Working version of ParseSamples

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ParseSamples.scala

@@ -3,72 +3,44 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import nl.lumc.sasc.biopet.core.ToolCommand
 import scala.io.Source
-import java.io.PrintWriter
-import argonaut._, Argonaut._
+import nl.lumc.sasc.biopet.core.config.Config
 
 object ParseSamples extends ToolCommand {
-  case class Args(librariesTsv: File = null) extends AbstractArgs
+  case class Args(inputFiles: List[File] = Nil) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('i', "librariesTsv") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
-      c.copy(librariesTsv = x)
-    } text ("output file, default to stdout")
+    opt[File]('i', "inputFiles") required () unbounded () valueName ("<file>") action { (x, c) =>
+      c.copy(inputFiles = x :: c.inputFiles)
+    } text ("Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed")
   }
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
     val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
 
-    // Libraries tsv
-    val reader = Source.fromFile(commandArgs.librariesTsv)
-    val lines = reader.getLines.toList
-    val header = lines.head.split("\t")
-    val sampleColumn = header.indexOf("sample")
-    val libraryColumn = header.indexOf("library")
-    if (sampleColumn == -1) throw new IllegalStateException("sample column does not exist in: " + commandArgs.librariesTsv)
-    if (libraryColumn == -1) throw new IllegalStateException("library column does not exist in: " + commandArgs.librariesTsv)
-
-    val librariesValues = (for (tsvLine <- lines.tail) yield {
-      val values = tsvLine.split("\t")
-      val sample = values(sampleColumn)
-      val library = values(libraryColumn)
-      val libraryValues = (for (t <- 0 until values.size if t != sampleColumn if t != libraryColumn) yield (header(t) -> values(t))).toMap
-      ((sample, library) -> libraryValues)
-    }).toMap
-
-    for (((sample, library), values) <- librariesValues) {
-      println("sample=" + sample + ", library=" + library + " = " + values)
-      // format: OFF
-      val summary =
-        ("samples" := (sample :=
-          ("libraries" := (library := (
-            jEmptyObject)) ->: jEmptyObject)->: jEmptyObject) ->: jEmptyObject) ->: jEmptyObject
-      // format: ON
-      val summeryText = summary.spaces2
-      println(summeryText)
-      //logger.debug("\n" + summeryText)
-      //val writer = new PrintWriter(out)
-      //writer.write(summeryText)
-      //writer.close()
-      //logger.debug("Stop")
-    }
-
-    def getSampleJson(sample: String): Json = {
-      val libraries = (for (((s, l), values) <- librariesValues if s == sample) yield getLibraryJson(sample, l)).toList
-      (sample := libraries) ->: jEmptyObject
-    }
-
-    def getLibraryJson(sample: String, library: String): Json = {
-      (library := "bla") ->: jEmptyObject
+    val fileMaps = for (inputFile <- commandArgs.inputFiles) yield {
+      val reader = Source.fromFile(inputFile)
+      val lines = reader.getLines.toList
+      val header = lines.head.split("\t")
+      val sampleColumn = header.indexOf("sample")
+      val libraryColumn = header.indexOf("library")
+      if (sampleColumn == -1) throw new IllegalStateException("sample column does not exist in: " + inputFile)
+
+      val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
+        val values = tsvLine.split("\t")
+        val sample = values(sampleColumn)
+        val library = if (libraryColumn != -1) values(libraryColumn) else null
+        val valuesMap = (for (t <- 0 until values.size if t != sampleColumn if t != libraryColumn) yield (header(t) -> values(t))).toMap
+        val map: Map[String, Any] = if (library != null) {
+          Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
+        } else {
+          Map("samples" -> Map(sample -> valuesMap))
+        }
+        map
+      }
+      librariesValues.foldLeft(Map[String, Any]())((acc, kv) => Config.mergeMaps(acc, kv))
     }
-
-    val samples = (for (((s, l), values) <- librariesValues) yield s).toSet
-
-    val samplesJson = (for (s <- samples) yield getSampleJson(s))
-
-    val summary = ("samples" := samplesJson) ->: jEmptyObject
-
-    println(summary.spaces2)
-
+    val map = fileMaps.foldLeft(Map[String, Any]())((acc, kv) => Config.mergeMaps(acc, kv))
+    val json = Config.mapToJson(map)
+    println(json.spaces2)
   }
-
 }