Merge pull request #171 from medizininformatik-initiative/release-v2.3.0

Release v2.3.0

.github/integration-test/basic-auth/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.26.2"
+    image: "samply/blaze:0.28"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"

.github/integration-test/no-auth/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.26.2"
+    image: "samply/blaze:0.28"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"

.github/integration-test/oauth/docker-compose.yml

@@ -72,7 +72,7 @@ services:
       keycloak:
         condition: service_healthy
   data-store:
-    image: "samply/blaze:0.26.2"
+    image: "samply/blaze:0.28"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"

.github/workflows/build.yml

@@ -6,7 +6,7 @@ on:
     - main
     - develop
     tags:
-    - '*.*.*'
+    - 'v*.*.*'
   pull_request:
     branches:
     - main

CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## v2.3.0
+
+### Enhancements
+
+* Update Ontology to Version v2.2.0
+
+## v2.3.0-rc.1
+
+### Enhancements
+
+* Update Ontology to Version v2.2.0-RC ([#163](https://github.com/medizininformatik-initiative/flare/issues/163))
+
+The full changelog can be found [here](https://github.com/medizininformatik-initiative/flare/milestone/14?closed=1).
+
 ## v2.2.0
 
 ### Enhancements

DEVELOPMENT.md

@@ -10,7 +10,7 @@
 * create a PR from the release branch into main
 * merge that PR
 * create and push a tag called `v<version>` like `v0.1.1` on main at the merge commit
-* create a new branch called `next-dev` on top of the release branch
+* create a new branch called `next-dev` on top of the main branch
 * change the version in the POM to the next SNAPSHOT version which usually increments the minor version  
 * merge the `next-dev` branch back into develop
 * create release notes on GitHub

README.md

@@ -29,7 +29,7 @@ mvn clean install
 ## Run
 
 ```sh
-docker run -p 8080:8080 ghcr.io/medizininformatik-initiative/flare:2.2
+docker run -p 8080:8080 ghcr.io/medizininformatik-initiative/flare:2.3
 ```
 
 ## Environment Variables

docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.26"
+    image: "samply/blaze:0.28"
     environment:
       BASE_URL: "http://localhost:8082"
       JAVA_TOOL_OPTIONS: "-Xmx1g"

pom.xml

@@ -7,21 +7,21 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.0</version>
+    <version>3.3.1</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>flare</artifactId>
-  <version>2.2.0</version>
+  <version>2.3.0</version>
 
   <name>Flare</name>
   <description>Flare</description>
 
   <properties>
     <java.version>17</java.version>
     <testcontainers.version>1.19.8</testcontainers.version>
-    <ontology.version>2.1.27</ontology.version>
+    <ontology.version>2.2.0</ontology.version>
   </properties>
 
   <dependencies>

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:0.26")
+    private final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.28")
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withExposedPorts(8080)

src/test/java/de/medizininformatikinitiative/flare/service/StructuredQueryServiceIT.java

@@ -39,7 +39,7 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
-import java.util.zip.ZipFile;
+import java.util.stream.Stream;
 
 import static java.util.function.Function.identity;
 import static org.assertj.core.api.Assertions.assertThat;
@@ -60,7 +60,7 @@ class StructuredQueryServiceIT {
 
     @Container
     @SuppressWarnings("resource")
-    private static final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.26")
+    private static final GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.28")
             .withImagePullPolicy(PullPolicy.alwaysPull())
             .withEnv("LOG_LEVEL", "debug")
             .withEnv("DB_SEARCH_PARAM_BUNDLE", "/app/custom-search-parameters.json")
@@ -97,10 +97,12 @@ private static Path resourcePathFlareApplication(String name) throws URISyntaxEx
     }
 
     public static List<StructuredQuery> getTestQueriesReturningOnePatient() throws URISyntaxException, IOException {
-        try (var zipFile = new ZipFile(resourcePathFlareApplication("testCases").resolve("returningOnePatient.zip").toString())) {
-            return zipFile.stream().map(entry -> {
+        Path directoryPath = Paths.get(resourcePathFlareApplication("testCases").resolve("returningOnePatient").toString());
+
+        try (Stream<Path> paths = Files.list(directoryPath)) {
+            return paths.map(path -> {
                 try {
-                    return new ObjectMapper().readValue(zipFile.getInputStream(entry), StructuredQuery.class);
+                    return new ObjectMapper().readValue(Files.readString(path), StructuredQuery.class);
                 } catch (IOException e) {
                     throw new RuntimeException(e);
                 }
@@ -134,15 +136,6 @@ void execute_Criterion() {
         assertThat(result).isOne();
     }
 
-    @Test
-    void execute_Criterion_WithValueFilter() {
-        var query = StructuredQuery.of(CriterionGroup.of(CriterionGroup.of(Criterion.of(ContextualConcept.of(OBSERVATION, Concept.of(COVID)), ValueFilter.ofConcept(INVALID)))));
-
-        var result = service.execute(query).block();
-
-        assertThat(result).isOne();
-    }
-
     @Test
     void execute_genderTestCase() throws URISyntaxException, IOException {
         var query = parseSq(Files.readString(resourcePathFlareApplication("testCases").resolve("returningOther").resolve("2-gender.json")));

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/1-age.json

@@ -0,0 +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#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/Diagnose-f728b4fa-4248-5e3a-0a5d-2f346baa9455

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "I08.0", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm"}], "context": {"code": "Diagnose", "display": "Diagnose", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/MedicationAdministration-aedab7b5-e2aa-55a7-4951-03edfd05a5f5

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "P01CA", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/atc"}], "context": {"code": "Medikamentenverabreichung", "display": "Verabreichung von Medikamenten", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/ObservationLab-0a02da60-749d-4601-df98-377981bd5336

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "800-3", "display": "", "system": "http://loinc.org"}], "context": {"code": "Laboruntersuchung", "display": "Laboruntersuchung", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/Procedure-d7de701d-8eaf-b323-5f65-380029c836e0

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "5-403.05", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/ops"}], "context": {"code": "Procedure", "display": "Prozedur", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/Specimen-e3e70682-c209-4cac-629f-6fbed82c07cd

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "396997002", "display": "", "system": "http://snomed.info/sct"}], "context": {"code": "Specimen", "display": "Bioprobe", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}

src/test/resources/de/medizininformatikinitiative/flare/testCases/returningOnePatient/Todesursache-31307e46-af79-7546-7e51-68dc5690f74d

@@ -0,0 +1 @@
+{"inclusionCriteria": [[{"attributeFilters": [], "termCodes": [{"code": "S14.11", "display": "", "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm"}], "context": {"code": "Diagnose", "display": "Diagnose", "system": "fdpg.mii.cds", "version": "1.0.0"}}]], "version": "http://to_be_decided.com/draft-1/schema#"}