From 9e5f2608cb8cfb76e5f1f54da57710ba38a78e2a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 7 Oct 2014 00:42:18 +0200
Subject: [PATCH] Improve main command line interface
---
.../sasc/biopet/core/BiopetExecutable.scala | 81 ++++++++++++++++---
.../sasc/biopet/core/PipelineCommand.scala | 3 +-
.../lumc/sasc/biopet/core/ToolCommand.scala | 12 +++
3 files changed, 81 insertions(+), 15 deletions(-)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index f1cd08b71..b71c87f12 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -15,7 +15,7 @@ import nl.lumc.sasc.biopet.pipelines.sage.Sage
object BiopetExecutable {
- val pipelines: Map[String,PipelineCommand] = Map(
+ val pipelines: Map[String, PipelineCommand] = Map(
"flexiprep" -> Flexiprep,
"mapping" -> Mapping,
"gentrap" -> Gentrap,
@@ -29,25 +29,80 @@ object BiopetExecutable {
"sage" -> Sage,
"basty" -> Basty
)
-
+
+ val tools: Map[String, ToolCommand] = Map(
+ )
+
/**
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
+
+ def toBulletedList(m: Map[String, Any], kind: String = "", bullet: String = "-") =
+ "Available %s:\n ".format(kind) + bullet + " " +
+ m.keys.toVector.sorted.mkString("\n " + bullet + " ")
+
+ lazy val pipelineList: String = toBulletedList(pipelines, "pipelines")
+
+ lazy val toolList: String = toBulletedList(tools, "tools")
+
+ lazy val addendum: String =
+ """Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git"""".stripMargin
+
+ lazy val baseUsage: String =
+ """
+ |Usage: java -jar BiopetFramework.jar {pipeline,tool} {pipeline/tool name} {pipeline/tool-specific options}
+ |
+ |%s
+ |
+ |%s
+ """.stripMargin.format("%s", addendum)
+
+ lazy val mainUsage: String =
+ baseUsage.format(pipelineList + "\n\n" + toolList)
+
+ lazy val pipelineUsage: String = baseUsage
+ .replaceFirst("""\{pipeline,tool\}""", "pipeline")
+ .replace("""pipeline/tool""", "pipeline")
+ .format(pipelineList)
+
+ lazy val toolUsage: String = baseUsage
+ .replaceFirst("""\{pipeline,tool\}""", "tool")
+ .replace("""pipeline/tool""", "tool")
+ .format(toolList)
+
if (args.isEmpty) {
- System.err.println(pipelineList)
+ System.err.println(mainUsage)
System.exit(1)
}
- else if (pipelines.contains(args.head)) pipelines(args.head).main(args.tail)
- else {
- System.err.println("Pipeline '" + args.head + "' does not exist")
- System.err.println(pipelineList)
- System.exit(1)
- }
-
- def pipelineList: String = {
- val pipelinesArray = for ((k,v) <- pipelines) yield k
- "Available pipelines:" + pipelinesArray.mkString("\n- ", "\n- ", "\n") + "please supply a valid pipeline"
+
+ args match {
+ case Array("pipeline", pipelineName, pipelineArgs @ _*) =>
+ if (pipelines.contains(pipelineName))
+ if (pipelineArgs.isEmpty)
+ pipelines(pipelineName).main(Array("--help"))
+ else
+ pipelines(pipelineName).main(pipelineArgs.toArray)
+ else
+ System.err.println(s"ERROR: pipeline '$pipelineName' does not exist")
+ System.err.println(pipelineUsage)
+ System.exit(1)
+ case Array("pipeline") =>
+ System.err.println(pipelineUsage)
+ System.exit(1)
+ case Array("tool", toolName, toolArgs @ _*) =>
+ if (tools.contains(toolName))
+ tools(toolName).main(toolArgs.toArray)
+ else
+ System.err.println(s"ERROR: tool '$toolName' does not exist")
+ System.err.println(toolUsage)
+ System.exit(1)
+ case Array("tool") =>
+ System.err.println(toolUsage)
+ System.exit(1)
+ case _ =>
+ println(mainUsage)
+ System.exit(1)
}
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 45c689886..7279704ea 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -7,9 +7,8 @@ trait PipelineCommand extends Logging {
def main(args: Array[String]): Unit = {
var argv: Array[String] = Array()
- //argv ++= Array("-S", tempFile.getAbsolutePath)
argv ++= Array("-S", pipeline)
argv ++= args
- return BiopetQCommandLine.main(argv)
+ BiopetQCommandLine.main(argv)
}
}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
new file mode 100644
index 000000000..af55981e7
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -0,0 +1,12 @@
+package nl.lumc.sasc.biopet.core
+
+import org.broadinstitute.gatk.queue.util.Logging
+
+
+abstract trait ToolCommand extends Logging {
+
+ lazy val toolName = this.getClass.getName
+ .split("\\$").last.split("\\.").last
+
+ def main(args: Array[String])
+}
--
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