From 594fb4a5472750d0200a3fc7f97532637626d362 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Sep 2010 02:56:51 +0000
Subject: [PATCH] More plots in report

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4225 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/GATKRunReport.R | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/R/GATKRunReport.R b/R/GATKRunReport.R
index 418257a56..a809b8aa8 100644
--- a/R/GATKRunReport.R
+++ b/R/GATKRunReport.R
@@ -1,6 +1,7 @@
 args = commandArgs(TRUE);
 
 onCMDLine = ! is.na(args[1])
+if (! is.na(args[3]) ) { name = args[3] } else { name = "" }
 
 if ( onCMDLine ) { 
    print(paste("Reading data from", args[1]))
@@ -27,7 +28,7 @@ myTable <- function(x, y, reqRowNonZero = F) {
     table <- prop.table(table(x, y), 2)
     ncols = dim(table)[2]
 
-    print(table)    
+    #print(table)    
     if ( reqRowNonZero )
         table = table[addmargins(table)[1:dim(table)[1],ncols] > 0,]
 
@@ -40,7 +41,9 @@ plotTable <- function(table, name) {
     ncols = dim(table)[2]
     nrows = dim(table)[1]
     cols = rainbow(nrows)
-    plot( as.numeric(table[1,]), type="n", ylim=c(0,1), main = name, ylab="Frequency", xlab="Date", xaxt="n")
+    tableMin = min(apply(table, 2, min))
+    tableMax = max(apply(table, 2, max))
+    plot( as.numeric(apply(table, 2, sum)), ylim=c(tableMin, tableMax), type="n", main = name, ylab="Frequency", xlab="Date", xaxt="n")
     axis(1, 1:ncols, labels=colnames(table))
     for ( i in 1:nrows )
         points(table[i,], type="b", col=cols[i])
@@ -52,6 +55,12 @@ RUNNING_GATK_RUNTIME <- 60 * 5 #  5 minutes => bad failure
 
 if ( onCMDLine ) pdf(args[2])
 
+successfulRuns <- function(d) {
+    x <- rep("Successful", length(d$exception.msg))
+    x[! is.na(d$exception.msg)] <- "Failed"
+    return(x)
+}
+
 generateOneReport <- function(d, header, includeByWeek = T) {
     head <- function(s) {
         return(paste("Section:", header, ":", s))
@@ -62,17 +71,21 @@ generateOneReport <- function(d, header, includeByWeek = T) {
 
     par("mar", c(5, 4, 4, 2))
     frame()
-    title(paste("Section:", header), cex=2)
+    title(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records"), cex=2)
     
-    reportCountingPlot(d$walker.name, head("Walker invocations"))
-    reportCountingPlot(d$svn.version, head("GATK SVN version"))
-
     # cuts by time
-    plotTable(myTable(d$svn.version, d$start.time), head("SVN version by day"))
     if ( includeByWeek ) {
+        plotTable(table(rep("GATK Invocations", length(d$start.time)), cut(d$start.time, "weeks")), head("GATK Invocations by week"))
+        plotTable(myTable(successfulRuns(d), cut(d$start.time, "weeks")), head("Successful and failing GATK invocations per week"))
+        
         plotTable(myTable(d$svn.version, cut(d$start.time, "weeks")), head("SVN version by week"))
         plotTable(myTable(excepted$walker.name, cut(excepted$start.time, "weeks"), reqRowNonZero = T), head("Walkers with exceptions by week"))
     }
+    plotTable(table(rep("GATK Invocations", length(d$start.time)), d$start.time), head("GATK Invocations by day"))
+    plotTable(myTable(d$svn.version, d$start.time), head("SVN version by day"))
+
+    reportCountingPlot(d$walker.name, head("Walker invocations"))
+    reportCountingPlot(d$svn.version, head("GATK SVN version"))
 
     # reportCountingPlot(d$java.tmp.directory, head("Java tmp directory"))
     reportCountingPlot(d$working.directory, head("Working directory"))