Dependencies/upgrade spring boot

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

@@ -11,9 +11,10 @@
  */
 public class FileSizeFormatter {
 
-  private static final long KILOBYTE = 1_000L;
-  private static final long MEGABYTE = 1_000_000L;
-  private static final long GIGABYTE = 1_000_000_000L;
+  private static final long base = 1024;
+  private static final long KILOBYTE = base;
+  private static final long MEGABYTE = base * KILOBYTE;
+  private static final long GIGABYTE = base * MEGABYTE;
 
   private FileSizeFormatter() {
     // Utility class - no instantiation
@@ -43,4 +44,4 @@
     }
     return String.format(Locale.US, "%.2f GB", bytes / (double) GIGABYTE);
   }
-}
+}

datamanager-app/frontend/themes/datamanager/components/dialog.css

@@ -494,6 +494,16 @@ Since we want to remove the spacing between the cancel and confirm button we rep
   width: 100%;
 }
 
+.upload-component .restrictions:has(:only-child) {
+  justify-content: flex-end;
+}
+
+.upload-component .upload-component-error {
+  font-size: smaller;
+  color: var(--lumo-error-color);
+  padding: var(--lumo-space-xs);
+}
+
 .measurement-upload-dialog .upload-items-display .uploaded-items-section .section-title {
   color: var(--lumo-secondary-text-color);
   font-size: var(--lumo-font-size-s);
@@ -514,8 +524,7 @@ Since we want to remove the spacing between the cancel and confirm button we rep
 }
 
 .measurement-upload-dialog .upload-items-display .uploaded-measurement-items .measurement-item,
-.register-samples-dialog .uploaded-items-section .uploaded-item,
-.edit-samples-dialog .uploaded-items-section .uploaded-item {
+.uploaded-items-section .uploaded-item {
   font-size: var(--lumo-font-size-s);
   display: flex;
   padding-top: var(--lumo-space-m);

datamanager-app/src/main/java/life/qbic/datamanager/configuration/UploadConfiguration.java

@@ -0,0 +1,28 @@
+package life.qbic.datamanager.configuration;
+
+import java.util.Objects;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.util.unit.DataSize;
+
+@Configuration
+public class UploadConfiguration {
+
+  private final DataSize maxInMemoryThreshold;
+  private final DataSize maxFileSize;
+
+  public UploadConfiguration(
+      @Value("${qbic.upload.in-memory-limit}") DataSize maxInMemoryThreshold,
+      @Value("${qbic.upload.max-file-size}") DataSize maxFileSize) {
+    this.maxInMemoryThreshold = Objects.requireNonNull(maxInMemoryThreshold);
+    this.maxFileSize = Objects.requireNonNull(maxFileSize);
+  }
+
+  public DataSize maxInMemoryThreshold() {
+    return maxInMemoryThreshold;
+  }
+
+  public DataSize maxFileSize() {
+    return maxFileSize;
+  }
+}

datamanager-app/src/main/java/life/qbic/datamanager/files/export/download/ByteArrayDownloadStreamProvider.java

@@ -11,4 +11,9 @@ public interface ByteArrayDownloadStreamProvider extends DownloadStreamProvider
   default InputStream getStream() {
     return new ByteArrayInputStream(getBytes());
   }
+
+  @Override
+  default String getContentType() {
+    return "application/octet-stream";
+  }
 }

datamanager-app/src/main/java/life/qbic/datamanager/files/export/download/DownloadStreamProvider.java

@@ -1,11 +1,15 @@
 package life.qbic.datamanager.files.export.download;
 
 import java.io.InputStream;
+import java.util.Optional;
 
 public interface DownloadStreamProvider {
 
   String getFilename();
 
   InputStream getStream();
 
+  String getContentType();
+
+  Optional<Long> contentLength();
 }

datamanager-app/src/main/java/life/qbic/datamanager/files/export/download/WorkbookDownloadStreamProvider.java

@@ -19,4 +19,8 @@ default InputStream getStream() {
       throw new RuntimeException(e);
     }
   }
+
+  default String getContentType() {
+    return "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet";
+  }
 }

datamanager-app/src/main/java/life/qbic/datamanager/security/SecurityConfiguration.java

@@ -1,10 +1,10 @@
 package life.qbic.datamanager.security;
 
+import static com.vaadin.flow.spring.security.VaadinSecurityConfigurer.vaadin;
 import static java.util.Objects.requireNonNull;
 
 import com.vaadin.flow.spring.security.VaadinAwareSecurityContextHolderStrategyConfiguration;
 import com.vaadin.flow.spring.security.VaadinDefaultRequestCache;
-import com.vaadin.flow.spring.security.VaadinWebSecurity;
 import life.qbic.datamanager.views.login.LoginLayout;
 import life.qbic.identity.application.security.QBiCPasswordEncoder;
 import life.qbic.identity.application.user.IdentityService;
@@ -16,13 +16,13 @@
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
 import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.security.web.SecurityFilterChain;
 import org.springframework.security.web.authentication.AuthenticationSuccessHandler;
-import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
 
 @EnableWebSecurity
 @Configuration
 @Import(VaadinAwareSecurityContextHolderStrategyConfiguration.class)
-public class SecurityConfiguration extends VaadinWebSecurity {
+public class SecurityConfiguration {
 
   final VaadinDefaultRequestCache defaultRequestCache;
   private final IdentityService identityService;
@@ -44,6 +44,30 @@ public SecurityConfiguration(
     this.identityService = requireNonNull(identityService);
   }
 
