Create mock.nf in project folder instead of meta folder

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

@@ -2,17 +2,14 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.math.BigInteger;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
 import java.util.List;
 import java.util.Vector;
 
+import com.askimed.nf.test.util.HashUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.askimed.nf.test.config.Config;
-import com.askimed.nf.test.config.FileStaging;
 import com.askimed.nf.test.util.FileUtil;
 
 public abstract class AbstractTest implements ITest {
@@ -57,6 +54,8 @@ public abstract class AbstractTest implements ITest {
 
 	public File projectDir = new File(System.getProperty("user.dir"));
 
+	public File mockFile;
+
 	public boolean skipped = false;
 
 	protected File config = null;
@@ -106,33 +105,16 @@ public void defineDirectories(File testDirectory) throws IOException {
 		outputDir = constructDirectory(launchDir, DIRECTORY_OUTPUT);
 		workDir = constructDirectory(launchDir, DIRECTORY_WORK);
 
+		mockFile = new File( ".nf-test-" + getHash() + ".nf");
+		mockFile.deleteOnExit();
 	}
 
 	@Override
 	public void setup(Config config) throws IOException {
-
-		initDirectory("Launch Directory", launchDir);
-		initDirectory("Meta Directory", metaDir);
-		initDirectory("Output Directory", outputDir);
-		initDirectory("Working Directory", workDir);
-		FileStaging[] sharedDirectories = new FileStaging[]{
-				new FileStaging("bin", config != null ? config.getStageMode() : FileStaging.MODE_COPY),
-				new FileStaging("lib",  config != null ? config.getStageMode() : FileStaging.MODE_COPY),
-				new FileStaging("assets", config != null ? config.getStageMode() : FileStaging.MODE_COPY)
-		};
-		try {
-			// copy bin, assets and lib to metaDir
-			shareDirectories(sharedDirectories, metaDir);
-			if (config != null) {
-				// copy user defined staging directories
-				log.debug("Stage {} user provided files...", config.getStageBuilder().getPaths().size());
-				shareDirectories(config.getStageBuilder().getPaths(), metaDir);
-			}
-			shareDirectories(parent.getStageBuilder().getPaths(), metaDir);
-		} catch (Exception e) {
-			throw new IOException("Testcase setup failed: Directories could not be shared:\n" + e);
-		}
-
+		setupDirectory("Launch Directory", launchDir);
+		setupDirectory("Meta Directory", metaDir);
+		setupDirectory("Output Directory", outputDir);
+		setupDirectory("Working Directory", workDir);
 	}
 
 	@Override
@@ -145,13 +127,13 @@ public void execute() throws Throwable {
 		}
 	}
 
-	public File constructDirectory(File root, String... childs) {
+	private File constructDirectory(File root, String... childs) {
 		String path = FileUtil.path(root.getAbsolutePath(), FileUtil.path(childs));
 		File directory = new File(path).getAbsoluteFile();
 		return directory;
 	}
 
-	public void initDirectory(String name, File directory) throws IOException {
+	private void setupDirectory(String name, File directory) throws IOException {
 
 		try {
 			FileUtil.deleteDirectory(directory);
@@ -164,7 +146,7 @@ public void initDirectory(String name, File directory) throws IOException {
 
 	@Override
 	public void cleanup() {
-		// FileUtil.deleteDirectory(metaDir);
+
 	}
 
 	@Override
@@ -191,25 +173,10 @@ public String getHash() {
 			throw new RuntimeException("Error generating hash");
 		}
 
-		return hash(parent.getFilename() + getName());
+		return HashUtil.getMd5(parent.getFilename() + getName());
 
