Adding test for PipelineStatus

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

+package nl.lumc.sasc.biopet.core
+
+import java.io.{File, PrintWriter}
+
+import com.google.common.io.Files
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvan_thof on 10-1-17.
+  */
+class PipelineStatusTest extends TestNGSuite with Matchers {
+  @Test
+  def testDefault: Unit = {
+    val outputDir = Files.createTempDir()
+    outputDir.deleteOnExit()
+    PipelineStatusTest.writeDeps(outputDir)
+
+    PipelineStatus.main(Array("-o", outputDir.toString, "-d", outputDir.toString))
+  }
+
+  @Test
+  def testDepsFileArg: Unit = {
+    val outputDir = Files.createTempDir()
+    outputDir.deleteOnExit()
+    val depsfile = PipelineStatusTest.writeDeps(outputDir)
+
+    PipelineStatus.main(Array("-o", outputDir.toString, "-d", outputDir.toString, "--depsFile", depsfile.toString))
+  }
+
+}
+
+object PipelineStatusTest {
+
+  def writeDeps(outputDir: File): File = {
+    require(outputDir.exists())
+    val depsFile = new File(outputDir, ".log/test.1234567890/graph/deps.json")
+    depsFile.getParentFile.mkdirs()
+    val writer = new PrintWriter(depsFile)
+    writer.println(defaultDeps(outputDir))
+    writer.close()
+    depsFile
+  }
+
+  def defaultDeps(outputDir: File) =
+    s"""
+       |{
+       |  "jobs" : {
+       |    "gzip_1" : {
+       |      "fail_files" : [
+       |        "$outputDir/.file.out.gz.fail",
+       |        "$outputDir/..file.out.gz.Gzip.out.fail"
+       |      ],
+       |      "done_at_start" : false,
+       |      "output_used_by_jobs" : [
+       |        
+       |      ],
+       |      "outputs" : [
+       |        "$outputDir/file.out.gz",
+       |        "$outputDir/.file.out.gz.Gzip.out"
+       |      ],
+       |      "command" : "\n\n '/bin/gzip'  -c  '$outputDir/file.out'  >  '$outputDir/file.out.gz' ",
+       |      "stdout_file" : "$outputDir/.file.out.gz.Gzip.out",
+       |      "depends_on_intermediate" : false,
+       |      "fail_at_start" : false,
+       |      "inputs" : [
+       |        "$outputDir/file.out"
+       |      ],
+       |      "depends_on_jobs" : [
+       |        "cat_1"
+       |      ],
+       |      "intermediate" : false,
+       |      "done_files" : [
+       |        "$outputDir/.file.out.gz.done",
+       |        "$outputDir/..file.out.gz.Gzip.out.done"
+       |      ],
+       |      "main_job" : true
+       |    },
+       |    "cat_1" : {
+       |      "fail_files" : [
+       |        "$outputDir/.file.out.fail",
+       |        "$outputDir/..file.out.Cat.out.fail"
+       |      ],
+       |      "done_at_start" : false,
+       |      "output_used_by_jobs" : [
+       |        "gzip_1"
+       |      ],
+       |      "outputs" : [
+       |        "$outputDir/file.out",
+       |        "$outputDir/.file.out.Cat.out"
+       |      ],
+       |      "command" : "\n\n '/bin/cat'  'test.deps'  >  '$outputDir/file.out' ",
+       |      "stdout_file" : "$outputDir/.file.out.Cat.out",
+       |      "depends_on_intermediate" : false,
+       |      "fail_at_start" : false,
+       |      "inputs" : [
+       |        "test.deps"
+       |      ],
+       |      "depends_on_jobs" : [
+       |        
+       |      ],
+       |      "intermediate" : false,
+       |      "done_files" : [
+       |        "$outputDir/.file.out.done",
+       |        "$outputDir/..file.out.Cat.out.done"
+       |      ],
+       |      "main_job" : true
+       |    }
+       |  },
+       |  "files" : [
+       |    {
+       |      "output_jobs" : [
+       |        "cat_1"
+       |      ],
+       |      "path" : "$outputDir/file.out",
+       |      "input_jobs" : [
+       |        "gzip_1"
+       |      ],
+       |      "exists_at_start" : false,
+       |      "pipeline_input" : false,
+       |      "intermediate" : false
+       |    },
+       |    {
+       |      "output_jobs" : [
+       |        "gzip_1"
+       |      ],
+       |      "path" : "$outputDir/.file.out.gz.Gzip.out",
+       |      "input_jobs" : [
+       |        
+       |      ],
+       |      "exists_at_start" : false,
+       |      "pipeline_input" : false,
+       |      "intermediate" : false
+       |    },
+       |    {
+       |      "output_jobs" : [
+       |        "gzip_1"
+       |      ],
+       |      "path" : "$outputDir/file.out.gz",
+       |      "input_jobs" : [
+       |        
+       |      ],
+       |      "exists_at_start" : false,
+       |      "pipeline_input" : false,
+       |      "intermediate" : false
+       |    },
+       |    {
+       |      "output_jobs" : [
+       |        
+       |      ],
+       |      "path" : "$outputDir/test.deps",
+       |      "input_jobs" : [
+       |        "cat_1"
+       |      ],
+       |      "exists_at_start" : false,
+       |      "pipeline_input" : true,
+       |      "intermediate" : false
+       |    },
+       |    {
+       |      "output_jobs" : [
+       |        "cat_1"
+       |      ],
+       |      "path" : "$outputDir/.file.out.Cat.out",
+       |      "input_jobs" : [
+       |        
+       |      ],
+       |      "exists_at_start" : false,
+       |      "pipeline_input" : false,
+       |      "intermediate" : false
+       |    }
+       |  ]
+       |}
+     """.stripMargin
+}