a/.github/scripts/execute-cohort-query-enabled.sh
+++ b/.github/scripts/execute-cohort-query-enabled.sh
@@ -1,18 +1,16 @@
 #!/bin/bash -e
 
 SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
-. "util.sh"
-
+. "$SCRIPT_DIR/util.sh"
 
 BASE="http://localhost:8080"
-curl_response=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
+CURL_RESPONSE=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
 
 ACTUAL_PAT_ID_ARRAY=()
 
 while IFS= read -r line; do
     ACTUAL_PAT_ID_ARRAY+=("$line")
-done < <(echo "$curl_response" | jq -r '.[]')
-
+done < <(echo "$CURL_RESPONSE" | jq -r '.[]')
 
 EXPECTED_PAT_ID_ARRAY=(
                           "DEZLXBBZCMJRHIWP" "DEZLXBBZGCL4O6LJ" "DEZLXBC7JY7I7VTM" "DEZLXBCWHPIDEXQP"
@@ -35,5 +33,4 @@ EXPECTED_PAT_ID_ARRAY=(
                           "DEZLXBS5QKVCQCTT"
                       )
 
-
 test_array "cohort test" ACTUAL_PAT_ID_ARRAY EXPECTED_PAT_ID_ARRAY
diff --git a/.github/scripts/execute-cohort-query-not-enabled.sh b/.github/scripts/execute-cohort-query-not-enabled.sh
index 5b1d8aac..438e277a 100755
--- a/.github/scripts/execute-cohort-query-not-enabled.sh
+++ b/.github/scripts/execute-cohort-query-not-enabled.sh
@@ -1,12 +1,10 @@
 #!/bin/bash -e
 
 SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
-. "util.sh"
-
+. "$SCRIPT_DIR/util.sh"
 
 BASE="http://localhost:8080"
-curl_response=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
-
-status_code=$(curl -s -o /dev/null -w "%{http_code}" "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"../integration-test/query-$1.json")
+STATUS_CODE=$(curl -s -o /dev/null -w "%{http_code}" "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
+EXPECTED_STATUS_CODE=404
 
-test "cohort endpoint status code" $status_code 404
+test "cohort endpoint status code" $STATUS_CODE $EXPECTED_STATUS_CODE

From 00a98d7ce6776170a410382e8c475a765bc2bec4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 20:46:16 +0100
Subject: [PATCH 29/43] change test to check response array and array length
 with strings of size id length

---
 .../scripts/execute-cohort-query-enabled.sh   | 26 ++--------------
 .github/scripts/util.sh                       | 31 ++++++++++---------
 .github/workflows/build.yml                   |  2 +-
 3 files changed, 20 insertions(+), 39 deletions(-)

diff --git a/.github/scripts/execute-cohort-query-enabled.sh b/.github/scripts/execute-cohort-query-enabled.sh
index fbc8a547..d7689677 100755
--- a/.github/scripts/execute-cohort-query-enabled.sh
+++ b/.github/scripts/execute-cohort-query-enabled.sh
@@ -4,33 +4,13 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
 . "$SCRIPT_DIR/util.sh"
 
 BASE="http://localhost:8080"
+EXPECTED_ARRAY_LENGTH=$2
+EXPECTED_ID_LENGTH=$3
 CURL_RESPONSE=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
-
 ACTUAL_PAT_ID_ARRAY=()
 
 while IFS= read -r line; do
     ACTUAL_PAT_ID_ARRAY+=("$line")
 done < <(echo "$CURL_RESPONSE" | jq -r '.[]')
 
