Merge branch 'patch-versioning' into 'develop'

Patch versioning

For issue #143

See merge request !140

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

@@ -16,11 +16,13 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.{ PrintWriter, StringWriter }
-import java.util.Properties
-import nl.lumc.sasc.biopet.core.BiopetExecutable._
-import org.apache.log4j.Logger
 import scala.io.Source
 
+import org.apache.log4j.Logger
+
+import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
+import nl.lumc.sasc.biopet.core.BiopetExecutable._
+
 trait BiopetExecutable extends Logging {
 
   def pipelines: List[MainCommand]
@@ -49,7 +51,7 @@ trait BiopetExecutable extends Logging {
         u.mkString("\n\n")
       }
       """
-        |Usage   : java -jar BiopetFramework.jar {%s} <name> [args]
+        |Usage   : java -jar <path/to/biopet.jar> {%s} <name> [args]
         |Version : %s
         |
         |%s
@@ -59,7 +61,7 @@ trait BiopetExecutable extends Logging {
         |  - license
         |
         |Questions or comments? Email sasc@lumc.nl or check out the project page at https://git.lumc.nl/biopet/biopet.git
-      """.stripMargin.format(modules.keys.mkString(","), getVersion, usage)
+      """.stripMargin.format(modules.keys.mkString(","), FullVersion, usage)
     }
 
     def checkModule(module: String) {
@@ -81,7 +83,7 @@ trait BiopetExecutable extends Logging {
 
     args match {
       case Array("version") => {
-        println("version: " + getVersion)
+        println("version: " + FullVersion)
       }
       case Array("license") => {
         println(getLicense)
@@ -118,30 +120,16 @@ trait BiopetExecutable extends Logging {
     }
   }
 
-  def checkDirtyBuild(logger: Logger) {
-    val prop = new Properties()
-    prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
-    val describeShort = prop.getProperty("git.commit.id.describe-short")
-    if (describeShort.endsWith("-dirty")) {
-      logger.warn("**********************************************************")
-      logger.warn("* This JAR was built while there are uncommited changes. *")
-      logger.warn("* Reproducible results are *not* guaranteed.             *")
-      logger.warn("**********************************************************")
+  def checkDirtyBuild(logger: Logger): Unit =
+    if (LastCommitHash.endsWith("-dirty")) {
+      logger.warn("***********************************************************")
+      logger.warn("* This JAR was built while there were uncommited changes. *")
+      logger.warn("* Reproducible results are *not* guaranteed.              *")
+      logger.warn("***********************************************************")
     }
-  }
 }
 
 object BiopetExecutable {
-  def getVersion = {
-    getClass.getPackage.getImplementationVersion + " (" + getCommitHash + ")"
-  }
-
-  def getCommitHash = {
-    val prop = new Properties()
-    prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
-    prop.getProperty("git.commit.id.abbrev")
-  }
-
   def getLicense: String = {
     val stream = getClass.getClassLoader.getResourceAsStream("nl/lumc/sasc/biopet/License.txt")
     Source.fromInputStream(stream).getLines().mkString("\n", "\n", "\n")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

@@ -15,6 +15,8 @@
  */
 package nl.lumc.sasc.biopet.core
 
+import nl.lumc.sasc.biopet.FullVersion
+
 /**
  * Trait for biopet tools, sets some default args
  */
@@ -45,7 +47,7 @@ trait ToolCommand extends MainCommand with Logging {
       sys.exit(1)
     } text ("Print usage")
     opt[Unit]('v', "version") foreach { _ =>
-      System.err.println("Version: " + BiopetExecutable.getVersion)
+      System.err.println("Version: " + FullVersion)
       sys.exit(1)
     } text ("Print version")
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

@@ -45,23 +45,24 @@
 
 package nl.lumc.sasc.biopet.core.workaround
 
-import java.io.File
+import collection.JavaConversions._
+import java.io.{ File, FileOutputStream }
+import java.net.URL
+import java.util.{ ResourceBundle, Arrays }
+
+import org.apache.commons.io.FilenameUtils
 import org.broadinstitute.gatk.utils.commandline._
 import org.broadinstitute.gatk.queue.util._
 import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
-import collection.JavaConversions._
 import org.broadinstitute.gatk.utils.classloader.PluginManager
 import org.broadinstitute.gatk.utils.exceptions.UserException
 import org.broadinstitute.gatk.utils.io.IOUtils
 import org.broadinstitute.gatk.utils.help.ApplicationDetails
-import java.io.FileOutputStream
-import java.net.URL
-import java.util.{ ResourceBundle, Arrays }
 import org.broadinstitute.gatk.utils.text.TextFormattingUtils
-import org.apache.commons.io.FilenameUtils
-import nl.lumc.sasc.biopet.core.BiopetExecutable
+
+import nl.lumc.sasc.biopet.FullVersion
 
 /**
  * Entry point of Queue.  Compiles and runs QScripts passed in to the command line.
@@ -291,7 +292,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
   }
 
   private def createQueueHeader(): Seq[String] = {
-    Seq("Biopet version: " + BiopetExecutable.getVersion, "",
+    Seq("Biopet version: " + FullVersion, "",
       "Based on GATK Queue",
       //                     String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
       "Copyright (c) 2012 The Broad Institute",

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/package.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc
+
+import java.util.Properties
+
+/**
+ * Common values and functions for the biopet package
+ *
+ * @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
+ */
+package object biopet {
+
+  /** Latest git commit hash, with '-dirty' appended if any uncommited changes were present */
+  val LastCommitHash: String = {
+    val prop = new Properties()
+    prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
+
+    val hash = prop.getProperty("git.commit.id.abbrev")
+    if (prop.getProperty("git.commit.id.describe-short").endsWith("-dirty")) s"$hash-dirty"
+    else hash
+  }
+
+  /** Package version */
+  // needs the Option here since the value is `null` when we run from an unpackaged JAR
+  val Version: String = Option(getClass.getPackage.getImplementationVersion).getOrElse("unpackaged")
+
+  /** Full version (raw version and latest commit hash) */
+  val FullVersion: String = s"$Version ($LastCommitHash)"
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -16,7 +16,6 @@
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
 import java.io.File
-import java.util.Properties
 import scala.language.reflectiveCalls
 
 import org.broadinstitute.gatk.queue.QScript
@@ -24,6 +23,7 @@ import org.broadinstitute.gatk.queue.function.QFunction
 import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
 import scalaz._, Scalaz._
 
+import nl.lumc.sasc.biopet.FullVersion
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.core.summary._
@@ -234,16 +234,6 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     "isoform_fpkm_cufflinks_blind_heatmap" -> isoFpkmCufflinksBlindHeatmapJob
   )
 
-  private def version: String = {
-    val baseVersion = getClass.getPackage.getImplementationVersion
-    val commitHash = {
-      val prop = new Properties()
-      prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
-      prop.getProperty("git.commit.id.abbrev")
-    }
-    s"$baseVersion ($commitHash)"
-  }
-
   /** Output summary file */
   def summaryFile: File = new File(outputDir, "gentrap.summary.json")
 
@@ -268,7 +258,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     "strand_protocol" -> strandProtocol.toString,
     "call_variants" -> callVariants,
     "remove_ribosomal_reads" -> removeRibosomalReads,
-    "version" -> version
+    "version" -> FullVersion
   )
 
   /** Job for writing PDF report template */