patvars

backend/src/main/scala/cromwell/backend/standard/callcaching/StandardFileHashingActor.scala

@@ -72,11 +72,11 @@ abstract class StandardFileHashingActor(standardParams: StandardFileHashingActor
       }
 
     // Hash Success
-    case (fileHashRequest: SingleFileHashRequest, response @ IoSuccess(_, result: String)) =>
+    case (fileHashRequest: SingleFileHashRequest, IoSuccess(_, result: String)) =>
       context.parent ! FileHashResponse(HashResult(fileHashRequest.hashKey, HashValue(result)))
 
     // Hash Failure
-    case (fileHashRequest: SingleFileHashRequest, response @ IoFailure(_, failure: Throwable)) =>
+    case (fileHashRequest: SingleFileHashRequest, IoFailure(_, failure: Throwable)) =>
       context.parent ! HashingFailedMessage(fileHashRequest.file.value, failure)
 
     case other =>

backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala

@@ -37,7 +37,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateDocker(dockerValue,
         "Failed to get Docker mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get Docker mandatory key from runtime attributes")
       }
     }
@@ -47,7 +47,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateDocker(dockerValue,
         "Failed to get Docker mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting docker runtime attribute to be a String")
       }
     }
@@ -87,7 +87,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateFailOnStderr(failOnStderrValue,
         "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
       }
     }
@@ -146,7 +146,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
         "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) =>
           assert(e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
       }
@@ -167,7 +167,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
         "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
       }
     }
@@ -197,7 +197,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(memoryValue,
         "Failed to get memory mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute value greater than 0 but got -1")
       }
     }
@@ -218,7 +218,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(memoryValue,
         "Failed to get memory mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute value greater than 0 but got 0.0")
       }
     }
@@ -228,7 +228,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(memoryValue,
         "Failed to get memory mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: value should be of the form 'X Unit' where X is a number, e.g. 8 GB")
       }
     }
@@ -238,7 +238,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(memoryValue,
         "Failed to get memory mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: Not supported WDL type value")
       }
     }
@@ -248,7 +248,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(memoryValue,
         "Failed to get memory mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get memory mandatory key from runtime attributes")
       }
     }
@@ -268,7 +268,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateCpu(cpuValue,
         "Failed to get cpu mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting cpu runtime attribute value greater than 0")
       }
     }
@@ -278,7 +278,7 @@ class RuntimeAttributesValidationSpec extends WordSpecLike with Matchers with Be
       val result = RuntimeAttributesValidation.validateMemory(cpuValue,
         "Failed to get cpu mandatory key from runtime attributes".invalidNel)
       result match {
-        case Valid(x) => fail("A failure was expected.")
+        case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get cpu mandatory key from runtime attributes")
       }
     }

backend/src/test/scala/cromwell/backend/wdl/FileSizeSpec.scala

@@ -73,16 +73,16 @@ class FileSizeSpec extends FlatSpec with Matchers {
 
     def testOver() = {
       testInner(n + 1, {
-        case Failure(s: FileSizeTooBig) => //success
+        case Failure(_: FileSizeTooBig) => //success
         case t => throw new RuntimeException(s"should not have eaten this file that is too big! msg: $t")
       })
     }
 
     def testUnder() = {
       testInner(n - 1, {
         case Success(_) =>
-        case Failure(nfe: NumberFormatException) => //we're not testing parsing
-        case Failure(uoe: UnsupportedOperationException) => //we're not testing tsv compatibility
+        case Failure(_: NumberFormatException) => //we're not testing parsing
+        case Failure(_: UnsupportedOperationException) => //we're not testing tsv compatibility
         case Failure(t) => throw t
       })
     }

core/src/main/scala/cromwell/core/ConfigUtil.scala

@@ -37,14 +37,14 @@ object ConfigUtil {
     def validateString(key: String): ValidatedNel[String, String] = try {
       config.getString(key).validNel
     } catch {
-      case e: ConfigException.Missing => s"Could not find key: $key".invalidNel
+      case _: ConfigException.Missing => s"Could not find key: $key".invalidNel
     }
 
     def validateConfig(key: String): ValidatedNel[String, Config] = try {
       config.getConfig(key).validNel
     } catch {
-      case e: ConfigException.Missing => s"Could not find key: $key".invalidNel
-      case e: ConfigException.WrongType => s"key $key cannot be parsed to a Config".invalidNel
+      case _: ConfigException.Missing => s"Could not find key: $key".invalidNel
+      case _: ConfigException.WrongType => s"key $key cannot be parsed to a Config".invalidNel
     }
 
