Harmonize excel data export and include missed properties (#999)

* replace measurement templates

* Move sample templates

* Remove templates and correct autosizing of columns

* Switch to new xlsx generation for sample metadata download

* remove duplicate class

* File name by experiment name instead of project code

* Adapt to confounding variables

* Move ROCrate export

* remove unused field

* Use downloadComponent

* Move classes

* Remove FileDownloadStreamProvider.java

* Reduce complexity

* Centralize file name formatting

* Adapt filename for proteomics measurements

* Change file name pattern

---------

Co-authored-by: KochTobi <[email protected]>

Author: KochTobi

user-interface/src/main/bundles/dev.bundle

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.export;
+package life.qbic.datamanager.files;
 
 import java.io.IOException;
 import java.nio.file.Files;

user-interface/src/main/java/life/qbic/datamanager/export/FileFormatSupplier.java

@@ -0,0 +1,59 @@
+package life.qbic.datamanager.files.export;
+
+import java.util.Collections;
+import java.util.List;
+import life.qbic.datamanager.files.export.FileSupplier.FormatException;
+import org.docx4j.openpackaging.exceptions.Docx4JException;
+import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
+import org.docx4j.openpackaging.parts.WordprocessingML.MainDocumentPart;
+
+@FunctionalInterface
+public interface DocxBuilder<T> {
+
+
+  record Section(String title, List<?> content) {
+
+    public Object titleAsParagraph(MainDocumentPart mainDocumentPart) {
+      return mainDocumentPart.createStyledParagraphOfText("Heading1", title);
+    }
+
+    @Override
+    public List<?> content() {
+      return Collections.unmodifiableList(content);
+    }
+  }
+
+  private static void addSection(MainDocumentPart mainDocumentPart, Section section) {
+    mainDocumentPart.addObject(section.titleAsParagraph(mainDocumentPart));
+    section.content().forEach(mainDocumentPart::addObject);
+  }
+
+  static Object createTitle(MainDocumentPart mainDocumentPart, String title) {
+    return mainDocumentPart.createStyledParagraphOfText("Title", title);
+  }
+
+  static Object createSubtitle(MainDocumentPart mainDocumentPart, String subTitle) {
+    return mainDocumentPart.createStyledParagraphOfText("Subtitle", subTitle);
+  }
+
+
+  List<Object> createContent(MainDocumentPart mainDocumentPart, T input);
+
+  default WordprocessingMLPackage buildFrom(T payload) {
+    try {
+      var result = WordprocessingMLPackage.createPackage();
+      var mainDocument = result.getMainDocumentPart();
+      List<Object> content = createContent(mainDocument, payload);
+      for (Object part : content) {
+        if (part instanceof Section section) {
+          addSection(mainDocument, section);
+        } else {
+          mainDocument.addObject(part);
+        }
+      }
+      return result;
+    } catch (Docx4JException e) {
+      throw new FormatException("Creating docx package failed. ", e);
+    }
+  }
+}

user-interface/src/main/java/life/qbic/datamanager/export/docx/DocxSupplier.java

@@ -0,0 +1,31 @@
+package life.qbic.datamanager.files.export;
+
+import java.io.File;
+import org.docx4j.openpackaging.exceptions.Docx4JException;
+import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
+
+public class DocxFileSupplier implements FileSupplier {
+
+  private final WordprocessingMLPackage wordPackage;
+
+  DocxFileSupplier(WordprocessingMLPackage wordPackage) {
+    this.wordPackage = wordPackage;
+
+  }
+
+  public static DocxFileSupplier supplying(WordprocessingMLPackage wordPackage) {
+    return new DocxFileSupplier(wordPackage);
+  }
+
+
+  @Override
+  public File getFile(String fileName) {
+    try {
+      File file = new File(fileName);
+      wordPackage.save(file);
+      return file;
+    } catch (Docx4JException e) {
+      throw new FormatException("Creating docx package failed.", e);
+    }
+  }
+}

user-interface/src/main/java/life/qbic/datamanager/export/yaml/YamlSupplier.java

@@ -0,0 +1,38 @@
+package life.qbic.datamanager.files.export;
+
+import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
+
+public class FileNameFormatter {
+
+  private static final String SPACE_REPLACEMENT = "-";
+  private static final String PART_JOINER = "_";
+
+  private static final DateTimeFormatter DATE_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd");
+
+  private FileNameFormatter() {
+
+  }
+
+
+  public static String formatWithTimestampedContext(LocalDate timestamp, String projectPart,
+      String experimentPart, String type, String extension) {
+    return DATE_FORMATTER.format(timestamp)
+        + PART_JOINER
+        + replaceSpaces(projectPart)
+        + PART_JOINER
+        + replaceSpaces(experimentPart)
+        + PART_JOINER
+        + replaceSpaces(type)
+        + "." + replaceSpaces(extension);
+  }
+
+  private static String replaceSpaces(String projectPart) {
+    return projectPart.replaceAll("\\s", SPACE_REPLACEMENT);
+  }
+
+  public static String formatWithVersion(String filename, int version,
+      String extension) {
+    return replaceSpaces(filename) + "_" + "v" + version + "." + replaceSpaces(extension);
+  }
+}

user-interface/src/main/java/life/qbic/datamanager/export/TempDirectory.java user-interface/src/main/java/life/qbic/datamanager/files/TempDirectory.java

@@ -0,0 +1,20 @@
+package life.qbic.datamanager.files.export;
+
+import java.io.File;
+
+@FunctionalInterface
+public interface FileSupplier {
+
+  File getFile(String fileName);
+
+  class FormatException extends RuntimeException {
+
+    public FormatException(String message) {
+      super(message);
+    }
+
+    public FormatException(String message, Throwable cause) {
+      super(message, cause);
+    }
+  }
+}