Merge branch 'patch-meta_in_summary' into 'develop'

Patch meta in summary

This pull request adds a `meta` entry to the root of each summary JSON file. The contents of the meta is:

`last_commit_hash`: the commit hash of the repository when the JAR was built. If the repository has uncommitted changes, `-dirty` is appended to the commit hash.

`pipeline_version`: the version of the pipeline (the one we put in the `pom.xml` file).

This information is static across all modules and subpipelines to any given pipeline run, so I decided to put this in the root.

See merge request !144

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

@@ -15,17 +15,17 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{ FileInputStream, PrintWriter, File }
-import java.security.MessageDigest
+import java.io.{ File, PrintWriter }
+import scala.collection.mutable
+import scala.io.Source
 
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, SampleLibraryTag }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
-import scala.collection.mutable
-import scala.io.Source
+import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 
 /**
  * Created by pjvan_thof on 2/14/15.
@@ -106,9 +106,13 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
         (v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
     }).foldRight(pipelineMap)((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
 
-    val combinedMap = (for (qscript <- qscript.summaryQScripts) yield {
-      ConfigUtils.fileToConfigMap(qscript.summaryFile)
-    }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b))
+    val combinedMap = Map("meta" -> Map(
+      "last_commit_hash" -> LastCommitHash,
+      "pipeline_version" -> Version
+    )) ++
+      (for (qscript <- qscript.summaryQScripts) yield {
+        ConfigUtils.fileToConfigMap(qscript.summaryFile)
+      }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b))
 
     val writer = new PrintWriter(out)
     writer.println(ConfigUtils.mapToJson(combinedMap).spaces4)