Add possibility to disable auto-sort for channels (#63)

* Add possibility to disable sorted channels

* Fix typo in config properties

* Clean up code

* Add missing delete file

* Add autoSort to documentation

* Change order of items to ensure they are not sorted by default

* Remove duplicate code from tests

docs/configuration.md

@@ -22,8 +22,9 @@ config {
     // run all test with the defined docker profile from the main nextflow.config
     profile "docker"
     // disable tracing options in case container does not include `procps` Linux tool.
-    withTrace = false
-
+    withTrace false
+    //disable sorted channels
+    autoSort false
 }
 ```
 
@@ -49,20 +50,21 @@ nextflow_process {
     script "main.nf"
     process "my_process"
     config "path/to/test/nextflow.config"
-
+    autoSort false
     ...
 
 }
 ```
 
-It is also possible to overwrite the `config` property for a specific test:
+It is also possible to overwrite the `config` or `autoSort` property for a specific test:
 
 ```
 nextflow_process {
 
    test("my test") {
 
       config "path/to/test/nextflow.config"
+      autoSort false
       ...
 
     }

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

@@ -17,6 +17,7 @@
 import com.askimed.nf.test.core.TestExecutionEngine;
 import com.askimed.nf.test.core.reports.TapTestReportWriter;
 import com.askimed.nf.test.core.reports.XmlReportWriter;
+import com.askimed.nf.test.lang.TestSuiteBuilder;
 import com.askimed.nf.test.plugins.PluginManager;
 import com.askimed.nf.test.util.AnsiColors;
 
@@ -48,7 +49,7 @@ public class RunTestsCommand implements Callable<Integer> {
 	private String tap = null;
 
 	@Option(names = {
-		"--junitxml" }, description = "Write test results in Junit Xml Format", required = false, showDefaultValue = Visibility.ALWAYS)
+			"--junitxml" }, description = "Write test results in Junit Xml Format", required = false, showDefaultValue = Visibility.ALWAYS)
 	private String junitXml = null;
 
 	@Option(names = { "--update-snapshot",
@@ -96,7 +97,10 @@ public Integer call() throws Exception {
 						System.out.println("Found " + testPaths.size() + " files in test directory.");
 					}
 
+					TestSuiteBuilder.setConfig(config);
+
 				} else {
+					TestSuiteBuilder.setConfig(null);
 					System.out.println(AnsiColors.yellow("Warning: This pipeline has no nf-test config file."));
 				}
 

src/main/java/com/askimed/nf/test/config/Config.java

@@ -26,6 +26,8 @@ public class Config {
 
 	private boolean withTrace = true;
 
+	private boolean autoSort = true;
+
 	private PluginManager pluginManager = new PluginManager(PluginManager.FORCE_UPDATE);
 
 	private String configFile = DEFAULT_NEXTFLOW_CONFIG;
@@ -62,6 +64,10 @@ public String getProfile() {
 		}
 	}
 
+	public void withTrace(boolean withTrace) {
+		this.withTrace = withTrace;
+	}
+
 	public void setWithTrace(boolean withTrace) {
 		this.withTrace = withTrace;
 	}
@@ -70,6 +76,18 @@ public boolean isWithTrace() {
 		return withTrace;
 	}
 
+	public void setAutoSort(boolean autoSort) {
+		this.autoSort = autoSort;
+	}
+
+	public void autoSort(boolean autoSort) {
+		this.autoSort = autoSort;
+	}
+
+	public boolean isAutoSort() {
+		return autoSort;
+	}
+
 	public void libDir(String libDir) {
 		this.libDir = libDir;
 	}

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

@@ -29,6 +29,10 @@ public abstract class AbstractTest implements ITest {
 
 	private boolean updateSnapshot = false;
 
+	private boolean debug = false;
+
+	private boolean withTrace = true;
+
 	public AbstractTest() {
 
 	}
@@ -158,6 +162,28 @@ public ITestSuite getTestSuite() {
 		return suite;		
 	}
 
+	public void debug(boolean debug) {
+		setDebug(debug);
+	}
+
+	@Override
+	public void setDebug(boolean debug) {
+		this.debug = debug;
+	}
+
+	public boolean isDebug() {
+		return debug;
+	}
+
+	@Override
+	public void setWithTrace(boolean withTrace) {
+		this.withTrace = withTrace;
+	}
+
+	public boolean isWithTrace() {
+		return withTrace;
+	}
+
 	protected void shareDirectories(String[] directories, String metaDir) throws IOException {
 		for (String directory : directories) {
 			File localDirectory = new File(directory);

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

@@ -4,6 +4,8 @@
 import java.util.List;
 import java.util.Vector;
 
+import com.askimed.nf.test.config.Config;
+
 public abstract class AbstractTestSuite implements ITestSuite {
 
 	private String name;
@@ -18,6 +20,13 @@ public abstract class AbstractTestSuite implements ITestSuite {
 
 	private String filename;
 
+	private boolean autoSort = true;
+
+	@Override
+	public void configure(Config config) {
+		autoSort = config.isAutoSort();
+	}
+
 	public void name(String name) {
 		this.name = name;
 	}
@@ -46,6 +55,15 @@ public String getProfile() {
 		return profile;
 	}
 
+	public void autoSort(boolean autoSort) {
+		this.autoSort = autoSort;
+	}
+
+	public boolean isAutoSort() {
+		return autoSort;
+	}
+
+
 	@Override
 	public void setGlobalConfigFile(File globalConfig) {
 		this.globalConfig = globalConfig;

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

@@ -3,18 +3,22 @@
 import java.io.File;
 import java.util.List;
 
+import com.askimed.nf.test.config.Config;
+
 public interface ITestSuite {
 