-EXPECTED_PAT_ID_ARRAY=(
-                          "DEZLXBBZCMJRHIWP" "DEZLXBBZGCL4O6LJ" "DEZLXBC7JY7I7VTM" "DEZLXBCWHPIDEXQP"
-                          "DEZLXBD2ZFD7ICE5" "DEZLXBD6YMHCAI5B" "DEZLXBDDTY5KODRB" "DEZLXBDGKPNNPOLS"
-                          "DEZLXBDLW2IYJNEV" "DEZLXBDQSTBEEKD3" "DEZLXBDVCCO6KA5K" "DEZLXBDYX5VLFMDF"
-                          "DEZLXBEGC5T2PBAM" "DEZLXBEJDWUZP7A5" "DEZLXBEKK3HVHOCL" "DEZLXBESEJYLN2RV"
-                          "DEZLXBEZ5C5V77WP" "DEZLXBF4MNTUBRUT" "DEZLXBFBLJUS3IS6" "DEZLXBFE2ON4CWLO"
-                          "DEZLXBG3MKK6PUVX" "DEZLXBG7NVKBU3JG" "DEZLXBGKPFVZ7AI3" "DEZLXBGKU74A44Z7"
-                          "DEZLXBGQ44BQHYDL" "DEZLXBGQDKOZHFU6" "DEZLXBGTXJS2VHEG" "DEZLXBGVQRWEBUGV"
-                          "DEZLXBH6JTYKLN37" "DEZLXBHP4DGCTTRN" "DEZLXBHQG2CBAKXS" "DEZLXBI4I24ZCM3H"
-                          "DEZLXBI5A2TSPB5S" "DEZLXBIIP6ZUTPIA" "DEZLXBIMZPVN64B3" "DEZLXBIT7CK3VRVH"
-                          "DEZLXBIUGA4R4KTC" "DEZLXBJJWNJTPMYC" "DEZLXBK3LRLPGP2U" "DEZLXBK4R55CSR2X"
-                          "DEZLXBKAF4GKMAQD" "DEZLXBKFWGK4TDK5" "DEZLXBKIQNZAHQJV" "DEZLXBL7YHECLK7W"
-                          "DEZLXBLD72E7CEJT" "DEZLXBLFX7YBP6HI" "DEZLXBLNYKQLJS5T" "DEZLXBLQGE5EKJGE"
-                          "DEZLXBM7F2I6MGPG" "DEZLXBMJLDY5OXHS" "DEZLXBMOJAE635MI" "DEZLXBMQR4FTZKEP"
-                          "DEZLXBN5O5IJB2OM" "DEZLXBN7PFFZDAYM" "DEZLXBNCGIA6Y2P7" "DEZLXBNIU42GXBTO"
-                          "DEZLXBNM37HOP6GW" "DEZLXBNU37U7ZIFR" "DEZLXBNY4SPRN7MD" "DEZLXBOS3OMTQZ42"
-                          "DEZLXBPJTYSY4PUU" "DEZLXBPJZEVQ6JYY" "DEZLXBPNIOO7JG4O" "DEZLXBPSXO5T4ZIO"
-                          "DEZLXBQI5WPVLRR4" "DEZLXBQWR5KHBB44" "DEZLXBR4IC6RUSTD" "DEZLXBRJ4TA7BJYV"
-                          "DEZLXBS5QKVCQCTT"
-                      )
-
-test_array "cohort test" ACTUAL_PAT_ID_ARRAY EXPECTED_PAT_ID_ARRAY
+test_array "cohort test" ACTUAL_PAT_ID_ARRAY "$EXPECTED_ID_LENGTH" "$EXPECTED_ARRAY_LENGTH"
diff --git a/.github/scripts/util.sh b/.github/scripts/util.sh
index 5bc3ad8c..91aa0381 100644
--- a/.github/scripts/util.sh
+++ b/.github/scripts/util.sh
@@ -11,28 +11,29 @@ test() {
 
 test_array() {
   local name="$1"
-  local array1_name="$2"
-  local array2_name="$3"
+  local array_name="$2"
+  local expected_length_id="$3"
+  local expected_array_length="$4"
 