+  @Bean
+  public SecurityFilterChain vaadinSecurityFilterChain(HttpSecurity http) throws Exception {
+    http.requestCache(c -> c.requestCache(defaultRequestCache));
+
+    http.authorizeHttpRequests(v -> v
+        .requestMatchers(
+            "/oauth2/authorization/orcid",
+            "/oauth2/code/**",
+            "/link/**",
+            "/images/*.png")
+        .permitAll()
+    );
+
+    http.oauth2Login(oauth2 -> oauth2.
+        loginPage("/login").permitAll()
+        .defaultSuccessUrl("/")
+        .successHandler(authenticationSuccessHandler())
+        .failureUrl("/login?errorOauth2=true&error"));
+
+    http.with(vaadin(), vaadin -> vaadin
+        .loginView(LoginLayout.class, contextPath + "/login?logout=true"));
+    return http.build();
+  }
+
   @Bean
   public PasswordEncoder passwordEncoder() {
     return new QBiCPasswordEncoder();
@@ -56,34 +80,4 @@ private AuthenticationSuccessHandler authenticationSuccessHandler() {
     storedRequestAwareOidcAuthenticationSuccessHandler.setRequestCache(defaultRequestCache);
     return storedRequestAwareOidcAuthenticationSuccessHandler;
   }
-
-  @Override
-  protected void configure(HttpSecurity http) throws Exception {
-    // Use Vaadin’s request cache (so redirects back to the original Flow route work)
-    http.requestCache(c -> c.requestCache(defaultRequestCache));
-
-    http.authorizeHttpRequests(v -> v
-        .requestMatchers(VaadinWebSecurity.getDefaultWebSecurityIgnoreMatcher()).permitAll()
-        .requestMatchers(
-            new AntPathRequestMatcher("/oauth2/authorization/orcid"),
-            new AntPathRequestMatcher("/oauth2/code/**"),
-            new AntPathRequestMatcher("/link/**"),
-            new AntPathRequestMatcher("/images/*.png"))
-        .permitAll()
-    );
-
-    http.oauth2Login(oAuth2Login -> {
-      oAuth2Login.loginPage("/login").permitAll();
-      oAuth2Login.defaultSuccessUrl("/");
-      oAuth2Login.successHandler(
-          authenticationSuccessHandler());
-      oAuth2Login.failureUrl("/login?errorOauth2=true&error");
-    });
-
-    // Let Vaadin register its filters/matchers
-    super.configure(http);
-
-    // Set the login view
-    setLoginView(http, LoginLayout.class, contextPath + "/login?logout=true");
-  }
 }

datamanager-app/src/main/java/life/qbic/datamanager/views/LandingPageTitleAndLogo.java

@@ -4,7 +4,8 @@
 import com.vaadin.flow.component.html.Div;
 import com.vaadin.flow.component.html.Image;
 import com.vaadin.flow.component.html.Span;
-import com.vaadin.flow.server.StreamResource;
+import com.vaadin.flow.server.streams.DownloadHandler;
+import com.vaadin.flow.server.streams.DownloadResponse;
 
 /**
  * Landing Page Title and Logo
@@ -33,9 +34,11 @@ public LandingPageTitleAndLogo() {
   }
 
   private Image getUTLogo() {
-    StreamResource utResource = new StreamResource("university_tuebingen_logo.svg",
-        () -> getClass().getClassLoader().getResourceAsStream(UT_LOGO_PATH));
-    Image utLogo = new Image(utResource, "university_tuebingen_logo");
+    DownloadHandler downloadHandler = DownloadHandler.fromInputStream(event ->
+        new DownloadResponse(getClass().getClassLoader().getResourceAsStream(UT_LOGO_PATH),
+            "university_tuebingen_logo.svg",
+            "image/svg+xml", -1));
+    Image utLogo = new Image(downloadHandler, "university_tuebingen_logo");
     utLogo.addClassName("ut-logo");
     return utLogo;
   }

datamanager-app/src/main/java/life/qbic/datamanager/views/account/UserAvatar.java

@@ -2,7 +2,8 @@
 
 import com.vaadin.flow.component.avatar.Avatar;
 import com.vaadin.flow.component.avatar.AvatarGroup;
-import com.vaadin.flow.server.StreamResource;
+import com.vaadin.flow.server.streams.DownloadHandler;
+import com.vaadin.flow.server.streams.DownloadResponse;
 import java.io.ByteArrayInputStream;
 import java.nio.charset.StandardCharsets;
 import life.qbic.datamanager.views.identicon.IdenticonGenerator;
@@ -19,20 +20,26 @@ public UserAvatar() {
   }
 
   public void setUserId(String userId) {
-    setImageResource(getImageResource(userId));
+    setImageHandler(getDownloadHandler(userId));
   }
 
-  private static StreamResource getImageResource(String name) {
-    return new StreamResource("user-identicon.svg",
-        () -> new ByteArrayInputStream(IdenticonGenerator.generateIdenticonSVG(name).getBytes(
-            StandardCharsets.UTF_8)));
+  private static DownloadHandler getDownloadHandler(String userid) {
+    return DownloadHandler.fromInputStream(event ->
+    {
+      byte[] imageBytes = IdenticonGenerator.generateIdenticonSVG(userid).getBytes(
+          StandardCharsets.UTF_8);
+      return new DownloadResponse(
+          new ByteArrayInputStream(imageBytes),
+          "user-identicon.svg", null, imageBytes.length);
+    });
   }
 
   public static class UserAvatarGroupItem extends AvatarGroup.AvatarGroupItem {
 
     public UserAvatarGroupItem(String userName, String userId) {
+      //new logic -> first more important; image then name -> image; name then image -> name is shown
+      setImageHandler(UserAvatar.getDownloadHandler(userId));
       super.setName(userName);
-      setImageResource(UserAvatar.getImageResource(userId));
     }
   }
 }