 	public List<ITest> getTests();
 
 	public String getName();
-	
+
 	public void setProfile(String profile);
-	
+
 	public void setGlobalConfigFile(File config);
 
 	public void setFilename(String filename);
-	
+
 	public String getFilename();
-
+
+	public void configure(Config config);
+
 }

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

@@ -5,6 +5,7 @@
 import org.codehaus.groovy.control.CompilerConfiguration;
 import org.codehaus.groovy.control.customizers.ImportCustomizer;
 
+import com.askimed.nf.test.config.Config;
 import com.askimed.nf.test.core.ITestSuite;
 import com.askimed.nf.test.lang.function.FunctionTestSuite;
 import com.askimed.nf.test.lang.pipeline.PipelineTestSuite;
@@ -18,56 +19,58 @@
 
 public class TestSuiteBuilder {
 
-	static ITestSuite nextflow_pipeline(
-			@DelegatesTo(value = PipelineTestSuite.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+	private static Config config = null;
 
-		final PipelineTestSuite suite = new PipelineTestSuite();
+	public static void setConfig(Config config) {
+		TestSuiteBuilder.config = config;
+	}
 
-		closure.setDelegate(suite);
-		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
-		closure.call();
+	public static ITestSuite nextflow_pipeline(final Closure closure) {
+
+		PipelineTestSuite suite = new PipelineTestSuite();
+		executeClosure(suite, closure);
 
 		return suite;
 
 	}
 
-	static ITestSuite nextflow_workflow(
-			@DelegatesTo(value = PipelineTestSuite.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
+	public static ITestSuite nextflow_workflow(Closure closure) {
 
-		final WorkflowTestSuite suite = new WorkflowTestSuite();
+		WorkflowTestSuite suite = new WorkflowTestSuite();
+		executeClosure(suite, closure);
 
-		closure.setDelegate(suite);
-		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
-		closure.call();
+		return suite;
+
+	}
+
+	public static ITestSuite nextflow_process(Closure closure) {
+
+		ProcessTestSuite suite = new ProcessTestSuite();
+		executeClosure(suite, closure);
 
 		return suite;
 
 	}
 
-	static ITestSuite nextflow_process(
+	public static ITestSuite nextflow_function(
 			@DelegatesTo(value = PipelineTestSuite.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
 
-		final ProcessTestSuite suite = new ProcessTestSuite();
+		FunctionTestSuite suite = new FunctionTestSuite();
 
-		closure.setDelegate(suite);
-		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
-		closure.call();
+		executeClosure(suite, closure);
 
 		return suite;
 
 	}
 
-	static ITestSuite nextflow_function(
-			@DelegatesTo(value = PipelineTestSuite.class, strategy = Closure.DELEGATE_ONLY) final Closure closure) {
-
-		final FunctionTestSuite suite = new FunctionTestSuite();
+	private static void executeClosure(ITestSuite suite, Closure closure) {
+		if (config != null) {
+			suite.configure(config);
+		}
 
 		closure.setDelegate(suite);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 		closure.call();
-
-		return suite;
-
 	}
 
 	public static ITestSuite parse(File script) throws Exception {

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

@@ -26,10 +26,6 @@ public class FunctionTest extends AbstractTest {
 
 	private String function = null;
 
-	private boolean debug = false;
-
-	private boolean withTrace = true;
-
 	private TestCode setup;
 
 	private TestCode cleanup;
@@ -83,15 +79,6 @@ public void when(@DelegatesTo(value = FunctionTest.class, strategy = Closure.DEL
 		when = new TestCode(closure);
 	}
 
-	public void debug(boolean debug) {
-		setDebug(debug);
-	}
-
-	@Override
-	public void setDebug(boolean debug) {
-		this.debug = debug;
-	}
-
 	@Override
 	public void execute() throws Throwable {
 
@@ -105,19 +92,22 @@ public void execute() throws Throwable {
 		}
 
 		context.init(baseDir, outputDir.getAbsolutePath());
-		
+
 		if (setup != null) {
 			setup.execute(context);
 		}
 
-
 		if (when != null) {
 			when.execute(context);
 		}
 
 		context.evaluateParamsClosure();
 		context.evaluateFunctionClosure();
 
+		if (isDebug()) {
+			System.out.println();
+		}
+
 		// Create workflow mock
 		File workflow = new File(metaDir, "mock.nf");
 		writeWorkflowMock(workflow);
@@ -137,12 +127,12 @@ public void execute() throws Throwable {
 		nextflow.addConfig(parent.getGlobalConfigFile());
 		nextflow.addConfig(parent.getLocalConfig());
 		nextflow.addConfig(getConfig());
-		if (withTrace) {
+		if (isWithTrace()) {
 			nextflow.setTrace(traceFile);
 		}
 		nextflow.setOut(outFile);
 		nextflow.setErr(errFile);
-		nextflow.setSilent(!debug);
+		nextflow.setSilent(!isDebug());
 		nextflow.setLog(logFile);
 		nextflow.setWork(workDir);
 		nextflow.setParamsFile(paramsFile);
@@ -160,7 +150,7 @@ public void execute() throws Throwable {
 		context.getWorkflow().exitStatus = exitCode;
 		context.getWorkflow().success = (exitCode == 0);
 		context.getWorkflow().failed = (exitCode != 0);
-		if (debug) {
+		if (isDebug()) {
 			System.out.println(AnsiText.padding("Output Channels:", 4));
 			context.getProcess().getOut().view();
 		}
@@ -207,9 +197,4 @@ protected void writeWorkflowMock(File file) throws IOException, CompilationFaile
 
 	}
 
-	@Override
-	public void setWithTrace(boolean withTrace) {
-		this.withTrace = withTrace;
-	}
-
 }