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Update Version 2
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added option for auto checking and updating of project downloads
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@mriedel56
mriedel56 authored Sep 12, 2018
1 parent b9db342 commit fda07cd
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Showing 3 changed files with 296 additions and 7 deletions.
202 changes: 202 additions & 0 deletions sub_sess_id.sh
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proj=$1
subid=$2

if [[ $proj == "ABCD_NDAR" ]]; then
tmp_label=$subid
if [[ $tmp_label == "1" ]]; then
sub="YCW83AC7"
sess="S1"
elif [[ $tmp_label == "S1" ]]; then
sub="INV6F1LPHLT"
sess="S1"
elif [[ $tmp_label == "S_1" ]]; then
sub="FDM0PRRA"
sess="S1"
else
sub=$subid
if [[ $sub == *_S* ]]; then
sess=S${sub##*_S}
sub=${sub%_S*}
elif [[ $sub == *-S* ]]; then
sess=S${sub##*-S}
sub=${sub%-S*}
else
sess="S1"
fi
fi
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Parra_MMMM" ]]; then
sub=${subid#$proj-}
sess=${sub##*-}
sub=${sub%-*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Pettit_tDCS" ]]; then
sub=${subid#$proj-}
sess=${sub##*_}
sub=${sub%_*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Sibley_Teen" ]]; then
if [[ $subid == *Sibley_TEEN* ]]; then
sub=${subid#Sibley_TEEN-}
else
sub=${subid#$proj-}
fi
sess=${sub##*-}
sub=${sub%-*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Sutherland_MIP" ]]; then
sub=${subid#$proj-}
sess=S${sub##*S}
if [[ $sub == *-S* ]]; then
sub=${sub%-*}
else
sub=${sub%S*}
fi
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Sutherland_ACE" ]]; then
sub=${subid#$proj-}
sess=${sub##*-}
sub=${sub%-*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Soto_GRT" ]]; then
sub=${subid#$proj-}
if [[ $sub == *0003S1-S1 ]]; then
sub=${sub%-*}
sess="S1"
elif [[ $sub == *0003S1-S2 ]]; then
sub=${sub%-*}
sess="S2"
elif [[ $sub == *0003S2-S2 ]]; then
sub=${sub%-*}
sess="S3"
elif [[ $sub == *0003-S1-S1 ]]; then
sub=${sub%-*}
sub=${sub%-*}
sess="S4"
elif [[ $sub == *0003-S2-S2 ]]; then
sub=${sub%-*}
sub=${sub%-*}
sess="S5"
elif [[ $sub == *0003S3-S3 ]]; then
sub=${sub%-*}
sess="S6"
elif [[ $sub == *0003S4-S4 ]]; then
sub=${sub%-*}
sess="S7"
else
sess=${sub##*-}
sub=${sub%-*}
if [[ $sub == *-S* ]]; then
sess=${sub##*-}
sub=${sub%-*}
elif [[ $sub == *S* ]]; then
sub=${sub%S*}
fi
fi
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Dick_AHEAD" ]]; then
sub=${subid##*$proj-}
if [[ $sub == *_S1 ]]; then
if [[ $sub == *-2_S1 ]]; then
sess="S2"
sub=${sub%-2_S1*}
else
sess="S1"
sub=${sub%-_*}
fi
elif [[ $sub == *_1 ]]; then
echo $subid >> $data_qc/qc-processed/$proj-processed
proj_data=$(cat $data_qc/qc-processed/$proj-processed)
continue
else
sess=${sub##*-}
sub=${sub%-*}
if [[ $sub == *-S* ]]; then
if [[ $sub != *-ST* ]]; then
sub=${sub%-*}
fi
fi
fi
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Dick_TRAIN" ]]; then
sub=${subid#$proj-}
sess=${sub##*-}
sub=${sub%-*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "Mattfeld_RTV" ]]; then
sub=${subid#$proj-}
sess=${sub##*-}
if [[ $sess != S* ]]; then
sub=$sub-S1
sess=${sub##*-}
fi
sub=${sub%-*}
sub=$(echo ${sub//[-_]/})
elif [[ $proj == "McMakin_EMU" ]]; then
tmp_label=$subid
if [[ $tmp_label == "McMakin_EMU_R01_PT-S1-S1" ]]; then
sub="R01_PT"
sess="S1"
elif [[ $tmp_label == "1" ]]; then
sub="000-1001"
sess="S1"
elif [[ $tmp_label == "2" ]]; then
sub="000-1005"
sess="S2"
elif [[ $tmp_label == "S_1" ]]; then
sub="000-1004"
sess="S1"
elif [[ $tmp_label == "S_2" ]]; then
sub="000-1004"
sess="S2"
else
if [[ $tmp_label == MCMAKIN_EMU* ]]; then
sub=${subid#MCMAKIN_EMU-}
else
sub=${subid#$proj-}
fi
if [[ $sub == *_Day2* ]]; then
sess="S2"
sub=${sub%_*}
elif [[ $sub == *_1-S1 ]]; then
sess="S1"
sub=${sub%_*}
elif [[ $sub == *_2-S2 ]]; then
sess="S2"
sub=${sub%_*}
elif [[ $sub == *_1 ]]; then
sess="S1"
sub=${sub%_*}
if [[ $sub == *_* ]]; then
sub=${sub%_*}
fi
elif [[ $sub == *_2 ]]; then
sess="S2"
sub=${sub%_*}
if [[ $sub == *_* ]]; then
sub=${sub%_*}
fi
elif [[ $sub == *_S1 ]]; then
sess="S1"
sub=${sub%_*}
elif [[ $sub == *_S2 ]]; then
sess="S2"
sub=${sub%_*}
else
sess=${sub##*-}
sub=${sub%-*}
if [[ $sub == *-S* ]]; then
sub=${sub%-*}
elif [[ $sub == *S* ]]; then
sub=${sub%S*}
fi
fi
fi
sub=$(echo ${sub//[-_]/})
if [[ $sub == "000" ]]; then
sub="0001002"
sess="S3"
fi
fi

