Refactoring super long methods

.github/workflows/build.yml

@@ -15,16 +15,18 @@ on:
 
 jobs:
   build:
-    name: Build and Test
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: ['11', '16', '17' ]
 
+    name: Java ${{ matrix.java }} Build and Test
     steps:
       - name: Set up java
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
-          java-version: 11.0.2
-          java-package: jdk
-          architecture: x64
+          distribution: 'temurin'
+          java-version: ${{ matrix.java }}
       - name: Set up python
         uses: actions/setup-python@v2
         with:
@@ -39,7 +41,7 @@ jobs:
       - name: Build with Gradle
         run: ./gradlew build -x test
       - name: Test
-        run: ./gradlew check
+        run: ./gradlew --info check
       - name: Publish Unit Test Results
         uses: EnricoMi/[email protected]
         if: always()

.github/workflows/cwl_compliance.yml

@@ -19,11 +19,10 @@ jobs:
 
     steps:
       - name: Set up java
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
-          java-version: 11.0.2
-          java-package: jdk
-          architecture: x64
+          distribution: 'temurin'
+          java-version: '17'
       - name: Set up python
         uses: actions/setup-python@v2
         with:

.gitignore

@@ -6,7 +6,12 @@ build/
 .settings
 *.iws
 .DS_Store
+.vscode
 
+# Ignore yarn
+src/main/frontend/yarn-v1.22.0/
+
+# Xenonflow logs
 log/
 db/
 xenon-flow.log

build.gradle

@@ -4,7 +4,7 @@ plugins {
     id 'idea'
     id 'eclipse'
     id 'application'
-    id 'org.springframework.boot' version '2.2.4.RELEASE'
+    id 'org.springframework.boot' version '2.3.12.RELEASE'
     id 'io.spring.dependency-management' version '1.0.7.RELEASE'
     id 'jacoco'
     id "com.github.node-gradle.node" version "2.2.2"
@@ -15,7 +15,7 @@ sourceCompatibility = JavaVersion.VERSION_11
 targetCompatibility = JavaVersion.VERSION_11
 
 application {
-	mainClassName = 'nl.esciencecenter.computeservice.rest.Application'
+	mainClass = 'nl.esciencecenter.computeservice.rest.Application'
 }
 
 
@@ -43,26 +43,27 @@ dependencies {
     implementation group: 'nl.esciencecenter.xenon.adaptors', name: 'xenon-adaptors-cloud', version: '3.0.2'
 
     //Spring(boot)
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.2.4.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-validation', version: '2.3.12.RELEASE'
     implementation group: 'io.springfox', name: 'springfox-boot-starter', version: '3.0.0'
 
     //Jackson, match version used in Spring
-    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.8'
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.9.8'
-    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.9.8'
+    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.11.4'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.11.4'
+    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.11.4'
 
     //compile group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310'
     implementation group: 'javax.validation', name: 'validation-api', version: '2.0.1.Final'
 
 	//JPA, hibernate and h2 database persistance libraries
-	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.2.4.RELEASE'
+	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.3.12.RELEASE'
 	runtimeOnly group: 'com.h2database', name: 'h2', version: '1.4.199'
 
 	// Security
-	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.2.4.RELEASE'
+	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.3.12.RELEASE'
 
 	// Admin Interface
 
@@ -75,18 +76,20 @@ dependencies {
 	testImplementation group: 'org.hamcrest', name:'hamcrest', version:'2.2'
     testImplementation group: 'org.hamcrest', name:'hamcrest-library', version:'2.2'
     testImplementation group: 'junit', name:'junit', version:'4.13'
-    testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.2.4.RELEASE'
+    testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.3.12.RELEASE'
+
+    runtimeOnly group: 'org.springframework.boot', name: 'spring-boot-properties-migrator', version: '2.3.12.RELEASE'
 }
 
 bootJar {
-	baseName = 'xenonflow'
+    baseName = 'xenonflow'
 }
 
 // Include some more files in the distribution zip
 // Don't use include an extra directory in the dist zip.
 distributions {
     boot {
-    	baseName = 'xenonflow'
+    	distributionBaseName = 'xenonflow'
         contents {
 			from(['config/config.yml', 'config/application.properties']) {
 				into '/config'

