Feature/fix testing (#314) (#315)

* add new test case

* use new surefire version to re-enable tests

* reroll unnecessary changes and bump

pom.xml

@@ -7,7 +7,7 @@
 
   <groupId>life.qbic</groupId>
   <artifactId>data-model-lib</artifactId>
-  <version>2.17.0</version> <!-- <<QUBE_FORCE_BUMP>> -->
+  <version>2.17.0</version>
   <name>data-model-lib</name>
   <url>http://github.com/qbicsoftware/data-model-lib</url>
   <description>Data models. A collection of QBiC's central data models and DTOs. </description>
@@ -171,7 +171,7 @@
       </plugin>
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
-        <version>2.22.2</version>
+        <version>3.0.0-M5</version>
         <configuration>
           <includes>
             <include>**/*Spec</include>

src/test/groovy/life/qbic/datamodel/datasets/datastructure/OxfordNanoporeExperimentSpec.groovy

@@ -16,13 +16,13 @@ class OxfordNanoporeExperimentSpec extends Specification {
      * according to the schema
      */
     @Shared
-    Map minimalWorkingSimpleDataStructure
+    Map minimalSimpleDataStructure
     /**
-     * Newer map that stores the Oxford Nanopore folder structure
-     * according to the schema that puts some reports in its own folder and adds a new report
+     * Newer map that stores the Oxford Nanopore folder structure according to the
+     * schema that puts some reports in its own folder and adds a barcode alignment report
      */
     @Shared
-    Map minimalWorkingSimpleDataStructureWithReportsFolder
+    Map extendedDataStructureWithReportsFolder
     /**
      * Map that that stores the Oxford Nanopore folder structure
      * according to the schema containing unclassified read information
@@ -37,23 +37,24 @@ class OxfordNanoporeExperimentSpec extends Specification {
     Map minimalWorkingPooledDataStructure
 
     def setupSpec() {
-        InputStream stream = Thread.currentThread().getContextClassLoader().getResourceAsStream("valid-example.json")
-        minimalWorkingSimpleDataStructure = (Map) new JsonSlurper().parse(stream)
+        def folder = "nanopore/"
+        InputStream stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example.json")
+        minimalSimpleDataStructure = (Map) new JsonSlurper().parse(stream)
         // new example with slightly different structure
-        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream("valid-example-newer.json")
-        minimalWorkingSimpleDataStructureWithReportsFolder = (Map) new JsonSlurper().parse(stream)
+        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example-v2.json")
+        extendedDataStructureWithReportsFolder = (Map) new JsonSlurper().parse(stream)
         // read in unclassified example
-        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream("valid-example-unclassified.json")
+        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example-unclassified.json")
         unclassifiedWorkingDataStructure = (Map) new JsonSlurper().parse(stream)
         // read in pooled example
-        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream("valid-example-pooled.json")
+        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example-pooled.json")
         minimalWorkingPooledDataStructure = (Map) new JsonSlurper().parse(stream)
         stream.close()
     }
 
     def "Create simple sample Oxford Nanopore experiment successfully"() {
         given:
-        final def example = minimalWorkingSimpleDataStructure
+        final def example = minimalSimpleDataStructure
 
         when:
         final def experiment = OxfordNanoporeExperiment.create(example)
@@ -65,9 +66,9 @@ class OxfordNanoporeExperimentSpec extends Specification {
         assert measurements[0].libraryPreparationKit == "SQK-LSK109"
     }
 
-    def "Create simple sample Oxford Nanopore experiment successfully for newer structure"() {
+    def "Create sample Oxford Nanopore experiment successfully for newer structure"() {
         given:
-        final def example = minimalWorkingSimpleDataStructureWithReportsFolder
+        final def example = extendedDataStructureWithReportsFolder
 
         when:
         final def experiment = OxfordNanoporeExperiment.create(example)
@@ -76,7 +77,7 @@ class OxfordNanoporeExperimentSpec extends Specification {
         then:
         assert experiment.sampleCode == "QABCD001AB"
         assert measurements.size() == 1
-        assert measurements[0].libraryPreparationKit == "SQK-LSK109-XL"
+        assert measurements[0].asicTemp == "32.631687"
     }
 
     def "Create a simple pooled Oxford Nanopore experiment successfully"() {