Merge pull request #1174 from qbicsoftware/development

Release

Author: KochTobi

GoogleStyle.xml

@@ -233,7 +233,8 @@ Therefore, in order to be able to run the application, a keystore must be set-up
 
 #### Setup keystore
 
-Before the Java keystore can be referenced in Data Manager's configuration, it has to be created in the first place.
+Before the Java keystore can be referenced in Data Manager's configuration, it has to be created in
+the first place.
 
 You will need [keytool](https://docs.oracle.com/en/java/javase/11/tools/keytool.html) for this step.
 
@@ -245,7 +246,8 @@ Start the setup with a dummy entry for creation of a keystore file in PKSC12 for
 
 This secures the keystore with the `mysecretpassword` password. Change it to something only you have
 access and with
-Please choose a strong password. The application will fail for passwords with entropy below 100. The entropy of your password is calculated as follows
+Please choose a strong password. The application will fail for passwords with entropy below 100. The
+entropy of your password is calculated as follows
 
 $$
 H = -\sum_{i=1}^{n} P(x_i) \log_2 P(x_i) \times n > 100.,
@@ -271,7 +273,9 @@ Verify:
 ```bash
 keytool -list -keystore keystore.p12 -storetype PKCS12 -storepass mysecretpassword
 ```
+
 which should show something like:
+
 ```text
 Keystore type: PKCS12
 Keystore provider: SUN

README.md

@@ -0,0 +1,71 @@
+package life.qbic.application.commons;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.ByteBuffer;
+import java.util.Iterator;
+import java.util.Objects;
+
+/**
+ * An input stream generated from a (lazy) iterator of {@link ByteBuffer}s.
+ */
+public class ByteBufferIteratorInputStream extends InputStream {
+
+  private final Iterator<ByteBuffer> bufferIterator;
+  private ByteBuffer currentBuffer;
+
+  public ByteBufferIteratorInputStream(Iterator<ByteBuffer> iterator) {
+    this.bufferIterator = iterator;
+  }
+
+  @Override
+  public int read(byte[] b, int off, int len) throws IOException {
+    Objects.checkFromIndexSize(off, len, b.length);
+    if (len == 0) {
+      return 0;
+    }
+    boolean bufferAvailable = makeBufferAvailable();
+    if (!bufferAvailable) {
+      return -1;
+    }
+
+    int requestedBytes = Math.min(currentBuffer.remaining(), len);
+    currentBuffer.get(currentBuffer.position(), b, off, requestedBytes);
+    currentBuffer.position(currentBuffer.position() + requestedBytes);
+
+    return requestedBytes;
+  }
+
+  @Override
+  public int read() {
+    boolean bufferAvailable = makeBufferAvailable();
+    if (!bufferAvailable) {
+      return -1;
+    }
+    var currentPosition = currentBuffer.position();
+    var value = currentBuffer.get(currentPosition) & 0xFF;
+    currentBuffer.position(currentPosition + 1);
+    return value;
+  }
+
+  /**
+   * Ensures a readable buffer is set.
+   *
+   * @return true if a readable buffer is selected; false if no readable buffer is available.
+   */
+  private boolean makeBufferAvailable() {
+    var buffer = currentBuffer;
+    if (buffer != null && !buffer.hasRemaining()) {
+      // the current buffer is read completely
+      buffer = null;
+    }
+    while (buffer == null) {
+      if (!bufferIterator.hasNext()) {
+        return false;
+      }
+      buffer = bufferIterator.next();
+    }
+    currentBuffer = buffer;
+    return true;
+  }
+}

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

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.files.export;
+package life.qbic.application.commons;
 
 import java.time.LocalDate;
 import java.time.format.DateTimeFormatter;
@@ -15,6 +15,14 @@ private FileNameFormatter() {
 
   }
 
+  public static String formatWithTimestampedSimple(LocalDate localDate, String project, String type, String extension) {
+    return DATE_FORMATTER.format(localDate)
+        + PART_JOINER
+        + replaceForbiddenCharacters(project)
+        + PART_JOINER
+        + replaceForbiddenCharacters(type)
+        + "." + replaceForbiddenCharacters(extension);
+  }
 
   public static String formatWithTimestampedContext(LocalDate timestamp, String projectPart,
       String experimentPart, String type, String extension) {
@@ -33,7 +41,7 @@ private static String replaceForbiddenCharacters(String input) {
   }
 
   private static String replaceSpaces(String projectPart) {
-    return projectPart.replaceAll("\\s", SPACE_REPLACEMENT);
+    return projectPart.trim().replaceAll("\\s", SPACE_REPLACEMENT);
   }
 
   private static String replaceSlashes(String input) {

user-interface/src/main/java/life/qbic/datamanager/files/export/FileNameFormatter.java renamed to application-commons/src/main/java/life/qbic/application/commons/FileNameFormatter.java

