feat: add download provider, upload components, measurement presenter, QC dialogs, and haproxy config

Author: KochTobi-Agent

datamanager-app/src/main/java/life/qbic/datamanager/download/DownloadProvider.java

@@ -0,0 +1,45 @@
+package life.qbic.datamanager.download;
+
+import com.vaadin.flow.component.UI;
+import com.vaadin.flow.component.html.Anchor;
+import com.vaadin.flow.server.StreamResource;
+import java.io.ByteArrayInputStream;
+import life.qbic.application.commons.ApplicationException;
+
+/**
+ * The DownloadProvider class extends the Anchor class and provides functionality for triggering
+ * any kind of download based on a provided DownloadContentProvider
+ */
+public class DownloadProvider extends Anchor {
+
+  private final transient DownloadContentProvider downloadContentProvider;
+
+  public DownloadProvider(DownloadContentProvider downloadContentProvider) {
+    super("_blank", "Download");
+    this.downloadContentProvider = downloadContentProvider;
+    /*
+     * Using setVisisble(false), vaadin prevents any client side actions.
+     * This prevents us from using JavaScript to click the link, which is the only option
+     * for using anchors now.
+     * Thus, we prevent the display of the link with `display: none`.
+     * The link is still on the page but invisible.
+     */
+    getStyle().set("display", "none");
+
+    setTarget("_blank");
+    getElement().setAttribute("download", true);
+  }
+
+  public void trigger() {
+    byte[] content = downloadContentProvider.getContent();
+    if(content.length > 0) {
+      UI ui = getUI().orElseThrow(() -> new ApplicationException(
+          "Download component triggered but not attached to any UI."));
+      StreamResource resource = new StreamResource(downloadContentProvider.getFileName(),
+          () -> new ByteArrayInputStream(content));
+      this.setHref(resource);
+      ui.getPage().executeJs("$0.click()", this.getElement());
+    }
+  }
+
+}

datamanager-app/src/main/java/life/qbic/datamanager/views/general/upload/EditableMultiFileMemoryBuffer.java

@@ -0,0 +1,64 @@
+package life.qbic.datamanager.views.general.upload;
+
+import com.vaadin.flow.component.upload.MultiFileReceiver;
+import com.vaadin.flow.component.upload.receivers.FileData;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.Serial;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Optional;
+import java.util.stream.Stream;
+
+/**
+ * <b>Editable multi-file memory buffer</b>
+ * <p>
+ * An improved {@link MultiFileReceiver} enables removing cached file content, which Vaadin's
+ * {@link com.vaadin.flow.component.upload.receivers.MultiFileMemoryBuffer} does not provide.
+ *
+ * @since 1.0.0
+ */
+public class EditableMultiFileMemoryBuffer implements MultiFileReceiver {
+
+  @Serial
+  private static final long serialVersionUID = 2041166242210420469L;
+  private final Map<String, FileData> files = new HashMap<>();
+
+  @Override
+  public OutputStream receiveUpload(String fileName, String mimeType) {
+    ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+    this.files.put(fileName, new FileData(fileName, mimeType, byteArrayOutputStream));
+    return byteArrayOutputStream;
+  }
+
+  public Optional<OutputStream> outputStream(String fileName) {
+    return Optional.ofNullable(files.getOrDefault(fileName, null)).map(FileData::getOutputBuffer);
+  }
+
+  public Optional<InputStream> inputStream(String fileName) {
+    return Optional.ofNullable(files.getOrDefault(fileName, null))
+        .map(fileData -> (ByteArrayOutputStream) fileData.getOutputBuffer())
+        .map(outputStream -> new ByteArrayInputStream(outputStream.toByteArray()));
+  }
+
+  public void remove(String fileName) {
+    files.remove(fileName);
+  }
+
+  /**
+   * Clears the complete buffer and removes any content cashed in the buffer.
+   * <p>
+   * All cached files and their content are removed from the buffer.
+   *
+   * @since 1.0.0
+   */
+  public void clear() {
+    files.clear();
+  }
+
+  public Stream<String> fileNames() {
+    return this.files.keySet().stream();
+  }
+}

datamanager-app/src/main/java/life/qbic/datamanager/views/general/upload/FileMemoryBuffer.java

@@ -0,0 +1,52 @@
+package life.qbic.datamanager.views.general.upload;
+
+import static java.util.Objects.nonNull;
+
+import com.vaadin.flow.component.upload.Receiver;
+import com.vaadin.flow.component.upload.receivers.FileData;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.Optional;
+
+/**
+ * Simple in-memory buffer for receiving uploaded content in the application.
+ */
+public class FileMemoryBuffer implements Receiver {
+
+  private FileData fileData;
+
+  @Override
+  public OutputStream receiveUpload(String fileName, String mimeType) {
+    ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+    this.fileData = new FileData(fileName, mimeType, byteArrayOutputStream);
+    return byteArrayOutputStream;
+  }
+
+  public boolean hasUploadedData() {
+    return nonNull(fileData);
+  }
+
+  public Optional<InputStream> getInputStream() {
+    return Optional.ofNullable(fileData)
+        .map(FileData::getOutputBuffer)
+        .filter(ByteArrayOutputStream.class::isInstance)
+        .map(ByteArrayOutputStream.class::cast)
+        .map(ByteArrayOutputStream::toByteArray)
+        .map(ByteArrayInputStream::new);
+  }
+
+  public Optional<String> getFileName() {
+    return Optional.ofNullable(fileData.getFileName());
+  }
+
+  public Optional<String> getMimeType() {
+    return Optional.ofNullable(fileData.getMimeType());
+  }
+
+  public void clear() {
+    fileData = null;
+  }
+
+}