Add stage to testsuite

docs/docs/configuration.md

@@ -145,3 +145,28 @@ In this example:
 
 - The `symlink` directive creates a symlink named "original_data.txt" in the `meta` directory pointing to the file located at "data/original_data.txt."
 - The `copy` directive copies the "config.yml" file from the "resources" directory to the `meta` directory.
+
+### Testsuite
+
+Furthermore, it is also possible to stage files that are specific to a single testsuite:
+
+```
+nextflow_workflow {
+
+    name "Test workflow HELLO_WORKFLOW"
+
+    script "./hello.nf"
+    workflow "HELLO_WORKFLOW"
+
+    stage {
+        symlink "test-assets/test.txt"
+    }
+
+    test("Should print out test file") {
+        expect {
+            assert workflow.success
+        }
+    }
+
+}
+```

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

@@ -1,8 +1,6 @@
 package com.askimed.nf.test.config;
 
 import java.io.File;
-import java.util.List;
-import java.util.Vector;
 
 import org.codehaus.groovy.control.CompilerConfiguration;
 import org.codehaus.groovy.control.customizers.ImportCustomizer;

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

@@ -111,6 +111,7 @@ public void setup(Config config, File testDirectory) throws IOException {
 				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);
 		}
@@ -247,7 +248,7 @@ public void setWithTrace(boolean withTrace) {
 	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());

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

@@ -5,6 +5,7 @@
 import java.util.Vector;
 
 import com.askimed.nf.test.config.Config;
+import com.askimed.nf.test.config.StageBuilder;
 import com.askimed.nf.test.lang.extensions.SnapshotFile;
 
 import groovy.lang.Closure;
@@ -41,6 +42,8 @@ public abstract class AbstractTestSuite implements ITestSuite {
 
 	private List<NamedClosure> testClosures = new Vector<NamedClosure>();
 
+	private StageBuilder stageBuilder = new StageBuilder();
+
 	private Config config;
 
 	@Override
@@ -137,6 +140,16 @@ public String getOptions() {
 		return options;
 	}
 
+	public void stage(Closure closure) {
+		closure.setDelegate(stageBuilder);
+		closure.setResolveStrategy(Closure.DELEGATE_ONLY);
+		closure.call();
+	}
+
+	public StageBuilder getStageBuilder() {
+		return stageBuilder;
+	}
+
 	@Override
 	public void setGlobalConfigFile(File globalConfig) {
 		this.globalConfig = globalConfig;

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

@@ -34,7 +34,7 @@ public void testWorkflowSucces() throws Exception {
 		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testWorkflowWithRelativePath() throws Exception {
 
@@ -43,15 +43,15 @@ public void testWorkflowWithRelativePath() throws Exception {
 		assertEquals(0, exitCode);
 
 	}
-  
+
 	@Test
-  public void testWorkflowUnamedOutputs() throws Exception {
+	public void testWorkflowUnamedOutputs() throws Exception {
 		App app = new App();
 		int exitCode = app.run(new String[] { "test", "test-data/workflow/unnamed/trial.unnamed.nf.test" });
 		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testWorkflowAndSnapshot() throws Exception {
 
@@ -60,7 +60,7 @@ public void testWorkflowAndSnapshot() throws Exception {
 		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testWorkflowWithNoOutputs() throws Exception {
 
@@ -83,91 +83,104 @@ public void testOverrideWorkflow() throws Exception {
 	public void testLibs() throws Exception {
 
 		App app = new App();
-		int exitCode = app.run(new String[] { "test", "test-data/workflow/libs/hello.nf.test", "--lib", "lib" ,"--debug"});
+		int exitCode = app
+				.run(new String[] { "test", "test-data/workflow/libs/hello.nf.test", "--lib", "lib", "--debug" });
 		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testParamsIssue34() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/issue34/trial.nf.test"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/issue34/trial.nf.test" });
+		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testParamsIssue34Setup() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/issue34/trial.setup.nf.test"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/issue34/trial.setup.nf.test" });
+		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testHangingWorkflowIssue57() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/hanging/meaningless_workflow.nf.test","--debug"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app
+				.run(new String[] { "test", "test-data/workflow/hanging/meaningless_workflow.nf.test", "--debug" });
+		assertEquals(0, exitCode);
 
 	}
 
 	@Test
 	public void testWorkflowNonUniqueFilenames() throws Exception {
 
 		App app = new App();
-		int exitCode = app.run(new String[] { "test", "test-data/workflow/non-unique-filenames/main.nf.test"});
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/non-unique-filenames/main.nf.test" });
 		assertEquals(0, exitCode);
 
 	}
-
-
+
 	@Test
 	public void testIssue125() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/issue125/example_wf.nf.test"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/issue125/example_wf.nf.test" });
+		assertEquals(0, exitCode);
 
 	}
-
-
+
 	@Test
 	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);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test" });
+		assertEquals(1, exitCode);
 
 	}
-	
+
 	@Test
 	public void testStagingWitMappingFolder() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config", "test-data/workflow/staging/nf-test.folder.config","--debug"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config",
+				"test-data/workflow/staging/nf-test.folder.config", "--debug" });
+		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testStagingWitMappingFile() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config", "test-data/workflow/staging/nf-test.file.config"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config",
+				"test-data/workflow/staging/nf-test.file.config" });
+		assertEquals(0, exitCode);
 
 	}
-	
+
 	@Test
 	public void testStagingWitMappingFileAndMode() throws Exception {
 
-	  App app = new App();
-	  int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config", "test-data/workflow/staging/nf-test.file.mode.config"});
-	  assertEquals(0, exitCode);
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello.nf.test", "--config",
+				"test-data/workflow/staging/nf-test.file.mode.config" });
+		assertEquals(0, exitCode);
+
+	}
+
+	@Test
+	public void testStagingInTestsuite() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/staging/hello-stage.nf.test" });
+		assertEquals(0, exitCode);
 
 	}
+
 }

test-data/workflow/staging/hello-stage.nf.test

@@ -0,0 +1,19 @@
+nextflow_workflow {
+
+  name "Test workflow HELLO_WORKFLOW"
+
+  script "./hello.nf"
+  workflow "HELLO_WORKFLOW"
+
+  stage {
+    symlink "test-assets/test.txt"
+  }
+
+  test("Should print out test file") {
+    expect {
+      assert workflow.success
+    }
+
+  }
+
+}

test-data/workflow/staging/hello.nf

@@ -0,0 +1,19 @@
+process HELLO {
+
+  input:
+    file input
+
+  script:
+  """
+  cat ${input}
+  """
+
+}
+
+workflow HELLO_WORKFLOW {
+
+  HELLO(
+    file("${baseDir}/test-assets/test.txt")
+  )
+
+}

test-data/workflow/staging/hello.nf.test

@@ -0,0 +1,15 @@
+nextflow_workflow {
+
+  name "Test workflow HELLO_WORKFLOW"
+
+  script "./hello.nf"
+  workflow "HELLO_WORKFLOW"
+
+  test("Should print out test file") {
+    expect {
+      assert workflow.success
+    }
+
+  }
+
+}