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Commit 0bc37c76 authored by Peter van 't Hof's avatar Peter van 't Hof
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Init version of report module

parent aa506e53
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public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/biopet.css 0 → 100644
View file @ 0bc37c76
header {
background-color:black;
color:white;
text-align:center;
padding:5px;
}
nav {
line-height:30px;
background-color:#eeeeee;
width:100%;
padding:5px;
}
nav ul ul {
display: none;
}
nav ul li:hover > ul {
display: block;
}
nav ul {
background: #efefef;
background: linear-gradient(top, #efefef 0%, #bbbbbb 100%);
background: -moz-linear-gradient(top, #efefef 0%, #bbbbbb 100%);
background: -webkit-linear-gradient(top, #efefef 0%,#bbbbbb 100%);
box-shadow: 0px 0px 9px rgba(0,0,0,0.15);
padding: 0 20px;
border-radius: 10px;
list-style: none;
position: relative;
display: inline-table;
}
nav ul:after {
content: ""; clear: both; display: block;
}
nav ul li {
float: left;
}
nav ul li:hover {
background: #4b545f;
background: linear-gradient(top, #4f5964 0%, #5f6975 40%);
background: -moz-linear-gradient(top, #4f5964 0%, #5f6975 40%);
background: -webkit-linear-gradient(top, #4f5964 0%,#5f6975 40%);
}
nav ul li:hover a {
color: #fff;
}
nav ul li a {
display: block; padding: 25px 40px;
color: #757575; text-decoration: none;
}
nav ul ul {
background: #5f6975; border-radius: 0px; padding: 0;
position: absolute; top: 100%;
}
nav ul ul li {
float: none;
border-top: 1px solid #6b727c;
border-bottom: 1px solid #575f6a;
position: relative;
}
nav ul ul li a {
padding: 15px 40px;
color: #fff;
}
nav ul ul li a:hover {
background: #4b545f;
}
nav ul ul ul {
position: absolute; left: 100%; top:0;
}
section {
width:350px;
float:left;
padding:10px;
}
footer {
background-color:black;
color:white;
clear:both;
text-align:center;
padding:5px;
}
table, td, th {
border: 1px solid green;
border-collapse: collapse;
}
th {
background-color: green;
border: 1px solid white;
color: white;
}
\ No newline at end of file
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp 0 → 100644
View file @ 0bc37c76
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var indexPage: ReportPage %>
<%@ var reportName: String %>
<%@ var page: ReportPage %>
<%@ var path: List[String] %>
<%@ var args: Map[String, Any] %>
#{
val rootPath = "./" + Array.fill(path.size)("../").mkString("")
def createMenu(page: ReportPage, path: List[String] = Nil): String = {
val buffer: StringBuffer = new StringBuffer()
buffer.append("<ul>")
for (subPage <- page.subPages) {
val href: String = {
if (path.isEmpty) rootPath + subPage._1 + "/index.html"
else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
}
buffer.append("<li><a href=\"" + href + "\">" + subPage._1 + "</a>")
buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil))
buffer.append("</li>")
}
buffer.append("</ul>")
buffer.toString
}
def getSubPage(path:List[String]): ReportPage = {
path.foldLeft(indexPage)(_.subPages(_))
}
}#
<!DOCTYPE html>
<html>
<head>
<link rel="stylesheet" type="text/css" href="${rootPath}css/biopet.css">
</head>
<body>
<header><h1>${reportName}</h1></header>
<nav>
<ul>
#for (t <- 0 to path.size)
<li>
#if (t == 0)
<a href="${rootPath}index.html">Home</a>
${unescape(createMenu(indexPage))}
#else
<a href="${rootPath}${path.slice(0, t).mkString("","/","/")}index.html">${path(t - 1)}</a>
${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t)))}
#end
</li>
#end
</ul>
</nav>
#for ((name, url) <- page.sections)
<section id="${name}">
${name}
</section>
#end
<footer>Footer</footer>
</body>
</html>
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala 0 → 100644
View file @ 0bc37c76
package nl.lumc.sasc.biopet.core.report
import nl.lumc.sasc.biopet.core.summary.Summary
/**
* Created by pjvan_thof on 3/30/15.
