195 lines
6.9 KiB
R
195 lines
6.9 KiB
R
require("plotrix")
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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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# The unknown records are from the Broad
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d$domain.name[d$domain.name == "unknown"] = "broadinstitute.org"
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noRecords <- function(name) {
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print(paste("No records", name))
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frame()
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title(paste("No records of", name), cex=2)
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}
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reportCountingPlot <- function(values, name, moreMargin = 0, ...) {
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#print(length(values))
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if ( length(values) > 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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t = table(factor(values))
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barplot(sort(t), horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", log="x", ...)
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par("mar" = oldMar)
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par("las" = 1)
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} else {
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noRecords(name)
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}
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}
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reportConditionalCountingPlot <- function(values, conditions, name, moreMargin = 0, ...) {
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if ( length(values) > 0 ) {
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t = table(values, conditions)
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t = t[, order(colSums(t))]
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#print(list(t = t))
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if ( ! is.null(dim(t)) ) {
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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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nconds = dim(t)[2]
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cols = rainbow(nconds)
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barplot(t, legend.text = T, horiz=TRUE, cex.names = 0.5, main = name, xlab="Counts", col=cols, cex=0.5, ...)
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par("mar" = oldMar)
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par("las" = 1)
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} else {
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noRecords(name)
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}
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} else {
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noRecords(name)
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}
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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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if ( ! is.null(nrows) ) {
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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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}
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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$exception.msg))
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x[d$exception.msg != "NA" & d$is.user.exception == "true"] <- "Failed with UserException"
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x[d$exception.msg != "NA" & d$is.user.exception == "false"] <- "Failed with StingException"
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x[d$exception.msg != "NA" & (d$is.user.exception == "NA" | is.na(d$is.user.exception))] <- "Failed with StingException before UserException code"
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return(x)
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}
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addSection <- function(name) {
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par("mar", c(5, 4, 4, 2))
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frame()
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title(name, cex=2)
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}
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dropit <- function (d, columns = names(d), ...)
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{
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d[columns] = lapply(d[columns], "[", drop=TRUE, ...)
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d
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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, "\n", s))
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}
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excepted <- dropit(subset(d, exception.msg != "NA"))
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UserExceptions <- dropit(subset(excepted, is.user.exception == "true"))
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StingExceptions <- dropit(subset(excepted, is.user.exception == "false" | is.user.exception == "NA" | is.na(is.user.exception)))
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addSection(paste("GATK run report", name, "for", Sys.Date(), "\nwith", dim(d)[1], "run repository records"))
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reportCountingPlot(d$walker.name, head("Walker invocations"))
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reportConditionalCountingPlot(d$user.name, d$walker.name, head("Walker invocations by user"))
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reportCountingPlot(d$svn.version, head("SVN version"))
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reportConditionalCountingPlot(d$svn.version, d$user.name, head("SVN by user"))
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# cuts by time
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if ( includeByWeek ) {
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plotTable(table(rep("GATK Invocations", length(d$end.time)), cut(d$end.time, "weeks")), head("GATK Invocations by week"))
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plotTable(myTable(successfulRuns(d), cut(d$end.time, "weeks")), head("Successful and failing GATK invocations per week"))
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plotTable(myTable(d$svn.version, cut(d$end.time, "weeks")), head("SVN version by week"))
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}
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plotTable(table(rep("GATK Invocations", length(d$end.time)), d$end.time), head("GATK Invocations by day"))
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plotTable(myTable(d$svn.version, d$end.time), head("SVN version by day"))
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#
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# Exception handling
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#
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addExceptionSection <- function(subd, subname, exceptionColor) {
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addSection(paste(subname))
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#print(list(subd = length(subd$end.time), name=subname))
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reportCountingPlot(subd$walker.name, head(paste("Walkers with", subname)), col=exceptionColor)
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reportCountingPlot(subd$exception.at, head(paste(subname, "locations")), 12, col=exceptionColor)
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#reportCountingPlot(subd$exception.msg, head(paste(subname, "messages")), 12, col=exceptionColor)
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reportConditionalCountingPlot(subd$user.name, subd$exception.at, head(paste("Walker invocations by user for", subname)), 12)
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if ( includeByWeek && length(subd$end.time) > 0 ) {
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plotTable(myTable(subd$walker.name, cut(subd$end.time, "weeks"), reqRowNonZero = T), head(paste("Walkers with", subname,"by week")), col=exceptionColor)
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}
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}
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addExceptionSection(excepted, "Exceptions", "grey")
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reportCountingPlot(excepted$user.name, head("Usernames generating exceptions"), col="grey")
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addExceptionSection(StingExceptions, "StingExceptions", "red")
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addExceptionSection(UserExceptions, "UserExceptions", "blue")
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Gb <- 1024^3
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reportHist(d$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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reportCountingPlot(d$user.name, head("user"))
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reportCountingPlot(d$domain.name, head("Domain name"))
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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$machine, head("Machine"))
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#reportCountingPlot(d$working.directory, head("Working directory"))
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}
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RUNME = F
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if ( RUNME ) {
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lastWeek = levels(cut(d$end.time, "weeks"))[-1]
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generateOneReport(d, "Overall")
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#generateOneReport(subset(d, end.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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