Preparations for singularity support

.circleci/config.yml

@@ -22,7 +22,7 @@ jobs: # a collection of steps
       - run:
           name: Run tests
           command: |
-            ./gradlew build test $GRADLE_ARGS
+            ./gradlew build check test allBoms $GRADLE_ARGS
       - save_cache:
           paths:
             - ~/.gradle/wrapper
@@ -34,26 +34,42 @@ jobs: # a collection of steps
       - store_test_results:
           # Upload test results for display in Test Summary: https://circleci.com/docs/2.0/collect-test-data/
           path: build/test-results/test
-      - store_artifacts: # Upload test results for display in Artifacts: https://circleci.com/docs/2.0/artifacts/
+      - store_artifacts:
+          # Upload test results for display in Artifacts: https://circleci.com/docs/2.0/artifacts/
           path: build/test-results/test
           when: always
-      - persist_to_workspace: # Pass artifact over to next job via workspace.
-          root: build/libs
+      - persist_to_workspace:
+          # Pass artifact over to next job via workspace.
+          root: build/
           paths:
-            - "*.jar"
-      # See https://circleci.com/docs/2.0/deployment-integrations/ for deploy examples
+            - "libs/*.jar"
+            - "reports/cyclonedx/*"
+            - "reports/tests/test/*"
+
+  # See https://circleci.com/docs/2.0/deployment-integrations/ for deploy examples
   publish-github-release:  # https://circleci.com/blog/publishing-to-github-releases-via-circleci/
     docker:
       - image: cibuilds/github:0.13
     resource_class: small
     steps:
       - attach_workspace:
-          at: build/libs
+          at: build/
       - run:
           name: "Publish Release on GitHub"
           command: |
             VERSION=$(ls ./build/libs/*.jar | sed -r 's/.*BatchEuphoria-([[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+(-.+)?).jar/\1/')
-            ghr -t "$GITHUB_TOKEN" -u "$CIRCLE_PROJECT_USERNAME" -r "$CIRCLE_PROJECT_REPONAME" -c "$CIRCLE_SHA1" -n "$VERSION" -delete "$VERSION" ./build/libs/*.jar
+            tar -C build/reports/tests/ -cvzf test-report.tgz test/
+            tar -C build/reports/ -cvzf cyclonedx-sbom.tgz cyclonedx/
+            ghr \
+              -t "$GITHUB_TOKEN" \
+              -u "$CIRCLE_PROJECT_USERNAME" \
+              -r "$CIRCLE_PROJECT_REPONAME" \
+              -c "$CIRCLE_SHA1" \
+              -n "$VERSION" \
+              -delete "$VERSION" \
+              ./build/libs/*.jar \
+              ./cyclonedx-sbom.tgz \
+              ./test-report.tgz
 
 workflows:
   version: 2

README.md

@@ -10,6 +10,7 @@ Currently this library supports the following job schedulers:
 * direct execution
 
 ### Dependencies
+
 * [RoddyToolLib](https://github.com/TheRoddyWMS/RoddyToolLib)
 
 ## Build
@@ -89,6 +90,15 @@ To start the integration tests, please fill in host and user settings (password
 
 # Change Logs
 
+* 0.2.0
+  - major: `CommandI` classes to model commands and code
+  - minor: `ApptainerCommandBuilder` to create a wrapping command to run code in containers
+    * Submission as container works for LSF and SLURM. PBS and SGE might work, but were not tested. It won't work for REST-based submission to LSF, though.
+  - patch: Library updates
+  - patch: Fix `--propagate=none` for SLURM to `--propagate=NONE`
+  - patch: Added Gradle task `:allBoms` for CycloneDX SBOM generation
+  - patch: Added cyclonedx SBOM and test-report tarballs to GitHub releases
+
 * 0.1.4
   - patch: Changed the conversion of EpochSeconds to ZonedDateTime for the value "0".
     * For eligibleTime it is set to null
@@ -100,7 +110,7 @@ To start the integration tests, please fill in host and user settings (password
     * Reworked queryExtendedJobStateById to always execute both scontrol and sacct and combine the output
     * Some refactoring and added comments
     * Fixed time parsing for jobs longer than 24h
-    * Added --propagate=none" to getAdditionalCommandParameters
+    * Added `--propagate=none` to getAdditionalCommandParameters
     * Added tests
 
 * 0.1.2

build.gradle

@@ -4,20 +4,27 @@
  * Distributed under the MIT License (license terms are at https://www.github.com/theroddywms/Roddy/LICENSE.txt).
  */
 
+import org.cyclonedx.gradle.CycloneDxTask
+
 plugins {
-    id 'org.ajoberstar.grgit' version '1.7.2'
+    id 'org.ajoberstar.grgit' version '4.1.1'
+    id 'org.cyclonedx.bom' version '1.8.2'
+    id 'maven-publish'
 }
 
 apply plugin: 'groovy'
 apply plugin: 'idea'
 apply plugin: 'application'
-apply plugin: 'maven'
 
 group = "com.github.theroddywms"
 
 mainClassName = 'de.dkfz.roddy.BEIntegrationTestStarter'
-sourceCompatibility = '1.8'
-targetCompatibility = '1.8'
+
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(8)
+    }
+}
 
 /*
  * Gets the version name from the current Git tag. If the current commit is not tagged,
@@ -30,10 +37,12 @@ def getVersionName() {
 
 rootProject.version = getVersionName()
 
