124 lines
4.8 KiB
R
124 lines
4.8 KiB
R
args = commandArgs(TRUE);
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onCMDLine = ! is.na(args[1])
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if (! is.na(args[3]) ) { name = args[3] } else { name = "" }
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if ( onCMDLine ) {
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print(paste("Reading data from", args[1]))
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d = read.table(args[1], header=T, sep="\t")
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d$start.time = as.Date(d$start.time)
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d$end.time = as.Date(d$end.time)
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} # only read into d if its' available, otherwise assume the data is already loaded
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reportCountingPlot <- function(values, name, moreMargin = 0, ...) {
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par(las=2) # make label text perpendicular to axis
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oldMar <- par("mar")
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par(mar=c(5,8+moreMargin,4,2)) # increase y-axis margin.
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barplot(sort(table(values)), horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", ...)
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par("mar" = oldMar)
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par("las" = 1)
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}
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reportHist <- function(values, name, ...) {
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if ( ! all(is.na(values) ) )
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hist(values, main=name, 20, xlab="", col="cornflowerblue", ...)
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}
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myTable <- function(x, y, reqRowNonZero = F) {
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table <- prop.table(table(x, y), 2)
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ncols = dim(table)[2]
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#print(table)
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if ( reqRowNonZero )
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table = table[addmargins(table)[1:dim(table)[1],ncols] > 0,]
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return(table)
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}
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# todo -- must be robust to smaller sizes
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plotTable <- function(table, name) {
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ncols = dim(table)[2]
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nrows = dim(table)[1]
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cols = rainbow(nrows)
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tableMin = min(apply(table, 2, min))
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tableMax = max(apply(table, 2, max))
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plot( as.numeric(apply(table, 2, sum)), ylim=c(tableMin, tableMax), type="n", main = name, ylab="Frequency", xlab="Date", xaxt="n")
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axis(1, 1:ncols, labels=colnames(table))
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for ( i in 1:nrows )
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points(table[i,], type="b", col=cols[i])
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legend("topright", row.names(table), fill=cols, cex=0.5)
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#return(table)
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}
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RUNNING_GATK_RUNTIME <- 60 * 5 # 5 minutes => bad failure
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if ( onCMDLine ) pdf(args[2])
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successfulRuns <- function(d) {
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x <- rep("Successful", length(d$exception.msg))
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x[! is.na(d$exception.msg)] <- "Failed"
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return(x)
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}
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generateOneReport <- function(d, header, includeByWeek = T) {
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head <- function(s) {
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return(paste("Section:", header, ":", s))
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}
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excepted <- subset(d, exception.msg != "NA")
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badExcepted <- subset(excepted, run.time > RUNNING_GATK_RUNTIME)
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par("mar", c(5, 4, 4, 2))
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frame()
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title(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records"), cex=2)
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# cuts by time
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if ( includeByWeek ) {
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plotTable(table(rep("GATK Invocations", length(d$start.time)), cut(d$start.time, "weeks")), head("GATK Invocations by week"))
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plotTable(myTable(successfulRuns(d), cut(d$start.time, "weeks")), head("Successful and failing GATK invocations per week"))
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plotTable(myTable(d$svn.version, cut(d$start.time, "weeks")), head("SVN version by week"))
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plotTable(myTable(excepted$walker.name, cut(excepted$start.time, "weeks"), reqRowNonZero = T), head("Walkers with exceptions by week"))
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}
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plotTable(table(rep("GATK Invocations", length(d$start.time)), d$start.time), head("GATK Invocations by day"))
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plotTable(myTable(d$svn.version, d$start.time), head("SVN version by day"))
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reportCountingPlot(d$walker.name, head("Walker invocations"))
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reportCountingPlot(d$svn.version, head("GATK SVN version"))
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# reportCountingPlot(d$java.tmp.directory, head("Java tmp directory"))
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reportCountingPlot(d$working.directory, head("Working directory"))
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reportCountingPlot(d$user.name, head("user"))
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reportCountingPlot(d$host.name, head("host"))
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reportCountingPlot(d$java, head("Java version"))
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reportCountingPlot(d$machine, head("Machine"))
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Gb <- 1024^3
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reportHist(d$total.memory / Gb, head("Used memory"))
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reportHist(d$max.memory / Gb, head("Max memory"))
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min <- 60
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reportHist(log10(d$run.time / min), head("Run time (log10[min])"))
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exceptionColor = "red"
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reportCountingPlot(excepted$walker.name, head("Walker exceptions"), col=exceptionColor)
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reportCountingPlot(subset(excepted, run.time > RUNNING_GATK_RUNTIME)$walker.name, paste(head("Long-running walker exceptions (>"),RUNNING_GATK_RUNTIME,"seconds runtime)"), col=exceptionColor)
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reportCountingPlot(subset(excepted, run.time < RUNNING_GATK_RUNTIME)$walker.name, paste(head("Start-up walker exceptions (<"),RUNNING_GATK_RUNTIME,"seconds runtime)"), col=exceptionColor)
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reportCountingPlot(excepted$user.name, head("Usernames generating exceptions"), col=exceptionColor)
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reportCountingPlot(excepted$exception.msg, head("Exception messages"), 12)
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reportCountingPlot(excepted$exception.at, head("Exception locations"), 12)
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}
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RUNME = T
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if ( RUNME ) {
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lastWeek = levels(cut(d$start.time, "weeks"))[-1]
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generateOneReport(d, "Overall")
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#generateOneReport(subset(d, start.time >= lastWeek), "Just last week to date", includeByWeek = F)
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}
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if ( onCMDLine ) dev.off()
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