Testing the complete graph itself

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala

@@ -6,6 +6,8 @@ import com.google.common.io.Files
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
+import PipelineStatusTest.Status
+import nl.lumc.sasc.biopet.utils.IoUtils._
 
 /**
   * Created by pjvan_thof on 10-1-17.
@@ -18,6 +20,7 @@ class PipelineStatusTest extends TestNGSuite with Matchers {
     PipelineStatusTest.writeDeps(outputDir)
 
     PipelineStatus.main(Array("-o", outputDir.toString, "-d", outputDir.toString))
+    checkOutput(outputDir)
   }
 
   @Test
@@ -27,12 +30,52 @@ class PipelineStatusTest extends TestNGSuite with Matchers {
     val depsfile = PipelineStatusTest.writeDeps(outputDir)
 
     PipelineStatus.main(Array("-o", outputDir.toString, "-d", outputDir.toString, "--depsFile", depsfile.toString))
+    checkOutput(outputDir)
+  }
+
+  def checkOutput(outputDir: File,
+                  cat: Status.Value = Status.Pending,
+                  gzip: Status.Value = Status.Pending,
+                  zcat: Status.Value = Status.Pending): Unit = {
+    val jobsGvFile = new File(outputDir, "jobs.gv")
+    val mainJobsGvFile = new File(outputDir, "main_jobs.gv")
+    val compressJobsGvFile = new File(outputDir, "compress.jobs.gv")
+    val compressMainJobsGvFile = new File(outputDir, "compress.main_jobs.gv")
+    jobsGvFile should exist
+    mainJobsGvFile should exist
+    compressJobsGvFile should exist
+    compressMainJobsGvFile should exist
+
+    val jobsGvLines = getLinesFromFile(jobsGvFile)
+    require(jobsGvLines.exists(_.contains("cat_1 -> gzip_1")))
+    require(jobsGvLines.exists(_.contains("gzip_1 -> zcat_1")))
+    require(jobsGvLines.forall(!_.contains("cat_1 -> zcat_1")))
+
+    val mainJobsGvLines = getLinesFromFile(mainJobsGvFile)
+    require(mainJobsGvLines.exists(_.contains("cat_1 -> zcat_1")))
+    require(mainJobsGvLines.forall(!_.contains("cat_1 -> gzip_1")))
+    require(mainJobsGvLines.forall(!_.contains("gzip_1 -> zcat_1")))
+
+    val compressJobsGvLines = getLinesFromFile(compressJobsGvFile)
+    require(compressJobsGvLines.exists(_.contains("cat -> gzip")))
+    require(compressJobsGvLines.exists(_.contains("gzip -> zcat")))
+    require(compressJobsGvLines.forall(!_.contains("cat -> zcat")))
+
+    val compressMainJobsGvLines = getLinesFromFile(compressMainJobsGvFile)
+    require(compressMainJobsGvLines.exists(_.contains("cat -> zcat")))
+    require(compressMainJobsGvLines.forall(!_.contains("cat -> gzip")))
+    require(compressMainJobsGvLines.forall(!_.contains("gzip -> zcat")))
+
   }
 
 }
 
 object PipelineStatusTest {
 
+  object Status extends Enumeration {
+    val Failed, Done, Pending = Value
+  }
+
   def writeDeps(outputDir: File): File = {
     require(outputDir.exists())
     val depsFile = new File(outputDir, ".log/test.1234567890/graph/deps.json")
@@ -47,6 +90,36 @@ object PipelineStatusTest {
     s"""
        |{
        |  "jobs" : {
+       |    "zcat_1" : {
+       |      "fail_files" : [
+       |        "$outputDir/.file.out.zcat.fail",
+       |        "$outputDir/..file.out.zcat.Zcat.out.fail"
+       |      ],
+       |      "done_at_start" : false,
+       |      "output_used_by_jobs" : [
+       |
+       |      ],
+       |      "outputs" : [
+       |        "$outputDir/file.out.zcat",
+       |        "$outputDir/.file.out.zcat.Zcat.out"
+       |      ],
+       |      "command" : "'/bin/zcat'  '$outputDir/file.out.gz'  >  '$outputDir/file.out.zcat' ",
+       |      "stdout_file" : "$outputDir/.file.out.zcat.Zcat.out",
+       |      "depends_on_intermediate" : false,
+       |      "fail_at_start" : false,
+       |      "inputs" : [
+       |        "$outputDir/file.out.gz"
+       |      ],
+       |      "depends_on_jobs" : [
+       |        "gzip_1"
+       |      ],
+       |      "intermediate" : false,
+       |      "done_files" : [
+       |        "$outputDir/.file.out.zcat.done",
+       |        "$outputDir/..file.out.zcat.Zcat.out.done"
+       |      ],
+       |      "main_job" : true
+       |    },
        |    "gzip_1" : {
        |      "fail_files" : [
        |        "$outputDir/.file.out.gz.fail",
@@ -54,13 +127,13 @@ object PipelineStatusTest {
        |      ],
        |      "done_at_start" : false,
        |      "output_used_by_jobs" : [
-       |        
+       |        "zcat_1"
        |      ],
        |      "outputs" : [
        |        "$outputDir/file.out.gz",
        |        "$outputDir/.file.out.gz.Gzip.out"
        |      ],
-       |      "command" : "\n\n '/bin/gzip'  -c  '$outputDir/file.out'  >  '$outputDir/file.out.gz' ",
+       |      "command" : "'/bin/gzip'  -c  '$outputDir/file.out'  >  '$outputDir/file.out.gz' ",
        |      "stdout_file" : "$outputDir/.file.out.gz.Gzip.out",
        |      "depends_on_intermediate" : false,
        |      "fail_at_start" : false,
@@ -70,12 +143,12 @@ object PipelineStatusTest {
        |      "depends_on_jobs" : [
        |        "cat_1"
        |      ],
-       |      "intermediate" : false,
+       |      "intermediate" : true,
        |      "done_files" : [
        |        "$outputDir/.file.out.gz.done",
        |        "$outputDir/..file.out.gz.Gzip.out.done"
        |      ],
-       |      "main_job" : true
+       |      "main_job" : false
        |    },
        |    "cat_1" : {
        |      "fail_files" : [
@@ -90,7 +163,7 @@ object PipelineStatusTest {
        |        "$outputDir/file.out",
        |        "$outputDir/.file.out.Cat.out"
        |      ],
-       |      "command" : "\n\n '/bin/cat'  'test.deps'  >  '$outputDir/file.out' ",
+       |      "command" : "'/bin/cat'  'test.deps'  >  '$outputDir/file.out' ",
        |      "stdout_file" : "$outputDir/.file.out.Cat.out",
        |      "depends_on_intermediate" : false,
        |      "fail_at_start" : false,

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala

@@ -14,7 +14,9 @@
  */
 package nl.lumc.sasc.biopet.utils
 
-import java.io.{ File, FileInputStream, FileOutputStream, InputStream }
+import java.io.{File, FileInputStream, FileOutputStream, InputStream}
+
+import scala.io.Source
 
 /**
  * This object contains generic io methods
@@ -68,4 +70,17 @@ object IoUtils {
         if (fname.toLowerCase.endsWith(ext)) fname.dropRight(ext.length)
         else fname
     }
+
+  /**
+    * This return the contends of a file as a List[String]
+    *
+    * @param file
+    * @return
+    */
+  def getLinesFromFile(file: File): List[String] = {
+    val reader = Source.fromFile(file)
+    val lines = reader.getLines().toList
+    reader.close()
+    lines
+  }
 }