@Test
public void testMonitoring() throws IOException {
String listCommand =
"-p net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker -- --tp 1000";
String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS);
Log.info(listOutput);
}
@Test
public void testLaunchScheduled() throws IOException {
// launch-scheduled
String schedCommand =
"-p net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher -- --launch-scheduled";
String schedOutput = ITUtility.runSeqWareJar(schedCommand, ReturnValue.SUCCESS);
Log.info(schedOutput);
}
@Test
public void testPackageBundleAndInstallSeparately() throws IOException {
separateTempDir = Files.createTempDir();
Log.info("Trying to package archetype at: " + separateTempDir.getAbsolutePath());
PluginRunner it = new PluginRunner();
String SEQWARE_VERSION = it.getClass().getPackage().getImplementationVersion();
Assert.assertTrue("unable to detect seqware version", SEQWARE_VERSION != null);
Log.info("SeqWare version detected as: " + SEQWARE_VERSION);
File packageDir = Files.createTempDir();
// for this test, we're going to create, install and package just one archetype. Doing more
// seems redundant for this test
String[] archetypes = {
"java-workflow" /*, "simplified-ftl-workflow", "legacy-ftl-workflow", "simple-legacy-ftl-workflow"*/
};
for (String archetype : archetypes) {
String workflow = "seqware-archetype-" + archetype;
// generate and install archetypes to local maven repo
String command =
"mvn archetype:generate -DarchetypeCatalog=local -Dpackage=com.seqware.github -DgroupId=com.github.seqware -DarchetypeArtifactId="
+ workflow
+ " -Dversion=1.0-SNAPSHOT -DarchetypeGroupId=com.github.seqware -DartifactId="
+ workflow
+ " -DworkflowDirectoryName="
+ workflow
+ " -DworkflowName="
+ workflow
+ " -DworkflowVersion=1.0-SNAPSHOT -B -Dgoals=install";
String genOutput = ITUtility.runArbitraryCommand(command, 0, separateTempDir);
Log.info(genOutput);
// install the workflows to the database and record their information
File workflowDir = new File(separateTempDir, workflow);
File targetDir = new File(workflowDir, "target");
File bundleDir =
new File(
targetDir,
"Workflow_Bundle_" + workflow + "_1.0-SNAPSHOT_SeqWare_" + SEQWARE_VERSION);
String packageCommand =
"-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
+ packageDir
+ " -p "
+ bundleDir.getAbsolutePath();
String packageOutput = ITUtility.runSeqWareJar(packageCommand, ReturnValue.SUCCESS);
Log.info(packageOutput);
// locate the zip bundle and then install it
File zippedBundle = new File(packageDir, bundleDir.getName() + ".zip");
Assert.assertTrue(
"zipped bundle " + zippedBundle.getAbsolutePath() + ".zip", zippedBundle.exists());
String installCommand =
"-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
+ zippedBundle
+ " -i";
String installOutput = ITUtility.runSeqWareJar(installCommand, ReturnValue.SUCCESS);
Log.info(installOutput);
}
FileUtils.deleteDirectory(packageDir);
}