-  # Get the length of both arrays
-  local len1=$(eval "echo \${#$array1_name[@]}")
-  local len2=$(eval "echo \${#$array2_name[@]}")
+  # Get the length of the array (number of elements)
+  local len=$(eval "echo \${#$array_name[@]}")
 
-  # Check if the arrays have the same length
-  if [ "$len1" -ne "$len2" ]; then
-    echo "Fail: the $name arrays have different lengths ($len1 vs $len2)"
+  # Check if the array has the expected number of elements
+  if [ "$len" -ne "$expected_array_length" ]; then
+    echo "Fail: the $name array has an unexpected number of elements ($len vs $expected_array_length)"
     exit 1
   fi
 
-  # Compare each element
-  for i in $(seq 0 $((len1 - 1))); do
-    local val1=$(eval "echo \${$array1_name[$i]}")
-    local val2=$(eval "echo \${$array2_name[$i]}")
-    if [ "$val1" != "$val2" ]; then
-      echo "Fail: the $name arrays differ at index $i: $val1 != $val2"
+  # Compare the length of each string in the array
+  for i in $(seq 0 $((len - 1))); do
+    local val=$(eval "echo \${$array_name[$i]}")
+
+    # Check if the string has the same expected length
+    if [ ${#val} -ne "$expected_length_id" ]; then
+      echo "Fail: the string at index $i in the $name array does not have the expected length of $expected_length_id: ${#val} != $expected_length_id"
       exit 1
     fi
   done
 
-  echo "OK: the $name arrays are equal"
+  echo "OK: all strings in the $name array have the expected length of $expected_length_id, and the array has the expected number of elements ($expected_array_length)"
 }
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index aaf28c74..eebe2356 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -168,7 +168,7 @@ jobs:
 
       - name: Query for Viral sinusitis (disorder) cohort enabled
         if: ${{ matrix.test == 'no-auth-cohort-enabled' }}
-        run: .github/scripts/execute-cohort-query-enabled.sh 444814009
+        run: .github/scripts/execute-cohort-query-enabled.sh 444814009 69 16
 
   push-image:
     needs:

From f3c3a2a84eff285591eac85b533865d52e585d12 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 21:26:53 +0100
Subject: [PATCH 30/43] simplify execution and only check enxpoint not enabled
 no auth

---
 .../scripts/execute-cohort-query-enabled.sh   |  9 +++---
 .../execute-cohort-query-not-enabled.sh       |  2 +-
 .github/scripts/util.sh                       | 29 -------------------
 .github/workflows/build.yml                   |  2 +-
 4 files changed, 6 insertions(+), 36 deletions(-)

diff --git a/.github/scripts/execute-cohort-query-enabled.sh b/.github/scripts/execute-cohort-query-enabled.sh
index d7689677..f3b731b9 100755
--- a/.github/scripts/execute-cohort-query-enabled.sh
+++ b/.github/scripts/execute-cohort-query-enabled.sh
@@ -7,10 +7,9 @@ BASE="http://localhost:8080"
 EXPECTED_ARRAY_LENGTH=$2
 EXPECTED_ID_LENGTH=$3
 CURL_RESPONSE=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
-ACTUAL_PAT_ID_ARRAY=()
 
-while IFS= read -r line; do
-    ACTUAL_PAT_ID_ARRAY+=("$line")
-done < <(echo "$CURL_RESPONSE" | jq -r '.[]')
+ACTUAL_PAT_ID_ARRAY_LENGTH=$(echo "$CURL_RESPONSE" | jq '. | length')
+ACTUAL_PAT_ID_ARRAY_ID_LENGTH=$(echo "$CURL_RESPONSE" | jq '.[] | length' | uniq)
 
