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biopet.biopet
Commits
acf21ee3
Commit
acf21ee3
authored
Feb 02, 2016
by
Wai Yi Leung
Browse files
Report update, sorting order (display)
parent
c736d0cb
Changes
4
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public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @
acf21ee3
...
...
@@ -15,7 +15,7 @@
buffer.append("
<ul
class=
\"dropdown-menu\"
>
")
}
for (subPage
<-
page.subPages
)
{
for (subPage
<-
page.subPages
.sortBy
(
_._1
)
)
{
val
href:
String =
{
if
(
path.isEmpty
)
rootPath
+
subPage._1
+
"/
index.html
"
else
rootPath
+
path.mkString
("","/","/")
+
subPage._1
+
"/
index.html
"
...
...
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
View file @
acf21ee3
...
...
@@ -5,7 +5,7 @@
<%@ var pipeline: String %>
#{
val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get.asInstanceOf[Map[String, Map[String, Any]]]
val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get
OrElse(Map.empty)
.asInstanceOf[Map[String, Map[String, Any]]]
}#
<table class="table">
...
...
public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
View file @
acf21ee3
...
...
@@ -2,6 +2,7 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<table class="table">
<tbody>
...
...
@@ -9,7 +10,7 @@
<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>${summary.getValue("meta", "output_dir")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue(
"shiva"
, "settings", "reference", "species")} - ${summary.getValue(
"shiva"
, "settings", "reference", "name")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue(
pipeline
, "settings", "reference", "species")} - ${summary.getValue(
pipeline
, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
...
...
@@ -18,7 +19,7 @@
<div class="col-md-1"></div>
<div class="col-md-6">
<p>
In this web document you can find your <em>
Shiva
</em> pipeline report.
In this web document you can find your <em>
${pipeline}
</em> pipeline report.
Different categories of data can be found in the left-side menu.
Statistics per sample and library can be accessed through the top-level menu.
Some statistics for target regions can be found in the regions tab.
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
acf21ee3
...
...
@@ -56,7 +56,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
))
),
pageArgs
pageArgs
++
Map
(
"pipeline"
->
pipelineName
)
)
}
...
...
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