Tweaked command line interface.

Author: balhoff

README.md

@@ -14,6 +14,8 @@ Development versions of pxftools may depend on the latest snapshot version of th
 
 ## Running
 
+You can download a prepackaged [release](https://github.com/phenopackets/pxftools/releases).
+
 To build the command-line executable, run:
 
 `sbt stage`
@@ -34,16 +36,19 @@ Usage
 
 Options
 
-   --format=STRING : Output format. Set the output format to one of:
-                     yaml
-                     json
-                     turtle
-   --out=STRING    : Output file. Omit to write to standard out.
+   --informat=STRING  : Input format. By default both yaml and json will be attempted. Set the input format to one of:
+                        yaml
+                        json
+                        hpo-phenote
+   --out=STRING       : Output file. Omit to write to standard out.
+   --outformat=STRING : Output format. Set the output format to one of:
+                        yaml
+                        json
+                        turtle
 
 Commands
 
-   convert [command options] : Read in a PXF file and output in the specified format.
-      --in=STRING : Input file. Pass '-' or omit to read from standard in.
+   convert <infile> : Read in a PXF file and output in the specified format.
 
    merge <files> ... : Read in multiple PXF files and output as a single merged PXF file in the specified format.
 ```

build.sbt

@@ -4,7 +4,7 @@ organization  := "org.phenopackets"
 
 name          := "pxftools"
 
-version       := "0.0.2"
+version       := "0.0.3"
 
 scalaVersion  := "2.11.8"
 

src/main/scala/org/phenopackets/pxftools/command/Common.scala

@@ -30,15 +30,16 @@ trait Common extends Command {
 
   var out = opt[String](description = "Output file. Omit to write to standard out.", default = "")
 
-  var informat = opt[Option[String]](description = "Input format. By default both yaml and json will be attempted. Set the input format to one of:\nyaml\njson\nhpo-phenote")
+  var informat = opt[String](description = "Input format. By default both yaml and json will be attempted. Set the input format to one of:\nyaml\njson\nhpo-phenote", default = "guess")
   var outformat = opt[String](description = "Output format. Set the output format to one of:\nyaml\njson\nturtle", default = "yaml")
 
-  def inputReader: Option[PhenoPacketReader] = informat.map(_ match {
-    case "yaml"        => YamlReader.readInputStream
-    case "json"        => JsonReader.readInputStream
-    case "hpo-phenote" => HPOAnnotations.read
+  def inputReader: Option[PhenoPacketReader] = informat match {
+    case "yaml"        => Option(YamlReader.readInputStream)
+    case "json"        => Option(JsonReader.readInputStream)
+    case "hpo-phenote" => Option(HPOAnnotations.read)
+    case "guess"       => None
     case _             => throw new ParsingException("Invalid input format.")
-  })
+  }
 
   def outputWriter: PhenoPacketWriter = outformat match {
     case "yaml"   => YamlGenerator.render

src/main/scala/org/phenopackets/pxftools/command/SingleInput.scala

@@ -21,11 +21,12 @@ import org.phenopackets.api.io.YamlReader
 
 trait SingleInput extends Command {
 
-  var in = opt[String](description = "Input file. Pass '-' or omit to read from standard in.", default = "-")
+  var infile = arg[Option[String]](description = "Input file. Omit to read from standard in.")
 
-  def determineInput: InputStream = in match {
-    case "-" => System.in
-    case _   => new FileInputStream(new File(in))
+  def determineInput: InputStream = infile match {
+    case Some("-")      => System.in
+    case Some(filepath) => new FileInputStream(new File(filepath))
+    case None           => System.in
   }
 
 }

src/main/scala/org/phenopackets/pxftools/util/HPOAnnotations.scala

@@ -33,7 +33,9 @@ object HPOAnnotations extends LazyLogging {
   def importFromTable(table: CSVReader): PhenoPacket = {
     val packetURI = s"urn:uuid:${UUID.randomUUID.toString}"
     val packet = ResourceFactory.createResource(packetURI)
+    println(packet)
     val triples = table.iteratorWithHeaders.flatMap(rowToTriples(_, packet)).toSeq
+    println(triples)
     val model = ModelFactory.createDefaultModel()
     model.add(triples.asJava)
     RDFReader.readModel(model, packetURI)