Refactore directory creation and fix remaining tests

src/main/java/com/askimed/nf/test/commands/RunTestsCommand.java

@@ -77,7 +77,6 @@ public Integer execute() throws Exception {
 
 			String defaultProfile = null;
 			File defaultConfigFile = null;
-			File workDir = new File(".nf-test");
 			String libDir = lib;
 			boolean defaultWithTrace = true;
 			try {
@@ -89,7 +88,6 @@ public Integer execute() throws Exception {
 					defaultProfile = config.getProfile();
 					defaultConfigFile = config.getConfigFile();
 					defaultWithTrace = config.isWithTrace();
-					workDir = new File(config.getWorkDir());
 					if (!libDir.isEmpty()) {
 						libDir += ":";
 					}
@@ -146,7 +144,6 @@ public Integer execute() throws Exception {
 			engine.setScripts(scripts);
 			engine.setTagQuery(tagQuery);
 			engine.setDebug(debug);
-			engine.setWorkDir(workDir);
 			engine.setUpdateSnapshot(updateSnapshot);
 			engine.setLibDir(libDir);
 			engine.setPluginManager(manager);

src/main/java/com/askimed/nf/test/core/AbstractTest.java

@@ -8,7 +8,6 @@
 import java.util.List;
 import java.util.Vector;
 
-import com.askimed.nf.test.config.Config;
 import com.askimed.nf.test.util.FileUtil;
 
 public abstract class AbstractTest implements ITest {
@@ -23,9 +22,9 @@ public abstract class AbstractTest implements ITest {
 
 	public String baseDir = System.getProperty("user.dir");
 
-	public boolean skipped = false;
+	public String projectDir = System.getProperty("user.dir");
 
-	private ITestSuite suite;
+	public boolean skipped = false;
 
 	public static String[] SHARED_DIRECTORIES = { "bin", "lib", "assets" };
 
@@ -56,41 +55,18 @@ public File getConfig() {
 		return config;
 	}
 
-	protected String getWorkDir() {
-
-		File workDir = new File("nf-test");
-
-		try {
-
-			Config config = Config.parse(new File(Config.FILENAME));
-			workDir = new File(config.getWorkDir());
-		} catch (Exception e) {
-
-		}
-		return workDir.getAbsolutePath();
-	}
-
 	@Override
-	public void setup(File baseDir) throws IOException {
-
-		String launchDir = FileUtil.path(baseDir.getAbsolutePath(), "tests", getHash());
+	public void setup(String testDirectory) throws IOException {
 
-		try {
-			this.launchDir = new File(launchDir);
-			FileUtil.deleteDirectory(this.launchDir);
-			FileUtil.createDirectory(this.launchDir);
-		} catch (Exception e) {
-			throw new IOException("Launch Directory '" + launchDir + "' could not be deleted or created:\n" + e);
-		}
+		launchDir = new File(FileUtil.path(testDirectory, "tests", getHash()));
+		metaDir = new File(FileUtil.path(launchDir.getAbsolutePath(), "meta"));
+		outputDir = new File(FileUtil.path(launchDir.getAbsolutePath(), "output"));
+		workDir = new File(FileUtil.path(launchDir.getAbsolutePath(), "work"));
 
-		String metaDir = FileUtil.path(launchDir, "meta");
-		this.metaDir = new File(metaDir);
-		try {
-			FileUtil.deleteDirectory(this.metaDir);
-			FileUtil.createDirectory(this.metaDir);
-		} catch (Exception e) {
-			throw new IOException("Meta Directory '" + metaDir + "' could not be deleted:\n" + e);
-		}
+		initDirectory("Launch Directory", launchDir);
+		initDirectory("Meta Directory", metaDir);
+		initDirectory("Output Directory", outputDir);
+		initDirectory("Working Directory", workDir);
 
 		try {
 			// copy bin and lib to metaDir. TODO: use symlinks and read additional "mapping"
@@ -100,24 +76,16 @@ public void setup(File baseDir) throws IOException {
 			throw new IOException("Directories could not be shared:\n" + e);
 		}
 
-		String outputDir = FileUtil.path(launchDir, "output");
+	}
 
+	public void initDirectory(String name, File directory) throws IOException {
 		try {
-			this.outputDir = new File(outputDir);
-			FileUtil.deleteDirectory(this.outputDir);
-			FileUtil.createDirectory(this.outputDir);
+			FileUtil.deleteDirectory(directory);
+			FileUtil.createDirectory(directory);
 		} catch (Exception e) {
-			throw new IOException("Output Directory '" + outputDir + "' could not be deleted:\n" + e);
+			throw new IOException(name + " '" + directory + "' could not be deleted or created:\n" + e);
 		}
 
