Update Nanopore structure to final version

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

@@ -244,6 +244,7 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
     FAST5_FILE(FQDN_FILES + ".Fast5File"),
     FASTQ_FILE(FQDN_FILES + ".FastQFile"),
     FASTQ_ZIPPED_FILE(FQDN_FILES + ".FastQZippedFile"),
+    BAM_FILE(FQDN_FILES + ".BamFile"),
     POD5_FILE(FQDN_FILES + ".Pod5File"),
     FINAL_SUMMARY_LOG(FQDN_FILES + ".FinalSummaryLog"),
     MUX_SCAN_DATA_LOG(FQDN_FILES + ".MuxScanDataLog"),
@@ -308,6 +309,8 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
     POD5_PASS_FOLDER(FQDN_FOLDERS + ".Pod5PassFolder"),
     POD5_FAIL_FOLDER(FQDN_FOLDERS + ".Pod5FailFolder"),
     POD5_SKIP_FOLDER(FQDN_FOLDERS + ".Pod5SkipFolder"),
+    BAM_PASS_FOLDER(FQDN_FOLDERS + ".BamPassFolder"),
+    BAM_FAIL_FOLDER(FQDN_FOLDERS + ".BamFailFolder"),
     OTHER_REPORTS_FOLDER(FQDN_FOLDERS + ".OtherReportsFolder"),
     BASECALLING_FOLDER(FQDN_FOLDERS + ".BasecallingFolder"),
 

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

@@ -102,6 +102,12 @@ final class OxfordNanoporeMeasurement {
                 case Pod5SkipFolder:
                     folders["pod5skip"] = element as Pod5SkipFolder
                     break
+                case BamPassFolder:
+                    folders["bampass"] = element as BamPassFolder
+                    break
+                case BamFailFolder:
+                    folders["bamfail"] = element as BamFailFolder
+                    break
                 case DataFile:
                     logFilesCollection.add(element as DataFile)
                     break
@@ -118,10 +124,13 @@ final class OxfordNanoporeMeasurement {
         if (areFast5FoldersInMeasurement() && areFastQFoldersInMeasurement()) {
             isValid = true
         }
-        //// We need to ensure that pod5_skip and fast5_skip information is provided if dorado basecaller was used
+        //// We need to ensure that pod5_pass and pod5_fail information is provided if dorado basecaller was used
         if (arePod5FoldersInMeasurement()) {
             isValid = true
         }
+        if (areBamFoldersInMeasurement()) {
+            isValid = true
+        }
         if (isValid == false) {
             throw new IllegalStateException("No valid data is contained in measurement")
         }
@@ -137,7 +146,11 @@ final class OxfordNanoporeMeasurement {
     }
     // Condition three: Don't allow empty Pod5 skip and fast5 skip folder
     private boolean arePod5FoldersInMeasurement() {
-        return isDataFolderInMeasurement("fast5skip") || isDataFolderInMeasurement("pod5skip")
+        return isDataFolderInMeasurement("pod5pass") || isDataFolderInMeasurement("pod5fail")
+    }
+
+    private boolean areBamFoldersInMeasurement() {
+        return isDataFolderInMeasurement("bampass") || isDataFolderInMeasurement("bamfail")
     }
 
     private boolean isDataFolderInMeasurement(String string) {
@@ -159,6 +172,10 @@ final class OxfordNanoporeMeasurement {
      *      "fast5pass": DataFolder
      *      "fastqfail": DataFolder
      *      "fastqpass": DataFolder
+     *      "bamfail": DataFolder
+     *      "bampass": DataFolder
+     *      "pod5fail": DataFolder
+     *      "pod5pass": DataFolder
      * "Other sample code":   // In case of pooled samples
      *      ...
      * @return nested Map with sample codes and data folders
@@ -310,25 +327,18 @@ final class OxfordNanoporeMeasurement {
     private Map<String, Map<String, DataFolder>> prepareRawData(String sampleId) {
         final def result = new HashMap()
         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)
+                "fast5fail": (folders.get("fast5fail") as DataFolder),
+                "fast5pass": (folders.get("fast5pass") as DataFolder),
+                "fast5skip": (folders.get("fast5skip") as DataFolder),
+                "fastqpass": (folders.get("fastqpass") as DataFolder),
+                "fastqfail": (folders.get("fastqfail") as DataFolder),
+                "pod5pass": (folders.get("pod5pass") as DataFolder),
+                "pod5fail": (folders.get("pod5fail") as DataFolder),
+                "pod5skip": (folders.get("pod5skip") as DataFolder),
+                "bampass": (folders.get("bampass") as DataFolder),
+                "bamfail": (folders.get("bamfail") as DataFolder)
         ]
         if (hasBasecallingData) dataFolders.put("basecalling", (folders.get("basecalling") as DataFolder))
-        //Only add dorado based minimal required datafolders if present
-        if (folders.get("fast5skip") != null) {
-            dataFolders.put("fast5skip", (folders.get("fast5skip") as DataFolder))
-        }
-        if (folders.get("pod5skip") != null) {
-            dataFolders.put("pod5skip", (folders.get("pod5skip") as DataFolder))
-        }
-        if (folders.get("pod5fail") != null) {
-            dataFolders.put("pod5fail", (folders.get("pod5fail") as DataFolder))
-        }
-        if (folders.get("pod5pass") != null) {
-            dataFolders.put("pod5pass", (folders.get("pod5pass") as DataFolder))
-        }
         result.put(sampleId, dataFolders)
         return result
     }

src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nanopore/BamFile.groovy

@@ -0,0 +1,30 @@
+package life.qbic.datamodel.datasets.datastructure.files.nanopore
+
+import life.qbic.datamodel.datasets.datastructure.files.DataFile
+
+/**
+ * A specialisation of a DataFile, represents an Oxford Nanopore bam file
+ *
+ */
+class BamFile extends DataFile {
+
+    final private static String FILE_TYPE = "bam"
+
+    final private static String NAME_SCHEMA = /.*\.bam$/
+
+    protected BamFile(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static BamFile create(String name, String relativePath) {
+        return new BamFile(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore summary schema!")
+        }
+    }
+
+}

src/main/groovy/life/qbic/datamodel/datasets/datastructure/folders/nanopore/BamFailFolder.groovy

