Make runID optional for nf-core registration (#374)

src/main/groovy/life/qbic/datamodel/datasets/NfCorePipelineResult.groovy

@@ -45,6 +45,7 @@ final class NfCorePipelineResult {
 
     private SampleIds sampleIds
 
+    // The RunId is only generated if the result was generated by a NF-Tower instance
     private RunId runId
 
     private PipelineInformationFolder pipelineInformationFolder
@@ -53,7 +54,7 @@ final class NfCorePipelineResult {
 
     private List<DataFolder> processFolders
 
-    NfCorePipelineResult(PipelineInformationFolder pipelineInformationFolder, QualityControlFolder qualityControlFolder, List<DataFolder> processFolders,  RunId runId, SampleIds sampleIds) {
+    NfCorePipelineResult(PipelineInformationFolder pipelineInformationFolder, QualityControlFolder qualityControlFolder, List<DataFolder> processFolders, RunId runId, SampleIds sampleIds) {
         Objects.requireNonNull(pipelineInformationFolder, "Please provide a PipelineInformation folder.")
         Objects.requireNonNull(qualityControlFolder, "Please provide a QualityControl folder")
         Objects.requireNonNull(processFolders, "Please provide a List of process folders")
@@ -67,6 +68,17 @@ final class NfCorePipelineResult {
         this.sampleIds = sampleIds
     }
 
+    NfCorePipelineResult(PipelineInformationFolder pipelineInformationFolder, QualityControlFolder qualityControlFolder, List<DataFolder> processFolders, SampleIds sampleIds) {
+        Objects.requireNonNull(pipelineInformationFolder, "Please provide a PipelineInformation folder.")
+        Objects.requireNonNull(qualityControlFolder, "Please provide a QualityControl folder")
+        Objects.requireNonNull(processFolders, "Please provide a List of process folders")
+        Objects.requireNonNull(sampleIds, "Please provide a sampleIds file")
+        this.pipelineInformationFolder = pipelineInformationFolder
+        this.qualityControlFolder = qualityControlFolder
+        this.processFolders = processFolders
+        this.sampleIds = sampleIds
+    }
+
     /**
      * Static factory method that creates a new nfcoreExperiment instance from the bioinformatic pipeline output.
      * See this @{link <a href="https://github.com/qbicsoftware/data-model-lib/blob/master/src/test/resources/examples/resultset/valid-resultset-example.json">example</a>}
@@ -80,14 +92,13 @@ final class NfCorePipelineResult {
 
         //Check if all required folders are in root directory
         Objects.requireNonNull(bioinformaticPipelineOutput.get("pipelineInformation"), "The root folder must contain a PipelineInformation folder.")
-        Objects.requireNonNull(bioinformaticPipelineOutput.get("qualityControl"),"The root folder must contain a QualityControl folder.")
+        Objects.requireNonNull(bioinformaticPipelineOutput.get("qualityControl"), "The root folder must contain a QualityControl folder.")
         Objects.requireNonNull(bioinformaticPipelineOutput.get("processFolders"), "The root folder must contain at least one process folder.")
         //Check if all required files are in the pipeline_info directory
         Map pipelineInfoMap = bioinformaticPipelineOutput["pipelineInformation"] as Map
         Objects.requireNonNull(pipelineInfoMap.get("softwareVersions"), "The pipeline_info folder must contain a softwareVersions.yml file.")
         Objects.requireNonNull(pipelineInfoMap.get("executionReport"), "The pipeline_info folder must contain a executionReport.html file.")
         //Check if all required files are in root directory
-        Objects.requireNonNull(bioinformaticPipelineOutput.get("runId"), "The root folder must contain a run_id.txt file.")
         Objects.requireNonNull(bioinformaticPipelineOutput.get("sampleIds"), "The root folder must contain an sample_ids.txt file.")
 
         //Parse all folders in the root directory
@@ -108,12 +119,16 @@ final class NfCorePipelineResult {
         pipelineInformation.softwareVersions = softwareVersions as SoftwareVersions
         pipelineInformation.executionReport = executionReport as ExecutionReport
 
-        //Parse all files in the root directory
-        DataFile runId = parseFile(bioinformaticPipelineOutput.get("runId") as Map) as RunId
+        //Parse all mandatory files in the root directory
         DataFile sampleIds = parseFile(bioinformaticPipelineOutput.get("sampleIds") as Map) as SampleIds
 
-        //Create new NfCorePipelineResult with parsed information
-        return new NfCorePipelineResult(pipelineInformation, qualityControl, processFolders, runId, sampleIds)
+        // Parse optional Files in the root directory and generate NfCorePipelineResult accordingly
+        if (bioinformaticPipelineOutput.get("runId") != null) {
+            DataFile runId = parseFile(bioinformaticPipelineOutput.get("runId") as Map) as RunId
+            return new NfCorePipelineResult(pipelineInformation, qualityControl, processFolders, runId, sampleIds)
+        } else {
+            return new NfCorePipelineResult(pipelineInformation, qualityControl, processFolders, sampleIds)
+        }
     }
 
     /**
@@ -165,11 +180,12 @@ final class NfCorePipelineResult {
     /*
      * Helper method that creates a DataFile instance from a map
      */
+
     private static DataFile parseFile(Map fileTree) throws IllegalArgumentException {
         String name = fileTree.get("name")
         String fileType = fileTree.get("fileType")
         String path = fileTree.get("path")
-        
+
         for (String nfCoreFileType : nfCoreFileTypes) {
             Class<?> c = Class.forName(nfCoreFileType)
             Method method = c.getDeclaredMethod("create", String.class, String.class)
@@ -183,15 +199,15 @@ final class NfCorePipelineResult {
             }
         }
         // We have to check for files of unknown type since this Parser will encounter variable file output dependent on the pipeline
-        if(!fileType)
-        {
-        throw new IllegalArgumentException("File $name with path $path is of unknown nfcore file type.")
+        if (!fileType) {
+            throw new IllegalArgumentException("File $name with path $path is of unknown nfcore file type.")
         }
     }
 
