improvements to the report code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
parent
4e83ba411f
commit
b57a0a0310
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@ -6,7 +6,7 @@ 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$start.time = as.Date(d$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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@ -14,11 +14,26 @@ 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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barplot(sort(table(factor(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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reportConditionalCountingPlot <- function(values, conditions, 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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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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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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}
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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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@ -37,18 +52,20 @@ myTable <- function(x, y, reqRowNonZero = F) {
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# todo -- must be robust to smaller sizes
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plotTable <- function(table, name) {
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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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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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@ -61,38 +78,61 @@ successfulRuns <- function(d) {
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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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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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return(paste("Section:", header, "\n", 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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UserExceptions <- subset(excepted, is.user.exception == "true")
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StingExceptions <- 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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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$start.time, "weeks")), head("Successful and failing GATK invocations per week"))
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plotTable(table(rep("GATK Invocations", length(d$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$svn.version, cut(d$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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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$start.time)), d$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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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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reportCountingPlot(d$walker.name, head("Walker invocations"))
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reportCountingPlot(d$svn.version, head("GATK SVN version"))
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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("Walker invocations by user"), 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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# 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$total.memory / Gb, head("Used memory"))
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@ -100,21 +140,20 @@ generateOneReport <- function(d, header, includeByWeek = T) {
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min <- 60
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reportHist(log10(d$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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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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reportCountingPlot(d$working.directory, head("Working directory"))
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}
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RUNME = T
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if ( RUNME ) {
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lastWeek = levels(cut(d$start.time, "weeks"))[-1]
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lastWeek = levels(cut(d$end.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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#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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@ -5,6 +5,7 @@ from itertools import *
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from xml.etree.ElementTree import *
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import gzip
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import datetime
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import re
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MISSING_VALUE = "NA"
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RUN_REPORT_LIST = "GATK-run-reports"
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@ -101,9 +102,20 @@ def eltIsException(elt):
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def parseException(elt):
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msgElt = elt.find("message")
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msgText = "MISSING"
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userException = "NA"
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if msgElt != None: msgText = msgElt.text
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return msgText, elt.find("stacktrace").find("string").text
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stackTrace = elt.find("stacktrace").find("string").text
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if elt.find("is-user-exception") != None:
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#print elt.find("is-user-exception")
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userException = elt.find("is-user-exception").text
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return msgText, stackTrace, userException
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def javaExceptionFile(javaException):
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m = re.search("\((.*\.java:.*)\)", javaException)
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if m != None:
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return m.group(1)
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else:
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javaException
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class RecordDecoder:
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def __init__(self):
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@ -118,6 +130,12 @@ class RecordDecoder:
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def formatExceptionAt(elt):
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return '%s' % parseException(elt)[1]
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def formatExceptionAtBrief(elt):
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return '%s' % javaExceptionFile(parseException(elt)[1])
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def formatExceptionUser(elt):
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return '%s' % parseException(elt)[2]
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def add(names, func):
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for name in names:
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@ -132,7 +150,7 @@ class RecordDecoder:
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add(["run-time", "java-tmp-directory", "working-directory", "user-name", "host-name"], id)
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add(["java", "machine"], toString)
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add(["max-memory", "total-memory", "iterations", "reads"], id)
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addComplex("exception", ["exception-msg", "exception-at"], [formatExceptionMsg, formatExceptionAt])
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addComplex("exception", ["exception-msg", "exception-at", "exception-at-brief", "is-user-exception"], [formatExceptionMsg, formatExceptionAt, formatExceptionAtBrief, formatExceptionUser])
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# add(["command-line"], toString)
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def decode(self, report):
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@ -234,17 +252,18 @@ class ExceptionReport(StageHandler):
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commonExceptions = sorted(commonExceptions, None, lambda x: x.counts)
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for common in commonExceptions:
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msg, at, svns, walkers, counts, ids, duration, users = common.toStrings()
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msg, at, svns, walkers, counts, ids, duration, users, userError = common.toStrings()
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print >> self.out, ''.join(['*'] * 80)
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print >> self.out, 'Exception :', msg
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print >> self.out, ' at :', at
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print >> self.out, ' walkers :', walkers
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print >> self.out, ' svns :', svns
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print >> self.out, ' duration :', duration
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print >> self.out, ' occurrences :', counts
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print >> self.out, ' users :', users
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print >> self.out, ' ids :', ids
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print >> self.out, 'Exception :', msg
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print >> self.out, ' is-user-exception? :', userError
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print >> self.out, ' at :', at
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print >> self.out, ' walkers :', walkers
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print >> self.out, ' svns :', svns
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print >> self.out, ' duration :', duration
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print >> self.out, ' occurrences :', counts
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print >> self.out, ' users :', users
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print >> self.out, ' ids :', ids
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class CommonException:
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MAX_SET_ITEMS_TO_SHOW = 5
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@ -254,6 +273,7 @@ class CommonException:
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self.at = ex['exception-at']
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self.svns = set([ex['svn-version']])
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self.users = set([ex['user-name']])
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self.userError = ex['is-user-exception']
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self.counts = 1
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self.times = set([decodeTime(ex['start-time'])])
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self.walkers = set([ex['walker-name']])
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@ -285,11 +305,17 @@ class CommonException:
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return ','.join(s)
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def duration(self):
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x = sorted(self.times)
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return "-".join(map(lambda x: x.strftime("%m/%d/%y"), [x[0], x[-1]]))
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x = sorted(filter(lambda x: x != "ND", self.times))
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if len(x) >= 2:
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return "-".join(map(lambda x: x.strftime("%m/%d/%y"), [x[0], x[-1]]))
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elif len(x) == 1:
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return x[0]
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else:
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return "ND"
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def toStrings(self):
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return [self.bestExample(self.msgs), self.at, self.setString(self.svns), self.setString(self.walkers), self.counts, self.setString(self.ids), self.duration(), self.setString(self.users)]
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return [self.bestExample(self.msgs), self.at, self.setString(self.svns), self.setString(self.walkers), self.counts, self.setString(self.ids), self.duration(), self.setString(self.users), self.userError]
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addHandler('exceptions', ExceptionReport)
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@ -354,7 +380,10 @@ def resolveFiles(paths):
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return allFiles
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def decodeTime(time):
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return datetime.datetime.strptime(time.split()[0], "%Y/%m/%d")
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if time == "ND":
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return "ND"
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else:
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return datetime.datetime.strptime(time.split()[0], "%Y/%m/%d")
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#return datetime.datetime.strptime(time, "%Y/%m/%d %H.%M.%S")
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def passesFilters(elt):
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@ -377,7 +406,12 @@ def readReports(files):
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for file in files:
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if OPTIONS.verbose: print 'Reading file', file
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input = openFile(file)
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tree = ElementTree(file=input)
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try:
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tree = ElementTree(file=input)
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except:
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print "EXCEPTING FILE", file
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raise
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elem = tree.getroot()
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if elem.tag == RUN_REPORT_LIST:
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for sub in elem:
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