Update NF-Core Parser to use new NF-Core output (#104)

* Adapt filesuffixes to sarekv3

* Adapt Parser and test to sarekv3

* Update pom.xml to data-model-lib release

* Update groovy version in pom.xml to the one also supplied by the data-model-lib release

pom.xml

@@ -15,6 +15,7 @@
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>
     <log4j.version>2.17.1</log4j.version>
+    <groovy.version>3.0.10</groovy.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
   </properties>
@@ -83,7 +84,7 @@
       <dependency>
         <groupId>org.codehaus.groovy</groupId>
         <artifactId>groovy-bom</artifactId>
-        <version>3.0.9</version>
+        <version>${groovy.version}</version>
         <type>pom</type>
         <scope>import</scope>
       </dependency>
@@ -93,7 +94,7 @@
     <dependency>
       <groupId>org.codehaus.groovy</groupId>
       <artifactId>groovy-all</artifactId>
-      <version>3.0.9</version>
+      <version>${groovy.version}</version>
       <type>pom</type>
     </dependency>
 
@@ -127,7 +128,7 @@
     <dependency>
       <artifactId>data-model-lib</artifactId>
       <groupId>life.qbic</groupId>
-      <version>2.19.0</version>
+      <version>2.20.0</version>
     </dependency>
     <dependency>
       <groupId>org.mockito</groupId>

src/main/groovy/life/qbic/utils/BioinformaticAnalysisParser.groovy

@@ -81,7 +81,6 @@ class BioinformaticAnalysisParser implements DatasetParser<NfCorePipelineResult>
     enum RequiredPipelineFileKeys {
         SOFTWARE_VERSIONS("softwareVersions"),
         EXECUTION_REPORT("executionReport"),
-        PIPELINE_REPORT("pipelineReport")
 
         private String keyName
 
@@ -184,19 +183,14 @@ class BioinformaticAnalysisParser implements DatasetParser<NfCorePipelineResult>
      *     "path": "./pipeline_info",
      *     "children": [],
      *     "softwareVersions": {
-     *       "name": "software_versions.csv",
-     *       "fileType": "csv",
-     *       "path": "./pipeline_info/software_versions.csv"
+     *       "name": "software_versions.yml",
+     *       "fileType": "yml",
+     *       "path": "./pipeline_info/software_versions.yml"
      *     },
-     *     "pipelineReport": {
-     *       "name": "pipeline_report.txt",
-     *       "fileType": "txt",
-     *       "path": "./pipeline_info/pipeline_report.txt"*
-     *       },
      *     "executionReport": {
-     *       "name": "execution_report.txt",
-     *       "fileType": "txt",
-     *       "path": "./pipeline_info/execution_report.txt"
+     *       "name": "execution_report.html",
+     *       "fileType": "html",
+     *       "path": "./pipeline_info/execution_report.html"
      *     }
      *   }
      * @param pipelineInformation the folder containing the pipeline information
@@ -207,15 +201,12 @@ class BioinformaticAnalysisParser implements DatasetParser<NfCorePipelineResult>
 
         pipelineInformation.get("children").each { Map child ->
             switch (child.get("name")) {
-                case "software_versions.csv":
+                case "software_versions.yml":
                     insertAsProperty(pipelineInformation, child, RequiredPipelineFileKeys.SOFTWARE_VERSIONS.getKeyName())
                     break
-                case "execution_report.txt":
+                case "execution_report.html":
                     insertAsProperty(pipelineInformation, child, RequiredPipelineFileKeys.EXECUTION_REPORT.getKeyName())
                     break
-                case "pipeline_report.txt":
-                    insertAsProperty(pipelineInformation, child, RequiredPipelineFileKeys.PIPELINE_REPORT.getKeyName())
-                    break
                 default:
                     //ignoring other children
                     break

src/test/groovy/life/qbic/utils/BioinformaticAnalysisSpec.groovy

@@ -2,7 +2,6 @@ package life.qbic.utils
 
 import life.qbic.datamodel.datasets.NfCorePipelineResult
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.ExecutionReport
-import life.qbic.datamodel.datasets.datastructure.files.nfcore.PipelineReport
 import life.qbic.datamodel.datasets.datastructure.files.nfcore.SoftwareVersions
 import life.qbic.datamodel.datasets.datastructure.folders.DataFolder
 import life.qbic.datamodel.datasets.datastructure.folders.nfcore.PipelineInformationFolder
@@ -57,16 +56,12 @@ class BioinformaticAnalysisSpec extends Specification {
         //Files in Root folders can be parsed
 
         SoftwareVersions softwareVersions = pipelineInfo.getSoftwareVersions()
-        assert softwareVersions.getRelativePath() == "./pipeline_info/software_versions.csv"
-        assert softwareVersions.getName() == "software_versions.csv"
-
-        PipelineReport pipelineReport = pipelineInfo.getPipelineReport()
-        assert pipelineReport.getRelativePath() == "./pipeline_info/pipeline_report.txt"
-        assert pipelineReport.getName() == "pipeline_report.txt"
+        assert softwareVersions.getRelativePath() == "./pipeline_info/software_versions.yml"
+        assert softwareVersions.getName() == "software_versions.yml"
 
         ExecutionReport executionReport = pipelineInfo.getExecutionReport()
-        assert executionReport.getRelativePath() == "./pipeline_info/execution_report.txt"
-        assert executionReport.getName() == "execution_report.txt"
+        assert executionReport.getRelativePath() == "./pipeline_info/execution_report.html"
+        assert executionReport.getName() == "execution_report.html"
 
 
     }
@@ -109,7 +104,7 @@ class BioinformaticAnalysisSpec extends Specification {
 
     def "parsing a file throws a DataParserException"() {
         given:
-        def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/pipeline_info/execution_report.txt")
+        def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/pipeline_info/execution_report.html")
         when:
         bioinformaticAnalysisParser.parseFrom(pathToDirectory)
         then: