Provide RO-Crate export for project summary

docs/fair/research-objects.md

@@ -0,0 +1,29 @@
+# RO-crates support in the data manager app
+
+[RO-crates](https://www.researchobject.org/ro-crate/) (RO: Research Object) provide a way structured and machine-actionable way to bundle metadata and files in one single digital object. We will
+look into how RO-Crates can be supported in the data manager.
+
+## RO-Crate structure
+
+The latest version up to the writing of this document is [RO-Crate 1.2-DRAFT](https://www.researchobject.org/ro-crate/specification/1.2-DRAFT/index.html). The last stable release is [RO-Crate 1.1](https://www.researchobject.org/ro-crate/specification/1.1/index.html).
+
+
+## Use case: project information 
+
+Project information such as title, identifier and contact person(s) are very basic and high-level metadata often
+used throughout a research project life cycle. This information is frequently consumed by humans (e.g. project managers, principal investigators, funding agencies) as well as machines to process or re-use it (e.g. in computational workflows).
+
+How can this metadata be provided in a FAIR compliant manner and serving both: humans and machines optimally.
+
+### Suggested RO-Crate implementation
+
+Possible structure for an RO-Crate containing QBiC project information:
+
+![Example project information RO-Crate](project-information-example-ro-crate.png)
+
+This simple RO-Crate consists of only three files:
+
+ - _ro-crate-metadata.json_: part of the RO-Crate specification, this file describes the content of the RO-crate object. You will see this file in every RO-Crate.
+ - _project-information.yml_: some machine-actionable high level metadata about a QBiC project, e.g. title, identifier, contact
+ - _project-information.docx_: some human-readable, visually appealing information about a QBiC project
+

pom.xml

@@ -173,6 +173,7 @@
         <artifactId>jackson-annotations</artifactId>
         <version>${jackson.version}</version>
       </dependency>
+
     </dependencies>
 
   </dependencyManagement>

user-interface/frontend/themes/datamanager/components/button.css

@@ -6,6 +6,11 @@
   flex: 1 1;
 }
 
+.button-bar {
+  display: inline-flex;
+  column-gap: var(--lumo-space-s);
+}
+
 .navigation-button .button {
   box-shadow: var(--lumo-box-shadow-xs);
 }

user-interface/pom.xml

@@ -159,6 +159,61 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-oauth2-client</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>
+    <dependency>
+      <groupId>org.docx4j</groupId>
+      <artifactId>docx4j-JAXB-ReferenceImpl</artifactId>
+      <version>11.4.11</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>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-test</artifactId>

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

@@ -0,0 +1,26 @@
+package life.qbic.datamanager.export;
+
+import java.io.File;
+import life.qbic.datamanager.export.model.ResearchProject;
+
+/**
+ * <b>File format supplier</b>
+ * <p>
+ * Interface describing the API of suppliers for different file formats.
+ *
+ * @since 1.6.0
+ */
+public interface FileFormatSupplier {
+
+  File from(String fileName, ResearchProject researchProject) throws FormatException;
+
+  class FormatException extends RuntimeException {
+
+    public FormatException(String message) {
+    }
+
+    public FormatException(String message, Throwable cause) {
+    }
+  }
+
+}

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

@@ -0,0 +1,52 @@
+package life.qbic.datamanager.export;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.UUID;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+/**
+ * <b>Temporary Director</b>
+ * <p>
+ * Provides a temporary directory for the application to use when files need to be created for
+ * exporting them.
+ *
+ * @since <version tag>
+ */
+@Component
+public class TempDirectory {
+
+  private final Path tempDir;
+
+  public TempDirectory(@Value("${service.host.temp.dir}") String tempDirectoryPath)
+      throws IOException {
+    Path tempDirPath = Path.of(tempDirectoryPath);
+    if (!Files.exists(tempDirPath)) {
+      throw new IOException(tempDirectoryPath + " does not exist");
+    }
+    if (!Files.isWritable(tempDirPath)) {
+      throw new IOException(tempDirectoryPath + " is not writable");
+    }
+    if (!Files.isExecutable(tempDirPath)) {
+      throw new IOException(tempDirectoryPath + " is not executable");
+    }
+    tempDir = tempDirPath;
+  }
+
+  /**
+   * Creates a new directory in the configured temporary directory location.
+   * <p>
+   * The method minimises the probability for collisions, so the client does not need to take care
+   * about potential existing directories.
+   *
+   * @return the path to the newly created directory in the app's global temporary directory
+   * @throws IOException in case the directory could not be created
+   * @since 1.6.0
+   */
+  public Path createDirectory() throws IOException {
+    return Files.createDirectory(tempDir.resolve(UUID.randomUUID().toString()));
+  }
+
+}