     /*
      * Helper method that creates a DataFolder instance from a map
      */
+
     private static DataFolder parseFolder(Map fileTree) throws IllegalArgumentException {
 
         def name = fileTree.get("name") as String
@@ -215,25 +231,27 @@ final class NfCorePipelineResult {
      * Helper method that tries to create a DataFolder instance
      * based on the DataFolder's different static factory create methods.
      */
+
     private static Optional<DataFolder> tryToCreateDataFolder(Method method,
                                                               String name,
                                                               String relativePath,
                                                               List children) {
         Optional<DataFolder> folder = Optional.empty()
-            try {
-                // We only have named Folders
-                def dataFolder = method.invoke(null, name, relativePath, children) as DataFolder
-                folder = Optional.of(dataFolder)
-            } catch (InvocationTargetException e2) {
-                // Do nothing
-            }
+        try {
+            // We only have named Folders
+            def dataFolder = method.invoke(null, name, relativePath, children) as DataFolder
+            folder = Optional.of(dataFolder)
+        } catch (InvocationTargetException e2) {
+            // Do nothing
+        }
 
         return folder
     }
 
     /*
      * Helper method that parses the children of a folder.
      */
+
     private static List parseChildren(List<Map> children) {
         def parsedChildren = []
         children.each { Map unknownChild ->

src/main/resources/schemas/bioinformatics-analysis-result-set.schema.json

@@ -115,7 +115,6 @@
     "pipelineInformation",
     "qualityControl",
     "processFolders",
-    "sampleIds",
-    "runId"
+    "sampleIds"
   ]
 }

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

@@ -35,6 +35,9 @@ class NfCorePipelineResultSpec extends Specification {
     @Shared
     Map missingQualityControlDataStructure
 
+    @Shared
+    Map validDataStructureWithoutRunId
+
     def setupSpec() {
         InputStream validStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("examples/resultset/valid-resultset-example.json")
         validDataStructure = (Map) new JsonSlurper().parse(validStream)
@@ -55,6 +58,10 @@ class NfCorePipelineResultSpec extends Specification {
         InputStream missingQualityControlStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("examples/resultset/missing-quality-control-resultset-example.json")
         missingQualityControlDataStructure = (Map) new JsonSlurper().parse(missingQualityControlStream)
         missingQualityControlStream.close()
+
+        InputStream validStreamWithoutRunId = Thread.currentThread().getContextClassLoader().getResourceAsStream("examples/resultset/valid-resultset-no-run_id-example.json")
+        validDataStructureWithoutRunId = (Map) new JsonSlurper().parse(validStreamWithoutRunId)
+        validStreamWithoutRunId.close()
     }
 
     def "Create NfCorePipelineOutput from Map successfully"() {
@@ -122,4 +129,24 @@ class NfCorePipelineResultSpec extends Specification {
         thrown(NullPointerException)
     }
 
+    def "Create NfCorePipelineOutput from Map without RunId successfully"() {
+        given:
+        final Map validExample = validDataStructureWithoutRunId
+
+        when:
+        final NfCorePipelineResult validPipelineResult = NfCorePipelineResult.createFrom(validExample)
+        SampleIds sampleIds = validPipelineResult.getSampleIds()
+        List<DataFolder> processFolders = validPipelineResult.getProcessFolders()
+        QualityControlFolder qualityControlFolder = validPipelineResult.getQualityControlFolder()
+        PipelineInformationFolder pipelineInformationFolder = validPipelineResult.getPipelineInformation()
+
+        then:
+        sampleIds.name == "sample_ids.txt"
+        processFolders.get(0).name == "salmon"
+        qualityControlFolder.name == "multiqc"
+        pipelineInformationFolder.getSoftwareVersions().name == "software_versions.yml"
+        pipelineInformationFolder.getExecutionReport().name == "execution_report.html"
+        assert validPipelineResult.runId == null
+    }
+
 }

src/test/resources/examples/resultset/valid-resultset-no-run_id-example.json

@@ -0,0 +1,52 @@
+{
+  "pipelineInformation": {
+    "name": "pipeline_info",
+    "path": "./pipeline_info",
+    "children": [],
+    "softwareVersions": {
+      "name": "software_versions.yml",
+      "fileType": "yml",
+      "path": "./pipeline_info/software_versions.yml"
+    },
+    "executionReport": {
+      "name": "execution_report.html",
+      "fileType": "html",
+      "path": "./pipeline_info/execution_report.html"
+    }
+  },
+  "qualityControl": {
+    "name": "multiqc",
+    "path": "./multiqc",
+    "children": [
+      {
+        "name": "star_salmon",
+        "path": "./multiqc/star_salmon",
+        "children": [
+          {
+            "name": "multiqc_report.html",
+            "path": "./multiqc/star_salmon/multiqc_report.html",
+            "fileType": "html"
+          }
+        ]
+      }
+    ]
+  },
+  "processFolders": [
+    {
+      "name": "salmon",
+      "path": "./salmon",
+      "children": [
+        {
+          "name": "salmon.merged.gene_tpm.tsv",
+          "fileType": "tsv",
+          "path": "./salmon/salmon.merged.gene_tpm.tsv"
+        }
+      ]
+    }
+  ],
+  "sampleIds": {
+    "name": "sample_ids.txt",
+    "fileType": "txt",
+    "path": "./sample_ids.txt"
+  }
+}