From c3f100e55e3e2945178c8d0c7428626df371ce18 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 16 Aug 2015 16:21:28 +0200
Subject: [PATCH] Adding md5sum checking
---
.../lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
.../biopet/core/summary/SummaryQScript.scala | 18 ++++++++--
.../biopet/core/summary/WriteSummary.scala | 5 +--
.../sasc/biopet/extensions/CheckMd5.scala | 33 +++++++++++++++++++
4 files changed, 53 insertions(+), 5 deletions(-)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/CheckMd5.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8961f2550..a5aa3efdb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -89,7 +89,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
- inputFiles.foreach{ i =>
+ inputFiles.foreach { i =>
if (!i.file.exists()) BiopetQScript.addError(s"Input file does not exist: ${i.file}")
if (!i.file.canRead()) BiopetQScript.addError(s"Input file can not be read: ${i.file}")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index c59438133..844a664c4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.Md5sum
+import nl.lumc.sasc.biopet.extensions.{ CheckMd5, Md5sum }
import scala.collection.mutable
@@ -27,7 +27,7 @@ import scala.collection.mutable
*
* Created by pjvan_thof on 2/14/15.
*/
-trait SummaryQScript extends BiopetQScript {
+trait SummaryQScript extends BiopetQScript { qscript =>
/** Key is sample/library, None is sample or library is not applicable */
private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
@@ -116,6 +116,20 @@ trait SummaryQScript extends BiopetQScript {
//TODO: add more checksums types
}
+ for (inputFile <- inputFiles) {
+ inputFile.md5 match {
+ case Some(checksum) => {
+ val checkMd5 = new CheckMd5
+ checkMd5.inputFile = inputFile.file
+ require(SummaryQScript.md5sumCache.contains(inputFile.file), "Md5 job is not executed, checksum file can't be found")
+ checkMd5.md5file = SummaryQScript.md5sumCache(inputFile.file)
+ checkMd5.md5sum = checksum
+ add(checkMd5)
+ }
+ case _ =>
+ }
+ }
+
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList) {
summarizable match {
case f: BiopetCommandLineFunctionTrait => f.beforeGraph()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 0dad01e5b..d987dcef3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -153,10 +153,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
def parseFile(file: File): Map[String, Any] = {
val map: mutable.Map[String, Any] = mutable.Map()
map += "path" -> file.getAbsolutePath
- if (md5sum) map += "md5" -> parseChecksum(SummaryQScript.md5sumCache(file))
+ if (md5sum) map += "md5" -> WriteSummary.parseChecksum(SummaryQScript.md5sumCache(file))
map.toMap
}
-
+}
+object WriteSummary {
/** Retrive checksum from file */
def parseChecksum(checksumFile: File): String = {
Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/CheckMd5.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/CheckMd5.scala
new file mode 100644
index 000000000..b6a108642
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/CheckMd5.scala
@@ -0,0 +1,33 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
+
+/**
+ * This class checks md5sums and give an exit code 1 when md5sum is not the same
+ *
+ * Created by pjvanthof on 16/08/15.
+ */
+class CheckMd5 extends InProcessFunction {
+ @Input(required = true)
+ var inputFile: File = _
+
+ @Input(required = true)
+ var md5file: File = _
+
+ @Argument(required = true)
+ var md5sum: String = _
+
+ /** Exits whenever the input md5sum is not the same as the output md5sum */
+ def run: Unit = {
+ val outputMd5sum = WriteSummary.parseChecksum(md5file).toLowerCase
+
+ if (outputMd5sum != md5sum.toLowerCase) {
+ logger.error(s"Input file: '$inputFile' md5sum is not as expected, aborting pipeline")
+ System.exit(1)
+ }
+ }
+}
\ No newline at end of file
--
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