process_inflammation.sh

# bash script to process inflammation data
# call with "http://npk.io/RBzU+"

echo Clean previous runs
rm -r data*

echo Download data
curl -L $1 -o data.zip

sleep 2

echo Unzip
unzip -x data.zip
cd data

sleep 2

echo Available files
ls -a -F

sleep 2

echo Cleanup
rm ._*.csv

mkdir bad_data
mv *broken* *metadata* bad_data/

sleep 2

echo Renaming
todays_date=`date +%Y-%m-%d`
for f in *.csv
do
	mv $f ${f/-/_${todays_date}_}
done

echo Files after renaming
ls *csv

sleep 2

echo Processing
for f in *.csv
do
	echo Processing $f
	/c/Program\ Files/R/R-3.1.0/bin/Rscript.exe plot_inflammation.r $f
    sleep 1
done

echo Move figures
mkdir figures
mv *png figures/

echo Completed