Added dot executable to generate plots

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineStatus.scala

@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
 import scala.concurrent.{Await, Future}
 import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.duration._
+import scala.sys.process.Process
 
 /**
   * Created by pjvan_thof on 7-12-16.
@@ -16,7 +17,8 @@ object PipelineStatus extends ToolCommand {
                   depsFile: Option[File] = None,
                   outputDir: File = null,
                   follow: Boolean = false,
-                  refreshTime: Int = 30) extends AbstractArgs
+                  refreshTime: Int = 30,
+                  plots: Boolean = true) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('d', "pipelineDir") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
@@ -34,7 +36,9 @@ object PipelineStatus extends ToolCommand {
     opt[Int]("refresh") maxOccurs 1 action { (x, c) =>
       c.copy(refreshTime = x)
     } text "Time to check again, default set on 30 seconds"
-
+    opt[Unit]("skipPlots") maxOccurs 1 action { (x, c) =>
+      c.copy(plots = false)
+    } text "This will follow a run"
   }
 
   def main(args: Array[String]): Unit = {
@@ -45,7 +49,7 @@ object PipelineStatus extends ToolCommand {
 
     val depsFile = cmdArgs.depsFile.getOrElse(getDepsFileFromDir(cmdArgs.pipelineDir))
     val deps = readDepsFile(depsFile)
-    writePipelineStatus(deps, cmdArgs.outputDir, follow = cmdArgs.follow, refreshTime = cmdArgs.refreshTime)
+    writePipelineStatus(deps, cmdArgs.outputDir, follow = cmdArgs.follow, refreshTime = cmdArgs.refreshTime, plots = cmdArgs.plots)
     logger.info("Done")
   }
 
@@ -75,12 +79,15 @@ object PipelineStatus extends ToolCommand {
                           alreadyDone: Set[String] = Set(),
                           alreadyFailed: Set[String] = Set(),
                           follow: Boolean = false,
-                          refreshTime: Int = 30): Unit = {
+                          refreshTime: Int = 30,
+                          plots: Boolean = true): Unit = {
 
     val jobDone = jobsDone(deps)
     val jobFailed = jobsFailed(deps, jobDone)
     val jobsStart = jobsReadyStart(deps, jobDone)
 
+    var futures: List[Future[Any]] = Nil
+
     val jobsDeps = deps.jobs.map(x => x._1 -> (x._2.dependsOnJobs match {
       case l: List[_] => l.map(_.toString)
       case _          => throw new IllegalStateException("Value 'depends_on_jobs' is not a list")
@@ -88,8 +95,8 @@ object PipelineStatus extends ToolCommand {
     val jobsWriter = new PrintWriter(new File(outputDir, s"jobs.json"))
     jobsWriter.println(ConfigUtils.mapToJson(jobsDeps).spaces2)
     jobsWriter.close()
-    writeGraphvizFile(jobsDeps, new File(outputDir, s"jobs.gv"), jobDone, jobFailed, jobsStart, deps)
-    writeGraphvizFile(compressOnType(jobsDeps), new File(outputDir, s"compress.jobs.gv"), jobDone, jobFailed, jobsStart, deps)
+    futures :+= writeGraphvizFile(jobsDeps, new File(outputDir, s"jobs.gv"), jobDone, jobFailed, jobsStart, deps, plots)
+    futures :+= writeGraphvizFile(compressOnType(jobsDeps), new File(outputDir, s"compress.jobs.gv"), jobDone, jobFailed, jobsStart, deps, plots)
 
     val mainJobs = deps.jobs.filter(_._2.mainJob == true).map {
       case (name, job) =>
@@ -99,8 +106,8 @@ object PipelineStatus extends ToolCommand {
     val mainJobsWriter = new PrintWriter(new File(outputDir, s"main_jobs.json"))
     mainJobsWriter.println(ConfigUtils.mapToJson(mainJobs).spaces2)
     mainJobsWriter.close()
-    writeGraphvizFile(mainJobs, new File(outputDir, s"main_jobs.gv"), jobDone, jobFailed, jobsStart, deps)
-    writeGraphvizFile(compressOnType(mainJobs), new File(outputDir, s"compress.main_jobs.gv"), jobDone, jobFailed, jobsStart, deps)
+    futures :+= writeGraphvizFile(mainJobs, new File(outputDir, s"main_jobs.gv"), jobDone, jobFailed, jobsStart, deps, plots)
+    futures :+= writeGraphvizFile(compressOnType(mainJobs), new File(outputDir, s"compress.main_jobs.gv"), jobDone, jobFailed, jobsStart, deps, plots)
 
     val totalJobs = deps.jobs.size
     val totalStart = jobsStart.size
@@ -110,6 +117,7 @@ object PipelineStatus extends ToolCommand {
 
     logger.info(s"Total job: ${totalJobs}, Pending: ${totalPending}, Ready to run / running: ${totalStart}, Done: ${totalDone}, Failed ${totalFailed}")
 
+    futures.foreach(x => Await.ready(x, Duration.Inf))
     if (follow) {
       Thread.sleep(refreshTime * 1000)
       writePipelineStatus(deps, outputDir, jobDone, jobFailed, follow)
@@ -146,7 +154,8 @@ object PipelineStatus extends ToolCommand {
                         jobDone: Set[String],
                         jobFailed: Set[String],
                         jobsStart: Set[String],
-                        deps: Deps): Unit = {
+                        deps: Deps,
+                        plots: Boolean): Future[Unit] = Future {
     val writer = new PrintWriter(outputFile)
     writer.println("digraph graphname {")
     jobDone
@@ -166,6 +175,13 @@ object PipelineStatus extends ToolCommand {
     jobsDeps.foreach { case (a, b) => b.foreach(c => writer.println(s"  $c -> $a;")) }
     writer.println("}")
     writer.close()
+
+    writeGvToPlot(outputFile)
+  }
+
+  def writeGvToPlot(input: File): Unit = {
+    Process(Seq("dot", "-Tpng", "-O", input.getAbsolutePath)).run()
+    Process(Seq("dot", "-Tsvg", "-O", input.getAbsolutePath)).run()
   }
 
   def jobsReadyStart(deps: Deps, jobsDone: Set[String]): Set[String] = {
@@ -191,8 +207,7 @@ object PipelineStatus extends ToolCommand {
   def jobsFailed(deps: Deps, dones: Set[String], alreadyFailed: Set[String] = Set()): Set[String] = {
     val f = deps.jobs.filterNot(x => dones.contains(x._1))
       .filterNot(x => alreadyFailed.contains(x._1)).map(x => x._1 -> x._2.isFailed)
-    val bla = f.map(x => x._1 -> Await.result(x._2, Duration.Inf)).filter(_._2).keySet
-    bla ++ alreadyFailed
+    f.map(x => x._1 -> Await.result(x._2, Duration.Inf)).filter(_._2).keySet ++ alreadyFailed
   }
 
   class Job(val name: String, map: Map[String, Any]) {
@@ -212,8 +227,6 @@ object PipelineStatus extends ToolCommand {
     def intermediate = ConfigUtils.any2boolean(map("intermediate"))
 
     def isDone: Future[Boolean] = Future { doneFiles.forall(_.exists()) }
-    def isFailed: Future[Boolean] = Future {
-      failFiles.exists(_.exists())
-    }
+    def isFailed: Future[Boolean] = Future { failFiles.exists(_.exists()) }
   }
 }