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

@@ -0,0 +1,67 @@
+package life.qbic.datamanager.export.docx;
+
+import java.io.File;
+import life.qbic.datamanager.export.FileFormatSupplier;
+import life.qbic.datamanager.export.model.ContactPoint;
+import life.qbic.datamanager.export.model.ResearchProject;
+import org.docx4j.openpackaging.exceptions.Docx4JException;
+import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
+import org.docx4j.openpackaging.parts.WordprocessingML.MainDocumentPart;
+
+/**
+ * <b>DOCX formatter implementation</b>
+ * <p>
+ * Creates DOCX representations of various content types in a Data Manager's project.
+ *
+ * @since 1.0.0
+ */
+public class DocxSupplier implements FileFormatSupplier {
+
+  public static DocxSupplier create() {
+    return new DocxSupplier();
+  }
+
+  @Override
+  public File from(String fileName, ResearchProject researchProject) {
+    try {
+      var wordPackage = WordprocessingMLPackage.createPackage();
+      var mainDocument = wordPackage.getMainDocumentPart();
+      addTitle(mainDocument, researchProject);
+      addProjectId(mainDocument, researchProject);
+      addSection(mainDocument, "Description", researchProject.description());
+      addSectionTitle(mainDocument, "Contact Points");
+      researchProject.contactPoint()
+          .forEach(contactPoint -> addContactPoint(mainDocument, contactPoint));
+      File file = new File(fileName);
+      wordPackage.save(file);
+      return file;
+    } catch (Docx4JException e) {
+      throw new FormatException("Creating docx package failed. ", e);
+    }
+  }
+
+  private void addTitle(MainDocumentPart mainDocumentPart, ResearchProject researchProject) {
+    mainDocumentPart.addStyledParagraphOfText("Title", researchProject.name());
+  }
+
+  private void addProjectId(MainDocumentPart mainDocumentPart, ResearchProject researchProject) {
+    mainDocumentPart.addStyledParagraphOfText("Subtitle",
+        "Project ID: " + researchProject.identifier());
+  }
+
+  private void addSection(MainDocumentPart mainDocumentPart, String sectionTitle,
+      String sectionContent) {
+    mainDocumentPart.addStyledParagraphOfText("Heading1", sectionTitle);
+    mainDocumentPart.addParagraphOfText(sectionContent);
+  }
+
+  private void addSectionTitle(MainDocumentPart mainDocumentPart, String title) {
+    mainDocumentPart.addStyledParagraphOfText("Heading1", title);
+  }
+
+  private void addContactPoint(MainDocumentPart mainDocumentPart, ContactPoint contactPoint) {
+    var contactPointFormatted = "%s (%s) - %s".formatted(contactPoint.name(),
+        contactPoint.contactType(), contactPoint.email());
+    mainDocumentPart.addParagraphOfText(contactPointFormatted);
+  }
+}

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

@@ -0,0 +1,44 @@
+package life.qbic.datamanager.export.model;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+/**
+ * A schema.org <a href="https://schema.org/ContactPoint">ContactPoint</a> representation in Java.
+ *
+ * @since 1.6.0.
+ */
+public class ContactPoint {
+
+  @JsonProperty(value = "@type")
+  private final String type = "ContactPoint";
+
+  @JsonProperty(value = "name")
+  private String name;
+
+  @JsonProperty(value = "email")
+  private String email;
+
+  @JsonProperty(value = "contactType")
+  private String contactType;
+
+  public static ContactPoint from(String name, String email, String contactType) {
+    ContactPoint contactPoint = new ContactPoint();
+    contactPoint.name = name;
+    contactPoint.email = email;
+    contactPoint.contactType = contactType;
+    return contactPoint;
+  }
+
+  public String name() {
+    return name;
+  }
+
+  public String email() {
+    return email;
+  }
+
+  public String contactType() {
+    return contactType;
+  }
+
+}

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

@@ -0,0 +1,53 @@
+package life.qbic.datamanager.export.model;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import java.util.List;
+
+/**
+ * A schema.org <a href="https://schema.org/ResearchProject">ResearchProject</a> representation in Java.
+ *
+ * @since 1.6.0.
+ */
+public class ResearchProject {
+
+  @JsonProperty(value = "@type")
+  private final String type = "ResearchProject";
+
+  @JsonProperty(value = "name")
+  private String name;
+
+  @JsonProperty(value = "identifier")
+  private String identifier;
+
+  @JsonProperty(value = "description")
+  private String description;
+
+  @JsonProperty(value = "contactPoint")
+  private List<ContactPoint> contactPoint;
+
+  public static ResearchProject from(String name, String identifier, String description, List<ContactPoint> contactPoint) {
+    ResearchProject project = new ResearchProject();
+    project.name = name;
+    project.identifier = identifier;
+    project.description = description;
+    project.contactPoint = contactPoint.stream().toList();
+    return project;
+  }
+
+  public String name() {
+    return name;
+  }
+
+  public String identifier() {
+    return identifier;
+  }
+
+  public String description() {
+    return description;
+  }
+
+  public List<ContactPoint> contactPoint() {
+    return contactPoint.stream().toList();
+  }
+
+}