Merge branch 'development' into feature/#988-close-dialogs-in-the-mea…

…surement-view-on-browser-navigation
qbicsoftware · Jan 27, 2025 · eb6b83f · eb6b83f
2 parents 1838fca + dc2808b
commit eb6b83f
Show file tree

Hide file tree

Showing 28 changed files with 537 additions and 141 deletions.
diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - development
+      - main
   pull_request:
     branches:
       - development

diff --git a/THIRD-PARTY.txt b/THIRD-PARTY.txt
diff --git a/application-commons/pom.xml b/application-commons/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>application-commons</artifactId>

diff --git a/broadcasting/pom.xml b/broadcasting/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>broadcasting</artifactId>

diff --git a/domain-concept/pom.xml b/domain-concept/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <artifactId>domain-concept</artifactId>

diff --git a/email-service-provider/pom.xml b/email-service-provider/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <groupId>life.qbic.infrastructure</groupId>
@@ -21,13 +21,13 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>identity</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>project-management</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

diff --git a/finances-api/pom.xml b/finances-api/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <groupId>life.qbic.finances</groupId>

diff --git a/finances-infrastructure/pom.xml b/finances-infrastructure/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <artifactId>finances-infrastructure</artifactId>
@@ -20,7 +20,7 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>finances</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

diff --git a/finances/pom.xml b/finances/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>finances</artifactId>
@@ -38,7 +38,7 @@
     <dependency>
       <groupId>life.qbic.finances</groupId>
       <artifactId>finances-api</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/identity-api/pom.xml b/identity-api/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <groupId>life.qbic.datamanager</groupId>
@@ -21,7 +21,7 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>application-commons</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/identity-infrastructure/pom.xml b/identity-infrastructure/pom.xml
@@ -6,14 +6,14 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <artifactId>identity-infrastructure</artifactId>
   <dependencies>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>identity</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

diff --git a/identity/pom.xml b/identity/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 
@@ -45,25 +45,25 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>broadcasting</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>application-commons</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>logging</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>domain-concept</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -86,7 +86,7 @@
     <dependency>
       <groupId>life.qbic.datamanager</groupId>
       <artifactId>identity-api</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/logging/pom.xml b/logging/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>logging</artifactId>
@@ -31,7 +31,7 @@
       <dependency>
         <groupId>ch.qos.logback</groupId>
         <artifactId>logback-core</artifactId>
-        <version>1.5.11</version>
+        <version>1.5.16</version>
       </dependency>
     </dependencies>
   </dependencyManagement>
@@ -53,7 +53,7 @@
     <dependency>
       <groupId>life.qbic.logging</groupId>
       <artifactId>subscription-api</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
   <groupId>life.qbic</groupId>
   <artifactId>datamanager</artifactId>
   <name>Data Manager</name>
-  <version>1.6.6</version>
+  <version>1.7.2</version>
   <modules>
     <module>user-interface</module>
     <module>identity</module>
@@ -146,14 +146,14 @@
       <dependency>
         <groupId>org.apache.groovy</groupId>
         <artifactId>groovy-all</artifactId>
-        <version>4.0.23</version>
+        <version>4.0.24</version>
         <type>pom</type>
         <scope>test</scope>
       </dependency>
       <dependency>
         <groupId>org.jobrunr</groupId>
         <artifactId>jobrunr-spring-boot-3-starter</artifactId>
-        <version>7.3.1</version>
+        <version>7.3.2</version>
       </dependency>
       <dependency>
         <groupId>com.fasterxml.jackson.core</groupId>
@@ -182,6 +182,25 @@
   </dependencyManagement>
   <build>
     <plugins>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>license-maven-plugin</artifactId>
+        <version>2.0.0</version> <!-- Use the latest version -->
+        <executions>
+          <execution>
+            <goals>
+              <goal>aggregate-add-third-party</goal>
+            </goals>
+          </execution>
+        </executions>
+        <configuration>
+          <!-- Configuration for licenses aggregation -->
+          <outputDirectory>${project.build.directory}/generated-sources/license</outputDirectory>
+          <thirdPartyFilename>THIRD-PARTY.txt</thirdPartyFilename>
+          <failIfWarning>false</failIfWarning> <!-- Optional: fail the build on issues -->
+          <includeTransitiveDependencies>true</includeTransitiveDependencies>
+        </configuration>
+      </plugin>
       <plugin>
         <groupId>org.codehaus.gmavenplus</groupId>
         <artifactId>gmavenplus-plugin</artifactId>
@@ -220,7 +239,7 @@
       </plugin>
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
-        <version>3.5.1</version>
+        <version>3.5.2</version>
         <configuration>
           <useModulePath>false</useModulePath>
           <includes>