*/
trait MultisampleReportBuilder extends ReportBuilder {
def generalPage: ReportPage
def samplePage(sampleId: String, args: Map[String, Any]) : ReportPage
def libraryPage(libraryId: String, args: Map[String, Any]) : ReportPage
def generateSamplesPage(args: Map[String, Any]) : ReportPage = {
val samplePages = summary.samples
.map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
.toMap
ReportPage(samplePages, Map(), args)
}
def generateLibraryPage(args: Map[String, Any]) : ReportPage = {
val libPages = summary.libraries(args("sampleId") match {
case Some(x) => x.toString
case None => throw new IllegalStateException("Sample not found")
})
.map(libId => (libId -> libraryPage(libId, args ++ Map("libId" -> Some(libId)))))
.toMap
ReportPage(libPages, Map(), args)
}
def indexPage = ReportPage(Map("General" -> generalPage, "Samples" -> generateSamplesPage(pageArgs)), Map(), pageArgs)
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 0 → 100644
View file @ 0bc37c76
package nl.lumc.sasc.biopet.core.report
import java.io.{ PrintWriter, File }
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.summary.Summary
import org.fusesource.scalate.{TemplateSource, TemplateEngine}
import scala.io.Source
/**
* Created by pjvan_thof on 3/27/15.
*/
trait ReportBuilder extends ToolCommand {
case class Args(summary: File = null, outputDir: File = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('s', "summary") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(summary = x)
}
opt[File]('o', "outputDir") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(outputDir = x)
}
}
private var setSummary: Summary = _
final def summary = setSummary
def pageArgs: Map[String, Any] = Map()
def main(args: Array[String]): Unit = {
logger.info("Start")
val argsParser = new OptParser
val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
require(cmdArgs.outputDir.exists(), "Output dir does not exist")
require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")
// Write css to output dir
val cssDir = new File (cmdArgs.outputDir, "css")
cssDir.mkdirs()
val cssWriter = new PrintWriter(new File(cssDir, "biopet.css"))
Source.fromInputStream(getClass.getResourceAsStream("biopet.css")).getLines().foreach(cssWriter.println(_))
cssWriter.close()
setSummary = new Summary(cmdArgs.summary)
generatePage(summary, indexPage, cmdArgs.outputDir,
args = pageArgs ++ Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage))
logger.info("Done")
}
protected val engine = new TemplateEngine()
def indexPage: ReportPage
def reportName: String
def generatePage(summary: Summary,
page: ReportPage,
outputDir: File,
path: List[String] = Nil,
args: Map[String, Any] = Map()): Unit = {
val templateText = Source.fromInputStream(getClass.getResourceAsStream("main.ssp")).getLines().mkString("\n")
val template = engine.compileText("ssp", templateText)
val pageArgs = args ++ page.args ++ Map("page" -> page, "path" -> path)
val output = engine.layout(template.source, pageArgs ++ Map("args" -> pageArgs))
val file = new File(outputDir, path.mkString("", File.separator, File.separator) + "index.html")
file.getParentFile.mkdirs()
val writer = new PrintWriter(file)
writer.println(output)
writer.close()
// Generating subpages
for ((name, subPage) <- page.subPages) {
generatePage(summary, subPage, outputDir, path ::: name :: Nil, pageArgs)
}
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala 0 → 100644
View file @ 0bc37c76
package nl.lumc.sasc.biopet.core.report
import java.net.URL
/**
* Created by pjvan_thof on 3/27/15.
*/
case class ReportPage(val subPages: Map[String, ReportPage],
val sections: Map[String, URL],
val args: Map[String, Any])
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