   }

core/src/main/scala/cromwell/core/CromwellUserGuardianStrategy.scala

@@ -5,7 +5,7 @@ import akka.actor.{ActorInitializationException, OneForOneStrategy, SupervisorSt
 
 class CromwellUserGuardianStrategy extends SupervisorStrategyConfigurator {
   override def create(): SupervisorStrategy = OneForOneStrategy() {
-    case aie: ActorInitializationException => Escalate
+    case _: ActorInitializationException => Escalate
     case t => akka.actor.SupervisorStrategy.defaultDecider.applyOrElse(t, (_: Any) => Escalate)
   }
 }

core/src/main/scala/cromwell/core/WorkflowOptions.scala

@@ -152,7 +152,7 @@ case class WorkflowOptions(jsObject: JsObject) {
   }
 
   lazy val defaultRuntimeOptions = jsObject.fields.get(defaultRuntimeOptionKey) match {
-    case Some(jsObj: JsObject) => TryUtil.sequenceMap(jsObj.fields map { case (k, v) => k -> WorkflowOptions.getAsJson(k, jsObj) })
+    case Some(jsObj: JsObject) => TryUtil.sequenceMap(jsObj.fields map { case (k, _) => k -> WorkflowOptions.getAsJson(k, jsObj) })
     case Some(jsVal) => Failure(new IllegalArgumentException(s"Unsupported JsValue for $defaultRuntimeOptionKey: $jsVal. Expected a JSON object."))
     case None => Failure(OptionNotFoundException(s"Cannot find definition for default runtime attributes"))
   }

core/src/main/scala/cromwell/core/actor/StreamActorHelper.scala

@@ -71,14 +71,14 @@ trait StreamActorHelper[T <: StreamContext] { this: Actor with ActorLogging =>
   }
 
   private def streamReceive: Receive = {
-    case EnqueueResponse(Enqueued, commandContext: T @unchecked) => // Good !
+    case EnqueueResponse(Enqueued, _: T @unchecked) => // Good !
     case EnqueueResponse(Dropped, commandContext) => backpressure(commandContext)
       
       // In any of the cases below, the stream is in a failed state, which will be caught by the watchCompletion hook and the
       // actor will be restarted
     case EnqueueResponse(QueueClosed, commandContext) => backpressure(commandContext)
-    case EnqueueResponse(QueueOfferResult.Failure(failure), commandContext) => backpressure(commandContext)
-    case FailedToEnqueue(throwable, commandContext) => backpressure(commandContext)
+    case EnqueueResponse(QueueOfferResult.Failure(_), commandContext) => backpressure(commandContext)
+    case FailedToEnqueue(_, commandContext) => backpressure(commandContext)
       
       // Those 2 cases should never happen, as long as the strategy is Resume, but in case it does...
     case StreamCompleted => restart(new IllegalStateException("Stream was completed unexpectedly"))

core/src/main/scala/cromwell/core/simpleton/WdlValueBuilder.scala

@@ -88,7 +88,7 @@ object WdlValueBuilder {
 
     // Group tuples by key using a Map with key type `K`.
     def group[K](tuples: Traversable[(K, SimpletonComponent)]): Map[K, Traversable[SimpletonComponent]] = {
-      tuples groupBy { case (i, _) => i } mapValues { _ map { case (i, s) => s} }
+      tuples groupBy { case (i, _) => i } mapValues { _ map { case (_, s) => s} }
     }
 
     outputType match {

core/src/test/scala/cromwell/core/simpleton/WdlValueBuilderSpec.scala

@@ -115,9 +115,9 @@ class WdlValueBuilderSpec extends FlatSpec with Matchers with Mockito {
 
   it should "round trip everything together with no losses" in {
 
-    val wdlValues = (simpletonConversions map { case SimpletonConversion(name, wdlValue, simpletons) => name -> wdlValue }).toMap
+    val wdlValues = (simpletonConversions map { case SimpletonConversion(name, wdlValue, _) => name -> wdlValue }).toMap
     val taskOutputs = wdlValues map { case (k, wv) => TaskOutput(k, wv.wdlType, IgnoredExpression, mock[Ast], None) }
-    val allSimpletons = simpletonConversions flatMap { case SimpletonConversion(name, wdlValue, simpletons) => simpletons }
+    val allSimpletons = simpletonConversions flatMap { case SimpletonConversion(_, _, simpletons) => simpletons }
 
