Fix testcases

genepi · Nov 12, 2023 · b269c9b · b269c9b
1 parent 6c7fed0
commit b269c9b
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java b/src/test/java/cloudgene/mapred/jobs/WorkflowEngineTest.java
@@ -8,6 +8,7 @@
 import java.util.List;
 import java.util.Map;
 
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import org.junit.jupiter.api.Test;
 
 import cloudgene.mapred.TestApplication;
@@ -470,10 +471,10 @@ public void testWriteTextToStdOutStep() throws Exception {
 
 		assertEquals(AbstractJob.STATE_SUCCESS, job.getState());
 
-		String stdout = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "std.out");
+		String stdout = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "logs", "std.out");
 		String contentStdOut = FileUtil.readFileAsString(stdout);
 
-		String log = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "job.txt");
+		String log = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "logs", "job.txt");
 		String contentlog = FileUtil.readFileAsString(log);
 
 		assertTrue(contentStdOut.contains("taks write to system out"));
@@ -670,10 +671,16 @@ public CloudgeneJob createJobFromWdl(WdlApp app, Map<String, String> inputs, Use
 		String localWorkspace = FileUtil.path(settings.getLocalWorkspace(), id);
 		FileUtil.createDirectory(localWorkspace);
 
+
+		// setup workspace
+		IWorkspace workspace = workspaceFactory.getDefault();
+		workspace.setJob(id);
+		workspace.setup();
+
 		CloudgeneJob job = new CloudgeneJob(user, id, app, inputs);
 		job.setId(id);
 		job.setName(id);
-		job.setWorkspace(workspaceFactory.getDefault());
+		job.setWorkspace(workspace);
 		job.setLocalWorkspace(localWorkspace);
 		job.setSettings(settings);
 		job.setApplication(app.getName() + " " + app.getVersion());

diff --git a/src/test/java/cloudgene/mapred/steps/TestCommand.java b/src/test/java/cloudgene/mapred/steps/TestCommand.java
@@ -7,6 +7,7 @@
 import java.util.List;
 import java.util.Map;
 
+import cloudgene.mapred.jobs.workspace.IWorkspace;
 import org.junit.jupiter.api.Test;
 
 import cloudgene.mapred.TestApplication;
@@ -57,13 +58,13 @@ public void testValidCommand() throws Exception {
 		assertEquals(messages.get(0).getType(), WorkflowContext.OK);
 		assertTrue(messages.get(0).getMessage().contains("Execution successful."));
 
-		String stdout = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "std.out");
+		String stdout = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "logs", "std.out");
 		String contentStdOut = FileUtil.readFileAsString(stdout);
 
 		// simple ls result check
 		assertTrue(contentStdOut.contains("invalid-command.yaml"));
 
-		String jobLog = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "job.txt");
+		String jobLog = FileUtil.path(application.getSettings().getLocalWorkspace(), job.getId(), "logs", "job.txt");
 		String contentjobLog = FileUtil.readFileAsString(jobLog);
 
 		// simple check if exit code = 0
@@ -139,9 +140,14 @@ public CloudgeneJob createJobFromWdl(WdlApp app, Map<String, String> inputs) thr
 		String localWorkspace = FileUtil.path(settings.getLocalWorkspace(), id);
 		FileUtil.createDirectory(localWorkspace);
 
+		// setup workspace
+		IWorkspace workspace = workspaceFactory.getDefault();
+		workspace.setJob(id);
+		workspace.setup();
+
 		CloudgeneJob job = new CloudgeneJob(user, id, app, inputs);
 		job.setId(id);
-		job.setWorkspace(workspaceFactory.getDefault());
+		job.setWorkspace(workspace);
 		job.setName(id);
 		job.setLocalWorkspace(localWorkspace);
 		job.setSettings(settings);