Add run method to setup block and fix relativ paths

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

@@ -76,7 +76,14 @@ public AbstractTest(AbstractTestSuite parent) {
 	}
 
 	public void config(String config) {
-		this.config = new File(config);
+		if (config == null) {
+			return;
+		}
+		if (parent.isRelative(config)) {
+			this.config = new File(parent.makeAbsolute(config));
+		} else {
+			this.config = new File(config);
+		}
 	}
 
 	public File getConfig() {
@@ -89,7 +96,7 @@ public void setup(File testDirectory) throws IOException {
 		if (testDirectory == null) {
 			throw new IOException("Testcase setup failed: No home directory set");
 		}
-				
+
 		launchDir = initDirectory("Launch Directory", testDirectory, DIRECTORY_TESTS, getHash());
 		metaDir = initDirectory("Meta Directory", launchDir, DIRECTORY_META);
 		outputDir = initDirectory("Output Directory", launchDir, DIRECTORY_OUTPUT);
@@ -154,11 +161,11 @@ public String getErrorReport() throws Throwable {
 
 	@Override
 	public String getHash() {
-		
+
 		if (parent == null || parent.getFilename() == null || getName() == null || getName().isEmpty()) {
 			throw new RuntimeException("Error generating hash");
 		}
-		
+
 		return hash(parent.getFilename() + getName());
 
 	}
@@ -254,7 +261,7 @@ public void setUpdateSnapshot(boolean updateSnapshot) {
 	public boolean isUpdateSnapshot() {
 		return updateSnapshot;
 	}
-	
+
 	@Override
 	public String toString() {
 		return getHash().substring(0, 8) + ": " + getName();

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

@@ -19,7 +19,7 @@ public abstract class AbstractTestSuite implements ITestSuite {
 
 	private File globalConfig = null;
 
-	private File localConfig = null;
+	private String localConfig = null;
 
 	private List<ITest> tests = new Vector<ITest>();
 
@@ -53,7 +53,7 @@ public void script(String script) {
 	}
 
 	public String getScript() {
-		if (script != null && isRelative(script)) {
+		if (isRelative(script)) {
 			return makeAbsolute(script);
 		} else {
 			return script;
@@ -70,7 +70,7 @@ public void evalualteTestClosures() throws Throwable {
 		for (NamedClosure namedClosure : testClosures) {
 			String testName = namedClosure.name;
 			Closure closure = namedClosure.closure;
-			
+
 			ITest test = getNewTestInstance(testName);
 			test.setup(getHomeDirectory());
 			closure.setDelegate(test);
@@ -95,7 +95,7 @@ public void profile(String profile) {
 	}
 
 	public void config(String config) {
-		this.localConfig = new File(config);
+		this.localConfig = config;
 	}
 
 	public void setName(String name) {
@@ -139,12 +139,15 @@ public File getGlobalConfigFile() {
 		return globalConfig;
 	}
 
-	public void setLocalConfig(File localConfig) {
-		this.localConfig = localConfig;
-	}
-
 	public File getLocalConfig() {
-		return localConfig;
+		if (localConfig == null) {
+			return null;
+		}
+		if (isRelative(localConfig)) {
+			return new File(makeAbsolute(localConfig));
+		} else {
+			return new File(localConfig);
+		}
 	}
 
 	public File getHomeDirectory() {
@@ -223,14 +226,17 @@ public boolean hasFailedTests() {
 		return failedTests;
 	}
 
-	protected String makeAbsolute(String path) {
+	public String makeAbsolute(String path) {
 		return new File(directory, path).getAbsolutePath();
 	}
 
-	protected boolean isRelative(String path) {
+	public boolean isRelative(String path) {
+		if (path == null) {
+			return false;
+		}
 		return path.startsWith("../") || path.startsWith("./");
 	}
-	
+
 	@Override
 	public String toString() {
 		return name;

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

@@ -0,0 +1,65 @@
+package com.askimed.nf.test.lang;
+
+import groovy.lang.Closure;
+
+public class Dependency {
+
+	private String script;
+
+	private String name;
+
+	private String mapping;
+
+	public Dependency(String name, Closure closure) {
+		this.name = name;
+		closure.setDelegate(this);
+		closure.setResolveStrategy(Closure.DELEGATE_FIRST);
+		closure.call();
+	}
+
+	public void script(String script) {
+		this.script = script;
+	}
+
+	public String getScript() {
+		return script;
+	}
+
+	public void setScript(String script) {
+		this.script = script;
+	}
+
+	public void process(Closure closure) {
+		closure.setDelegate(this);
+		closure.setResolveStrategy(Closure.DELEGATE_FIRST);
+		Object mapping = closure.call();
+		if (mapping != null) {
+			this.mapping = mapping.toString();
+		}
+	}
+
+	public void workflow(Closure closure) {
+		process(closure);
+	}
+
+	public void function(Closure closure) {
+		process(closure);
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getMapping() {
+		return mapping;
+	}
+
+	public void setMapping(String mapping) {
+		this.mapping = mapping;
+	}
+
+}

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

@@ -1,6 +1,10 @@
 package com.askimed.nf.test.lang.process;
 