-		String workDir = FileUtil.path(launchDir, "work");
-		try {
-			this.workDir = new File(workDir);
-			FileUtil.deleteDirectory(this.workDir);
-			FileUtil.createDirectory(this.workDir);
-		} catch (Exception e) {
-			throw new IOException("Working Directory '" + workDir + "' could not be deleted:\n" + e);
-		}
 	}
 
 	@Override
@@ -145,7 +113,7 @@ public String getErrorReport() throws Throwable {
 	@Override
 	public String getHash() {
 
-		return hash(suite.getFilename() + getName());
+		return hash(parent.getFilename() + getName());
 
 	}
 
@@ -195,14 +163,9 @@ public boolean isSkipped() {
 		return skipped;
 	}
 
-	@Override
-	public void setTestSuite(ITestSuite suite) {
-		this.suite = suite;
-	}
-
 	@Override
 	public ITestSuite getTestSuite() {
-		return suite;
+		return parent;
 	}
 
 	public void debug(boolean debug) {
@@ -227,11 +190,11 @@ public boolean isWithTrace() {
 		return withTrace;
 	}
 
-	protected void shareDirectories(String[] directories, String metaDir) throws IOException {
+	protected void shareDirectories(String[] directories, File metaDir) throws IOException {
 		for (String directory : directories) {
 			File localDirectory = new File(directory);
 			if (localDirectory.exists()) {
-				String metaDirectory = FileUtil.path(metaDir, directory);
+				String metaDirectory = FileUtil.path(metaDir.getAbsolutePath(), directory);
 				FileUtil.copyDirectory(localDirectory.getAbsolutePath(), metaDirectory);
 			}
 		}

src/main/java/com/askimed/nf/test/core/AbstractTestSuite.java

@@ -25,13 +25,16 @@ public abstract class AbstractTestSuite implements ITestSuite {
 	private String options = "";
 
 	private String directory = "";
+
+	private String homeDirectory = Config.DEFAULT_HOME;
 
 	private List<String> tags = new Vector<String>();
 
 	@Override
 	public void configure(Config config) {
 		autoSort = config.isAutoSort();
 		options = config.getOptions();
+		homeDirectory = config.getWorkDir();
 	}
 
 	public void name(String name) {
@@ -94,6 +97,10 @@ public void setLocalConfig(File localConfig) {
 	public File getLocalConfig() {
 		return localConfig;
 	}
+
+	public String getHomeDirectory() {
+		return homeDirectory;
+	}
 
 	@Override
 	public void setFilename(String filename) {
@@ -118,7 +125,6 @@ public List<ITest> getTests() {
 
 	protected void addTest(ITest test) {
 		tests.add(test);
-		test.setTestSuite(this);
 	}
 
 	public void tag(String tag) {

src/main/java/com/askimed/nf/test/core/ITest.java

@@ -1,10 +1,8 @@
 package com.askimed.nf.test.core;
 
-import java.io.File;
-
 public interface ITest extends ITaggable {
 
-	public void setup(File baseDir) throws Throwable;
+	public void setup(String homeDirectory) throws Throwable;
 
 	public void execute() throws Throwable;
 
@@ -22,8 +20,6 @@ public interface ITest extends ITaggable {
 
 	public String getHash();
 
-	public void setTestSuite(ITestSuite suite);
-
 	public ITestSuite getTestSuite();
 
 	public void setWithTrace(boolean withTrace);

src/main/java/com/askimed/nf/test/core/TestExecutionEngine.java

@@ -25,8 +25,6 @@ public class TestExecutionEngine {
 
 	private String profile = null;
 
-	private File workDir = null;
-
 	private File configFile = null;
 
 	private File baseDir = new File(System.getProperty("user.dir"));
@@ -57,10 +55,6 @@ public void setConfigFile(File configFile) {
 		this.configFile = configFile;
 	}
 
-	public void setWorkDir(File workDir) {
-		this.workDir = workDir;
-	}
-
 	public void setWithTrace(boolean withTrace) {
 		if (withTrace == false) {
 			System.out.println("Warning: Tracing is disabled. `workflow.trace` is not supported.");
@@ -179,7 +173,6 @@ public int execute() throws Throwable {
 				}
 				listener.executionStarted(test);
 				TestExecutionResult result = new TestExecutionResult(test);
-				test.setup(workDir);
 				test.setWithTrace(withTrace);
 				test.setUpdateSnapshot(updateSnapshot);
 				try {

src/main/java/com/askimed/nf/test/lang/ParamsMap.java

@@ -197,6 +197,9 @@ protected Map<String, Object> createNestedMap(Map<String, Object> map) {
 		Map<String, Object> nestedMap = new HashMap<String, Object>();
 		nestedMap.put("baseDir", baseDir);
 		nestedMap.put("outputDir", outputDir);
+		nestedMap.put("projectDir", projectDir);
+		nestedMap.put("launchDir", launchDir);
+		nestedMap.put("workDir", workDir);	
 		if (map != null) {
 			nestedMap.putAll(map);
 		}

src/main/java/com/askimed/nf/test/lang/function/FunctionTestSuite.java

@@ -1,5 +1,7 @@
 package com.askimed.nf.test.lang.function;
 
