Merge pull request #264 from kit-data-manager/development

Next Version (2.1.0 | 2.1.0-rc3)

Author: Pfeil

CITATION.cff

@@ -10,6 +10,6 @@ authors:
   given-names: "Sabrine"
   orcid: "https://orcid.org/0000-0002-4480-6116"
 title: "ro-crate-java"
-version: 1.0.3
+version: 2.1.0-rc3
 date-released: 2022-07-19
 url: "https://github.com/kit-data-manager/ro-crate-java"

build.gradle

@@ -43,7 +43,7 @@ ext {
 
 dependencies {
     // JUnit setup for testing
-    testImplementation(platform("org.junit:junit-bom:5.12.2"))
+    testImplementation(platform("org.junit:junit-bom:5.13.0"))
     testImplementation('org.junit.jupiter:junit-jupiter')
     testRuntimeOnly('org.junit.platform:junit-platform-launcher')
     // JSON object mapping / (de-)serialization
@@ -64,7 +64,7 @@ dependencies {
     // JSON-LD, Zenodo mapping
     implementation group: 'com.apicatalog', name: 'titanium-json-ld', version: '1.6.0'
     // metadata validation, profiles based on JSON schema
-    implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.6"
+    implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.7"
     implementation 'org.glassfish:jakarta.json:2.0.1'
     //JTE for template processing
     implementation('gg.jte:jte:3.2.1')
@@ -111,6 +111,22 @@ configurations {
     performanceTestImplementation.extendsFrom implementation
 }
 
+// Task for creating a resource file with the version info
+tasks.register("generateVersionProps", WriteProperties) { t ->
+    def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "main"].join(File.separator))
+    def outputFile = generatedResourcesDir.map { it.file("version.properties") }
+
+    t.destinationFile = outputFile.get().asFile
+    t.property("version", version)
+}
+
+tasks.register("generateVersionPropsTest", WriteProperties) { t ->
+    def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "test"].join(File.separator))
+    def outputFile = generatedResourcesDir.map { it.file("version.properties") }
+
+    t.destinationFile = outputFile.get().asFile
+    t.property("version", version)
+}
 
 tasks.register('performanceContextEntitiesBenchmark', JavaExec) {
     description = "Run the context entities benchmarks."
@@ -154,8 +170,13 @@ tasks.register('performanceReadWriteMultipleCratesBenchmark', JavaExec) {
     mainClass = 'edu.kit.datamanager.ro_crate.multiplecrates.MultipleCratesWriteAndRead'
 }
 
+compileJava {
+    dependsOn generateVersionProps
+}
+
 test {
     useJUnitPlatform()
+    dependsOn generateVersionPropsTest
     finalizedBy jacocoTestReport
 }
 
@@ -178,3 +199,5 @@ if (System.getProperty('profile') == "release") {
     println 'Using release profile for building ' + project.getName()
     apply from: 'gradle/profile-release.gradle'
 }
+
+apply from: 'gradle/updateCff.gradle'

gradle/profile-release.gradle

@@ -17,7 +17,7 @@
 apply plugin: 'net.researchgate.release'
 apply plugin: 'maven-publish'
 apply plugin: 'signing'
-   
+
 //for plugin net.researchgate.release 
 //see https://github.com/researchgate/gradle-release
 release {

