#!/bin/bash

#cell#

# COPY the data to local disk

# sudo chown -R dlituiev /home/dlituiev/.gsutil/tracker-files

TMPDIR=/tmp/kidney

XMLFILELIST=./xmlfiles.list

mkdir -p $TMPDIR 

LINE=2

for LINE in `seq 1 5`

do

    # PREV_SLIDEID=$(head  /home/dlituiev/metadata/xmlfiles.list | sed -n -e $((${LINE}-1))p | sed 's/\.xml//' )

    # rm "$HOME/tmpdata/${PREV_SLIDEID}.svs"

    SLIDEID=$(head  $XMLFILELIST | sed -n -e ${LINE}p | sed 's/\.xml//' ) || exit 1

    echo $SLIDEID

    SVS="$TMPDIR/${SLIDEID}.svs"

    XML="$TMPDIR/${SLIDEID}.xml"

    if [ -a "$SVS" ] ; then

        echo -e "${SVS}\talready exists"

    else

        gsutil cp gs://kidney-rejection/${SLIDEID}.xml $TMPDIR 

        gsutil cp gs://kidney-rejection/${SLIDEID}.svs $TMPDIR

    fi

    python3 $PWD/sample_from_slide.py --data-root "../data/" --all-grid $XML && rm $SVS

done

if [ $RMTMP ]

then

    rm -rf $TMPDIR

fi