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Commit 00804440 authored by Peter van 't Hof's avatar Peter van 't Hof
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Switch core to futures

parent cd7469b4
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @ 00804440
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var indexPage: ReportPage %>
<%@ var reportName: String %>
......@@ -15,11 +17,13 @@
buffer.append("<ul class=\"dropdown-menu list-group\">")
}
for (subPage <- page.subPages.sortBy(_._1)) {
for (subPageFuture <- page.subPages.sortBy(_._1)) {
val subPageName = subPageFuture._1
val subPage = Await.result(subPageFuture._2, Duration.Inf)
val href: String = {
if (path.isEmpty) rootPath + subPage._1 + "/index.html"
else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
if (path.isEmpty) rootPath + subPageName + "/index.html"
else rootPath + path.mkString("","/","/") + subPageName + "/index.html"
}
// buffer.append("<li")
......@@ -30,16 +34,16 @@
// buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil, first = false))
// buffer.append("</li>")
val listSubmenu = if(subPage._2.subPages.nonEmpty) "dropdown-submenu" else ""
val listSubmenu = if(subPage.subPages.nonEmpty) "dropdown-submenu" else ""
// val subMenuBadgeCount = if(subPage._2.subPages.nonEmpty && first) "<span class='badge'>%d</span>".format(subPage._2.subPages.size) else ""
val tabIndex = if (first) " tabindex='-1'" else ""
// val listGroupA = if(subPage._2.subPages.nonEmpty) "list-group-item" else ""
var menuItem: String = "<li class='%s'>".format(listSubmenu) +
"<a href='%s' class='%s'%s>".format(href, "", tabIndex) +
"%s".format(subPage._1) +
"%s".format(subPageName) +
"</a>" +
createMenu(subPage._2, path ::: subPage._1 :: Nil, first = false) +
createMenu(subPage, path ::: subPageName :: Nil, first = false) +
"</li>"
buffer.append(menuItem)
......@@ -54,7 +58,7 @@
path.foldLeft(indexPage)((c, p) => {
val foundPages = c.subPages.filter(_._1 == p)
require(foundPages.size == 1, "Name of page not found or duplicate is found, page:: " + p + " in path: " + path)
foundPages.head._2
Await.result(foundPages.head._2, Duration.Inf)
})
}
}#
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
View file @ 00804440
......@@ -14,8 +14,9 @@
*/
package nl.lumc.sasc.biopet.core.report
import scala.concurrent.Await
import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration
import scala.concurrent.ExecutionContext.Implicits.global
/**
* This trait will generate a report with added function to generate sample and library pages for those existing in the summary.
......@@ -25,7 +26,7 @@ import scala.concurrent.duration.Duration
trait MultisampleReportBuilder extends ReportBuilder {
/** Method to generate a single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage
def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage]
/** Default list of samples, can be override */
def samplesSections: List[(String, ReportSection)] = {
......@@ -35,7 +36,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
}
/** Method to generate a single library page */
def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]): ReportPage
def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]): Future[ReportPage]
/** Default list of libraries, can be override */
def librariesSections: List[(String, ReportSection)] = {
......@@ -45,7 +46,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
}
/** Generate the samples page including a single sample page for each sample in the summary */
def generateSamplesPage(args: Map[String, Any]): ReportPage = {
def generateSamplesPage(args: Map[String, Any]): Future[ReportPage] = Future {
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val samplePages = samples.map(_.id)
.map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId))))
......@@ -54,7 +55,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
}
/** Generate the libraries page for a single sample with a subpage for eacht library */
def generateLibraryPage(args: Map[String, Any]): ReportPage = {
def generateLibraryPage(args: Map[String, Any]): Future[ReportPage] = Future {
val sampleId = args("sampleId") match {
case Some(x: Int) => x
case None => throw new IllegalStateException("Sample not found")
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @ 00804440
......@@ -28,6 +28,7 @@ import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration
import scala.language.postfixOps
import scala.language.implicitConversions
import scala.concurrent.ExecutionContext.Implicits.global
/**
* This trait is meant to make an extension for a report object
......@@ -74,7 +75,7 @@ trait ReportBuilderExtension extends ToolCommandFunction {
trait ReportBuilder extends ToolCommand {
