Updates to fix API

.github/workflows/build-test-with-registry.yml

@@ -16,16 +16,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
-      uses: actions/setup-java@v3
+    - uses: actions/checkout@v7
+    - name: Set up JDK 21
+      uses: actions/setup-java@v6
       with:
-        java-version: '11'
-        distribution: 'adopt'
+        java-version: '21'
+        distribution: 'temurin'
         cache: gradle
     - name: Install local registry
       run: |
-        /bin/bash -c "$(curl -fsSL https://data.scrc.uk/static/localregistry.sh)"
+        /bin/bash -c "$(curl -fsSL https://data.fairdatapipeline.org/static/localregistry.sh)"
         ~/.fair/registry/scripts/start_fair_registry
     - name: Grant execute permission for gradlew
       run: chmod +x gradlew
@@ -34,6 +34,7 @@ jobs:
         export REGTOKEN=`cat ~/.fair/registry/token`
         export LOCALREG=FRESHASADAISY
         ./gradlew build
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v7
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         files: ./api/build/reports/jacoco/test/jacocoTestReport.xml,./dataregistry/build/reports/jacoco/test/jacocoTestReport.xml

.github/workflows/build-test.yml

@@ -16,12 +16,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up JDK 11
-        uses: actions/setup-java@v3
+      - uses: actions/checkout@v7
+      - name: Set up JDK 21
+        uses: actions/setup-java@v6
         with:
-          java-version: '11'
-          distribution: 'adopt'
+          java-version: '21'
+          distribution: 'temurin'
           cache: gradle
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew

.github/workflows/gradle-publish.yml

@@ -16,12 +16,12 @@ jobs:
       packages: write
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
-      uses: actions/setup-java@v3
+    - uses: actions/checkout@v7
+    - name: Set up JDK 21
+      uses: actions/setup-java@v6
       with:
-        java-version: '11'
-        distribution: 'adopt'
+        java-version: '21'
+        distribution: 'temurin'
         server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
         settings-path: ${{ github.workspace }} # location for the settings.xml file
 

.github/workflows/javadoc.yml

@@ -9,13 +9,13 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v6
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '21'
           cache: 'gradle'
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew

.gitignore

@@ -6,3 +6,7 @@ gradle
 build
 
 .idea
+api/bin
+dataregistry/bin
+dataregistry/build
+graphify-out

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "interactive"
+}

README.md

@@ -12,12 +12,12 @@ Documentation can be found on https://www.fairdatapipeline.org/docs/API/Java/
 
 JavaDocs are automatically published on https://www.fairdatapipeline.org/javaDataPipeline/
 
-To use a release version (latest: 1.0.0-rc3) include the following dependency (available from mavenCentral):
+To use a release version (latest: 1.0.0-rc4) include the following dependency (available from mavenCentral):
 
 ```gradle
 group: 'org.fairdatapipeline',
 name: 'api',
-version: '1.0.0-rc3'
+version: '1.0.0-rc4'
 ```
 
 ## javaSimpleModel

api/build.gradle

@@ -1,21 +1,22 @@
 plugins {
     id 'java'
-    id "com.diffplug.gradle.spotless" version "4.4.0"
+    id "com.diffplug.spotless" version "8.10.2"
     id "maven-publish"
     id "signing"
     id "jacoco"
 }
 
-group 'org.fairdatapipeline'
-version '1.0.0-rc3'
+group = 'org.fairdatapipeline'
+version = '1.0.0-rc4'
 