     import WdlValueSimpleton._
 

core/src/test/scala/cromwell/util/AkkaTestUtil.scala

@@ -8,7 +8,7 @@ object AkkaTestUtil {
   implicit class EnhancedTestProbe(probe: TestProbe) {
     def props = Props(new Actor with ActorLogging {
       def receive = {
-        case outbound if sender == probe.ref =>
+        case outbound @ _ if sender == probe.ref =>
           val msg = "Unexpected outbound message from Probe. You're doing something wrong!"
           log.error(msg)
           throw new RuntimeException(msg)

database/migration/src/main/scala/cromwell/database/migration/WdlTransformation.scala

@@ -18,7 +18,7 @@ private [migration] object WdlTransformation {
       case None => null
     }
   } recover {
-    case e: IOException => value
+    case _: IOException => value
   }
 
   def coerceStringToWdl(wdlString: String, wdlType: WdlType) = wdlType match {

database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala

@@ -44,10 +44,10 @@ class MetadataStatementForWorkflow(preparedStatement: PreparedStatement, workflo
 
   private def metadataType(value: Any) = {
     value match {
-      case WdlInteger(i) => "int"
-      case WdlFloat(f) => "number"
-      case WdlBoolean(b) => "boolean"
-      case value: WdlValue => "string"
+      case WdlInteger(_) => "int"
+      case WdlFloat(_) => "number"
+      case WdlBoolean(_) => "boolean"
+      case _: WdlValue => "string"
       case _: Int | Long => "int"
       case _: Double | Float => "number"
       case _: Boolean => "boolean"

database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala

@@ -49,7 +49,7 @@ trait SymbolTableMigration extends BatchedTaskChange {
       wdlType <- Try(WdlType.fromWdlString(row.getString("WDL_TYPE")))
       inflated <- row.getString("WDL_VALUE") match {
         case null => Success("") // Empty Strings are null in the DB
-        case nonNull => inflate(row.getString("WDL_VALUE"))
+        case nonNull @ _ => inflate(row.getString("WDL_VALUE"))
       }
     } yield WdlTransformation.coerceStringToWdl(inflated, wdlType)
 

database/migration/src/main/scala/cromwell/database/migration/restart/table/JobStoreSimpletonMigration.scala

@@ -51,7 +51,7 @@ class JobStoreSimpletonMigration extends AbstractRestartMigration {
 
     def buildJobStoreSimpletonEntries(name: String, wdlValue: WdlValue, wdlType: WdlType) = Option(wdlValue) match {
       case None => List(JobStoreSimpletonEntry(name, null, wdlType.toWdlString))
-      case Some(v) => wdlValue.simplify(name) map { s =>
+      case Some(_) => wdlValue.simplify(name) map { s =>
         JobStoreSimpletonEntry(s.simpletonKey, s.simpletonValue.valueString, s.simpletonValue.wdlType.toWdlString)
       }
     }

dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/FlowUtils.scala

@@ -17,8 +17,8 @@ object FlowUtils {
     import GraphDSL.Implicits._
 
     val partition = builder.add(Partition[(Try[T], U)](2, {
-      case (Success(v), _) => 0
-      case (Failure(f), _) => 1
+      case (Success(_), _) => 0
+      case (Failure(_), _) => 1
     }))
 
     val successOut: PortOps[(T, U)] = partition.out(0) collect {

dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/HttpFlowWithRetry.scala

@@ -25,7 +25,7 @@ object HttpFlowWithRetry {
       case StatusCodes.BadGateway => true
       case StatusCodes.GatewayTimeout => true
       case StatusCodes.RequestTimeout => true
-      case other => isTransient(response)
+      case other @ _ => isTransient(response)
     }
   }
 
@@ -100,7 +100,7 @@ case class HttpFlowWithRetry[T](
       // Successful return code
       case (httpResponse, flowContext) if httpResponse.status.isSuccess() || !shouldRetry(httpResponse, flowContext) => 0
       // Failed return code but retryable
-      case (httpResponse, flowContext) => 1
+      case (_, _) => 1
     }))
     