@@ -0,0 +1,39 @@
+package life.qbic.datamodel.datasets.datastructure.folders.nanopore
+
+import life.qbic.datamodel.datasets.datastructure.folders.DataFolder
+
+/**
+ * A special case of a DataFolder, its name is always bam_fail.
+ *
+ * Its children field contains either a list of type List<BamFiles> or List<BamFolder>
+ *
+ */
+class BamFailFolder extends DataFolder {
+
+    final private static String NAME_SCHEMA = /bam_fail/
+
+    protected BamFailFolder() {}
+
+    protected BamFailFolder(String name, String relativePath, List<?> children) {
+        super(name, relativePath, children)
+        validateName()
+    }
+
+    /**
+     * Creates a new instance of a BamFailFolder object
+     *
+     * @param name The folder name
+     * @param relativePath The relative path of the folder
+     * @param children A list with child elements of the folder
+     * @return A new instance of a BamFailFolder object
+     */
+    static BamFailFolder create(String name, String relativePath, List<?> children) {
+        new BamFailFolder(name, relativePath, children)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore BamFail directory schema!")
+        }
+    }
+}

src/main/groovy/life/qbic/datamodel/datasets/datastructure/folders/nanopore/BamPassFolder.groovy

@@ -0,0 +1,39 @@
+package life.qbic.datamodel.datasets.datastructure.folders.nanopore
+
+import life.qbic.datamodel.datasets.datastructure.folders.DataFolder
+
+/**
+ * A special case of a DataFolder, its name is always bam_pass.
+ *
+ * Its children field contains either a list of type List<BamFiles> or List<BamFolder>
+ *
+ */
+class BamPassFolder extends DataFolder {
+
+    final private static String NAME_SCHEMA = /bam_pass/
+
+    protected BamPassFolder() {}
+
+    protected BamPassFolder(String name, String relativePath, List<?> children) {
+        super(name, relativePath, children)
+        validateName()
+    }
+
+    /**
+     * Creates a new instance of a BamPassFolder object
+     *
+     * @param name The folder name
+     * @param relativePath The relative path of the folder
+     * @param children A list with child elements of the folder
+     * @return A new instance of a BamPassFolder object
+     */
+    static BamPassFolder create(String name, String relativePath, List<?> children) {
+        new BamPassFolder(name, relativePath, children)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore BamPass directory schema!")
+        }
+    }
+}

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

@@ -62,7 +62,10 @@ class OxfordNanoporeExperimentSpec extends Specification {
     Map minimalDataStructurePooled
 
     @Shared
-    Map minimalDoradoDataStructure
+    Map minimalPod5DoradoDataStructure
+
+    @Shared
+    Map minimalBamDoradoDataStructure
 
     @Shared
     Map fullDoradoDataStructure
@@ -96,8 +99,12 @@ class OxfordNanoporeExperimentSpec extends Specification {
         stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-minimal-structure-pooled.json")
         minimalDataStructurePooled = (Map) new JsonSlurper().parse(stream)
         // read in minimal required example with dorado based basecalling
-        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-minimal-structure-dorado-basecaller.json")
-        minimalDoradoDataStructure = (Map) new JsonSlurper().parse(stream)
+        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-minimal-structure-pod5-dorado-basecaller.json")
+        minimalPod5DoradoDataStructure = (Map) new JsonSlurper().parse(stream)
+        stream.close()
+        // read in minimal required example with dorado based basecalling
+        stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-minimal-structure-bam-dorado-basecaller.json")
+        minimalBamDoradoDataStructure = (Map) new JsonSlurper().parse(stream)
         stream.close()
         // read in minimal required example with dorado based basecalling
         stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example-dorado-basecaller.json")
@@ -210,9 +217,9 @@ class OxfordNanoporeExperimentSpec extends Specification {
         assert measurements[0].asicTemp == "32.631687"
     }
 
-    def "Create sample Oxford Nanopore experiment successfully for dorado basecaller generated minimal structure"() {
+    def "Create sample Oxford Nanopore experiment successfully for pod5 generated minimal structure"() {
         given:
-        final def example = minimalDoradoDataStructure
+        final def example = minimalPod5DoradoDataStructure
 
         when:
         final def experiment = OxfordNanoporeExperiment.create(example)
@@ -222,8 +229,24 @@ 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("pod5skip")
-        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fast5skip")
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("pod5pass")
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("pod5fail")
+    }
+
+    def "Create sample Oxford Nanopore experiment successfully for bam generated minimal structure"() {
+        given:
+        final def example = minimalBamDoradoDataStructure
+
+        when:
+        final def experiment = OxfordNanoporeExperiment.create(example)
+        final def measurements = experiment.getMeasurements()
+
+        then:
+        assert experiment.sampleCode == "QABCD001AB"
+        assert measurements.size() == 1
+        assert measurements[0].asicTemp == "32.631687"
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("bampass")
+        assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("bamfail")
     }
 
     def "Create sample Oxford Nanopore experiment successfully for dorado basecaller generated full structure"() {