+compileJava.options.compilerArgs = ["-release", targetCompatibility]
+
 // Set -Pchecked on the command line to change this compiler parameter.
-if (!project.hasProperty("checked") || !project.checked) {
-    compileJava.options.compilerArgs = ["-Xlint:unchecked"]
-    compileGroovy.options.compilerArgs = ["-Xlint:unchecked"]
+if (project.hasProperty("checked") && !project.checked) {
+    compileJava.options.compilerArgs += ["-Xlint:unchecked", "-Xlint:deprecation"]
+    compileGroovy.options.compilerArgs += ["-Xlint:unchecked", "-Xlint:deprecation"]
 }
 
 repositories {
@@ -46,41 +55,49 @@ configurations.all {
 }
 
 dependencies {
-    compile 'com.fasterxml.jackson.core:jackson-core:2.9.7'
-    compile 'com.fasterxml.jackson.core:jackson-annotations:2.9.7'
-    compile 'com.fasterxml.jackson.core:jackson-databind:2.9.7'
-    compile 'org.codehaus.groovy:groovy-all:2.4.9'
-    testCompile 'junit:junit:4.12'
-    testCompile 'org.spockframework:spock-core:1.1-groovy-2.4'
-    testRuntime "net.bytebuddy:byte-buddy:1.6.5"
-    testRuntime "org.objenesis:objenesis:2.5.1"
-    testCompile 'com.google.guava:guava:23.0'
-    testCompile 'org.slf4j:slf4j-nop:1.7.25'
-    compile 'org.slf4j:slf4j-api:1.7.25'
-    compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
-    compile group: 'commons-codec', name: 'commons-codec', version: '1.9'
-    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.3'
-    compile group: 'commons-cli', name: 'commons-cli', version: '1.2'
-    compile group: 'org.apache.commons', name: 'commons-text', version: '1.1'
-    compile 'com.google.guava:guava:23.0'
-    compile 'com.github.theroddywms:RoddyToolLib:2.4.0'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.9.7'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.9.7'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.12.7.1'
+    implementation 'org.codehaus.groovy:groovy-all:2.4.21'
+    testImplementation 'junit:junit:4.13.1'
+    testImplementation 'org.spockframework:spock-core:1.1-groovy-2.4'
+    testRuntimeOnly "net.bytebuddy:byte-buddy:1.6.5"
+    testRuntimeOnly "org.objenesis:objenesis:2.5.1"
+    testImplementation 'org.slf4j:slf4j-nop:1.7.25'
+    implementation 'org.slf4j:slf4j-api:1.7.25'
+    implementation group: 'commons-io', name: 'commons-io', version: '2.11.0'
+    implementation group: 'commons-codec', name: 'commons-codec', version: '1.15'
+    implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.13'
+    implementation group: 'commons-cli', name: 'commons-cli', version: '1.5.0'
+    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.11.0'
+    implementation group: 'com.google.guava', name: 'guava', version: '33.2.1-jre'
+    implementation 'com.github.theroddywms:RoddyToolLib:2.5.0'
+
+    // Runtime retention of @NotNull and annotations.
+    implementation 'com.github.bbottema:jetbrains-runtime-annotations:1.0.1'
 }
 
-task writePom {
-    doLast {
-        pom {
-            project {
-                version rootProject.version
-                inceptionYear '2017'
+model {
+    tasks.generatePomFileForMavenJavaPublication {
+        destination = file("$buildDir/pom.xml")
+    }
+}
+
+publishing {
+    publications {
+        mavenJava(org.gradle.api.publish.maven.MavenPublication) {
+            from components.java
+            pom {
+                name = 'BatchEuphoria'
+                url = "https://www.github.com/theroddywms/BatchEuphoria"
                 licenses {
                     license {
-                        name 'MIT License'
-                        url 'https://raw.githubusercontent.com/eilslabs/BatchEuphoria/master/LICENSE'
-                        distribution 'repo'
+                        name = 'MIT License'
+                        url = 'https://raw.githubusercontent.com/eilslabs/BatchEuphoria/master/LICENSE'
                     }
                 }
             }
-        }.writeTo("$buildDir/pom.xml")
+        }
     }
 }
 
@@ -89,13 +106,12 @@ jar {
 
     manifest {
         attributes("Implementation-Vendor": "German Cancer Research Center (DKFZ)")
-        attributes("Implementation-Title": baseName)
+        attributes("Implementation-Title": archiveBaseName.get())
         attributes 'Implementation-Version': rootProject.version
     }
 
-    dependsOn writePom
     into("META-INF/maven/$project.group/$project.name") {
-        from "$buildDir/pom.xml"
+        from generatePomFileForMavenJavaPublication
     }
 
 }
@@ -109,7 +125,7 @@ task listJars {
 
 task uberjar(type: Jar, dependsOn:[':compileJava',':compileGroovy']) {
     from files(sourceSets.main.output.dirs)
-    from configurations.runtime.asFileTree.files.collect { zipTree(it) }
+    from configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
 
     version = getVersionName()
 
@@ -119,3 +135,35 @@ task uberjar(type: Jar, dependsOn:[':compileJava',':compileGroovy']) {
     }
     exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
 }
+
+task listConfigurations {
+    group = "reporting"
+    description = "List all configurations, as needed for discerning development and production configurations by the SBOM tasks."
+    doLast {
+        configurations.each { Configuration c ->
+            println c.name
+        }
+    }
+}
+
+task allBoms() {
+    group = "reporting"
+    description = "A grouping task to execute the CycloneDxTask for each configuration"
+}
+
+rootProject.configurations.each { Configuration configuration ->
+    String name = configuration.name
+    task "${name}Bom"(type: CycloneDxTask) {
+        group = "reporting"
+        description = "Creates a CycloneDX SBOM for the configuration ${name}."
+
+        destination = file("${project.buildDir}/reports/cyclonedx")
+        outputName = name
+        includeConfigs = [name]
+        schemaVersion = "1.5"
+        outputFormat="json"
+        includeLicenseText = false
+        projectType = "application"
+    }
+    allBoms.dependsOn tasks.getByName("${name}Bom")
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists