Support xlsx upload for measurement metadata registration (#803)

Adds XLSX file upload support for measurement metadata registration.

Solves #677

Co-authored-by: KochTobi <[email protected]>
(cherry picked from commit 5de2e98)

application-commons/src/main/java/life/qbic/application/commons/ApplicationException.java

@@ -150,7 +150,8 @@ public enum ErrorCode {
     NO_ANALYTE_DEFINED,
     DATA_ATTACHED_TO_SAMPLES,
     SAMPLES_ATTACHED_TO_EXPERIMENT,
-    SERVICE_FAILED;
+    SERVICE_FAILED,
+    UNKNOWN_METADATA;
 
     @Override
     public String toString() {

project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java

@@ -554,7 +554,7 @@ private int readInjectionVolume(String value) throws NumberFormatException {
     if (value.isBlank()) {
       return -1;
     }
-    return Integer.parseInt(value);
+    return (int) Double.parseDouble(value);
   }
 
   /**

project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/SampleCode.java

@@ -19,15 +19,15 @@ protected SampleCode() {
     // needed for JPA
   }
 
-  private SampleCode(String code) {
+  private SampleCode(String code) throws IllegalArgumentException{
     Objects.requireNonNull(code, "Sample code must not be null");
     if (code.isBlank()) {
       throw new IllegalArgumentException("Sample code must not be blank");
     }
     this.code = code;
   }
 
-  public static SampleCode create(String code) {
+  public static SampleCode create(String code) throws IllegalArgumentException {
     return new SampleCode(code);
   }
 

user-interface/src/main/java/life/qbic/datamanager/parser/MeasurementMetadataConverter.java

@@ -0,0 +1,52 @@
+package life.qbic.datamanager.parser;
+
+import java.util.List;
+import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
+
+/**
+ * <b>Measurement Metadata Converter</b>
+ * <p>
+ * Measurement metadata converter enable the client to process a {@link ParsingResult} object and
+ * convert them into known implementations of the {@link MeasurementMetadata} interface.
+ *
+ * @since 1.4.0
+ */
+public interface MeasurementMetadataConverter {
+
+  /**
+   * Takes an instance of {@link ParsingResult} and tries to convert it to known implementations of
+   * the {@link MeasurementMetadata} interface.
+   * <p>
+   * Currently supported implementations are:
+   *
+   * <ul>
+   *   <li>NGS Measurement Metadata {@link life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata}</li>
+   *   <li>Proteomics Measurement Metadata {@link life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata}</li>
+   * </ul>
+   *
+   * @param parsingResult       the parsing result to take as input for the conversion.
+   * @param ignoreMeasurementId weather to ignore the measurement identifier or not
+   * @return a list of converted implementations of {@link MeasurementMetadata}.
+   * @throws UnknownMetadataTypeException if no matching implementation of
+   *                                      {@link MeasurementMetadata} can be associated from the
+   *                                      provided {@link ParsingResult#keys()}.
+   * @since 1.4.0
+   */
+  List<? extends MeasurementMetadata> convert(ParsingResult parsingResult,
+      boolean ignoreMeasurementId)
+      throws UnknownMetadataTypeException;
+
+  class UnknownMetadataTypeException extends RuntimeException {
+
+    public UnknownMetadataTypeException(String message) {
+      super(message);
+    }
+  }
+
+  class MissingSampleIdException extends RuntimeException {
+    public MissingSampleIdException(String message) {
+      super(message);
+    }
+  }
+
+}