finished docopt proxy impl

Author: holgerbrandl

src/main/kotlin/kscript/DocOpt.kt

@@ -12,18 +12,24 @@ import java.io.File
 /** Simple Kotlin facade for org.docopt.Docopt.Docopt(java.lang.String) .*/
 class DocOpt(args: Array<String>, val usage: String) {
 
-    val myDO by lazy {
-        Docopt(usage).parse(args.toList()).map {
-            it.key.removePrefix("--").replace("[<>]".toRegex(), "") to it.value?.toString()
+    val docopt = Docopt(usage)
+
+    private val myDO by lazy {
+        docopt.parse(args.toList()).map {
+            it.key.removePrefix("--").replace("[<>]".toRegex(), "") to it.value
         }.toMap()
     }
 
-    fun getString(key: String) = myDO[key]!!
-    fun getStrings(key: String) = myDO[key]!!
+    fun getString(key: String) = myDO[key]!!.toString()
+    fun getStrings(key: String) = (myDO[key]!! as List<*>).map { it as String }
+
+    fun getFile(key: String) = File(getString(key))
+    fun getFiles(key: String) = getStrings(key).map { File(it) }
+
 
-    fun getInt(key: String) = myDO[key]!!.toInt()
+    fun getInt(key: String) = myDO[key]!!.toString().toInt()
 
-    fun getNumber(key: String) = myDO[key]!!.toFloat()
+    fun getNumber(key: String) = myDO[key]!!.toString().toFloat()
 
-    fun getBoolean(key: String) = myDO[key]!!.toBoolean()
+    fun getBoolean(key: String) = myDO[key]!!.toString().toBoolean()
 }

src/main/kotlin/kscript/StreamUtil.kt

@@ -3,7 +3,6 @@ package kscript
 import java.io.BufferedReader
 import java.io.File
 import java.io.FileReader
-import kotlin.system.exitProcess
 
 
 // for top-level vs member extensions see https://kotlinlang.org/docs/reference/extensions.html#scope-of-extensions
@@ -20,18 +19,16 @@ fun argLines(arg: String, stdinNames: List<String> = listOf("-", "stdin")): Sequ
 
     stopIfNot(inputFile.canRead()) { "Can not read from '${arg}'" }
 
-    // not we don't close the buffer with this approach
+    // todo we don't close the buffer with this approach
     //    BufferedReader(FileReader(inputFile )).use { return it }
     return BufferedReader(FileReader(inputFile)).lineSequence()
 }
 
+fun mapLines(arg: String, stdinNames: List<String> = listOf("-", "stdin"), trafo: (String) -> String) =
+        argLines(arg, stdinNames).map { trafo(it) }.print()
 
-
-fun Sequence<String>.print() = forEach { println(it) }
+fun filterLines(arg: String, stdinNames: List<String> = listOf("-", "stdin"), trafo: (String) -> Boolean) =
+        argLines(arg, stdinNames).filter { trafo(it) }.print()
 
 
-fun processStdin(trafo: (String) -> String) {
-    generateSequence() { readLine() }.map {
-        println(trafo(it))
-    }
-}
+fun Sequence<String>.print() = forEach { println(it) }

src/main/kotlin/kscript/Support.kt

@@ -6,10 +6,8 @@ import kotlin.system.exitProcess
  * @author Holger Brandl
  */
 
-
-fun foo() = "1"
-
-public inline fun stopIfNot(value: Boolean, lazyMessage: () -> Any) {
+/** Similar to require but without a stacktrace. */
+inline fun stopIfNot(value: Boolean, lazyMessage: () -> Any) {
     if (!value) {
         System.err.println("[ERROR] " + lazyMessage().toString())
         exitProcess(1)

src/main/kotlin/kscript/experimental/Incubator.kt

@@ -18,3 +18,10 @@ fun <T> File.mapLines(trafo: (String) -> T) {
 fun String.processLines(trafo: (String) -> String) {
     split("\n").map { println(trafo(it)) }
 }
+
+
+fun processStdin(trafo: (String) -> String) {
+    generateSequence() { readLine() }.map {
+        println(trafo(it))
+    }
+}

src/test/kotlin/kscript/test/DocOptTest.kt

@@ -3,6 +3,7 @@ package kscript.test
 import io.kotlintest.matchers.shouldBe
 import io.kotlintest.specs.StringSpec
 import kscript.DocOpt
+import java.io.File
 
 /**
  * @author Holger Brandl
@@ -11,27 +12,37 @@ import kscript.DocOpt
 
 class DocOptTest : StringSpec() { init {
 
-    val args = "-n 7 --pc-only --gtf my.gtf a.fastq b.fastq".split(" ").toTypedArray()
 
     val usage = """
 Use star to align fastq files against a genome
 Usage: star_align.kts [options] <igenome> <fastq_files>...
 
 Options:
- --gtf <gtfFile>        Custom gtf file instead of igenome bundled copy
- --pc-only              Use protein coding genes only for mapping and quantification
- -n --num-fragments     Fragment count used for processing [default: 5]
+ --gtf <gtfFile>                   Custom gtf file instead of igenome bundled copy
+ --pc-only                         Use protein coding genes only for mapping and quantification
+ -n --num-fragments <num_frags>    Fragment count used for processing [default: 5]
 """
 
+    val args = "-n 7 --pc-only --gtf my.gtf genome.fasta a.fastq b.fastq".split(" ").toTypedArray()
+
+
     val docopt = DocOpt(args, usage)
 
+
+    // optional arg
     docopt.getString("gtf") shouldBe "my.gtf"
-    docopt.getStrings("fastq_files") shouldBe arrayOf("a.fastq", "b.fastq")
+    docopt.getFile("gtf") shouldBe File("my.gtf")
+
+    // mandatory arg
+    docopt.getString("igenome") shouldBe "genome.fasta"
+    docopt.getFile("igenome") shouldBe File("genome.fasta")
+
+    docopt.getStrings("fastq_files") shouldBe listOf("a.fastq", "b.fastq")
+    docopt.getFiles("fastq_files") shouldBe listOf(File("a.fastq"), File("b.fastq"))
+
 
-    docopt.getInt("fastq_files")
-    docopt.getNumber("num-fragments") shouldBe 7
-    docopt.getNumber("num-fragments") shouldBe 7
-    docopt.getNumber("-n")
+    docopt.getInt("num-fragments") shouldBe 7
+    docopt.getNumber("num-fragments").toString() shouldBe "7.0"
     docopt.getBoolean("pc-only") shouldBe true
 }
 }