From 7bea0e9577bdda29291eebe1782bc0966692f638 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Tue, 5 Jan 2016 10:55:57 +0100
Subject: [PATCH] manwe wrapper fixes
---
.../ManweActivateAfterAnnotImport.scala | 38 ++++++++++++++++---
.../toucan/ManweDownloadAfterAnnotate.scala | 36 +++++++++++++++---
2 files changed, 64 insertions(+), 10 deletions(-)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala
index 468549358..9ed3b00d0 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala
@@ -1,5 +1,7 @@
package nl.lumc.sasc.biopet.pipelines.toucan
+import java.io.File
+
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesActivate, ManweSamplesImport }
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -24,13 +26,39 @@ class ManweActivateAfterAnnotImport(root: Configurable,
override def beforeCmd: Unit = {
super.beforeCmd
- if (imported.output.exists()) {
- val reader = Source.fromFile(imported.output)
- this.uri = reader.getLines().toList.head.split(' ').last
- reader.close()
+ this.uri = getUri
+ }
+
+ def getUriFromFile(f: File): String = {
+ val r = if (f.exists()) {
+ val reader = Source.fromFile(f)
+ val it = reader.getLines()
+ if (it.isEmpty) {
+ throw new IllegalArgumentException("Empty manwe stderr file")
+ }
+ it.filter(_.contains("Added sample")).toList.head.split(" ").last
} else {
- this.uri = ""
+ ""
}
+ r
+ }
+
+ def getUri: String = {
+ val err: Option[File] = Some(imported.jobOutputFile)
+ uri = err match {
+ case None => ""
+ case Some(s) => s match {
+ case null => ""
+ case other => getUriFromFile(other)
+ }
+ case _ => ""
+ }
+
+ uri
+ }
+
+ override def subCommand = {
+ required("samples") + required("activate") + getUri
}
}
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
index bdb19ffa0..e49ff7e5e 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala
@@ -22,13 +22,39 @@ class ManweDownloadAfterAnnotate(root: Configurable,
override def beforeCmd: Unit = {
super.beforeCmd
- if (annotate.output.exists()) {
- val reader = Source.fromFile(annotate.output)
- this.uri = reader.getLines().toList.head.split(' ').last
- reader.close()
+ this.uri = getUri
+ }
+
+ def getUriFromFile(f: File): String = {
+ val r = if (f.exists()) {
+ val reader = Source.fromFile(f)
+ val it = reader.getLines()
+ if (it.isEmpty) {
+ throw new IllegalArgumentException("Empty manwe stderr file")
+ }
+ it.filter(_.contains("Annotated VCF file")).toList.head.split(" ").last
} else {
- this.uri = ""
+ ""
+ }
+ r
+ }
+
+ def getUri: String = {
+ val err: Option[File] = Some(annotate.jobOutputFile)
+ uri = err match {
+ case None => ""
+ case Some(s) => s match {
+ case null => ""
+ case other => getUriFromFile(other)
+ }
+ case _ => ""
}
+
+ uri
+ }
+
+ override def subCommand = {
+ required("data-sources") + required("download") + getUri
}
}
--
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