diff --git a/project-management-infrastructure/pom.xml b/project-management-infrastructure/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>life.qbic</groupId>
     <artifactId>datamanager</artifactId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
 
   <groupId>life.qbic.identity</groupId>
@@ -29,7 +29,7 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>project-management</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

diff --git a/project-management/pom.xml b/project-management/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>datamanager</artifactId>
     <groupId>life.qbic</groupId>
-    <version>1.6.6</version>
+    <version>1.7.2</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>project-management</artifactId>
@@ -37,13 +37,13 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>application-commons</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>logging</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -54,7 +54,7 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>domain-concept</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -77,13 +77,13 @@
     <dependency>
       <groupId>life.qbic.datamanager</groupId>
       <artifactId>identity-api</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic.finances</groupId>
       <artifactId>finances-api</artifactId>
-      <version>1.6.6</version>
+      <version>1.7.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

diff --git a/...src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java b/...src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java
@@ -23,6 +23,7 @@
 import life.qbic.projectmanagement.application.OrganisationLookupService;
 import life.qbic.projectmanagement.application.ProjectInformationService;
 import life.qbic.projectmanagement.application.ontology.SpeciesLookupService;
+import life.qbic.projectmanagement.application.ontology.TerminologyService;
 import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.domain.model.OntologyTerm;
@@ -65,28 +66,29 @@ public class MeasurementService {
   private final MeasurementDomainService measurementDomainService;
   private final MeasurementLookupService measurementLookupService;
   private final SampleInformationService sampleInformationService;
-  private final SpeciesLookupService speciesLookupService;
   private final OrganisationLookupService organisationLookupService;
   private final ProjectInformationService projectInformationService;
   private final MeasurementRepository measurementRepository;
+  private final TerminologyService terminologyService;
 
   @Autowired
   public MeasurementService(MeasurementDomainService measurementDomainService,
       SampleInformationService sampleInformationService,
-      SpeciesLookupService speciesLookupService,
       OrganisationLookupService organisationLookupService,
       MeasurementLookupService measurementLookupService,
       ProjectInformationService projectInformationService,
       MeasurementRepository measurementRepository,
+      TerminologyService terminologyService,
       ApplicationContext context) {
     this.measurementDomainService = Objects.requireNonNull(measurementDomainService);
     this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
-    this.speciesLookupService = Objects.requireNonNull(speciesLookupService);
     this.organisationLookupService = Objects.requireNonNull(organisationLookupService);
     this.measurementLookupService = Objects.requireNonNull(measurementLookupService);
     this.projectInformationService = Objects.requireNonNull(projectInformationService);
     this.measurementRepository = Objects.requireNonNull(measurementRepository);
     this.context = Objects.requireNonNull(context);
+    this.terminologyService = Objects.requireNonNull(terminologyService);
+
   }
 
   /**
@@ -778,7 +780,7 @@ private boolean allMeasurementCodesExist(List<String> measurementCode) {
   }
 
   private Optional<OntologyTerm> resolveOntologyCURI(String ontologyCURI) {
-    return speciesLookupService.findByCURI(ontologyCURI).map(OntologyTerm::from);
+    return terminologyService.findByCurie(ontologyCURI);
   }
 
   private Optional<SampleIdCodeEntry> queryIdCodePair(SampleCode sampleCode) {