Merge pull request #354 from qbicsoftware/development

Introduce minimal Schema for nanopore registration  (#350)

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

@@ -0,0 +1,29 @@
+package life.qbic.datamodel.datasets.datastructure.files.nanopore
+
+import life.qbic.datamodel.datasets.datastructure.files.DataFile
+
+/**
+ * Unspecific OptionalFile used to store unexpected file in the nanopore registration
+ *
+ * The high variety of the nanopore datasets registered made an optional all-purpose Datafile structure necessary.
+ *
+ */
+class OptionalFile extends DataFile {
+
+  protected OptionalFile() {}
+
+  protected OptionalFile(String name, String relativePath, String fileType) {
+    super(name, relativePath, fileType)
+  }
+
+  /**
+   * Creates a new instance of a OptionalFile object
+   * @param name The name of the file
+   * @param relativePath The relative path of the file
+   * @param fileType The suffix specifying the file type of the file
+   * @return A new instance of a OptionalFile object
+   */
+  static OptionalFile create(String name, String relativePath, String fileType) {
+    return new OptionalFile(name, relativePath, fileType)
+  }
+}

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

@@ -0,0 +1,29 @@
+package life.qbic.datamodel.datasets.datastructure.folders.nanopore
+
+import life.qbic.datamodel.datasets.datastructure.folders.DataFolder
+
+/**
+ * Unspecific Optional Folder used to store unexpected folders in the nanopore registration
+ *
+ * The high variety of the nanopore datasets registered made an optional all-purpose Datafolder structure necessary.
+ *
+ */
+class OptionalFolder extends DataFolder {
+
+  protected OptionalFolder() {}
+
+  protected OptionalFolder(String name, String relativePath, List children) {
+    super(name, relativePath, children)
+  }
+
+  /**
+   * Creates a new instance of a OptionalFolder object
+   * @param relativePath The relative path of the folder
+   * @param children A list with child elements of unknown type of the folder
+   * @return A new instance of a OptionalFolder object
+   */
+  static OptionalFolder create(String name, String relativePath, List<?> children) {
+    new OptionalFolder(name, relativePath, children)
+  }
+
+}

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

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+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.
+ */
+class OxfordNanoporeInstrumentOutputMinimal {
+
+  private static final String SCHEMA_PATH = "/schemas/nanopore-instrument-output_minimal_schema.json"
+
+  static InputStream getSchemaAsStream() {
+    return OxfordNanoporeInstrumentOutputMinimal.getResourceAsStream(SCHEMA_PATH)
+  }
+}