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|
#!/bin/sh
while [ $# -gt 0 ]
do
case "$1" in
-path )
shift
;;
-* )
exec >&2
echo "$0: Unrecognized option $1"
exit 1
;;
* )
break
;;
esac
done
if [ "$#" -gt 0 ]
then
target="$1"
MASTER=$(cd "$target" && pwd)
CONFIG=${MASTER}
shift
else
if [ -z "${EDIRECT_PUBMED_MASTER}" ]
then
echo "Must supply path to master archive area or set EDIRECT_PUBMED_MASTER environment variable"
exit 1
else
MASTER="${EDIRECT_PUBMED_MASTER}"
MASTER=${MASTER%/}
fi
fi
while [ $# -gt 0 ]
do
case "$1" in
-temp | -work | -working )
shift
;;
-* )
exec >&2
echo "$0: Unrecognized option $1"
exit 1
;;
* )
break
;;
esac
done
if [ "$#" -gt 0 ]
then
working="$1"
WORKING=$(cd "$working" && pwd)
shift
else
if [ -z "${EDIRECT_PUBMED_WORKING}" ]
then
WORKING=${MASTER}
else
WORKING="${EDIRECT_PUBMED_WORKING}"
WORKING=${WORKING%/}
fi
fi
echo "MASTER $MASTER"
echo "WORKING $WORKING"
for dir in Archive Postings
do
mkdir -p "$MASTER/$dir"
done
for dir in Current Data Indexed Inverted Merged Pubmed
do
mkdir -p "$WORKING/$dir"
done
date
seconds_start=$(date "+%s")
echo "Removing Intermediate Indices"
cd "$WORKING/Indexed"
target="$WORKING/Indexed"
find "$target" -name "*.e2x" -delete
find "$target" -name "*.e2x.gz" -delete
cd "$WORKING/Inverted"
target="$WORKING/Inverted"
find "$target" -name "*.inv" -delete
find "$target" -name "*.inv.gz" -delete
cd "$WORKING/Merged"
target="$WORKING/Merged"
find "$target" -name "*.mrg" -delete
find "$target" -name "*.mrg.gz" -delete
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
CLR=$seconds
seconds_start=$(date "+%s")
echo "Expanding Current PubMed Archive"
cd "$WORKING/Current"
gunzip *.xml.gz
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
EXP=$seconds
echo "CLR $CLR seconds"
echo "EXP $EXP seconds"
echo ""
date
|