-test_array "cohort test" ACTUAL_PAT_ID_ARRAY "$EXPECTED_ID_LENGTH" "$EXPECTED_ARRAY_LENGTH"
+test "cohort length" $ACTUAL_PAT_ID_ARRAY_LENGTH $EXPECTED_ARRAY_LENGTH
+test "cohort id length" $ACTUAL_PAT_ID_ARRAY_ID_LENGTH $EXPECTED_ID_LENGTH
diff --git a/.github/scripts/execute-cohort-query-not-enabled.sh b/.github/scripts/execute-cohort-query-not-enabled.sh
index 438e277a..158eb0f3 100755
--- a/.github/scripts/execute-cohort-query-not-enabled.sh
+++ b/.github/scripts/execute-cohort-query-not-enabled.sh
@@ -7,4 +7,4 @@ BASE="http://localhost:8080"
 STATUS_CODE=$(curl -s -o /dev/null -w "%{http_code}" "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
 EXPECTED_STATUS_CODE=404
 
-test "cohort endpoint status code" $STATUS_CODE $EXPECTED_STATUS_CODE
+test "cohort endpoint status code" "$STATUS_CODE" $EXPECTED_STATUS_CODE
diff --git a/.github/scripts/util.sh b/.github/scripts/util.sh
index 91aa0381..93519cd2 100644
--- a/.github/scripts/util.sh
+++ b/.github/scripts/util.sh
@@ -8,32 +8,3 @@ test() {
     exit 1
   fi
 }
-
-test_array() {
-  local name="$1"
-  local array_name="$2"
-  local expected_length_id="$3"
-  local expected_array_length="$4"
-
-  # Get the length of the array (number of elements)
-  local len=$(eval "echo \${#$array_name[@]}")
-
-  # Check if the array has the expected number of elements
-  if [ "$len" -ne "$expected_array_length" ]; then
-    echo "Fail: the $name array has an unexpected number of elements ($len vs $expected_array_length)"
-    exit 1
-  fi
-
-  # Compare the length of each string in the array
-  for i in $(seq 0 $((len - 1))); do
-    local val=$(eval "echo \${$array_name[$i]}")
-
-    # Check if the string has the same expected length
-    if [ ${#val} -ne "$expected_length_id" ]; then
-      echo "Fail: the string at index $i in the $name array does not have the expected length of $expected_length_id: ${#val} != $expected_length_id"
-      exit 1
-    fi
-  done
-
-  echo "OK: all strings in the $name array have the expected length of $expected_length_id, and the array has the expected number of elements ($expected_array_length)"
-}
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index eebe2356..8f18c202 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -163,7 +163,7 @@ jobs:
         run: .github/scripts/execute-query.sh 444814009 69
 
       - name: Query for Viral sinusitis (disorder) cohort not enabled
-        if: ${{ matrix.test != 'no-auth-cohort-enabled' }}
+        if: ${{ matrix.test == 'no-auth' }}
         run: .github/scripts/execute-cohort-query-not-enabled.sh 444814009
 
       - name: Query for Viral sinusitis (disorder) cohort enabled

From edff3e0d5ff4c3e0763484b515929c1acf5b40a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julian=20Gr=C3=BCndner?= <juliangruendner@googlemail.com>
Date: Thu, 14 Nov 2024 21:28:19 +0100
Subject: [PATCH 31/43] fix api.md

---
 docs/api.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/api.md b/docs/api.md
index 912df69c..b931654c 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -49,7 +49,7 @@ The result of that query could be:
 
 > [!CAUTION]
 > This feature is disabled by default. Be aware that it returns the actual patient IDs (techinal IDs of the FHIR server) for the patients.
-> To enable set the env var FLARE_COHORT_ENABLED=true
+> To enable set the env var FLARE_ENABLE_COHORT_ENDPOINT=true
 
 The ExecuteCohort-Endpoint returns a list of patient ids for patients fitting the criteria of the structured query that is passed in the body of a POST-Request. Also, the POST-Request must contain `application/sq+json` as Content-Type. It can be called like this:
 

From d83c005d72033351b18faf671fcbe19268465d63 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 14 Nov 2024 20:53:03 +0000
Subject: [PATCH 32/43] Update samply/blaze Docker tag to v0.30

