93 lines
3.1 KiB
Scala
93 lines
3.1 KiB
Scala
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package org.broadinstitute.sting.queue.function
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import java.io.File
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import org.broadinstitute.sting.queue.util._
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import org.broadinstitute.sting.queue.engine.{CommandLineRunner, QGraph}
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trait CommandLineFunction extends QFunction with DispatchFunction {
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/**
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* The command line to run locally or via grid computing.
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*/
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def commandLine: String
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/**
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* The directory where the command should run.
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*/
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@Internal
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var commandDirectory: File = new File(".")
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/**
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* Repeats parameters with a prefix/suffix if they are set otherwise returns "".
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* Skips null, Nil, None. Unwraps Some(x) to x. Everything else is called with x.toString.
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*/
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protected def repeat(prefix: String, params: Seq[_], suffix: String = "", separator: String = "") =
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params.filter(param => hasValue(param)).map(param => prefix + toValue(param) + suffix).mkString(separator)
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/**
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* Returns parameter with a prefix/suffix if it is set otherwise returns "".
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* Does not output null, Nil, None. Unwraps Some(x) to x. Everything else is called with x.toString.
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*/
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protected def optional(prefix: String, param: Any, suffix: String = "") =
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if (hasValue(param)) prefix + toValue(param) + suffix else ""
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/**
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* Sets a field value using the name of the field.
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* Field must be annotated with @Input, @Output, or @Internal
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* @returns true if the value was found and set
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*/
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def setValue(name: String, value: String) = {
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ReflectionUtils.getField(this, name) match {
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case Some(field) =>
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val isInput = ReflectionUtils.hasAnnotation(field, classOf[Input])
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val isOutput = ReflectionUtils.hasAnnotation(field, classOf[Output])
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val isInternal = ReflectionUtils.hasAnnotation(field, classOf[Internal])
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if (isInput || isOutput || isInternal) {
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ReflectionUtils.setValue(this, field, value)
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}
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true
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case None => false
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}
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}
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private lazy val fields = ReflectionUtils.getAllFields(this.getClass)
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private def internals = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Internal])
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def inputs = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Input])
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def outputs = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Output])
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override def missingValues = {
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val missingInputs = missingFields(inputs)
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val missingOutputs = missingFields(outputs)
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missingInputs | missingOutputs
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}
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private def missingFields(fields: Map[String, Any]) = {
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var missing = Set.empty[String]
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for ((name, value) <- fields) {
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val isOptional = ReflectionUtils.getField(this, name) match {
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case Some(field) => ReflectionUtils.hasAnnotation(field, classOf[Optional])
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case None => false
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}
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if (!isOptional)
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if (!hasValue(value))
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missing += name
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}
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missing
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}
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private def hasValue(param: Any) = param match {
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case null => false
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case Nil => false
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case None => false
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case _ => true
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}
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private def toValue(param: Any): String = param match {
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case null => ""
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case Nil => ""
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case None => ""
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case Some(x) => x.toString
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case x => x.toString
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}
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}
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