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de-CTKS map tests (broadinstitute#4530)
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centaur/src/main/resources/standardTestCases/map_workflow.test
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| name: map_workflow | ||
| testFormat: workflowsuccess | ||
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| files { | ||
| workflow: map_workflow/map_workflow.wdl | ||
| } | ||
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| metadata { | ||
| "outputs.wf.read_map.out_map.x": 500 | ||
| "outputs.wf.read_map.out_map.y": 600 | ||
| "outputs.wf.read_map.out_map.z": 700 | ||
| } |
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centaur/src/main/resources/standardTestCases/map_workflow/map_workflow.wdl
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| version 1.0 | ||
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| task make_files { | ||
| command { | ||
| for f in f1 f2 f3; do touch $f; done | ||
| } | ||
| output { | ||
| Array[File] files = ["f1", "f2", "f3"] | ||
| } | ||
| runtime { | ||
| docker: "python:2.7" | ||
| } | ||
| } | ||
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| task write_map { | ||
| input { | ||
| Map[File, String] file_to_name | ||
| } | ||
| command { | ||
| cat ${write_map(file_to_name)} | ||
| } | ||
| output { | ||
| String contents = read_string(stdout()) | ||
| } | ||
| runtime { | ||
| docker: "python:2.7" | ||
| } | ||
| } | ||
| task read_map { | ||
| command <<< | ||
| python <<CODE | ||
| map = {'x': 500, 'y': 600, 'z': 700} | ||
| print("\\n".join(["{}\\t{}".format(k,v) for k,v in map.items()])) | ||
| CODE | ||
| >>> | ||
| output { | ||
| Map[String, Int] out_map = read_map(stdout()) | ||
| } | ||
| runtime { | ||
| docker: "python:2.7" | ||
| } | ||
| } | ||
| workflow wf { | ||
| call make_files | ||
| Map[File, String] map = {make_files.files[0]: "alice", make_files.files[1]: "bob", make_files.files[2]: "chuck"} | ||
| call write_map {input: file_to_name = map} | ||
| call read_map | ||
| } |
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languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/MapWorkflowSpec.scala
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| package languages.wdl.draft2 | ||
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| import languages.wdl.draft2.MapWorkflowSpec._ | ||
| import org.scalatest.{FlatSpec, Matchers} | ||
| import wdl.draft2.model.expression.{NoFunctions, WdlFunctions} | ||
| import wdl.draft2.model.{Draft2ImportResolver, WdlNamespaceWithWorkflow} | ||
| import wom.types.{WomMapType, WomSingleFileType, WomStringType} | ||
| import wom.values.{WomMap, WomSingleFile, WomString, WomValue} | ||
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| import scala.util.{Success, Try} | ||
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| class MapWorkflowSpec extends FlatSpec with Matchers { | ||
| val namespace = WdlNamespaceWithWorkflow.load(WorkflowSource, Seq.empty[Draft2ImportResolver]).get | ||
| val expectedMap = WomMap(WomMapType(WomSingleFileType, WomStringType), Map( | ||
| WomSingleFile("f1") -> WomString("alice"), | ||
| WomSingleFile("f2") -> WomString("bob"), | ||
| WomSingleFile("f3") -> WomString("chuck") | ||
| )) | ||
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| "A static Map[File, String] declaration" should "be a valid declaration" in { | ||
| val declaration = namespace.workflow.declarations.find { | ||
| _.unqualifiedName == "map" | ||
| }.getOrElse { | ||
| fail("Expected declaration 'map' to be found") | ||
| } | ||
| val expression = declaration.expression.getOrElse { | ||
| fail("Expected an expression for declaration 'map'") | ||
| } | ||
| val value = expression.evaluate((_: String) => fail("No lookups"), NoFunctions).getOrElse { | ||
| fail("Expected expression for 'map' to evaluate") | ||
| } | ||
| expectedMap.womType.coerceRawValue(value).get shouldEqual expectedMap | ||
| } | ||
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| it should "be usable as an input" in { | ||
| val writeMapTask = namespace.findTask("write_map").getOrElse { | ||
| fail("Expected to find task 'write_map'") | ||
| } | ||
| class CannedFunctions extends WdlFunctions[WomValue] { | ||
| def write_map(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Success(WomSingleFile("/test/map/path")) | ||
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| override def getFunction(name: String): WdlFunction = name match { | ||
| case "write_map" => write_map | ||
| case _ => throw new UnsupportedOperationException("Only write_map should be called") | ||
| } | ||
| } | ||
| val command = writeMapTask.instantiateCommand(writeMapTask.inputsFromMap(Map("file_to_name" -> expectedMap)), new CannedFunctions).getOrElse { | ||
| fail("Expected instantiation to work") | ||
| } | ||
| command.head.commandString shouldEqual "cat /test/map/path" | ||
| } | ||
| } | ||
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| object MapWorkflowSpec { | ||
| val WorkflowSource = | ||
| s""" | ||
| |task write_map { | ||
| | Map[File, String] file_to_name | ||
| | command { | ||
| | cat $${write_map(file_to_name)} | ||
| | } | ||
| | output { | ||
| | String contents = read_string(stdout()) | ||
| | } | ||
| |} | ||
| | | ||
| |task read_map { | ||
| | command <<< | ||
| | python <<CODE | ||
| | map = {'x': 500, 'y': 600, 'z': 700} | ||
| | print("\\n".join(["{}\\t{}".format(k,v) for k,v in map.items()])) | ||
| | CODE | ||
| | >>> | ||
| | output { | ||
| | Map[String, Int] out_map = read_map(stdout()) | ||
| | } | ||
| |} | ||
| | | ||
| |workflow wf { | ||
| | Map[File, String] map = {"f1": "alice", "f2": "bob", "f3": "chuck"} | ||
| | call write_map {input: file_to_name = map} | ||
| | call read_map | ||
| |} | ||
| """.stripMargin | ||
| } |
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