+import java.util.List;
+import java.util.Vector;
+
 import com.askimed.nf.test.core.ITest;
+import com.askimed.nf.test.lang.Dependency;
 import com.askimed.nf.test.lang.TestContext;
 
 import groovy.lang.Closure;
@@ -11,6 +15,8 @@ public class ProcessContext extends TestContext {
 
 	private Closure processClosure;
 
+	private List<Dependency> dependencies = new Vector<Dependency>();
+
 	public ProcessContext(ITest test) {
 		super(test);
 	}
@@ -43,5 +49,14 @@ public void evaluateProcessClosure() {
 		}
 
 	}
-
+
+	public void run(String process, Closure closure) {		
+		Dependency dependency = new Dependency(process, closure);		
+		dependencies.add(dependency);
+	}
+
+	public List<Dependency> getDependencies() {
+		return dependencies;
+	}
+
 }

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

@@ -9,6 +9,7 @@
 import org.codehaus.groovy.control.CompilationFailedException;
 
 import com.askimed.nf.test.core.AbstractTest;
+import com.askimed.nf.test.lang.Dependency;
 import com.askimed.nf.test.lang.TestCode;
 import com.askimed.nf.test.nextflow.NextflowCommand;
 import com.askimed.nf.test.util.AnsiText;
@@ -82,7 +83,7 @@ public void autoSort(boolean autoSort) {
 	public void execute() throws Throwable {
 
 		super.execute();
-		
+
 		File script = new File(parent.getScript());
 
 		if (!script.exists()) {
@@ -91,6 +92,10 @@ public void execute() throws Throwable {
 
 		context.init(this);
 
+		if (parent.getSetup() != null) {
+			parent.getSetup().execute(context);
+		}
+
 		if (setup != null) {
 			setup.execute(context);
 		}
@@ -124,8 +129,8 @@ public void execute() throws Throwable {
 		nextflow.setProfile(parent.getProfile());
 		File projectConfig = new File("nextflow.config");
 		if (projectConfig.exists()) {
-			nextflow.addConfig(projectConfig);	
-		}		
+			nextflow.addConfig(projectConfig);
+		}
 		nextflow.addConfig(parent.getGlobalConfigFile());
 		nextflow.addConfig(parent.getLocalConfig());
 		nextflow.addConfig(getConfig());
@@ -177,9 +182,26 @@ protected void writeWorkflowMock(File file) throws IOException, CompilationFaile
 			script = new File(script).getAbsolutePath();
 		}
 
+		// update dependency paths
+		for (Dependency dependency : context.getDependencies()) {
+			String _script = dependency.getScript();
+			if (_script == null) {
+				dependency.setScript(script);
+			} else {
+				if (parent.isRelative(_script)) {
+					_script = parent.makeAbsolute(_script);
+				}
+				if (!_script.startsWith("/") && !_script.startsWith("./")) {
+					_script = new File(_script).getAbsolutePath();
+				}
+				dependency.setScript(_script);
+			}
+		}
+
 		Map<Object, Object> binding = new HashMap<Object, Object>();
 		binding.put("process", parent.getProcess());
 		binding.put("script", script);
+		binding.put("dependencies", context.getDependencies());
 
 		// Get body of when closure
 		binding.put("mapping", context.getProcess().getMapping());

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

@@ -4,13 +4,17 @@
 
 import com.askimed.nf.test.core.AbstractTestSuite;
 import com.askimed.nf.test.core.ITest;
+import com.askimed.nf.test.lang.TestCode;
 
 import groovy.lang.Closure;
+import groovy.lang.DelegatesTo;
 
 public class ProcessTestSuite extends AbstractTestSuite {
 
 	private String process;
 
+	private TestCode setup;
+
 	public void process(String process) {
 		this.process = process;
 	}
@@ -27,6 +31,14 @@ public void test(String name, Closure closure) throws IOException {
 		addTestClosure(name, closure);
 	}
 
+	public void setup(@DelegatesTo(value = ProcessTest.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+		setup = new TestCode(closure);
+	}
+
+	public TestCode getSetup() {
+		return setup;
+	}
+
 	@Override
 	protected ITest getNewTestInstance(String name) {
 		ProcessTest test = new ProcessTest(this);

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

@@ -1,6 +1,10 @@
 package com.askimed.nf.test.lang.workflow;
 
+import java.util.List;
+import java.util.Vector;
+
 import com.askimed.nf.test.core.ITest;
+import com.askimed.nf.test.lang.Dependency;
 import com.askimed.nf.test.lang.TestContext;
 
 import groovy.lang.Closure;
@@ -11,10 +15,12 @@ public class WorkflowContext extends TestContext {
 
 	private Workflow workflow = new Workflow();
 
+	private List<Dependency> dependencies = new Vector<Dependency>();
+
 	public WorkflowContext(ITest test) {
 		super(test);
 	}
-	
+
 	public void workflow(Closure<Object> closure) {
 		workflowClosure = closure;
 	}
@@ -40,4 +46,13 @@ public void setWorkflow(Workflow workflow) {
 		this.workflow = workflow;
 	}
 
+	public void run(String process, Closure closure) {
+		Dependency dependency = new Dependency(process, closure);
+		dependencies.add(dependency);
+	}
+
+	public List<Dependency> getDependencies() {
+		return dependencies;
+	}
+
 }