From d9532ecf537bcc47427128f08e59ae927f73eb3d Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Feb 2011 12:58:48 +0000
Subject: [PATCH] Better run reporting structure.  Now text report is attached
 as well as inline in the email, so you can easily view it in fix width fonts!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5158 348d0f76-0448-11de-a6fe-93d51630548a
---
 shell/runGATKReport.csh | 40 +++++++++++++++++++++++++++-------------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/shell/runGATKReport.csh b/shell/runGATKReport.csh
index b7cd22e00..f76227f57 100755
--- a/shell/runGATKReport.csh
+++ b/shell/runGATKReport.csh
@@ -12,29 +12,40 @@ setenv DATE `date +"%m_%d_%Y"`
 setenv ARCHIVE $ARCHIVE_DIR/$DATE
 setenv SUMMARY $SUMMARY_DIR/$DATE
 setenv GATK ~/dev/GenomeAnalysisTK/trunk
+setenv GATK_RELEASE_VERSION `ls -l /humgen/gsa-hpprojects/GATK/bin/current | sed 's/.*GenomeAnalysisTK-//'`
+
+rm -f report.txt 
 
 cd $DIR
 
-echo "Archiving recently submitted jobs"
-python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D
+echo "\n####################\nArchiving recently submitted jobs" >> report.txt
+#python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D >> report.txt
 
-echo "All runs"
-python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1
+echo "Released version, all runs" >> report.txt
+#python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --rev $GATK_RELEASE_VERSION >> report.txt
+#python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
+python $GATK/python/analyzeRunReports.py summary $ARCHIVE_DIR/*.gz --rev $GATK_RELEASE_VERSION >> report.txt
+python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
 
-echo "No-dev"
-python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 --no-dev
-python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz --max_days 1 -E sting --no-dev
+echo "\n####################\nAll runs" >> report.txt
+python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 >> report.txt
+python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --max_days 1 >> report.txt
 
-echo "Archive directory contents"
-du -sh $ARCHIVE_DIR
+echo "\n####################\nLast day, all versions" >> report.txt
+python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 --no-dev >> report.txt
+python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz --max_days 1 -E sting --no-dev >> report.txt
 
-foreach maxDays ( 7 30 360 ) 
+#echo "Archive directory contents"
+#du -sh $ARCHIVE_DIR
+
+if (1 == 1) then
+foreach maxDays ( 30 360 ) 
     echo "Creating table"
     setenv table $ARCHIVE.${maxDays}_days.table
-    python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays
+    python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays 
 
     echo "Creating summary"
-    Rscript $GATK/R/GATKRunReport.R $table $SUMMARY.${maxDays}_days.pdf "of previous $maxDays days" 
+    Rscript $GATK/R/GATKRunReport.R $table $SUMMARY.${maxDays}_days.pdf "of previous $maxDays days"
 
     echo "Creating exception report"
     python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.sting.exceptions.txt --max_days $maxDays -E sting --no-dev
@@ -42,5 +53,8 @@ foreach maxDays ( 7 30 360 )
 
     rm $table
 end
+endif
+
+#echo "GATK daily run report" | mutt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK Run report PDFs for $DATE" gsamembers
+cat report.txt | mutt -a report.txt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK run report for $DATE" depristo 
 
-echo "GATK daily run report" | mutt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK Run report PDFs for $DATE" gsamembers