Add more refactoring

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

@@ -12,6 +12,30 @@
 
 public abstract class AbstractTest implements ITest {
 
+	public static final String FILE_STD_ERR = "std.err";
+
+	public static final String FILE_STD_OUT = "std.out";
+
+	public static final String FILE_TRACE = "trace.csv";
+
+	public static final String FILE_NEXTFLOW_LOG = "nextflow.log";
+
+	public static final String FILE_MOCK = "mock.nf";
+
+	public static final String FILE_PARAMS = "params.json";
+
+	public static final String FILE_WORKFLOW_JSON = "workflow.json";
+
+	public static final String FILE_FUNCTION_JSON = "function.json";
+
+	public static final String DIRECTORY_WORK = "work";
+
+	public static final String DIRECTORY_OUTPUT = "output";
+
+	public static final String DIRECTORY_META = "meta";
+
+	public static final String DIRECTORY_TESTS = "tests";
+
 	public File launchDir;
 
 	public File metaDir;
@@ -20,9 +44,9 @@ public abstract class AbstractTest implements ITest {
 
 	public File workDir;
 
-	public String baseDir = System.getProperty("user.dir");
+	public File baseDir = new File(System.getProperty("user.dir"));
 
-	public String projectDir = System.getProperty("user.dir");
+	public File projectDir = new File(System.getProperty("user.dir"));
 
 	public boolean skipped = false;
 
@@ -56,17 +80,12 @@ public File getConfig() {
 	}
 
 	@Override
-	public void setup(String testDirectory) throws IOException {
+	public void setup(File testDirectory) throws IOException {
 
-		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"));
-
-		initDirectory("Launch Directory", launchDir);
-		initDirectory("Meta Directory", metaDir);
-		initDirectory("Output Directory", outputDir);
-		initDirectory("Working Directory", workDir);
+		launchDir = initDirectory("Launch Directory", testDirectory, DIRECTORY_TESTS, getHash());
+		metaDir = initDirectory("Meta Directory", launchDir, DIRECTORY_META);
+		outputDir = initDirectory("Output Directory", launchDir, DIRECTORY_OUTPUT);
+		workDir = initDirectory("Working Directory", launchDir, DIRECTORY_WORK);
 
 		try {
 			// copy bin and lib to metaDir. TODO: use symlinks and read additional "mapping"
@@ -78,10 +97,15 @@ public void setup(String testDirectory) throws IOException {
 
 	}
 
-	public void initDirectory(String name, File directory) throws IOException {
+	public File initDirectory(String name, File root, String... childs) throws IOException {
+
+		String path = FileUtil.path(root.getAbsolutePath(), FileUtil.path(childs));
+
+		File directory = new File(path).getAbsoluteFile();
 		try {
 			FileUtil.deleteDirectory(directory);
 			FileUtil.createDirectory(directory);
+			return directory;
 		} catch (Exception e) {
 			throw new IOException(name + " '" + directory + "' could not be deleted or created:\n" + e);
 		}
@@ -96,11 +120,11 @@ public void cleanup() {
 	@Override
 	public String getErrorReport() throws Throwable {
 		String result = null;
-		File outFile = new File(metaDir, "std.out");
+		File outFile = new File(metaDir, FILE_STD_OUT);
 		if (outFile.exists()) {
 			result = "Nextflow stdout:\n\n" + FileUtil.readFileAsString(outFile);
 		}
-		File errFile = new File(metaDir, "std.err");
+		File errFile = new File(metaDir, FILE_STD_ERR);
 		if (errFile.exists()) {
 			if (result == null) {
 				result = "";

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

@@ -23,18 +23,18 @@ public abstract class AbstractTestSuite implements ITestSuite {
 	private boolean autoSort = true;
 
 	private String options = "";
-	
+
 	private String directory = "";
-	
-	private String homeDirectory = Config.DEFAULT_HOME;
+
+	private File homeDirectory = new File(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();
+		homeDirectory = new File(config.getWorkDir());
 	}
 
 	public void name(String name) {
@@ -97,8 +97,8 @@ public void setLocalConfig(File localConfig) {
 	public File getLocalConfig() {
 		return localConfig;
 	}
-	
-	public String getHomeDirectory() {
+
+	public File getHomeDirectory() {
 		return homeDirectory;
 	}
 
