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|
#!/bin/sh
# Public domain notice for all NCBI EDirect scripts is located at:
# https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE
doall=false
dofresh=false
flag="none"
while [ $# -gt 0 ]
do
case "$1" in
-strict )
flag="strict"
shift
;;
-mixed )
flag="mixed"
shift
;;
-path )
shift
;;
-all )
doall=true
shift
;;
-fresh )
dofresh=true
shift
;;
-* )
exec >&2
echo "$0: Unrecognized option $1"
exit 1
;;
* )
break
;;
esac
done
if [ "$#" -gt 0 ]
then
argument="$1"
target=$(cd "$argument" && pwd)
target=${target%/}
case "$target" in
*/Archive ) ;;
* ) target=$target/Archive ;;
esac
else
if [ -z "${EDIRECT_PUBMED_MASTER}" ]
then
echo "Must supply path to archive files or set EDIRECT_PUBMED_MASTER environment variable"
exit 1
else
MASTER="${EDIRECT_PUBMED_MASTER}"
MASTER=${MASTER%/}
target="$MASTER/Archive"
fi
fi
osname=`uname -s | sed -e 's/_NT-.*$/_NT/; s/^MINGW[0-9]*/CYGWIN/'`
if [ "$osname" = "CYGWIN_NT" -a -x /bin/cygpath ]
then
target=`cygpath -w "$target"`
fi
target=${target%/}
HEAD=$(cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd">
<PubmedArticleSet>
EOF
)
TAIL=$(cat <<EOF
</PubmedArticleSet>
EOF
)
if [ "$doall" = true ]
then
mx=$(
for dr in "$target"/*
do
if [ -d "$dr" ]
then
bs=$(basename "$dr")
echo "$bs"
fi
done |
sort -n | tail -n 1
)
maximum=$(((mx + 1) * 1000000))
fr=0
chunk_size=250000
to=$((chunk_size - 1))
loop_max=$((maximum / chunk_size))
echo "$HEAD"
seq 1 $loop_max | while read n
do
seq -f "%0.f" $fr $to | rchive -gzip -fetch "$target"
fr=$((fr + chunk_size))
to=$((to + chunk_size))
perl -e "select(undef, undef, undef, 0.1)"
done
echo "$TAIL"
elif [ "$dofresh" = true ]
then
mx=$(
for dr in "$target"/*
do
if [ -d "$dr" ]
then
bs=$(basename "$dr")
echo "$bs"
fi
done |
sort -n | tail -n 1
)
maximum=$(((mx + 1) * 1000000))
fr=0
chunk_size=250000
to=$((chunk_size - 1))
loop_max=$((maximum / chunk_size))
seq 1 $loop_max | while read n
do
base=$(printf pubmed%03d $n)
if [ -f "$base.xml.gz" ]
then
fr=$((fr + chunk_size))
to=$((to + chunk_size))
continue
fi
if [ -f "$base.xml" ]
then
continue
fi
echo "$base XML"
seconds_start=$(date "+%s")
seq -f "%0.f" $fr $to | rchive -gzip -fetch "$target" -head "<PubmedArticleSet>" -tail "</PubmedArticleSet>" > "$base.xml"
fr=$((fr + chunk_size))
to=$((to + chunk_size))
seconds_end=$(date "+%s")
seconds=$((seconds_end - seconds_start))
echo "$seconds seconds"
fsize=$(wc -c < "$base.xml")
if [ "$fsize" -le 300 ]
then
rm "$base.xml.gz"
exit 0
fi
perl -e "select(undef, undef, undef, 0.1)"
done
else
echo "$HEAD"
rchive -gzip -flag "$flag" -fetch "$target"
echo "$TAIL"
fi
|