implicit def toOption[T](x: T): Option[T] = Option(x)
implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
// implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
case class Args(summaryDbFile: File = null,
outputDir: File = null,
......@@ -186,6 +187,7 @@ trait ReportBuilder extends ToolCommand {
_setSamples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
_setLibraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId, libId = libId), Duration.Inf)
// TODO: switch to future for base files
logger.info("Copy Base files")
// Static files that will be copied to the output folder, then file is added to [resourceDir] it's need to be added here also
......@@ -200,21 +202,23 @@ trait ReportBuilder extends ToolCommand {
createDirs = true)
)
total = ReportBuilder.countPages(indexPage)
val rootPage = indexPage
// total = ReportBuilder.countPages(rootPage)
logger.info(total + " pages to be generated")
done = 0
logger.info("Generate pages")
val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
val jobs = generatePage(summary, rootPage, cmdArgs.outputDir,
args = pageArgs ++ cmdArgs.pageArgs.toMap ++
Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage, "runId" -> cmdArgs.runId))
Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> rootPage, "runId" -> cmdArgs.runId))
logger.info(jobs + " Done")
Await.result(jobs, Duration.Inf)
}
/** This must be implemented, this will be the root page of the report */
def indexPage: ReportPage
def indexPage: Future[ReportPage]
/** This must be implemented, this will become the title of the report */
def reportName: String
......@@ -223,49 +227,50 @@ trait ReportBuilder extends ToolCommand {
* This method will render the page and the subpages recursivly
*
* @param summary The summary object
* @param page Page to render
* @param pageFuture Page to render
* @param outputDir Root output dir of the report
* @param path Path from root to current page
* @param args Args to add to this sub page, are args from current page are passed automaticly
* @return Number of pages including all subpages that are rendered
*/
def generatePage(summary: SummaryDb,
page: ReportPage,
pageFuture: Future[ReportPage],
outputDir: File,
path: List[String] = Nil,
args: Map[String, Any] = Map()): Int = {
val pageOutputDir = new File(outputDir, path.mkString(File.separator))
pageOutputDir.mkdirs()
val rootPath = "./" + Array.fill(path.size)("../").mkString
val pageArgs = args ++ page.args ++
Map("page" -> page,
"path" -> path,
"outputDir" -> pageOutputDir,
"rootPath" -> rootPath,
"allPipelines" -> pipelines,
"allModules" -> modules,
"allSamples" -> samples,
"allLibraries" -> libraries
)
// Generating subpages
val jobs = page.subPages.par.flatMap {
case (name, subPage) => Some(generatePage(summary, subPage, outputDir, path ::: name :: Nil, pageArgs))
case _ => None
args: Map[String, Any] = Map()): Future[_] = {
pageFuture.flatMap { page =>
val pageOutputDir = new File(outputDir, path.mkString(File.separator))
pageOutputDir.mkdirs()
val rootPath = "./" + Array.fill(path.size)("../").mkString
val pageArgs = args ++ page.args ++
Map("page" -> page,
"path" -> path,
"outputDir" -> pageOutputDir,
"rootPath" -> rootPath,
"allPipelines" -> pipelines,
"allModules" -> modules,
"allSamples" -> samples,
"allLibraries" -> libraries
)
// Generating subpages
val jobs = Future.sequence(page.subPages.map {
case (name, subPage) => generatePage(summary, subPage, outputDir, path ::: name :: Nil, pageArgs)
})
val renderFuture = Future {
val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/main.ssp",
pageArgs ++ Map("args" -> pageArgs))
val file = new File(pageOutputDir, "index.html")
val writer = new PrintWriter(file)
writer.println(output)
writer.close()
}
Future.sequence(renderFuture :: jobs :: Nil)
}
val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/main.ssp",
pageArgs ++ Map("args" -> pageArgs))
val file = new File(pageOutputDir, "index.html")
val writer = new PrintWriter(file)
writer.println(output)
writer.close()
done += 1
if (done % 100 == 0) logger.info(done + " Done, " + (done.toDouble / total * 100) + "%")
jobs.sum + 1
}
}
......@@ -276,9 +281,9 @@ object ReportBuilder {
engine.allowReload = false
/** This will give the total number of pages including all nested pages */
def countPages(page: ReportPage): Int = {
page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
}
// def countPages(page: ReportPage): Int = {
// page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
// }
/**
* This method will render a template that is located in the classpath / jar
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
View file @ 00804440
......@@ -14,6 +14,8 @@
*/
package nl.lumc.sasc.biopet.core.report
import scala.concurrent.Future
/**
* Created by pjvan_thof on 3/27/15.