@@ -15,5 +15,4 @@
  * @since 1.0.0
  */
 public record Offer(String id, String title, String objective, String experimentDescription) {
-
 }

finances-api/src/main/java/life/qbic/finances/api/Offer.java

@@ -32,6 +32,18 @@
       <version>1.9.4</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-core</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-annotations</artifactId>
+    </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>openbis-api</artifactId>
@@ -55,6 +67,81 @@
       <groupId>org.springframework.security</groupId>
       <artifactId>spring-security-oauth2-client</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.docx4j</groupId>
+      <artifactId>docx4j-JAXB-ReferenceImpl</artifactId>
+      <version>11.5.0</version>
+    </dependency>
+
+
+    <!-- Needed for building RO-Crates -->
+    <dependency>
+      <groupId>edu.kit.datamanager</groupId>
+      <artifactId>ro-crate-java</artifactId>
+      <version>1.1.1</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-log4j12</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>log4j</groupId>
+          <artifactId>log4j</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-jdk14</artifactId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.dataformat/jackson-dataformat-yaml -->
+    <dependency>
+      <groupId>com.fasterxml.jackson.dataformat</groupId>
+      <artifactId>jackson-dataformat-yaml</artifactId>
+    </dependency>
+
+
+    <!-- docx4j dependencies !-->
+    <!-- https://mvnrepository.com/artifact/org.docx4j/docx4j-core -->
+    <dependency>
+      <groupId>org.docx4j</groupId>
+      <artifactId>docx4j-core</artifactId>
+      <version>11.5.0</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-log4j12</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>log4j</groupId>
+          <artifactId>log4j</artifactId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <!-- Needed for docx4j !-->
+    <dependency>
+      <groupId>org.glassfish.jaxb</groupId>
+      <artifactId>jaxb-runtime</artifactId>
+      <version>4.0.5</version>
+    </dependency>
+    <dependency>
+      <groupId>jakarta.xml.bind</groupId>
+      <artifactId>jakarta.xml.bind-api</artifactId>
+      <version>4.0.2</version>
+    </dependency>
+
+    <!-- Needed for xlsx support !-->
+    <dependency>
+      <groupId>org.apache.poi</groupId>
+      <artifactId>poi</artifactId>
+      <version>5.4.0</version>
+    </dependency>
+    <!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
+    <dependency>
+      <groupId>org.apache.poi</groupId>
+      <artifactId>poi-ooxml</artifactId>
+      <version>5.4.0</version>
+    </dependency>
   </dependencies>
 
 </project>

project-management-infrastructure/pom.xml

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.files;
+package life.qbic.projectmanagement.infrastructure;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -8,7 +8,7 @@
 import org.springframework.stereotype.Component;
 
 /**
- * <b>Temporary Director</b>
+ * <b>Temporary Directory</b>
  * <p>
  * Provides a temporary directory for the application to use when files need to be created for
  * exporting them.

user-interface/src/main/java/life/qbic/datamanager/files/TempDirectory.java renamed to project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/TempDirectory.java

@@ -1,8 +1,8 @@
-package life.qbic.datamanager.files.export;
+package life.qbic.projectmanagement.infrastructure.api.fair.rocrate;
 
 import java.util.Collections;
 import java.util.List;
-import life.qbic.datamanager.files.export.FileSupplier.FormatException;
+import life.qbic.projectmanagement.infrastructure.api.fair.rocrate.FileSupplier.FormatException;
 import org.docx4j.openpackaging.exceptions.Docx4JException;
 import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
 import org.docx4j.openpackaging.parts.WordprocessingML.MainDocumentPart;

user-interface/src/main/java/life/qbic/datamanager/files/export/DocxBuilder.java renamed to project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/fair/rocrate/DocxBuilder.java

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.files.export;
+package life.qbic.projectmanagement.infrastructure.api.fair.rocrate;
 
 import java.io.File;
 import org.docx4j.openpackaging.exceptions.Docx4JException;

user-interface/src/main/java/life/qbic/datamanager/files/export/DocxFileSupplier.java renamed to project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/api/fair/rocrate/DocxFileSupplier.java

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.files.export;
+package life.qbic.projectmanagement.infrastructure.api.fair.rocrate;
 
 import java.io.File;