---
 .github/integration-test/basic-auth/docker-compose.yml          | 2 +-
 .../integration-test/no-auth-cohort-enabled/docker-compose.yml  | 2 +-
 .github/integration-test/no-auth/docker-compose.yml             | 2 +-
 .github/integration-test/oauth/docker-compose.yml               | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/integration-test/basic-auth/docker-compose.yml b/.github/integration-test/basic-auth/docker-compose.yml
index 0b332f26..9bd9b730 100644
--- a/.github/integration-test/basic-auth/docker-compose.yml
+++ b/.github/integration-test/basic-auth/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.29"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml b/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml
index d8e9cd14..95236ab7 100644
--- a/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml
+++ b/.github/integration-test/no-auth-cohort-enabled/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.29"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/.github/integration-test/no-auth/docker-compose.yml b/.github/integration-test/no-auth/docker-compose.yml
index d6495841..273c19e3 100644
--- a/.github/integration-test/no-auth/docker-compose.yml
+++ b/.github/integration-test/no-auth/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.29"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index 99b609b0..37fbbc09 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -72,7 +72,7 @@ services:
       keycloak:
         condition: service_healthy
   data-store:
-    image: "samply/blaze:0.29"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"

From 8b4b5fc337498b48908f4d0814031d41d8926c75 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 06:27:55 +0000
Subject: [PATCH 33/43] Update dependency
 org.springframework.boot:spring-boot-starter-parent to v3.3.5

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index dab95319..3c8f0266 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.4</version>
+    <version>3.3.5</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 

From 4905be91c80fb7971c0bf8ef469e8200fed4c5cb Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 06:42:15 +0000
Subject: [PATCH 34/43] Update eclipse-temurin Docker tag to v21.0.5_11-jre

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 4e71852c..2f8cc3d5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM eclipse-temurin:21.0.3_9-jre
+FROM eclipse-temurin:21.0.5_11-jre
 
 RUN apt-get update && apt-get upgrade -y && \
     apt-get purge wget libbinutils libctf0 libctf-nobfd0 libncurses6 -y && \

From e7826415ed86e2cdb3e7acb33db2042c7c8feac2 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 07:22:49 +0000
Subject: [PATCH 35/43] Update nginx Docker tag to v1.27.2

---
 .github/integration-test/basic-auth/docker-compose.yml | 2 +-
 .github/integration-test/oauth/docker-compose.yml      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/integration-test/basic-auth/docker-compose.yml b/.github/integration-test/basic-auth/docker-compose.yml
index 9bd9b730..b212f4a0 100644
--- a/.github/integration-test/basic-auth/docker-compose.yml
+++ b/.github/integration-test/basic-auth/docker-compose.yml
@@ -37,7 +37,7 @@ services:
     depends_on:
       - data-store
   proxy:
-    image: "nginx:1.27.1"
+    image: "nginx:1.27.2"
     volumes:
       - "./nginx.conf:/etc/nginx/nginx.conf"
       - "./proxy.htpasswd:/etc/auth/.htpasswd"
diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index 37fbbc09..24dfad06 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -50,7 +50,7 @@ services:
     volumes:
       - "./realm-test.json:/opt/keycloak/data/import/realm-test.json"
   proxy:
-    image: "nginx:1.27.1"
+    image: "nginx:1.27.2"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080"]
       interval: "5s"

From b409391f171323249db64b6f803f0a450097a6c4 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 09:58:40 +0000
Subject: [PATCH 36/43] Update testcontainers-java monorepo to v1.20.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 3c8f0266..e85da458 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,7 +20,7 @@
 
   <properties>
     <java.version>17</java.version>
-    <testcontainers.version>1.20.1</testcontainers.version>
+    <testcontainers.version>1.20.3</testcontainers.version>
     <ontology.version>3.0.0-alpha</ontology.version>
   </properties>
 