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/java/nl/esciencecenter/computeservice/service/staging/BaseStagingObject.java

@@ -2,7 +2,7 @@
 
 import org.commonwl.cwl.Parameter;
 
-public class BaseStagingObject implements StagingObject {
+public abstract class BaseStagingObject implements StagingObject {
 
 	protected long bytesCopied = 0;
 	protected String copyId;

src/main/java/nl/esciencecenter/computeservice/service/staging/CommandScriptStagingObject.java

@@ -1,13 +1,32 @@
 package nl.esciencecenter.computeservice.service.staging;
 
-import org.commonwl.cwl.Parameter;
+import java.util.Set;
 
+import org.slf4j.Logger;
+
+import nl.esciencecenter.xenon.XenonException;
+import nl.esciencecenter.xenon.filesystems.FileSystem;
 import nl.esciencecenter.xenon.filesystems.Path;
+import nl.esciencecenter.xenon.filesystems.PosixFilePermission;
 
 public class CommandScriptStagingObject extends StringToFileStagingObject {
 
-	public CommandScriptStagingObject(String source, Path targetPath, Parameter parameter) {
-		super(source, targetPath, parameter);
+	public CommandScriptStagingObject(String source, Path targetPath) {
+		super(source, targetPath, null);
 	}
 
+	public String stage(Logger jobLogger, FileSystem sourceFileSystem, FileSystem targetFileSystem,
+			Path sourceDirectory, Path targetDirectory) throws XenonException {
+		String id = super.stage(jobLogger, sourceFileSystem, targetFileSystem, sourceDirectory, targetDirectory);
+
+		Path targetPath = targetDirectory.resolve(getTargetPath());
+
+		Set<PosixFilePermission> permissions = targetFileSystem.getAttributes(targetPath).getPermissions();
+		permissions.add(PosixFilePermission.OWNER_EXECUTE);
+		permissions.add(PosixFilePermission.GROUP_EXECUTE);
+		permissions.add(PosixFilePermission.OTHERS_EXECUTE);
+		targetFileSystem.setPosixFilePermissions(targetPath, permissions);
+
+		return id;
+	}
 }

src/main/java/nl/esciencecenter/computeservice/service/staging/CwlFileStagingObject.java

@@ -1,38 +1,27 @@
 package nl.esciencecenter.computeservice.service.staging;
 
-import org.commonwl.cwl.Parameter;
+import org.slf4j.Logger;
 
+import nl.esciencecenter.xenon.XenonException;
+import nl.esciencecenter.xenon.filesystems.FileSystem;
 import nl.esciencecenter.xenon.filesystems.Path;
 
-public class CwlFileStagingObject extends BaseStagingObject {
-	private Path sourcePath;
-	private Path targetPath;
+public class CwlFileStagingObject extends FileStagingObject {
+	protected FileSystem cwlFileSystem;
 
-	public CwlFileStagingObject(Path sourcePath, Path targetPath, Parameter parameter) {
-		super(parameter);
-		this.sourcePath = sourcePath;
-		this.targetPath = targetPath;
-	}
-
-	public Path getSourcePath() {
-		return sourcePath;
-	}
-
-	public void setSourcePath(Path sourcePath) {
-		this.sourcePath = sourcePath;
-	}
-
-	public Path getTargetPath() {
-		return targetPath;
-	}
-
-	public void setTargetPath(Path targetPath) {
-		this.targetPath = targetPath;
+	public CwlFileStagingObject(Path sourcePath, Path targetPath, FileSystem cwlFileSystem) {
+		super(sourcePath, targetPath, null);
+		this.cwlFileSystem = cwlFileSystem;
 	}
 