 repositories {
     mavenCentral()
 }
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
     withJavadocJar()
     withSourcesJar()
 }
@@ -32,12 +33,12 @@ dependencies {
     implementation 'com.google.guava:guava:31.1-jre'
     implementation 'com.moandjiezana.toml:toml4j:0.7.2'
     implementation 'commons-io:commons-io:2.11.0'
-    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.0.0'
+    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.1.0'
     implementation 'org.apache.commons:commons-math3:3.6.1'
     implementation 'org.apache.maven:maven-artifact:3.8.4'
-    implementation 'org.glassfish.jersey.core:jersey-client:3.0.4'
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.0.4'
-    implementation 'org.glassfish.jersey:jersey-bom:3.0.4'
+    implementation 'org.glassfish.jersey.core:jersey-client:3.1.12'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.12'
+    implementation 'org.glassfish.jersey:jersey-bom:3.1.12'
     implementation 'org.immutables:value-annotations:2.9.0'
     implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.15.2'
     implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.15.2'
@@ -49,9 +50,10 @@ dependencies {
     implementation 'org.slf4j:slf4j-simple:1.7.36'
     testAnnotationProcessor 'org.immutables:value:2.9.0'
     testImplementation(platform('org.junit:junit-bom:5.8.1'))
+    testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
     testImplementation('org.junit.jupiter:junit-jupiter:5.8.2')
     testImplementation 'org.skyscreamer:jsonassert:1.5.0'
-    testImplementation 'org.mockito:mockito-core:4.3.1'
+    testImplementation 'org.mockito:mockito-core:5.11.0'
     testImplementation 'org.assertj:assertj-core:3.22.0'
     testImplementation 'org.javatuples:javatuples:1.2'
 }
@@ -67,14 +69,14 @@ test {
 jacocoTestReport {
     dependsOn test
     reports {
-        xml.enabled true
-        html.enabled false
+        xml.required = true
+        html.required = false
     }
 }
 
 spotless {
     java {
-        googleJavaFormat()
+        googleJavaFormat("1.36.1")
     }
 }
 
@@ -126,8 +128,8 @@ publishing {
         maven {
             url = 'https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/'
             credentials {
-                username findProperty('ossrhUsername')
-                password findProperty('ossrhPassword')
+                username = findProperty('ossrhUsername')
+                password = findProperty('ossrhPassword')
             }
         }
     }

api/src/main/java/org/fairdatapipeline/api/Coderun.java

@@ -239,8 +239,8 @@ private void prepare_code_run() {
     String remote_repo = this.config.run_metadata().remote_repo().orElse("");
     URL remote_repo_url;
     try {
-      remote_repo_url = new URL(remote_repo);
-    } catch (MalformedURLException e) {
+      remote_repo_url = URI.create(remote_repo).toURL();
+    } catch (MalformedURLException | IllegalArgumentException e) {
       throw (new ConfigException(
           "Remote repo must be a valid URL; (" + remote_repo + " isn't)", e));
     }

api/src/main/java/org/fairdatapipeline/api/Data_product.java

@@ -34,8 +34,10 @@ public abstract class Data_product implements AutoCloseable {
   Path filePath;
   CleanableFileChannel filechannel;
   Object_component whole_obj_oc;
+
   /** the name given by the user (asked for in the FileApi.get_dp_for_xxx() call) */
   final String givenDataProduct_name;
+
   /**
    * usually the same as the given name, unless the config use section has given an alternative data
    * product name to open.

api/src/main/java/org/fairdatapipeline/estimate/Estimate.java

@@ -14,7 +14,9 @@
 @JsonDeserialize
 @JsonSerialize
 public interface Estimate extends Component {
-  /** @return Number - the value that is stored in this component */
+  /**
+   * @return Number - the value that is stored in this component
+   */
   @JsonProperty("value")
   Number internalValue();
 

dataregistry/build.gradle

@@ -1,17 +1,18 @@
 plugins {
     id 'java'
-    id "com.diffplug.gradle.spotless" version "4.4.0"
+    id "com.diffplug.spotless" version "8.10.2"
     id "maven-publish"
     id "signing"
     id "jacoco"
 }
 
-group 'org.fairdatapipeline'
-version '1.0.0-rc3'
+group = 'org.fairdatapipeline'
+version = '1.0.0-rc4'
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
     withJavadocJar()
     withSourcesJar()
 }
@@ -26,13 +27,15 @@ repositories {
 
