From e09f609a74ef7e2484b3fb13b38184020bc554c4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 19 Feb 2015 17:04:46 +0100
Subject: [PATCH] Added scala docs
---
.../biopet/core/summary/Summarizable.scala | 10 +++++
.../biopet/core/summary/SummaryQScript.scala | 38 ++++++++++++++++++-
.../biopet/core/summary/WriteSummary.scala | 24 +++++++++++-
3 files changed, 69 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
index a1901ed79..918d57a6b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
@@ -5,12 +5,22 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
/**
+ * Trait for class to let them accept into a Summary
+ *
* Created by pjvan_thof on 2/14/15.
*/
trait Summarizable extends Configurable {
+ /**
+ * Must return files to store into summary
+ * @return
+ */
def summaryFiles: Map[String, File]
+ /**
+ * Must returns stats to store into summary
+ * @return
+ */
def summaryStats: Map[String, Any]
/**
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 82bdad86c..e5257b1f8 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
@@ -14,16 +14,30 @@ trait SummaryQScript extends BiopetQScript {
/** 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()
+
+ /** Qscripts summaries that need to be merge into this summary */
private[summary] var summaryQScripts: List[SummaryQScript] = Nil
+ /** Name of the pipeline in the summary */
var summaryName = configName
+ /** Must return a map with used settings for this pipeline */
def summarySettings: Map[String, Any]
+ /** File to put in the summary for thie pipeline */
def summaryFiles: Map[String, File]
+ /** Name of summary output file */
def summaryFile: File
+ /**
+ * Add a module to summary for this pipeline
+ *
+ * Auto detect sample and library from pipeline
+ *
+ * @param summarizable summarizable to add to summary for this pipeline
+ * @param name Name of module
+ */
def addSummarizable(summarizable: Summarizable, name: String): Unit = {
this match {
case tag: SampleLibraryTag => addSummarizable(summarizable, name, tag.sampleId, tag.libId)
@@ -31,19 +45,39 @@ trait SummaryQScript extends BiopetQScript {
}
}
+ /**
+ * Add a module to summary for this pipeline
+ *
+ * @param summarizable summarizable to add to summary for this pipeline
+ * @param name Name of module
+ * @param sampleId
+ */
def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String]): Unit = {
addSummarizable(summarizable, name, sampleId, None)
}
+ /**
+ * Add a module to summary for this pipeline
+ *
+ * @param summarizable summarizable to add to summary for this pipeline
+ * @param name Name of module
+ * @param sampleId
+ * @param libraryId
+ */
def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
}
+ /**
+ * Add an other qscript to merge in output summary
+ * @param summaryQScript
+ */
def addSummaryQScript(summaryQScript: SummaryQScript): Unit = {
summaryQScripts :+= summaryQScript
}
+ /** Add jobs to qscript to execute summary, also add checksum jobs */
def addSummaryJobs: Unit = {
val writeSummary = new WriteSummary(this)
@@ -73,11 +107,11 @@ trait SummaryQScript extends BiopetQScript {
add(writeSummary)
}
-
- protected[summary] val executables: mutable.Map[String, (File, String)] = mutable.Map()
}
object SummaryQScript {
import scala.collection.mutable.Map
+
+ /** Cache to have no duplicate jobs */
protected[summary] val md5sumCache: Map[File, File] = Map()
}
\ No newline at end of file
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 c73cc0505..5d41744a8 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
@@ -20,6 +20,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
require(root.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
+ /** To access qscript for this summary */
val qscript = root.asInstanceOf[SummaryQScript]
@Input(doc = "deps", required = false)
@@ -43,8 +44,8 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
super.freezeFieldValues()
}
+ /** Function to create summary */
def run(): Unit = {
-
val pipelineMap = {
val files = parseFiles(qscript.summaryFiles)
val settings = qscript.summarySettings
@@ -100,6 +101,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
}
}
+ /**
+ * Convert summarizable to a summary map
+ * @param summarizable
+ * @param name
+ * @return
+ */
def parseSummarizable(summarizable: Summarizable, name: String) = {
val data = summarizable.summaryStats
val files = parseFiles(summarizable.summaryFiles)
@@ -108,10 +115,20 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
(if (files.isEmpty) Map[String, Any]() else Map("files" -> Map(name -> files)))
}
+ /**
+ * Parse files map to summary map
+ * @param files
+ * @return
+ */
def parseFiles(files: Map[String, File]): Map[String, Map[String, Any]] = {
for ((key, file) <- files) yield key -> parseFile(file)
}
+ /**
+ * parse single file summary map
+ * @param file
+ * @return
+ */
def parseFile(file: File): Map[String, Any] = {
val map: mutable.Map[String, Any] = mutable.Map()
map += "path" -> file.getAbsolutePath
@@ -119,6 +136,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
map.toMap
}
+ /**
+ * Retrive checksum from file
+ * @param checksumFile
+ * @return
+ */
def parseChecksum(checksumFile: File): String = {
Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
}
--
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