92 lines
3.0 KiB
Scala
92 lines
3.0 KiB
Scala
package org.broadinstitute.sting.queue.pipeline
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import org.broadinstitute.sting.utils.Utils
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import org.testng.Assert
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import org.broadinstitute.sting.commandline.CommandLineProgram
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import org.broadinstitute.sting.queue.util.ProcessController
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import org.broadinstitute.sting.queue.QCommandLine
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object PipelineTest {
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private var runningCommandLines = Set.empty[QCommandLine]
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val run = System.getProperty("pipeline.run") == "run"
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/**
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* execute the test
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* @param name the name of the test
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* @param args the argument list
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* @param expectedException the expected exception or null if no exception is expected.
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*/
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def executeTest(name: String, args: String, expectedException: Class[_]) = {
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var command = Utils.escapeExpressions(args)
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// add the logging level to each of the integration test commands
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command = Utils.appendArray(command, "-l", "WARN", "-startFromScratch", "-tempDir", tempDir(name), "-runDir", runDir(name))
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if (run)
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command = Utils.appendArray(command, "-run", "-bsub")
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// run the executable
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var gotAnException = false
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val instance = new QCommandLine
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runningCommandLines += instance
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try {
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println("Executing test %s with Queue arguments: %s".format(name, Utils.join(" ",command)))
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CommandLineProgram.start(instance, command)
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} catch {
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case e =>
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gotAnException = true
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if (expectedException != null) {
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// we expect an exception
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println("Wanted exception %s, saw %s".format(expectedException, e.getClass))
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if (expectedException.isInstance(e)) {
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// it's the type we expected
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println(String.format(" => %s PASSED", name))
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} else {
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e.printStackTrace()
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Assert.fail("Test %s expected exception %s but got %s instead".format(
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name, expectedException, e.getClass))
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}
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} else {
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// we didn't expect an exception but we got one :-(
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throw new RuntimeException(e)
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}
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} finally {
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instance.shutdown()
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runningCommandLines -= instance
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}
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// catch failures from the integration test
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if (expectedException != null) {
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if (!gotAnException)
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// we expected an exception but didn't see it
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Assert.fail("Test %s expected exception %s but none was thrown".format(name, expectedException.toString))
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} else {
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if (CommandLineProgram.result != 0)
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throw new RuntimeException("Error running the GATK with arguments: " + args)
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}
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}
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def testDir(testName: String) = "pipelinetests/%s/".format(testName)
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def runDir(testName: String) = testDir(testName) + "run/"
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def tempDir(testName: String) = testDir(testName) + "temp/"
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Runtime.getRuntime.addShutdownHook(new Thread {
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/** Cleanup as the JVM shuts down. */
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override def run = {
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try {
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ProcessController.shutdown()
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} catch {
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case _ => /*ignore */
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}
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runningCommandLines.foreach(commandLine =>
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try {
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commandLine.shutdown()
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} catch {
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case _ => /* ignore */
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})
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}
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})
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}
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