@@ -117,7 +117,7 @@ public String getFilename() {
 	public String getDirectory() {
 		return directory;
 	}
-	
+
 	@Override
 	public List<ITest> getTests() {
 		return tests;
@@ -144,9 +144,9 @@ public ITaggable getParent() {
 	protected String makeAbsolute(String path) {
 		return new File(directory, path).getAbsolutePath();
 	}
-	
+
 	protected boolean isRelative(String path) {
 		return path.startsWith("../") || path.startsWith("./");
 	}
-	
+
 }

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

@@ -1,8 +1,10 @@
 package com.askimed.nf.test.core;
 
+import java.io.File;
+
 public interface ITest extends ITaggable {
 
-	public void setup(String homeDirectory) throws Throwable;
+	public void setup(File homeDirectory) throws Throwable;
 
 	public void execute() throws Throwable;
 

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

@@ -20,47 +20,39 @@ public class ParamsMap extends HashMap<String, Object> {
 
 	private static final long serialVersionUID = 1L;
 
-	public String baseDir = "";
+	public String baseDir;
 
-	public String outputDir = "";
+	public String outputDir;
 
-	public String projectDir = "";
+	public String projectDir;
 
-	public String launchDir = "";
+	public String launchDir;
 
-	public String workDir = "";
+	public String workDir;
 
-	public void setBaseDir(String baseDir) {
-		this.baseDir = baseDir;
-		put("baseDir", baseDir);
+	public void setBaseDir(File baseDir) {
+		this.baseDir = baseDir.getAbsolutePath();
+		put("baseDir", this.baseDir);
 	}
 
-	public void setOutputDir(String outputDir) {
-		this.outputDir = outputDir;
-		put("outputDir", outputDir);
+	public void setOutputDir(File outputDir) {
+		this.outputDir = outputDir.getAbsolutePath();
+		put("outputDir", this.outputDir);
 	}
 
-	public String getBaseDir() {
-		return baseDir;
+	public void setProjectDir(File projectDir) {
+		this.projectDir = projectDir.getAbsolutePath();
+		put("projectDir", this.projectDir);
 	}
 
-	public String getOutputDir() {
-		return outputDir;
+	public void setLaunchDir(File launchDir) {
+		this.launchDir = launchDir.getAbsolutePath();
+		put("launchDir", this.launchDir);
 	}
 
-	public void setProjectDir(String projectDir) {
-		this.projectDir = projectDir;
-		put("projectDir", projectDir);
-	}
-
-	public void setLaunchDir(String launchDir) {
-		this.launchDir = launchDir;
-		put("launchDir", launchDir);
-	}
-
-	public void setWorkDir(String workDir) {
-		this.workDir = workDir;
-		put("workDir", workDir);
+	public void setWorkDir(File workDir) {
+		this.workDir = workDir.getAbsolutePath();
+		put("workDir", this.workDir);
 	}
 
 	public void load(String filename) throws CompilationFailedException, ClassNotFoundException, IOException {
@@ -199,7 +191,7 @@ protected Map<String, Object> createNestedMap(Map<String, Object> map) {
 		nestedMap.put("outputDir", outputDir);
 		nestedMap.put("projectDir", projectDir);
 		nestedMap.put("launchDir", launchDir);
-		nestedMap.put("workDir", workDir);	
+		nestedMap.put("workDir", workDir);
 		if (map != null) {
 			nestedMap.putAll(map);
 		}

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

@@ -1,5 +1,6 @@
 package com.askimed.nf.test.lang;
 
+import java.io.File;
 import java.io.IOException;
 
 import org.codehaus.groovy.control.CompilationFailedException;
@@ -17,15 +18,15 @@ public class TestContext {
 
 	private Closure paramsClosure;
 