From f2df77f2fdd9d90accb32ffbd9a91ed34ff354b3 Mon Sep 17 00:00:00 2001
From: Alexander Kiel <alexanderkiel@gmx.net>
Date: Fri, 15 Nov 2024 11:19:29 +0100
Subject: [PATCH 37/43] Release v2.4.0-alpha.3

---
 CHANGELOG.md       | 9 +++++++++
 README.md          | 6 ++++++
 docker-compose.yml | 2 +-
 pom.xml            | 4 ++--
 4 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a27b3f6..a07cea60 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,16 @@
 # Changelog
 
+## v2.4.0-alpha.3
+
+### Enhancements
+
+* Add Feature Toggle for the Cohort Endpoint ([#217](https://github.com/medizininformatik-initiative/flare/pull/217))
+* Updated ontology to v3.0.0-alpha.1
+
 ## v2.4.0-alpha.2
 
+### Enhancements
+
 * Updated ontology to v3.0.0-alpha
 
 ## v2.4.0-alpha.1
diff --git a/README.md b/README.md
index 09db85eb..b560243e 100644
--- a/README.md
+++ b/README.md
@@ -79,6 +79,12 @@ have the .pem extension.
 
 * [REST API](docs/api.md)
 
+## FHIR Endpoint Requirements
+
+The FHIR endpoint used by FLARE (see `FLARE_FHIR_SERVER`) has to support the following parts of the FHIR specification:
+
+* the search result parameters `_count` and `_elements` should be supported for optimal performance
+
 ## License
 
 Copyright ???
diff --git a/docker-compose.yml b/docker-compose.yml
index 30622073..580ee74d 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.3.0-alpha.2
+    image: ghcr.io/medizininformatik-initiative/flare:2.4.0-alpha.3
     ports:
       - 8080:8080
     volumes:
diff --git a/pom.xml b/pom.xml
index e85da458..a4d26cd7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>flare</artifactId>
-  <version>2.4.0-alpha.2</version>
+  <version>2.4.0-alpha.3</version>
 
   <name>Flare</name>
   <description>Flare</description>
@@ -21,7 +21,7 @@
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.20.3</testcontainers.version>
-    <ontology.version>3.0.0-alpha</ontology.version>
+    <ontology.version>3.0.0-alpha.1</ontology.version>
   </properties>
 
   <dependencies>

From ab20e62fa7edcb2810aa28701ddc07398ca5c84e Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:49:47 +0000
Subject: [PATCH 38/43] Update keycloak/keycloak Docker tag to v25.0.6

---
 .github/integration-test/oauth/docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
index 24dfad06..a655ecb3 100644
--- a/.github/integration-test/oauth/docker-compose.yml
+++ b/.github/integration-test/oauth/docker-compose.yml
@@ -29,7 +29,7 @@ services:
       generate-cert:
         condition: service_completed_successfully
   keycloak:
-    image: "keycloak/keycloak:25.0.4"
+    image: "keycloak/keycloak:25.0.6"
     command: ["start", "--import-realm"]
     healthcheck:
       test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/9000;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]

From d6846784c89085e120ef5a881a1f827440de3c2d Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:38:00 +0000
Subject: [PATCH 39/43] Update dependency
 com.googlecode.maven-download-plugin:download-maven-plugin to v1.11.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a4d26cd7..d6d44744 100644
--- a/pom.xml
+++ b/pom.xml
@@ -197,7 +197,7 @@
       <plugin>
         <groupId>com.googlecode.maven-download-plugin</groupId>
         <artifactId>download-maven-plugin</artifactId>
-        <version>1.9.0</version>
+        <version>1.11.3</version>
         <executions>
           <execution>
             <id>download-ontology</id>