     // Merges requests coming from 3 input ports:

dockerHashing/src/test/scala/cromwell/docker/DockerHashMocks.scala

@@ -13,7 +13,7 @@ class HttpMock[T](responses: MockHttpResponse*) {
   private var responsesLeft = responses.toBuffer
   
   private def nextResponse(value: (HttpRequest, ContextWithRequest[T])): (Try[HttpResponse], ContextWithRequest[T]) = value match {
-    case (request, context) =>
+    case (request @ _, context) =>
       responsesLeft.headOption match {
         case Some(mockResponse) =>
           if (mockResponse.nb > 1)

engine/src/main/scala/cromwell/engine/io/IoActor.scala

@@ -44,8 +44,8 @@ final class IoActor(queueSize: Int, throttle: Option[Throttle])(implicit val mat
     
     // Partitions requests between gcs batch, and single nio requests
     val batchPartitioner = builder.add(Partition[IoCommandContext[_]](2, {
-      case gcsBatch: GcsBatchCommandContext[_, _] => 0
-      case other => 1
+      case _: GcsBatchCommandContext[_, _] => 0
+      case other @ _ => 1
     }))
     
     // Sub flow for batched gcs requests

engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala

@@ -206,7 +206,7 @@ class WorkflowActor(val workflowId: WorkflowId,
       pushWorkflowStart(workflowId)
       actor ! MaterializeWorkflowDescriptorCommand(workflowSourceFilesCollection, conf)
       goto(MaterializingWorkflowDescriptorState) using stateData.copy(currentLifecycleStateActor = Option(actor))
-    case Event(AbortWorkflowCommand, stateData) => goto(WorkflowAbortedState)
+    case Event(AbortWorkflowCommand, _) => goto(WorkflowAbortedState)
   }
 
   when(MaterializingWorkflowDescriptorState) {
@@ -217,7 +217,7 @@ class WorkflowActor(val workflowId: WorkflowId,
       goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
     case Event(MaterializeWorkflowDescriptorFailureResponse(reason: Throwable), data) =>
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason))))
-    case Event(AbortWorkflowCommand, stateData) =>
+    case Event(AbortWorkflowCommand, _) =>
       // No lifecycle sub-actors exist yet, so no indirection via WorkflowAbortingState is necessary:
       goto(WorkflowAbortedState)
   }
@@ -274,7 +274,7 @@ class WorkflowActor(val workflowId: WorkflowId,
   }
 
   when(WorkflowAbortingState) {
-    case Event(x: EngineLifecycleStateCompleteResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
+    case Event(_: EngineLifecycleStateCompleteResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, Map.empty, failures = None)
     case _ => stay()
   }

engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowFinalizationActor.scala

@@ -112,7 +112,7 @@ case class WorkflowFinalizationActor(workflowIdForLogging: WorkflowId,
     jobExecutionMap map {
       case (wd, executedKeys) => wd -> (executedKeys filter { jobKey => calls.contains(jobKey.call) })
     } filter {
-      case (wd, keys) => keys.nonEmpty
+      case (_, keys) => keys.nonEmpty
     }
   }
 

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStore.scala

@@ -142,7 +142,7 @@ final case class ExecutionStore(private val statusStore: Map[JobKey, ExecutionSt
         * NOTE: this algorithm was designed for ONE-LEVEL of scattering and probably does not
         * work as-is for nested scatter blocks
         */
-      case Some(ancestor: Scatter) => doneKeys.contains(prerequisiteScope.fullyQualifiedName -> entry.index)
+      case Some(_: Scatter) => doneKeys.contains(prerequisiteScope.fullyQualifiedName -> entry.index)
 
       /*
         * Otherwise, simply refer to the collector entry.  This means that 'entry' depends

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/OutputStore.scala

@@ -42,7 +42,7 @@ case class OutputStore(store: Map[OutputCallKey, List[OutputEntry]]) {
     
     def declarationOutputs(declaration: Declaration, outputs: List[OutputEntry]) = {
       outputs match {
-        case OutputEntry(name, _, Some(value)) :: Nil => Success(value)
+        case OutputEntry(_, _, Some(value)) :: Nil => Success(value)
         case _ => Failure(new RuntimeException(s"Could not find value for declaration ${declaration.fullyQualifiedName}"))
       }
     }