 	@Override
 	public String toString() {
 		return "CwlFileStagingObject [sourcePath=" + sourcePath + ", targetPath=" + targetPath
 				+ ", parameter=" + parameter + "]";
 	}
+
+	public String stage(Logger jobLogger, FileSystem sourceFileSystem, FileSystem targetFileSystem,
+			Path sourceDirectory, Path targetDirectory) throws XenonException {		
+		return super.stage(jobLogger, cwlFileSystem, targetFileSystem, sourceDirectory, targetDirectory);
+	}
 }

src/main/java/nl/esciencecenter/computeservice/service/staging/DirectoryStagingObject.java

@@ -1,7 +1,11 @@
 package nl.esciencecenter.computeservice.service.staging;
 
 import org.commonwl.cwl.Parameter;
+import org.slf4j.Logger;
 
+import nl.esciencecenter.xenon.XenonException;
+import nl.esciencecenter.xenon.filesystems.CopyMode;
+import nl.esciencecenter.xenon.filesystems.FileSystem;
 import nl.esciencecenter.xenon.filesystems.Path;
 
 public class DirectoryStagingObject extends BaseStagingObject implements FileOrDirectoryStagingObject {
@@ -35,4 +39,24 @@ public String toString() {
 		return "DirectoryStagingObject [sourcePath=" + sourcePath + ", targetPath=" + targetPath
 				+ ", parameter=" + parameter + "]";
 	}
+
+	public String stage(Logger jobLogger, FileSystem sourceFileSystem, FileSystem targetFileSystem,
+			Path sourceDirectory, Path targetDirectory) throws XenonException {		
+		Path sourcePath = getSourcePath();
+		if (!sourcePath.isAbsolute()) {
+			sourcePath = sourceDirectory.resolve(getSourcePath()).toAbsolutePath();
+		}
+		Path targetPath = targetDirectory.resolve(getTargetPath());
+		Path targetDir = targetPath.getParent();
+		if (!targetFileSystem.exists(targetDir)) {
+			targetFileSystem.createDirectories(targetDir);
+		}
+
+		jobLogger.info("Copying from " + sourcePath + " to " + targetPath);
+		String copyId = sourceFileSystem.copy(sourcePath, targetFileSystem, targetPath, CopyMode.REPLACE,
+				true);
+
+		setCopyId(copyId);
+		return copyId;
+	}
 }

src/main/java/nl/esciencecenter/computeservice/service/staging/FileStagingObject.java

@@ -1,12 +1,16 @@
 package nl.esciencecenter.computeservice.service.staging;
 
 import org.commonwl.cwl.Parameter;
+import org.slf4j.Logger;
 
+import nl.esciencecenter.xenon.XenonException;
+import nl.esciencecenter.xenon.filesystems.CopyMode;
+import nl.esciencecenter.xenon.filesystems.FileSystem;
 import nl.esciencecenter.xenon.filesystems.Path;
 
 public class FileStagingObject extends BaseStagingObject implements FileOrDirectoryStagingObject {
-	private Path sourcePath;
-	private Path targetPath;
+	protected Path sourcePath;
+	protected Path targetPath;
 
 	public FileStagingObject(Path sourcePath, Path targetPath, Parameter parameter) {
 		super(parameter);
@@ -35,4 +39,24 @@ public String toString() {
 		return "FileStagingObject [sourcePath=" + sourcePath + ", targetPath=" + targetPath
 				+ ", parameter=" + parameter + "]";
 	}
+
+	public String stage(Logger jobLogger, FileSystem sourceFileSystem, FileSystem targetFileSystem,
+			Path sourceDirectory, Path targetDirectory) throws XenonException {		
+		Path sourcePath = getSourcePath();
+		if (!sourcePath.isAbsolute()) {
+			sourcePath = sourceDirectory.resolve(getSourcePath()).toAbsolutePath();
+		}
+		Path targetPath = targetDirectory.resolve(getTargetPath());
+		Path targetDir = targetPath.getParent();
+		if (!targetFileSystem.exists(targetDir)) {
+			targetFileSystem.createDirectories(targetDir);
+		}
+
+		jobLogger.info("Copying from " + sourcePath + " to " + targetPath);
+		String copyId = sourceFileSystem.copy(sourcePath, targetFileSystem, targetPath, CopyMode.REPLACE,
+				false);
+
+		setCopyId(copyId);
+		return copyId;
+	}
 }