From aeee1d2426f95819427701c67ff5ea7d97bc48a6 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:55:28 +0000
Subject: [PATCH 40/43] Update dependency org.rocksdb:rocksdbjni to v9.7.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index d6d44744..43cbea61 100644
--- a/pom.xml
+++ b/pom.xml
@@ -61,7 +61,7 @@
     <dependency>
       <groupId>org.rocksdb</groupId>
       <artifactId>rocksdbjni</artifactId>
-      <version>9.5.2</version>
+      <version>9.7.3</version>
     </dependency>
 
     <dependency>

From 22dd1182ea0c80913f246433d751969e1b066ac4 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 15:16:17 +0000
Subject: [PATCH 41/43] Update dependency ubuntu to v24

---
 .github/workflows/build.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 8f18c202..eb60b19e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -16,7 +16,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
 
@@ -71,7 +71,7 @@ jobs:
 
   image-scan:
     needs: build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Download Flare Image
@@ -105,7 +105,7 @@ jobs:
 
   integration-test-default-config:
     needs: build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Check out Git repository
@@ -135,7 +135,7 @@ jobs:
           - basic-auth
           - oauth
           - no-auth-cohort-enabled
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Check out Git repository
@@ -176,7 +176,7 @@ jobs:
       - integration-test-default-config
       - integration-test
       - image-scan
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     if: ${{ ! startsWith(github.head_ref, 'dependabot/')}}
 
     steps:

From 94fef0ab5d6d47a40585c975d912ab599672b4da Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 19 Nov 2024 12:12:00 +0000
Subject: [PATCH 42/43] Update dependency
 com.googlecode.maven-download-plugin:download-maven-plugin to v1.12.0

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 43cbea61..d8d273e9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -197,7 +197,7 @@
       <plugin>
         <groupId>com.googlecode.maven-download-plugin</groupId>
         <artifactId>download-maven-plugin</artifactId>
-        <version>1.11.3</version>
+        <version>1.12.0</version>
         <executions>
           <execution>
             <id>download-ontology</id>

From fe4b78a524a998dc92f2eaa89a5b3726cad4cff7 Mon Sep 17 00:00:00 2001
From: Alexander Kiel <alexanderkiel@gmx.net>
Date: Wed, 20 Nov 2024 20:42:44 +0100
Subject: [PATCH 43/43] Release v2.4.0

---
 CHANGELOG.md       | 12 ++++++++++++
 docker-compose.yml |  2 +-
 pom.xml            |  4 ++--
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a07cea60..5f72d077 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # Changelog
 
+## v2.4.0
+
+### Enhancements
+
+* Updated ontology to v3.0.0
+* Add Feature Toggle for the Cohort Endpoint ([#217](https://github.com/medizininformatik-initiative/flare/pull/217))
+* Update mapping_tree creation ([#191](https://github.com/medizininformatik-initiative/flare/issues/191))
+* Add cohort extraction endpoint ([#178](https://github.com/medizininformatik-initiative/flare/issues/178))
+* docker-compose.yml should be for flare instead of blaze ([#184](https://github.com/medizininformatik-initiative/flare/issues/184))
+
+The full changelog can be found [here](https://github.com/medizininformatik-initiative/flare/milestone/15?closed=1).
+ 
 ## v2.4.0-alpha.3
 
 ### Enhancements
diff --git a/docker-compose.yml b/docker-compose.yml
index 580ee74d..ca1dfe08 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.4.0-alpha.3
+    image: ghcr.io/medizininformatik-initiative/flare:2.4.0
     ports:
       - 8080:8080
     volumes:
diff --git a/pom.xml b/pom.xml
index d8d273e9..7eac7274 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>flare</artifactId>
-  <version>2.4.0-alpha.3</version>
+  <version>2.4.0</version>
 
   <name>Flare</name>
   <description>Flare</description>
@@ -21,7 +21,7 @@
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.20.3</testcontainers.version>
-    <ontology.version>3.0.0-alpha.1</ontology.version>
+    <ontology.version>3.0.0</ontology.version>
   </properties>
 
   <dependencies>