Commit 414f406d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed null pointer

parent 134e9302
...@@ -167,7 +167,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co ...@@ -167,7 +167,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
(for (f <- qscript.functions.par) yield f match { (for (f <- qscript.functions.par) yield f match {
case f: BiopetJavaCommandLineFunction with Version => case f: BiopetJavaCommandLineFunction with Version =>
Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, f.getJavaVersion, Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, f.getJavaVersion,
javaMd5 = BiopetCommandLineFunction.executableMd5Cache.get(f.executable), jarPath = Some(f.jarFile.getAbsolutePath))) javaMd5 = BiopetCommandLineFunction.executableMd5Cache.get(f.executable), jarPath = Option(f.jarFile).map(_.getAbsolutePath)))
case f: BiopetCommandLineFunction with Version => case f: BiopetCommandLineFunction with Version =>
Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, Option(f.executable))) Some(db.createOrUpdateExecutable(qscript.summaryRunId, f.configNamespace, f.getVersion, Option(f.executable)))
case f: Configurable with Version => case f: Configurable with Version =>
...@@ -252,10 +252,10 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co ...@@ -252,10 +252,10 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
(v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key)) (v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
}).foldRight(pipelineMap)((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2)) }).foldRight(pipelineMap)((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
val combinedMap = (for (qscript <- qscript.summaryQScripts) yield { val combinedMap = //(for (qscript <- qscript.summaryQScripts) yield {
ConfigUtils.fileToConfigMap(qscript.summaryFile) // ConfigUtils.fileToConfigMap(qscript.summaryFile)
}).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b)) ++ // }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b)) ++
Map("meta" -> Map( jobsMap ++ Map("meta" -> Map(
"last_commit_hash" -> LastCommitHash, "last_commit_hash" -> LastCommitHash,
"pipeline_version" -> nl.lumc.sasc.biopet.Version, "pipeline_version" -> nl.lumc.sasc.biopet.Version,
"pipeline_name" -> qscript.summaryName, "pipeline_name" -> qscript.summaryName,
......
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