/*
* Copyright (C) 2013 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.pipeline.debugging_tutorial;
import com.google.common.io.Files;
import io.seqware.cli.Main;
import java.io.File;
import java.io.IOException;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.common.util.Log;
import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
import net.sourceforge.seqware.pipeline.plugins.ITUtility;
import org.junit.Assert;
import org.junit.Test;
/**
* These tests support the tutorial for debugging workflows.
*
* We will verify that error reporting in the WorkflowLauncher and stderr come back as expected.
*
* @author dyuen
*/
public class DebugWorkflowTutorialET {
@Test
public void runThroughFirstFailAtLaunchTutorial() throws IOException {
// here we test that the first error is properly propagated into the database and reported
ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
Main main = new Main();
String SEQWARE_VERSION = main.getClass().getPackage().getImplementationVersion();
Assert.assertTrue("unable to detect seqware version", SEQWARE_VERSION != null);
Log.info("SeqWare version detected as: " + SEQWARE_VERSION);
File tempDir = Files.createTempDir();
// create the workflow
String command = "mvn archetype:generate -DarchetypeCatalog=local -Dpackage=com.github.seqware"
+ " -DgupId=com.github.seqware -DarchetypeArtifactId=seqware-archetype-java-workflow "
+ "-Dversion=1.0-SNAPSHOT -DarchetypeGroupId=com.github.seqware -DartifactId=BuggyWorkflow "
+ "-Dworkflow-name=BuggyWorkflow -B";
String genOutput = ITUtility.runArbitraryCommand(command, 0, tempDir);
Log.info(genOutput);
// Replace contents of WorkflowClient from both workflows with code from tutorial
String tarTemplatePath = DebugWorkflowTutorialET.class.getResource("FailLaunch.template").getPath();
// determine existing file paths
File tarTarget = new File(tempDir, "BuggyWorkflow/src/main/java/com/github/seqware/BuggyWorkflowWorkflow.java");
// replace tutorial files
Files.copy(new File(tarTemplatePath), tarTarget);
// rebuild bundles
command = "mvn clean install";
genOutput = ITUtility.runArbitraryCommand(command, 0, new File(tempDir, "BuggyWorkflow"));
Log.info(genOutput);
// package bundles
String listCommand = " bundle launch --dir BuggyWorkflow/target/Workflow_Bundle_BuggyWorkflow_1.0-SNAPSHOT_SeqWare_"
+ SEQWARE_VERSION + "/";
String listOutput = ITUtility.runSeqwareCLI(listCommand, ReturnValue.RUNNERERR, tempDir);
Assert.assertTrue("Launch did not fail as expected", listOutput.contains("java.lang.ArithmeticException: / by zero"));
// clean-up on the way out
tempDir.deleteOnExit();
}
@Test
public void runThroughFirstFailAtRuntimeTutorial() throws IOException {
// here we test that the first error is properly propagated into the database and reported
ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
Main main = new Main();
String SEQWARE_VERSION = main.getClass().getPackage().getImplementationVersion();
Assert.assertTrue("unable to detect seqware version", SEQWARE_VERSION != null);
Log.info("SeqWare version detected as: " + SEQWARE_VERSION);
File tempDir = Files.createTempDir();
// create the workflow
String command = "mvn archetype:generate -DarchetypeCatalog=local -Dpackage=com.github.seqware"
+ " -DgupId=com.github.seqware -DarchetypeArtifactId=seqware-archetype-java-workflow "
+ "-Dversion=1.0-SNAPSHOT -DarchetypeGroupId=com.github.seqware -DartifactId=BuggyWorkflow "
+ "-Dworkflow-name=BuggyWorkflow -B";
String genOutput = ITUtility.runArbitraryCommand(command, 0, tempDir);
Log.info(genOutput);
// Replace contents of WorkflowClient from both workflows with code from tutorial
String tarTemplatePath = DebugWorkflowTutorialET.class.getResource("FailRun.template").getPath();
// determine existing file paths
File tarTarget = new File(tempDir, "BuggyWorkflow/src/main/java/com/github/seqware/BuggyWorkflowWorkflow.java");
// replace tutorial files
Files.copy(new File(tarTemplatePath), tarTarget);
// rebuild bundles
command = "mvn clean install";
genOutput = ITUtility.runArbitraryCommand(command, 0, new File(tempDir, "BuggyWorkflow"));
Log.info(genOutput);
// package bundles
String listCommand = " bundle launch --dir BuggyWorkflow/target/Workflow_Bundle_BuggyWorkflow_1.0-SNAPSHOT_SeqWare_"
+ SEQWARE_VERSION + "/";
String listOutput = ITUtility.runSeqwareCLI(listCommand, ReturnValue.FAILURE, tempDir);
Log.stderr(listOutput);
Assert.assertTrue("Workflow did not fail as expected",
listOutput.contains("The method 'do_run' exited abnormally so the Runner will terminate here!"));
listCommand = " workflow-run propagate-statuses";
listOutput = ITUtility.runSeqwareCLI(listCommand, ReturnValue.SUCCESS, tempDir);
Assert.assertTrue("Statuses not refreshed", listOutput.contains("Propagated workflow engine statuses"));
// check whether the error output contains the expected error
listCommand = " workflow-run stderr --accession 2";
listOutput = ITUtility.runSeqwareCLI(listCommand, ReturnValue.SUCCESS, tempDir);
Log.stderr(listOutput);
Assert.assertTrue("Did not create error output", listOutput.contains("Created file 2.err"));
// cat stderr and check for error
command = "cat 2.err";
genOutput = ITUtility.runArbitraryCommand(command, 0, tempDir);
Log.stderr(genOutput);
Assert.assertTrue("Did not see error in error output, saw: " + genOutput, genOutput.contains("missing operand"));
// clean-up on the way out
tempDir.deleteOnExit();
}
}