 	}
 
-	private String hash(String value) {
-
-		MessageDigest md;
-		try {
-			md = MessageDigest.getInstance("MD5");
-			md.update(value.getBytes());
-			byte[] md5sum = md.digest();
-			BigInteger bigInt = new BigInteger(1, md5sum);
-			return bigInt.toString(16);
-		} catch (NoSuchAlgorithmException e) {
-			e.printStackTrace();
-			return "??";
-		}
-	}
-
 	public void tag(String tag) {
 		tags.add(tag);
 	}
@@ -268,20 +235,6 @@ public boolean isWithTrace() {
 		return withTrace;
 	}
 
-	protected void shareDirectories(List<FileStaging> directories, File stageDir) throws IOException {
-		for (FileStaging directory : directories) {
-			String metaDirectory = FileUtil.path(stageDir.getAbsolutePath(), directory.getPath());
-			directory.stage(metaDirectory);
-		}
-	}
-
-	protected void shareDirectories(FileStaging[] directories, File stageDir) throws IOException {
-		for (FileStaging directory : directories) {
-			String metaDirectory = FileUtil.path(stageDir.getAbsolutePath(), directory.getPath());
-			directory.stage(metaDirectory);
-		}
-	}
-
 	@Override
 	public void setUpdateSnapshot(boolean updateSnapshot) {
 		this.updateSnapshot = updateSnapshot;

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

@@ -109,8 +109,10 @@ public void execute() throws Throwable {
 		}
 
 		// Create workflow mock
-		File workflow = new File(metaDir, FILE_MOCK);
-		writeWorkflowMock(workflow);
+		writeWorkflowMock(mockFile);
+
+		 // Copy mock file in meta folder for debugging
+		FileUtil.copy(mockFile, new File(metaDir, FILE_MOCK));
 
 		context.getParams().put("nf_test_output", metaDir.getAbsolutePath());
 
@@ -121,7 +123,7 @@ public void execute() throws Throwable {
 		File paramsFile = new File(metaDir, FILE_PARAMS);
 
 		NextflowCommand nextflow = new NextflowCommand();
-		nextflow.setScript(workflow.getAbsolutePath());
+		nextflow.setScript(mockFile.getAbsolutePath());
 		nextflow.setParams(context.getParams());
 		for (String profile: parent.getProfiles()) {
 			nextflow.addProfile(profile);

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

@@ -108,8 +108,10 @@ public void execute() throws Throwable {
 		context.evaluateProcessClosure();
 
 		// Create workflow mock
-		File workflow = new File(metaDir, FILE_MOCK);
-		writeWorkflowMock(workflow);
+		writeWorkflowMock(mockFile);
+
+		// Copy mock file in meta folder for debugging
+		FileUtil.copy(mockFile, new File(metaDir, FILE_MOCK));
 
 		context.getParams().put("nf_test_output", metaDir.getAbsolutePath());
 
@@ -124,7 +126,7 @@ public void execute() throws Throwable {
 		File paramsFile = new File(metaDir, FILE_PARAMS);
 
 		NextflowCommand nextflow = new NextflowCommand();
-		nextflow.setScript(workflow.getAbsolutePath());
+		nextflow.setScript(mockFile.getAbsolutePath());
 		nextflow.setParams(context.getParams());
 		for (String profile: parent.getProfiles()) {
 			nextflow.addProfile(profile);

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

@@ -121,8 +121,10 @@ public void execute() throws Throwable {
 		context.evaluateWorkflowClosure();
 
 		// Create workflow mock
-		File workflow = new File(metaDir, FILE_MOCK);
-		writeWorkflowMock(workflow);
+		writeWorkflowMock(mockFile);
+
+		// Copy mock file in meta folder for debugging
+		FileUtil.copy(mockFile, new File(metaDir, FILE_MOCK));
 
 		context.getParams().put("nf_test_output", metaDir.getAbsolutePath());
 		if (isDebug()) {
@@ -136,7 +138,7 @@ public void execute() throws Throwable {
 		File paramsFile = new File(metaDir, FILE_PARAMS);
 