*
......@@ -21,6 +23,6 @@ package nl.lumc.sasc.biopet.core.report
* @param sections Sections for this page
* @param args Arguments for this page, this arguments get passed to all section and subpages
*/
case class ReportPage(subPages: List[(String, ReportPage)],
case class ReportPage(subPages: List[(String, Future[ReportPage])],
sections: List[(String, ReportSection)],
args: Map[String, Any])
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
View file @ 00804440
......@@ -23,8 +23,9 @@ import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
import scala.concurrent.Await
import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration
import scala.concurrent.ExecutionContext.Implicits.global
/**
* Created by pjvanthof on 24/02/16.
......@@ -38,12 +39,12 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
def testGeneratePages(): Unit = {
val builder = new MultisampleReportBuilder {
def reportName: String = "test"
def indexPage: ReportPage = ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map())
def indexPage: Future[ReportPage] = Future(ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map()))
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage =
ReportPage("Libraries" -> generateLibraryPage(Map("sampleId" -> Some(sampleId))) :: Nil, Nil, Map())
def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage] =
Future(ReportPage("Libraries" -> generateLibraryPage(Map("sampleId" -> Some(sampleId))) :: Nil, Nil, Map()))
def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]) = ReportPage(Nil, Nil, Map())
def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]) = Future(ReportPage(Nil, Nil, Map()))
}
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
......
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
View file @ 00804440
......@@ -23,9 +23,11 @@ import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ DataProvider, Test }
import scala.concurrent.Await
import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration
import scala.concurrent.ExecutionContext.Implicits.global
/**
* Created by pjvanthof on 24/02/16.
*/
......@@ -47,8 +49,8 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
def testGeneratePages(sample: Option[String], lib: Option[String], nested: Boolean): Unit = {
val builder = new ReportBuilder {
def reportName: String = "test"
def indexPage: ReportPage = ReportPage(
(if (nested) "p1" -> ReportPage(Nil, Nil, Map()) :: Nil else Nil), Nil, Map())
def indexPage: Future[ReportPage] = Future(ReportPage(
(if (nested) "p1" -> Future(ReportPage(Nil, Nil, Map())) :: Nil else Nil), Nil, Map()))
}
val dbFile = File.createTempFile("summary.", ".db")
......@@ -77,22 +79,22 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
db.close()
}
@Test
def testCountPages: Unit = {
ReportBuilder.countPages(ReportPage(Nil, Nil, Map())) shouldBe 1
ReportBuilder.countPages(ReportPage(
"p1" -> ReportPage(Nil, Nil, Map()) :: Nil,
Nil, Map())) shouldBe 2
ReportBuilder.countPages(ReportPage(
"p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage(Nil, Nil, Map()) :: Nil,
Nil, Map())) shouldBe 3
ReportBuilder.countPages(ReportPage(
"p1" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
Nil, Map())) shouldBe 3
ReportBuilder.countPages(ReportPage(
"p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
Nil, Map())) shouldBe 4
}
// @Test
// def testCountPages: Unit = {
// ReportBuilder.countPages(ReportPage(Nil, Nil, Map())) shouldBe 1
// ReportBuilder.countPages(ReportPage(
// "p1" -> ReportPage(Nil, Nil, Map()) :: Nil,
// Nil, Map())) shouldBe 2
// ReportBuilder.countPages(ReportPage(
// "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage(Nil, Nil, Map()) :: Nil,
// Nil, Map())) shouldBe 3
// ReportBuilder.countPages(ReportPage(
// "p1" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
// Nil, Map())) shouldBe 3
// ReportBuilder.countPages(ReportPage(
// "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
// Nil, Map())) shouldBe 4
// }
@Test
def testRenderTemplate: Unit = {
......
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