+import java.io.IOException;
+
 import com.askimed.nf.test.core.AbstractTestSuite;
 
 import groovy.lang.Closure;
@@ -40,10 +42,12 @@ public void setScript(String script) {
 	}
 
 	public void test(String name,
-			@DelegatesTo(value = FunctionTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+			@DelegatesTo(value = FunctionTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure)
+			throws IOException {
 
 		final FunctionTest test = new FunctionTest(this);
 		test.name(name);
+		test.setup(getHomeDirectory());
 		closure.setDelegate(test);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 		closure.call();

src/main/java/com/askimed/nf/test/lang/pipeline/PipelineTest.java

@@ -95,7 +95,6 @@ public void execute() throws Throwable {
 		if (!script.startsWith("/") && !script.startsWith("./")) {
 			script = new File(script).getAbsolutePath();
 		}
-		System.out.println("Script: " + script);
 
 		NextflowCommand nextflow = new NextflowCommand();
 		nextflow.setScript(script);

src/main/java/com/askimed/nf/test/lang/pipeline/PipelineTestSuite.java

@@ -1,5 +1,7 @@
 package com.askimed.nf.test.lang.pipeline;
 
+import java.io.IOException;
+
 import com.askimed.nf.test.core.AbstractTestSuite;
 
 import groovy.lang.Closure;
@@ -26,10 +28,11 @@ public void setScript(String script) {
 	}
 
 	public void test(String name,
-			@DelegatesTo(value = PipelineTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+			@DelegatesTo(value = PipelineTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) throws IOException {
 
 		final PipelineTest test = new PipelineTest(this);
 		test.name(name);
+		test.setup(getHomeDirectory());
 		closure.setDelegate(test);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 		closure.call();

src/main/java/com/askimed/nf/test/lang/process/ProcessTest.java

@@ -171,7 +171,6 @@ protected void writeWorkflowMock(File file) throws IOException, CompilationFaile
 		if (!script.startsWith("/") && !script.startsWith("./")) {
 			script = new File(script).getAbsolutePath();
 		}
-		System.out.println("Script: " + script);
 
 		Map<Object, Object> binding = new HashMap<Object, Object>();
 		binding.put("process", parent.getProcess());

src/main/java/com/askimed/nf/test/lang/process/ProcessTestSuite.java

@@ -1,5 +1,7 @@
 package com.askimed.nf.test.lang.process;
 
+import java.io.IOException;
+
 import com.askimed.nf.test.core.AbstractTestSuite;
 
 import groovy.lang.Closure;
@@ -40,10 +42,11 @@ public void setScript(String script) {
 	}
 
 	public void test(String name,
-			@DelegatesTo(value = ProcessTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+			@DelegatesTo(value = ProcessTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) throws IOException {
 
 		final ProcessTest test = new ProcessTest(this);
 		test.name(name);
+		test.setup(getHomeDirectory());
 		closure.setDelegate(test);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 		closure.call();

src/main/java/com/askimed/nf/test/lang/workflow/WorkflowTest.java

@@ -100,7 +100,7 @@ public void execute() throws Throwable {
 		if (!script.exists()) {
 			throw new Exception("Script '" + script.getAbsolutePath() + "' not found.");
 		}
-
+		
 		context.init(this);
 
 		if (setup != null) {

src/main/java/com/askimed/nf/test/lang/workflow/WorkflowTestSuite.java

@@ -1,5 +1,7 @@
 package com.askimed.nf.test.lang.workflow;
 
+import java.io.IOException;
+
 import com.askimed.nf.test.core.AbstractTestSuite;
 
 import groovy.lang.Closure;
@@ -40,10 +42,11 @@ public void setScript(String script) {
 	}
 
 	public void test(String name,
-			@DelegatesTo(value = WorkflowTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+			@DelegatesTo(value = WorkflowTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) throws IOException {
 
 		final WorkflowTest test = new WorkflowTest(this);
 		test.name(name);
+		test.setup(getHomeDirectory());
 		closure.setDelegate(test);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 		closure.call();