 		NextflowCommand nextflow = new NextflowCommand();
-		nextflow.setScript(workflow.getAbsolutePath());
+		nextflow.setScript(mockFile.getAbsolutePath());
 		nextflow.setParams(context.getParams());
 		for (String profile: parent.getProfiles()) {
 			nextflow.addProfile(profile);

src/main/java/com/askimed/nf/test/util/FileUtil.java

@@ -1,14 +1,6 @@
 package com.askimed.nf.test.util;
 
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.PushbackInputStream;
+import java.io.*;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -189,4 +181,17 @@ public static String encodeBase64(byte[] bytes) {
 		return encodedContent;
 	}
 
+	public static void copy(File source, File dest) throws IOException {
+		try (InputStream is = new FileInputStream(source);
+			 OutputStream os = new FileOutputStream(dest)) {
+
+			byte[] buffer = new byte[1024];
+			int length;
+
+			// Read from the input stream and write to the output stream
+			while ((length = is.read(buffer)) > 0) {
+				os.write(buffer, 0, length);
+			}
+		}
+	}
 }

src/main/java/com/askimed/nf/test/util/HashUtil.java

@@ -0,0 +1,24 @@
+package com.askimed.nf.test.util;
+
+import java.math.BigInteger;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+
+public class HashUtil {
+
+    public static String getMd5(String value) {
+
+        MessageDigest md;
+        try {
+            md = MessageDigest.getInstance("MD5");
+            md.update(value.getBytes());
+            byte[] md5sum = md.digest();
+            BigInteger bigInt = new BigInteger(1, md5sum);
+            return bigInt.toString(16);
+        } catch (NoSuchAlgorithmException e) {
+            e.printStackTrace();
+            return "??";
+        }
+    }
+
+}

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

@@ -139,8 +139,9 @@ public void testIssue125() throws Exception {
 	public void testStagingWithoutMapping() throws Exception {
 
 		App app = new App();
-		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test" });
-		assertEquals(1, exitCode);
+		// TODO: remove this test. no staging needed.
+		//int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test" });
+		//assertEquals(1, exitCode);
 
 	}
 
@@ -183,4 +184,13 @@ public void testStagingInTestsuite() throws Exception {
 
 	}
 
+	@Test
+	public void testRegex() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/regex/workflow.nf.test" });
+		assertEquals(0, exitCode);
+
+	}
+
 }

test-data/workflow/regex/params.yaml

@@ -0,0 +1,2 @@
+localOutputDir: "example_output"
+someRegex: '^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\\.[a-zA-Z]{2,}\$'

test-data/workflow/regex/workflow.nf

@@ -0,0 +1,36 @@
+process exampleProc {
+
+    storeDir "${outputDir}/exampleProc"
+    input:
+        tuple(
+            val(outputDir),
+            val(localOutputDir),
+            val(someRegexString)
+        )
+
+    output:
+        tuple(
+            val(outputDir),
+            path("example_output/example*.txt")
+        )
+
+    shell:
+        """
+        mkdir -p !{localOutputDir}
+        echo !{someRegexString} > "!{localOutputDir}/example1.txt"
+        """
+}
+
+
+workflow PipeWf {
+    take:
+        inputCh
+
+    main:
+        inputCh
+            | exampleProc
+            | set { outputCh }
+
+    emit:
+        outputCh
+}

test-data/workflow/regex/workflow.nf.test

@@ -0,0 +1,27 @@
+nextflow_workflow {
+
+    name "Test workflow"
+    script "./workflow.nf"
+    workflow "PipeWf"
+
+    test("Output will exist in default outputDir") {
+
+        when {
+
+            params {
+                outDir = "$outputDir"
+                load("test-data/workflow/regex/params.yaml")
+            }
+            workflow {
+                """
+                input[0] = Channel.of([params.outDir,params.localOutputDir])
+                """
+            }
+        }
+
+        then {
+              assert workflow.success
+              assert path("${outputDir}/exampleProc/example_output").exists()
+            }
+    }
+}