-	public String baseDir = "";
+	public File baseDir;
 
-	public String projectDir = "";
+	public File projectDir;
 
-	public String launchDir = "";
+	public File launchDir;
 
-	public String workDir = "";
+	public File workDir;
 
-	public String outputDir = "";
+	public File outputDir;
 
 	public ITest test;
 
@@ -40,15 +41,15 @@ public TestContext(ITest test) {
 	public void init(AbstractTest test) {
 		params.setBaseDir(test.baseDir);
 		params.setProjectDir(test.baseDir);
-		params.setLaunchDir(test.launchDir.getAbsolutePath());
-		params.setWorkDir(test.workDir.getAbsolutePath());
-		params.setOutputDir(test.outputDir.getAbsolutePath());
+		params.setLaunchDir(test.launchDir);
+		params.setWorkDir(test.workDir);
+		params.setOutputDir(test.outputDir);
 
 		this.baseDir = test.baseDir;
 		this.projectDir = test.baseDir;
-		this.launchDir = test.launchDir.getAbsolutePath();
-		this.workDir = test.workDir.getAbsolutePath();
-		this.outputDir = test.outputDir.getAbsolutePath();
+		this.launchDir = test.launchDir;
+		this.workDir = test.workDir;
+		this.outputDir = test.outputDir;
 	}
 
 	public ParamsMap getParams() {

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

@@ -1,14 +1,13 @@
 package com.askimed.nf.test.lang;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import com.opencsv.exceptions.CsvValidationException;
+import com.askimed.nf.test.core.AbstractTest;
 
 import groovy.json.JsonSlurper;
 
@@ -34,7 +33,7 @@ public class WorkflowMeta {
 
 	public void loadFromFolder(File folder) {
 
-		File file = new File(folder, "workflow.json");
+		File file = new File(folder, AbstractTest.FILE_WORKFLOW_JSON);
 
 		if (file.exists()) {
 			JsonSlurper jsonSlurper = new JsonSlurper();
@@ -46,7 +45,7 @@ public void loadFromFolder(File folder) {
 			this.errorReport = getString(map, "errorReport");
 		}
 
-		File outFile = new File(folder, "std.out");
+		File outFile = new File(folder, AbstractTest.FILE_STD_OUT);
 		if (outFile.exists()) {
 			try {
 				stdout = Files.readAllLines(outFile.toPath());
@@ -55,7 +54,7 @@ public void loadFromFolder(File folder) {
 			}
 		}
 
-		File outFileStdErr = new File(folder, "std.err");
+		File outFileStdErr = new File(folder, AbstractTest.FILE_STD_ERR);
 		if (outFileStdErr.exists()) {
 			try {
 				stderr = Files.readAllLines(outFileStdErr.toPath());
@@ -64,18 +63,11 @@ public void loadFromFolder(File folder) {
 			}
 		}
 
-		File traceFile = new File(folder, "trace.csv");
+		File traceFile = new File(folder, AbstractTest.FILE_TRACE);
 		if (traceFile.exists()) {
 			try {
 				trace = new WorkflowTrace(traceFile);
-			} catch (CsvValidationException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			} catch (FileNotFoundException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			} catch (IOException e) {
-				// TODO Auto-generated catch block
+			} catch (Exception e) {
 				e.printStackTrace();
 			}
 		}

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

@@ -2,6 +2,7 @@
 
 import java.io.File;
 
+import com.askimed.nf.test.core.AbstractTest;
 import com.askimed.nf.test.lang.WorkflowMeta;
 
 import groovy.json.JsonSlurper;
@@ -40,13 +41,13 @@ public String toString() {
 	}
 
 	public void loadResult(File folder) {
-		File file = new File(folder, "function.json");
+		File file = new File(folder, AbstractTest.FILE_FUNCTION_JSON);
 
 		if (file.exists()) {
 			JsonSlurper jsonSlurper = new JsonSlurper();
 			result = jsonSlurper.parse(file);
 		}
-		
+
 	}
-	
+
 }