Merge pull request #348 from qbicsoftware/feature/nanopore-basecalling-methods

provide method to get basecalling folder and test it

Author: wow-such-code

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

@@ -29,6 +29,8 @@ final class OxfordNanoporeMeasurement {
 
     private boolean pooledSamplesMeasurement
 
+    private boolean hasBasecallingData
+
     protected OxfordNanoporeMeasurement(String name, String path, List children, Map metadata) {
         this.logFilesCollection = new ArrayList<>()
         this.folders = new HashMap<>()
@@ -39,6 +41,7 @@ final class OxfordNanoporeMeasurement {
 
         createContent()
         assessPooledStatus()
+        assessBasecallingStatus()
         assessState()
     }
 
@@ -53,12 +56,16 @@ final class OxfordNanoporeMeasurement {
     private void assessPooledStatus() {
         this.pooledSamplesMeasurement = containsAtLeastOneBarcodedFolder(folders["fast5pass"])
         // There can be still pooled samples in the failed folder, worst case is all
-        // samples failed, so we need to check there to
+        // samples failed, so we need to check there too
         if (! pooledSamplesMeasurement) {
             this.pooledSamplesMeasurement = containsAtLeastOneBarcodedFolder(folders["fast5fail"])
         }
     }
 
+    private void assessBasecallingStatus() {
+        this.hasBasecallingData = folders["basecalling"];
+    }
+
     private static boolean containsAtLeastOneBarcodedFolder(DataFolder folder) {
         if (!folder) {
             return false
@@ -86,6 +93,9 @@ final class OxfordNanoporeMeasurement {
                 case DataFile:
                     logFilesCollection.add(element as DataFile)
                     break
+                case BasecallingFolder:
+                    folders["basecalling"] = element as BasecallingFolder
+                    break
             }
         }
     }
@@ -273,13 +283,14 @@ final class OxfordNanoporeMeasurement {
 
     private Map<String, Map<String, DataFolder>> prepareRawData(String sampleId) {
         final def result = new HashMap()
-        final def folders = [
+        final def dataFolders = [
                 "fast5fail": (folders.get("fast5fail") as DataFolder),
                 "fast5pass": (folders.get("fast5pass") as DataFolder),
                 "fastqpass": (folders.get("fastqpass") as DataFolder),
                 "fastqfail": (folders.get("fastqfail") as DataFolder)
         ]
-        result.put(sampleId, folders)
+        if(hasBasecallingData) dataFolders.put("basecalling", (folders.get("basecalling") as DataFolder))
+        result.put(sampleId, dataFolders)
         return result
     }
 

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

@@ -147,6 +147,11 @@ class OxfordNanoporeExperimentSpec extends Specification {
         assert experiment.sampleCode == "QABCD001AB"
         assert measurements.size() == 1
         assert measurements[0].asicTemp == "32.631687"
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("basecalling")
+        assert !measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").get("basecalling").relativePath.isEmpty()
+        assert !measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").get("basecalling").children.isEmpty()
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").get("basecalling").name.size() > 0
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fastqfail")
     }
 
     def "Create a simple pooled Oxford Nanopore experiment successfully"() {

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

@@ -94,6 +94,7 @@ class OxfordNanoporeMeasurementSpec extends Specification {
         assert result.get("QABCD001AE").get("fast5pass") instanceof DataFolder
         assert result.get("QABCD001AE").get("fastqfail") instanceof DataFolder
         assert result.get("QABCD001AE").get("fastqpass") instanceof DataFolder
+        assert result.get("QABCD001AE").get("basecalling") == null
         assert measurement.relativePath == "path/20200219_1107_1-E3-H3_PAE26974_454b8dc6"
         assert libraryKit == "SQK-LSK109"
         assert adapter.equals("flongle")