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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=${WORKING%/}
fi
fi
for dir in Archive Postings
do
mkdir -p "$MASTER/$dir"
done
for dir in Indexed Inverted Merged Pubmed
do
mkdir -p "$WORKING/$dir"
done
if [ ! -f "$MASTER/Archive/CACHEDIR.TAG" ]
then
pm-prepare "$MASTER/Archive"
fi
seconds_start=$(date "+%s")
echo "Downloading PubMed Files"
cd "$WORKING/Pubmed"
download-pubmed baseline updatefiles
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
DWN=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Populating PubMed Archive"
pm-stash "$MASTER/Archive"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
POP=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Refreshing Versioned Records"
pm-refresh "$MASTER/Archive"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
REF=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Indexing PubMed Records"
pm-index "$MASTER/Archive" "$WORKING/Indexed"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
IDX=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Inverting PubMed Indices"
cd "$WORKING/Indexed"
pm-invert "$WORKING/Inverted"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
INV=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Merging Inverted Indices"
cd "$WORKING/Inverted"
pm-merge "$WORKING/Merged"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
MRG=$seconds
echo ""
seconds_start=$(date "+%s")
echo "Producing Postings Files"
cd "$WORKING/Merged"
pm-promote "$MASTER/Postings"
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
PST=$seconds
echo ""
echo "DWN $DWN seconds"
echo "POP $POP seconds"
echo "REF $REF seconds"
echo "IDX $IDX seconds"
echo "INV $INV seconds"
echo "MRG $MRG seconds"
echo "PST $PST seconds"
echo ""
phrase-search -path "$MASTER/Postings" -query "mapping of spatio-temporal pollution status AND 2008 [YEAR]" |
fetch-pubmed -path "$MASTER/Archive" |
xtract -pattern Author -if Affiliation -contains Medicine \
-pfx "Archive and Index are " -element Initials
echo ""
if [ -n "$CONFIG" ]
then
target=bash_profile
if ! grep "$target" "$HOME/.bashrc" >/dev/null 2>&1
then
if [ ! -f $HOME/.$target ] || grep 'bashrc' "$HOME/.$target" >/dev/null 2>&1
then
target=bashrc
fi
fi
echo ""
echo "For convenience, please execute the following to save the archive path to a variable:"
echo ""
echo " echo \"export EDIRECT_PUBMED_MASTER='${CONFIG}'\" >>" "\$HOME/.$target"
echo ""
fi
|
