Support nanopore data structure v3 (#328)

* add new version of valid nanopore structure

* implement additional v3 changes

* Update schema and test to current file structure

Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>

Author: wow-such-code

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

@@ -33,9 +33,14 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
             FQDN_FILES + ".MuxScanDataLog",
             FQDN_FILES + ".ReportMdLog",
             FQDN_FILES + ".ReportPDFLog",
+            FQDN_FILES + ".ReportHTMLLog",
+            FQDN_FILES + ".ReportJSONLog",
             FQDN_FILES + ".SequencingSummaryLog",
             FQDN_FILES + ".ThroughputLog",
-            FQDN_FILES + ".BarcodeAlignmentLog"
+            FQDN_FILES + ".BarcodeAlignmentLog",
+            FQDN_FILES + ".PoreActivityLog",
+            FQDN_FILES + ".SampleSheetLog",
+            FQDN_FILES + ".PoreScanDataLog"
     ]
 
     private final static Set nanoporeFolderTypes = [

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

@@ -0,0 +1,32 @@
+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 pore activity log file
+ *
+ */
+class PoreActivityLog extends DataFile {
+
+    final private static String FILE_TYPE = "csv"
+
+    final private static String NAME_SCHEMA = $/pore_activity_.*/$
+
+    protected PoreActivityLog() {}
+
+    protected PoreActivityLog(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static PoreActivityLog create(String name, String relativePath) {
+        return new PoreActivityLog(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore pore activity log name schema!")
+        }
+    }
+
+}

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

@@ -0,0 +1,32 @@
+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 pore scan data log file
+ *
+ */
+class PoreScanDataLog extends DataFile {
+
+    final private static String FILE_TYPE = "csv"
+
+    final private static String NAME_SCHEMA = $/pore_scan_data_.*/$
+
+    protected PoreScanDataLog() {}
+
+    protected PoreScanDataLog(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static PoreScanDataLog create(String name, String relativePath) {
+        return new PoreScanDataLog(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore pore scan data log name schema!")
+        }
+    }
+
+}

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

@@ -0,0 +1,31 @@
+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 report HTML log file
+ *
+ */
+class ReportHTMLLog extends DataFile {
+
+    final private static String FILE_TYPE = "html"
+
+    final private static String NAME_SCHEMA = $/report_.*/$
+
+    protected ReportHTMLLog() {}
+
+    protected ReportHTMLLog(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static ReportHTMLLog create(String name, String relativePath) {
+        return new ReportHTMLLog(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore report name schema!")
+        }
+    }
+}

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

@@ -0,0 +1,31 @@
+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 report JSON log file
+ *
+ */
+class ReportJSONLog extends DataFile {
+
+    final private static String FILE_TYPE = "json"
+
+    final private static String NAME_SCHEMA = $/report_.*/$
+
+    protected ReportJSONLog() {}
+
+    protected ReportJSONLog(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static ReportJSONLog create(String name, String relativePath) {
+        return new ReportJSONLog(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore report name schema!")
+        }
+    }
+}

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

@@ -0,0 +1,33 @@
+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 sample sheet log file
+ *
+ * @author: Andreas Friedrich
+ */
+class SampleSheetLog extends DataFile {
+
+    final private static String FILE_TYPE = "csv"
+
+    final private static String NAME_SCHEMA = $/sample_sheet_.*/$
+
+    protected SampleSheetLog() {}
+
+    protected SampleSheetLog(String name, String relativePath) {
+        super(name, relativePath, FILE_TYPE)
+        validateName()
+    }
+
+    static SampleSheetLog create(String name, String relativePath) {
+        return new SampleSheetLog(name, relativePath)
+    }
+
+    private void validateName() {
+        if (!(this.name =~ NAME_SCHEMA)) {
+            throw new IllegalArgumentException("Name must match the Nanopore sample sheet log name schema!")
+        }
+    }
+
+}

src/main/groovy/life/qbic/datamodel/instruments/OxfordNanoporeInstrumentOutputV3.groovy

@@ -0,0 +1,22 @@
+package life.qbic.datamodel.instruments
+
+
+/**
+ * Represents the Nanopore instrument output data structure schema.
+ *
+ * The original schema is defined in as resource and is
+ * referenced here, wrapped in a Groovy class for reference
+ * in applications that want to validate the instrument
+ * output structure against the schema.
+ *
+ * @author Sven Fillinger
+ * @since 1.9.0
+ */
+class OxfordNanoporeInstrumentOutputV3 {
+
+    private static final String SCHEMA_PATH = "/schemas/nanopore-instrument-output_v3.schema.json"
+
+    static InputStream getSchemaAsStream() {
+        return OxfordNanoporeInstrumentOutputV3.getResourceAsStream(SCHEMA_PATH)
+    }
+}