echo $sub $sess
86 changes: 79 additions & 7 deletions xnat_download.sh
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Original file line number Diff line number Diff line change
@@ -1,23 +1,95 @@
if [ ! -e ~/xnatpassfile ]; then
if [ ! -e ~/xnatpassfile ] & [ ! -e ~/xnatconfigfile ]; then
read -p 'Username: ' uservar
read -sp 'Password: ' passvar
printf "{\"password\": \"$passvar\", \"user\": \"$uservar\", \"server\": \"http://xnat.fiu.edu\"}" > ~/xnatpassfile
printf "{\"password\": \"$passvar\", \"user\": \"$uservar\", \"server\": \"http://xnat.fiu.edu\"}" > ~/xnatconfigfile
printf "+$uservar@http://xnat.fiu.edu:8080/xnat=$passvar" > ~/xnatpassfile
fi


while [[ $# -gt 0 ]]; do
case $1 in
-a|--auto) autocheck="$2"; shift;;
-p|--project) proj="$2" ; shift;;
-c|--credentials) passfile="$2" ; shift;;
-o|--outputdir) outdir="$2" ; shift;;
-s|--session) sess="$2" ; shift;;
-s|--session) expsess="$2" ; shift;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1. Try $0 -h" 1>&2; exit 1;;
(*) break;;
esac
shift
done

if [ -e ~/xnatpassfile ]; then
/xget-public/xget -passfile $passfile -s $sess -o $outdir -proj $proj
function download_experiment {

# create a temporary directory with the subject filters
# if the temporary directory exists (it should not), create it
if [ ! -d $outdir/$proj ]; then
mkdir -p $outdir/$proj
fi

# download the subject file into the temporary directory
/xget-public/xget -passfile ~/xnatpassfile -s ${exps[i]} -o $outdir/$proj -proj $proj
unzip $outdir/$proj/${exps[i]}_acq.zip -d $outdir/$proj/
rm $outdir/$proj/${exps[i]}_acq.zip
tar -C $outdir/$proj/${labels[i]} -cf $outdir/$proj/sub-"$sub"_ses-${sess}.tar scans/
rm -r $outdir/$proj/${labels[i]}
printf "sub-%s_ses-%s.tar\n" $sub $sess >> ~/XNAT-data-transfer/$proj-processed

# get date and time
date_time=
date_time=$(date)
# append the email message
echo "Data transferred from XNAT to FIU-HPC for Project: $proj Subject: $sub Session: $sess on $date_time" >> ~/XNAT-data-transfer/$proj-processed-message

}

# call a python script to get a list of experiments in the XNAT project
exps=($(python /scripts/xnat_list.py ~/xnatconfigfile $proj 'experiments'))
labels=($(python /scripts/xnat_list.py ~/xnatconfigfile $proj 'labels'))

#for each subject identified
for ((i=0;i<${#exps[@]};i++)); do
labelinfo=($(bash /scripts/sub_sess_id.sh $proj ${labels[i]}))
sub=${labelinfo[0]}
sess=${labelinfo[1]}
if [[ $autocheck == "y" ]] | [[ $autocheck == "yes" ]]; then

if [ -e ~/XNAT-data-transfer/$proj-processed ]; then
proj_data=`cat ~/XNAT-data-transfer/$proj-processed`
# if the subject has not previously been processed
if [[ $proj_data != *sub-"$sub"_ses-"$sess".tar* ]]; then
download_experiment
fi
else
mkdir ~/XNAT-data-transfer
download_experiment
fi

else
if [[ $expsess == XNAT_* ]]; then
if [[ ${exps[i]} == $expsess ]]; then
if [ ! -e ~/XNAT-data-transfer/$proj-processed ]; then
mkdir ~/XNAT-data-transfer
else
proj_data=`cat ~/XNAT-data-transfer/$proj-processed`
if [[ $proj_data != *sub-"$sub"_ses-"$sess".tar* ]]; then
download_experiment
else
echo "Experiment session has already been downloaded!"
exit
fi
fi
else
echo "Experiment session '$expsess' is not in project '$proj'!"
exit
fi
else
echo "Experiment session should start with 'XNAT_*'!"
exit
fi
fi
done

if [ -e ~/XNAT-data-transfer/$proj-processed-message ]; then
mail -s 'FIU XNAT-HPC Data Transfer Update Project $proj' $USER@fiu.edu < ~/XNAT-data-transfer/$proj-processed-message
rm ~/XNAT-data-transfer/$proj-processed-message
fi
15 changes: 15 additions & 0 deletions xnat_list.py
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#!/usr/bin/env python
from pyxnat import Interface
import sys

config_file = sys.argv[1]
project = sys.argv[2]
ref = sys.argv[3]

central = Interface(config=config_file)
select_exp = '/projects/' + project +'/experiments'
exps = central.select(select_exp).get()
if ref == 'experiments':
print " ".join([str(x) for x in exps])
elif ref == 'labels':
print " ".join([central.select(select_exp + '/' + x).label() for x in exps])

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