From 4c4053157c5f3c324a1d972e9d4b9cdd6c27d194 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 28 Oct 2015 12:57:33 +0100
Subject: [PATCH] Refactor the report generation a bit. Move pipeline specific
report components into the pipeline itself (not hosted in core anymore)
---
.../biopet/core/report/ReportBuilder.scala | 35 ++++++++++---------
.../biopet/pipelines/gears/gearsFront.ssp | 1 -
.../pipelines/gears}/report/ext/js/gears.js | 0
.../biopet/pipelines/gears/GearsReport.scala | 4 +++
4 files changed, 22 insertions(+), 18 deletions(-)
rename public/{biopet-core/src/main/resources/nl/lumc/sasc/biopet/core => gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears}/report/ext/js/gears.js (100%)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index 311e3e928..cea0efcd3 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -16,11 +16,13 @@
package nl.lumc.sasc.biopet.core.report
import java.io._
+
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ ToolCommand, Logging, IoUtils }
+import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand}
import org.broadinstitute.gatk.utils.commandline.Input
-import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
+import org.fusesource.scalate.{TemplateEngine, TemplateSource}
+
import scala.collection.mutable
/**
@@ -95,6 +97,19 @@ trait ReportBuilder extends ToolCommand {
private var _libId: Option[String] = None
protected def libId = _libId
+ def extFiles = List(
+ "css/bootstrap_dashboard.css",
+ "css/bootstrap.min.css",
+ "css/bootstrap-theme.min.css",
+ "css/sortable-theme-bootstrap.css",
+ "js/jquery.min.js",
+ "js/sortable.min.js",
+ "js/bootstrap.min.js",
+ "fonts/glyphicons-halflings-regular.woff",
+ "fonts/glyphicons-halflings-regular.ttf",
+ "fonts/glyphicons-halflings-regular.woff2"
+ ).map("/nl/lumc/sasc/biopet/core/report/ext/" + _)
+
/** Main function to for building the report */
def main(args: Array[String]): Unit = {
logger.info("Start")
@@ -123,23 +138,9 @@ trait ReportBuilder extends ToolCommand {
// Static files that will be copied to the output folder, then file is added to [resourceDir] it's need to be added here also
val extOutputDir: File = new File(cmdArgs.outputDir, "ext")
- val resourceDir: String = "/nl/lumc/sasc/biopet/core/report/ext/"
- val extFiles = List(
- "css/bootstrap_dashboard.css",
- "css/bootstrap.min.css",
- "css/bootstrap-theme.min.css",
- "css/sortable-theme-bootstrap.css",
- "js/jquery.min.js",
- "js/sortable.min.js",
- "js/bootstrap.min.js",
- "js/gears.js",
- "fonts/glyphicons-halflings-regular.woff",
- "fonts/glyphicons-halflings-regular.ttf",
- "fonts/glyphicons-halflings-regular.woff2"
- )
for (resource <- extFiles.par) {
- IoUtils.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), createDirs = true)
+ IoUtils.copyStreamToFile(getClass.getResourceAsStream(resource), new File(extOutputDir, resource), createDirs = true)
}
logger.info("Parsing summary")
diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
index 21feab6c9..67d011009 100644
--- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
+++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
@@ -9,7 +9,6 @@
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
- <tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
<br/>
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/gears.js b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js
similarity index 100%
rename from public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/gears.js
rename to public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index a04b89ec2..af2f17c25 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -14,6 +14,10 @@ object GearsReport extends ReportBuilder {
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
+ override def extFiles = super.extFiles ++ List(
+ "js/gears.js"
+ ).map("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + _)
+
def indexPage = {
ReportPage(
List() ++
--
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