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#!/bin/sh
cmd="$1"
shift
do_download() {
dir="$1"
msk="$2"
nquire -lst ftp.ncbi.nlm.nih.gov "$dir" |
grep "$msk" |
skip-if-file-exists | tee /dev/stderr |
nquire -asp ftp.ncbi.nlm.nih.gov "$dir"
}
prepare_book_list() {
echo "<OpenAccessSubset>"
while IFS=$'\t' read pth titl pblshr dt accn upd
do
if [ -n "$accn" ]
then
echo " <Book>"
echo " <Accn>$accn</Accn>"
echo " <Path>$pth</Path>"
echo " <Title>$titl</Title>"
echo " </Book>"
fi
done
echo "</OpenAccessSubset>"
}
case "$cmd" in
-h | -help | --help | help )
cat <<EOF
USAGE: $0
pmc-oa | pmc-bioc | bioconcepts | generif | meshtree | oa-list | oa-book | carotene
EOF
exit 0
;;
pmc-oa | -pmc-oa )
do_download "pub/pmc/oa_bulk" "xml.tar.gz"
exit 0
;;
pmc-bioc | -pmc-bioc )
do_download "pub/wilbur/BioC-PMC" "xml_unicode.tar.gz"
exit 0
;;
bioconcepts | -bioconcepts )
do_download "pub/lu/PubTatorCentral" "chemical2pubtatorcentral.gz"
do_download "pub/lu/PubTatorCentral" "disease2pubtatorcentral.gz"
do_download "pub/lu/PubTatorCentral" "gene2pubtatorcentral.gz"
exit 0
;;
generif | -generif | generifs | -generifs )
do_download "gene/GeneRIF" "generifs_basic.gz"
do_download "gene/DATA" "gene_info.gz"
if [ ! -f "geneconv.xml" ]
then
gunzip -c gene_info.gz |
grep -v NEWENTRY |
grep -v GeneID |
cut -f 2,3,9 |
transmute -t2x -set Set -rec Rec Code Name Desc |
transmute -format indent > geneconv.xml
fi
if [ ! -f "genename.txt" ]
then
cat geneconv.xml |
xtract -pattern Rec -element Code Name > genename.txt
fi
exit 0
;;
meshtree | -meshtree )
if [ ! -f "desc2021.xml" ]
then
echo "desc2021.xml"
nquire -dwn "ftp://nlmpubs.nlm.nih.gov" "online/mesh/MESH_FILES/xmlmesh" "desc2021.zip"
unzip -qq desc2021.zip
rm desc2021.zip
chmod og-wx desc2021.xml
chmod u-x desc2021.xml
fi
if [ ! -f "pa2021.xml" ]
then
echo "pa2021.xml"
nquire -dwn "ftp://nlmpubs.nlm.nih.gov" "online/mesh/MESH_FILES/xmlmesh" "pa2021.xml"
fi
if [ ! -f "qual2021.xml" ]
then
echo "qual2021.xml"
nquire -dwn "ftp://nlmpubs.nlm.nih.gov" "online/mesh/MESH_FILES/xmlmesh" "qual2021.xml"
fi
if [ ! -f "supp2021.xml" ]
then
echo "supp2021.xml"
nquire -dwn "ftp://nlmpubs.nlm.nih.gov" "online/mesh/MESH_FILES/xmlmesh" "supp2021.zip"
unzip -qq supp2021.zip
rm supp2021.zip
chmod og-wx supp2021.xml
chmod u-x supp2021.xml
fi
if [ ! -f "meshconv.xml" ]
then
cat supp2021.xml |
xtract -wrp "Set,Rec" -pattern SupplementalRecord \
-if "SupplementalRecord@SCRClass" -eq 1 \
-or "SupplementalRecord@SCRClass" -eq 3 \
-wrp "Code" -element "SupplementalRecord/SupplementalRecordUI" \
-wrp "Name" -encode "SupplementalRecordName/String" \
-wrp "Term" -encode "Term/String" > meshtemp.xml
cat desc2021.xml |
xtract -wrp "Set,Rec" -pattern DescriptorRecord \
-wrp "Code" -element "DescriptorRecord/DescriptorUI" \
-wrp "Name" -first "DescriptorName/String" \
-wrp "Term" -encode "Term/String" \
-wrp "Tree" -element "TreeNumberList/TreeNumber" >> meshtemp.xml
cat meshtemp.xml | xtract -wrp Set -pattern Rec -sort Code |
transmute -format indent > meshconv.xml
rm meshtemp.xml
fi
if [ ! -f "meshtree.txt" ]
then
cat meshconv.xml |