gradle/updateCff.gradle

@@ -0,0 +1,70 @@
+import java.time.LocalDate
+import java.time.format.DateTimeFormatter
+
+/**
+ * This file defines the updateCff task.
+ *
+ * This task hooks into the workflow of the release task,
+ * which, according to the source code of the release plugin,
+ * seems to be defined like this:
+ *
+ * tasks = [
+ * "${p}createScmAdapter" as String,
+ * "${p}initScmAdapter" as String,
+ * "${p}checkCommitNeeded" as String,
+ * "${p}checkUpdateNeeded" as String,
+ * "${p}checkoutMergeToReleaseBranch" as String,
+ * "${p}unSnapshotVersion" as String,
+ * "${p}confirmReleaseVersion" as String,
+ * -> we insert our task here <-
+ * "${p}checkSnapshotDependencies" as String,
+ * "${p}runBuildTasks" as String,
+ * "${p}preTagCommit" as String,
+ * "${p}createReleaseTag" as String,
+ * "${p}checkoutMergeFromReleaseBranch" as String,
+ * "${p}updateVersion" as String,
+ * "${p}commitNewVersion" as String
+ * ]
+ */
+
+tasks.register('updateCff') {
+    group = 'release'
+    description = 'Updates the version in CITATION.cff file'
+
+    outputs.file("CITATION.cff")
+
+    doLast {
+        def version = project.version.toString()
+        def today = LocalDate.now().format(DateTimeFormatter.ISO_DATE)
+
+        def cffFile = file('CITATION.cff')
+        def content = cffFile.text
+
+        // Update or insert version
+        if (content.contains('version:')) {
+            content = content.replaceAll(/(?m)^version:\s*.+$/, "version: ${version}")
+        } else {
+            content = content + "\nversion: ${version}"
+        }
+
+        // Update or insert date-released
+        if (content.contains('date-released:')) {
+            content = content.replaceAll(/(?m)^date-released:\s*.+$/, "date-released: ${today}")
+        } else {
+            content = content + "\ndate-released: ${today}"
+        }
+
+        cffFile.text = content
+        println "Updated CITATION.cff to version ${version} and date-released ${today}"
+    }
+}
+
+// Make sure your custom task runs after a specific task in the release sequence
+tasks.named('updateCff') {
+    mustRunAfter(tasks.named('confirmReleaseVersion'))
+}
+
+// Ensure subsequent tasks in the release sequence run after your custom task
+tasks.named('checkSnapshotDependencies') {
+    dependsOn('updateCff')
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.2-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/edu/kit/datamanager/ro_crate/Crate.java

@@ -22,6 +22,28 @@
  */
 public interface Crate {
 
+  /**
+   * Mark the crate as imported, i.e. it has been read from a file
+   * or is for other reasons not considered a new crate.
+   * <p>
+   * This is useful mostly for readers to indicate this in case
+   * the crate may not have any provenance information yet and
+   * should still be recognized as an imported crate.
+   *
+   * @return this crate, for convenience.
+   */
+  Crate markAsImported();
+
+  /**
+   * Check if the crate is marked as imported.
+   * <p>
+   * If true, it indicates that the crate has been read from a file
+   * or is for other reasons not considered a new crate.
+   *
+   * @return true if the crate is marked as imported, false otherwise.
+   */
+  boolean isImported();
+
   /**
    * Read version from the crate descriptor and return it as a class
    * representation.

src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java

@@ -50,6 +50,24 @@ public class RoCrate implements Crate {
 
     protected Collection<File> untrackedFiles;
 
+    /**
+     * Indicates whether this crate has been imported from an external source.
+     * This is used to determine if ro-crate-java should add a CreateAction
+     * or an UpdateAction in the provenance on export.
+     */
+    protected boolean isImported = false;
+
+    @Override
+    public RoCrate markAsImported() {
+        this.isImported = true;
+        return this;
+    }
+
+    @Override
+    public boolean isImported() {
+        return this.isImported;
+    }
+
     @Override
     public CratePreview getPreview() {
         return this.roCratePreview;
@@ -375,12 +393,14 @@ public RoCrateBuilder addDescription(String description) {
          * @return returns the builder for further usage.
          */
         public RoCrateBuilder addDataEntity(DataEntity dataEntity) {
+            this.metadataContext.checkEntity(dataEntity);
             this.payload.addDataEntity(dataEntity);
             this.rootDataEntity.addToHasPart(dataEntity.getId());
             return this;
         }
 
         public RoCrateBuilder addContextualEntity(ContextualEntity contextualEntity) {
+            this.metadataContext.checkEntity(contextualEntity);
             this.payload.addContextualEntity(contextualEntity);
             return this;
         }