 dependencies {
     testImplementation(platform('org.junit:junit-bom:5.8.1'))
+    testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.hamcrest:hamcrest:2.2'
-    testImplementation 'org.mockito:mockito-core:4.3.1'
-    implementation 'org.glassfish.jersey.core:jersey-client:3.0.4'
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.0.4'
-    implementation 'org.glassfish.jersey:jersey-bom:3.0.4'
-    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.0.0'
+    testImplementation 'org.mockito:mockito-core:5.11.0'
+    implementation 'org.glassfish.jersey.core:jersey-client:3.1.12'
+    implementation 'org.glassfish.jersey.connectors:jersey-jnh-connector:3.1.12'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.12'
+    implementation 'org.glassfish.jersey:jersey-bom:3.1.12'
+    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.1.0'
     implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.15.2'
     implementation 'com.fasterxml.jackson.core:jackson-databind:2.15.2'
     implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.2'
@@ -46,7 +49,7 @@ dependencies {
 
 spotless {
     java {
-        googleJavaFormat()
+        googleJavaFormat("1.36.1")
     }
 }
 
@@ -60,8 +63,8 @@ test {
 jacocoTestReport {
     dependsOn test
     reports {
-        xml.enabled true
-        html.enabled false
+        xml.required = true
+        html.required = false
     }
 }
 
@@ -113,8 +116,8 @@ publishing {
         maven {
             url = 'https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/'
             credentials {
-                username findProperty('ossrhUsername')
-                password findProperty('ossrhPassword')
+                username = findProperty('ossrhUsername')
+                password = findProperty('ossrhPassword')
             }
         }
     }

dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryAuthor.java

@@ -51,7 +51,9 @@ public void setName(String name) {
     this.name = name;
   }
 
-  /** @param identifier (optional): Full URL of identifier (e.g. ORCiD or ROR ID) of the Author. */
+  /**
+   * @param identifier (optional): Full URL of identifier (e.g. ORCiD or ROR ID) of the Author.
+   */
   public void setIdentifier(String identifier) {
     this.identifier = identifier;
   }

dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_repo_release.java

@@ -68,12 +68,16 @@ public void setVersion(String version) {
     this.version = version;
   }
 
-  /** @param website (optional): URL of the website for this code release, if applicable. */
+  /**
+   * @param website (optional): URL of the website for this code release, if applicable.
+   */
   public void setWebsite(URL website) {
     this.website = website;
   }
 
-  /** @param object APIURL of the associated Object. */
+  /**
+   * @param object APIURL of the associated Object.
+   */
   public void setObject(APIURL object) {
     this.object = object;
   }

dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_run.java

@@ -132,12 +132,16 @@ public APIURL getRo_crate() {
     return this.ro_crate;
   }
 
-  /** @param run_date Datetime of the CodeRun. */
+  /**
+   * @param run_date Datetime of the CodeRun.
+   */
   public void setRun_date(LocalDateTime run_date) {
     this.run_date = run_date;
   }
 
-  /** @param description (optional): Free text description of the CodeRun. */
+  /**
+   * @param description (optional): Free text description of the CodeRun.
+   */
   public void setDescription(String description) {
     this.description = description;
   }
@@ -166,12 +170,16 @@ public void setSubmission_script(APIURL submission_script) {
     this.submission_script = submission_script;
   }
 
-  /** @param inputs List of RegistryObject_component that the CodeRun used as inputs. */
+  /**
+   * @param inputs List of RegistryObject_component that the CodeRun used as inputs.
+   */
   public void setInputs(List<APIURL> inputs) {
     this.inputs = (inputs == null) ? null : new ArrayList<>(inputs);
   }
 
-  /** @param outputs List of RegistryObject_component that the CodeRun produced as outputs. */
+  /**
+   * @param outputs List of RegistryObject_component that the CodeRun produced as outputs.
+   */
   public void setOutputs(List<APIURL> outputs) {
     this.outputs = (outputs == null) ? null : new ArrayList<>(outputs);
   }

dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryData_product.java

@@ -122,12 +122,16 @@ public void setVersion(String version) {
     this.version = version;
   }
 
-  /** @param object APIURL of the associated Object. */
+  /**
+   * @param object APIURL of the associated Object.
+   */
   public void setObject(APIURL object) {
     this.object = object;
   }
 
-  /** @param namespace API URL of the Namespace of the DataProduct. */
+  /**
+   * @param namespace API URL of the Namespace of the DataProduct.
+   */
   public void setNamespace(APIURL namespace) {
     this.namespace = namespace;
   }