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Fixing errors in queueJobReport runtime unit

This commit is contained in:
Mark DePristo 2011-10-07 12:04:53 -07:00
parent ec14a4a606
commit ff3dccd062
1 changed files with 10 additions and 10 deletions
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20
public/R/queueJobReport.R
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@ -12,20 +12,20 @@ if ( onCMDLine ) {
inputFileName = args[1]
outputPDF = args[2]
} else {
inputFileName = "~/Desktop/Q-30033@gsa1.jobreport.txt"
inputFileName = "~/Desktop/broadLocal/GATK/unstable/wgs.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
outputPDF = NA
}
RUNTIME_UNITS = "(hours)"
ORIGINAL_UNITS_TO_SECONDS = 1/1000/60/60
ORIGINAL_UNITS_TO_RUNTIME_UNITS = 1/1000/60/60
#
# Helper function to aggregate all of the jobs in the report across all tables
#
allJobsFromReport <- function(report) {
names <- c("jobName", "startTime", "analysisName", "doneTime", "exechosts")
names <- c("jobName", "startTime", "analysisName", "doneTime", "exechosts", "runtime")
sub <- lapply(report, function(table) table[,names])
do.call("rbind", sub)
}
@ -44,8 +44,8 @@ plotJobsGantt <- function(gatkReport, sortOverall, includeText) {
}
allJobs$index = 1:nrow(allJobs)
minTime = min(allJobs$startTime)
allJobs$relStartTime = (allJobs$startTime - minTime) * ORIGINAL_UNITS_TO_SECONDS
allJobs$relDoneTime = (allJobs$doneTime - minTime) * ORIGINAL_UNITS_TO_SECONDS
allJobs$relStartTime = allJobs$startTime - minTime
allJobs$relDoneTime = allJobs$doneTime - minTime
allJobs$ganttName = paste(allJobs$jobName, "@", allJobs$exechosts)
maxRelTime = max(allJobs$relDoneTime)
p <- ggplot(data=allJobs, aes(x=relStartTime, y=index, color=analysisName))
@ -54,7 +54,7 @@ plotJobsGantt <- function(gatkReport, sortOverall, includeText) {
if ( includeText )
p <- p + geom_text(aes(x=relDoneTime, label=ganttName, hjust=-0.2), size=2)
p <- p + xlim(0, maxRelTime * 1.1)
p <- p + xlab(paste("Start time (relative to first job)", RUNTIME_UNITS))
p <- p + xlab(paste("Start time, relative to first job", RUNTIME_UNITS))
p <- p + ylab("Job number")
p <- p + opts(title=title)
print(p)
@ -121,7 +121,7 @@ plotGroup <- function(groupTable) {
if ( length(groupAnnotations) == 1 && dim(sub)[1] > 1 ) {
# todo -- how do we group by annotations?
p <- ggplot(data=sub, aes(x=runtime)) + geom_histogram()
p <- p + xlab("runtime in seconds") + ylab("No. of jobs")
p <- p + xlab(paste("runtime", RUNTIME_UNITS)) + ylab("No. of jobs")
p <- p + opts(title=paste("Job runtime histogram for", name))
print(p)
}
@ -141,9 +141,9 @@ print(paste("Project :", inputFileName))
convertUnits <- function(gatkReportData) {
convertGroup <- function(g) {
g$runtime = g$runtime * ORIGINAL_UNITS_TO_SECONDS
g$startTime = g$startTime * ORIGINAL_UNITS_TO_SECONDS
g$doneTime = g$doneTime * ORIGINAL_UNITS_TO_SECONDS
g$runtime = g$runtime * ORIGINAL_UNITS_TO_RUNTIME_UNITS
g$startTime = g$startTime * ORIGINAL_UNITS_TO_RUNTIME_UNITS
g$doneTime = g$doneTime * ORIGINAL_UNITS_TO_RUNTIME_UNITS
g
}
lapply(gatkReportData, convertGroup)