xtract -pattern Rec -if Tree -element Code -sep "," -element Tree > meshtree.txt
fi
if [ ! -f "meshname.txt" ]
then
cat meshconv.xml |
xtract -pattern Rec -if Name -element Code -sep "," -element Name > meshname.txt
fi
if [ ! -f "chemconv.xml" ]
then
cat supp2021.xml |
xtract -wrp "Set,Rec" -pattern SupplementalRecord \
-if "SupplementalRecord@SCRClass" -eq 1 \
-wrp "Code" -element "SupplementalRecord/SupplementalRecordUI" \
-wrp "Name" -encode "SupplementalRecordName/String" \
-wrp "Term" -encode "Term/String" > chemtemp.xml
cat desc2021.xml |
xtract -wrp "Set,Rec" -pattern DescriptorRecord \
-if TreeNumber -starts-with D \
-wrp "Code" -element "DescriptorRecord/DescriptorUI" \
-wrp "Name" -first "DescriptorName/String" \
-wrp "Term" -encode "Term/String" \
-wrp "Tree" -element "TreeNumberList/TreeNumber" >> chemtemp.xml
cat chemtemp.xml | xtract -wrp Set -pattern Rec -sort Code |
transmute -format indent > chemconv.xml
rm chemtemp.xml
fi
if [ ! -f "diszconv.xml" ]
then
cat supp2021.xml |
xtract -wrp "Set,Rec" -pattern SupplementalRecord \
-if "SupplementalRecord@SCRClass" -eq 3 \
-wrp "Code" -element "SupplementalRecord/SupplementalRecordUI" \
-wrp "Name" -encode "SupplementalRecordName/String" \
-wrp "Term" -encode "Term/String" > disztemp.xml
cat desc2021.xml |
xtract -wrp "Set,Rec" -pattern DescriptorRecord \
-if TreeNumber -starts-with C \
-wrp "Code" -element "DescriptorRecord/DescriptorUI" \
-wrp "Name" -first "DescriptorName/String" \
-wrp "Term" -encode "Term/String" \
-wrp "Tree" -element "TreeNumberList/TreeNumber" >> disztemp.xml
cat disztemp.xml | xtract -wrp Set -pattern Rec -sort Code |
transmute -format indent > diszconv.xml
rm disztemp.xml
fi
exit 0
;;
oa-list | -oa-list )
if [ ! -f "books.xml" ]
then
nquire -ftp ftp.ncbi.nlm.nih.gov pub/litarch file_list.txt |
prepare_book_list > books.xml
fi
exit 0
;;
oa-book | -oa-book )
accn="$1"
shift
if [ ! -f "books.xml" ]
then
nquire -ftp ftp.ncbi.nlm.nih.gov pub/litarch file_list.txt |
prepare_book_list > books.xml
fi
cat books.xml |
xtract -pattern Book -if Accn -equals "$accn" -element Path |
while read pth
do
if [ ! -f "$pth" ]
then
nquire -dwn ftp.ncbi.nlm.nih.gov "pub/litarch" "$pth"
fi
done
exit 0
;;
carotene | -carotene )
if [ ! -f "carotene.xml" ]
then
nquire -asp ftp.ncbi.nlm.nih.gov "entrez/entrezdirect/samples" "carotene.xml.zip"
unzip -qq carotene.xml.zip
rm carotene.xml.zip
fi
exit 0
;;
-natural-earth )
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_countries.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_disputed_areas.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_1_states_provinces.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_geography_marine_polys.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_lakes.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_minor_islands.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_reefs.zip"
curl -Ls -O "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_rivers_lake_centerlines.zip"
exit 0
;;
* )
break
;;
esac
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