From 393df460559b6681c97cd6cf5985b2477f427602 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Feb 2011 12:02:12 +0000
Subject: [PATCH] updates to handle only reporting on a specific SVN revision. 
 Updated the R script to show the domain name of the runner, now that S3
 logging is working

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/GATKRunReport.R           |  8 ++++++--
 python/analyzeRunReports.py | 17 ++++++++++++++++-
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/R/GATKRunReport.R b/R/GATKRunReport.R
index 10088d7e9..599abe25f 100644
--- a/R/GATKRunReport.R
+++ b/R/GATKRunReport.R
@@ -1,3 +1,4 @@
+require("plotrix")
 args = commandArgs(TRUE);
 
 onCMDLine = ! is.na(args[1])
@@ -10,6 +11,9 @@ if ( onCMDLine ) {
    d$end.time = as.Date(d$end.time)
 } # only read into d if its' available, otherwise assume the data is already loaded
 
+# The unknown records are from the Broad
+d$domain.name[d$domain.name == "unknown"] = "broadinstitute.org"
+
 noRecords <- function(name) {
     print(paste("No records", name))
     frame()
@@ -127,7 +131,6 @@ generateOneReport <- function(d, header, includeByWeek = T) {
     reportConditionalCountingPlot(d$user.name, d$walker.name, head("Walker invocations by user"))
     reportCountingPlot(d$svn.version, head("SVN version"))
 	reportConditionalCountingPlot(d$svn.version, d$user.name, head("SVN by user"))
-
     
     # cuts by time
     if ( includeByWeek ) {
@@ -170,6 +173,7 @@ generateOneReport <- function(d, header, includeByWeek = T) {
     reportHist(log10(d$run.time / min), head("Run time (log10[min])"))
 
     reportCountingPlot(d$user.name, head("user"))
+    reportCountingPlot(d$domain.name, head("Domain name"))
     #reportCountingPlot(d$host.name, head("host"))
 
     reportCountingPlot(d$java, head("Java version"))
@@ -177,7 +181,7 @@ generateOneReport <- function(d, header, includeByWeek = T) {
     #reportCountingPlot(d$working.directory, head("Working directory"))
 }
 
-RUNME = T
+RUNME = F
 if ( RUNME ) {
     lastWeek = levels(cut(d$end.time, "weeks"))[-1]
     generateOneReport(d, "Overall")
diff --git a/python/analyzeRunReports.py b/python/analyzeRunReports.py
index 683f40f35..fff4659e0 100755
--- a/python/analyzeRunReports.py
+++ b/python/analyzeRunReports.py
@@ -32,6 +32,10 @@ def main():
                         action='store_true', default=False,
                         help="if provided, only records not coming from a dev version of GATK will be included")
 
+    parser.add_option("", "--rev", dest="rev",
+                        type="string", default=None,
+                        help="if provided, only reports generated by this version of the GATK will be included")
+
     parser.add_option("-E", "", dest="exception_selection",
                         type='choice', choices=['all', 'user', 'sting'], default='all',
                         help="if provided, will only emit records matching of the provided class [default %default]")
@@ -142,6 +146,14 @@ class RecordDecoder:
 
         def formatExceptionUser(elt):
             return '%s' % parseException(elt)[2]
+            
+        def formatDomainName(elt):
+            if elt != None:
+                parts = elt.text.split(".")
+                if len(parts) >= 2:
+                    return '.'.join(parts[-2:])
+                else:
+                    return 'unknown'
         
         def add(names, func):
             for name in names:
@@ -153,7 +165,8 @@ class RecordDecoder:
     
         add(["id", "walker-name", "svn-version", "phone-home-type"], id)
         add(["start-time", "end-time"], toString)      
-        add(["run-time", "java-tmp-directory", "working-directory", "user-name", "host-name"], id)
+        add(["run-time", "java-tmp-directory", "working-directory", "user-name"], id)
+        addComplex("host-name", ["host-name", "domain-name"], [id, formatDomainName])
         add(["java", "machine"], toString)
         add(["max-memory", "total-memory", "iterations", "reads"], id)
         addComplex("exception", ["exception-msg", "exception-at", "exception-at-brief", "is-user-exception"], [formatExceptionMsg, formatExceptionAt, formatExceptionAtBrief, formatExceptionUser])
@@ -443,6 +456,8 @@ def passesFilters(elt):
     if OPTIONS.noDev and eltTagEquals(elt.find('argument-collection'),'phone-home-type','DEV'):
         #print 'skipping', elt
         return False
+    if OPTIONS.rev != None and not eltTagEquals(elt, 'svn-version', OPTIONS.rev):
+        return False
     if OPTIONS.maxDays != None:
         now = datetime.datetime.today()
         now = datetime.datetime(now.year, now.month, now.day)