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Improving type evaluation and lookup (#2807)
Fixing type evaluation problems
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173 changes: 173 additions & 0 deletions
173
wdl/src/test/scala/wdl/expression/DNAxTypeEvalTest.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| package wdl.expression | ||
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| import org.scalatest.{FlatSpec, Matchers} | ||
| import scala.util.{Success, Try} | ||
| import wdl.{Scope, Scatter, WdlCall, WdlExpression, WdlNamespace, WdlNamespaceWithWorkflow} | ||
| import wom.types._ | ||
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| class DNAxTypeEvalTest extends FlatSpec with Matchers { | ||
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| val wdlCode = | ||
| """|task Add { | ||
| | Int a | ||
| | Int b | ||
| | | ||
| | command { | ||
| | } | ||
| | output { | ||
| | Int result = a + b | ||
| | } | ||
| |} | ||
| | | ||
| |workflow dict { | ||
| | Map[Int, Int] mII = {1: 10, 2: 11} | ||
| | Map[Int, Float] mIF = {1: 1.2, 10: 113.0} | ||
| | | ||
| | scatter(pair in mII) { | ||
| | Int valueII = pair.right | ||
| | } | ||
| | | ||
| | scatter(pair in mIF) { | ||
| | call Add { | ||
| | input: a=pair.left, b=5 | ||
| | } | ||
| | } | ||
| | | ||
| | output { | ||
| | valueII | ||
| | } | ||
| |} | ||
| |""".stripMargin | ||
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| // Figure out the type of an expression | ||
| def evalType(expr: WdlExpression, parent: Scope) : Try[WomType] = { | ||
| expr.evaluateType(WdlNamespace.lookupType(parent), | ||
| new WdlStandardLibraryFunctionsType, | ||
| Some(parent)) | ||
| } | ||
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| it should "correctly evaluate expression types" in { | ||
| val ns = WdlNamespaceWithWorkflow.load(wdlCode, Seq.empty).get | ||
| val wf = ns.workflow | ||
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| val call:WdlCall = wf.findCallByName("Add") match { | ||
| case None => throw new Exception(s"Call Add not found in WDL file") | ||
| case Some(call) => call | ||
| } | ||
| val ssc:Scatter = wf.scatters.head | ||
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| call.inputMappings.foreach { case (_, expr) => | ||
| val t:Try[WomType] = evalType(expr, ssc) | ||
| t should equal(Success(WomIntegerType)) | ||
| } | ||
| } | ||
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| val wdlCode2 = | ||
| """|task Copy { | ||
| | File src | ||
| | String basename | ||
| | | ||
| | command <<< | ||
| | cp ${src} ${basename}.txt | ||
| | sort ${src} > ${basename}.sorted.txt | ||
| | >>> | ||
| | output { | ||
| | File outf = "${basename}.txt" | ||
| | File outf_sorted = "${basename}.sorted.txt" | ||
| | } | ||
| |} | ||
| | | ||
| | | ||
| |workflow files { | ||
| | File f | ||
| | | ||
| | call Copy { input : src=f, basename="tearFrog" } | ||
| | call Copy as Copy2 { input : src=Copy.outf, basename="mixing" } | ||
| | | ||
| | output { | ||
| | Copy2.outf_sorted | ||
| | } | ||
| |} | ||
| |""".stripMargin | ||
|
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| it should "correctly evaluate Strings and File types" in { | ||
| val ns = WdlNamespaceWithWorkflow.load(wdlCode2, Seq.empty).get | ||
| val wf = ns.workflow | ||
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| val copy2call:WdlCall = wf.findCallByName("Copy2") match { | ||
| case None => throw new Exception(s"Call Add not found in WDL file") | ||
| case Some(call) => call | ||
| } | ||
|
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| val e1 = copy2call.inputMappings("src") | ||
| val t1 = evalType(e1, copy2call) | ||
| t1 should equal(Success(WomFileType)) | ||
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| val e2 = copy2call.inputMappings("basename") | ||
| val t2 = evalType(e2, copy2call) | ||
| t2 should equal(Success(WomStringType)) | ||
| } | ||
|
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| val wdlCode3 = | ||
| """| | ||
| |task Inc { | ||
| | Int i | ||
| | | ||
| | command <<< | ||
| | python -c "print(${i} + 1)" | ||
| | >>> | ||
| | output { | ||
| | Int result = read_int(stdout()) | ||
| | } | ||
| |} | ||
| | | ||
| |task Mod7 { | ||
| | Int i | ||
| | | ||
| | command <<< | ||
| | python -c "print(${i} % 7)" | ||
| | >>> | ||
| | output { | ||
| | Int result = read_int(stdout()) | ||
| | } | ||
| |} | ||
| | | ||
| |workflow math { | ||
| | Int n = 5 | ||
| | | ||
| | scatter (k in range(length(n))) { | ||
| | call Mod7 {input: i=k} | ||
| | } | ||
| | | ||
| | scatter (k in Mod7.result) { | ||
| | call Inc {input: i=k} | ||
| | } | ||
| | | ||
| | output { | ||
| | Inc.result | ||
| | } | ||
| |} | ||
| |""".stripMargin | ||
|
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| it should "take context into account" in { | ||
| val ns = WdlNamespaceWithWorkflow.load(wdlCode3, Seq.empty).get | ||
| val wf = ns.workflow | ||
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| val incCall:WdlCall = wf.findCallByName("Inc") match { | ||
| case None => throw new Exception(s"Call Add not found in WDL file") | ||
| case Some(call) => call | ||
| } | ||
|
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| val e1 = incCall.inputMappings("i") | ||
| val t1 = evalType(e1, incCall) | ||
| t1 should equal(Success(WomIntegerType)) | ||
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| val output = wf.outputs.head | ||
| val e2 = output.requiredExpression | ||
| val t2 = evalType(e2, wf) | ||
| t2 should equal(Success(WomMaybeEmptyArrayType(WomIntegerType))) | ||
| } | ||
| } |
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