jackman/linux-bin
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

spring library

Browse Source
This commit is contained in:
ackman678
2021-04-08 20:52:17 -07:00
parent 6e92164bc3
commit 980e493cf7
5 changed files with 95 additions and 57 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
pdf2bib.sh
View File

@@ -31,23 +31,24 @@ echo "using $bibdFileOut"
#try to extract doi from pdf and retrieve a pubmed id
#for 'DOI:' syntax
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi:" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi:(.+)#\1#")
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi:" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|doi:(.+)|\1|")
doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi:? ?/?10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.*doi:? ?/?(10.+)#\1#")
# search for doi string between first page last page 10
doi=$(pdftotext -q -f 1 -l 10 $fn - | grep -iE "doi:? ?/?10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.*doi:? ?/?(10.+)|\1|")
#for 'https://doi.org' syntax
if [ -z "$doi" ]; then
doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi\.org/10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.+doi\.org/(10.+)#\1#")
doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi\.org/10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.+doi\.org/(10.+)|\1|")
fi
# for 'https://doi.org' syntax
# if [ -z "$doi" ]; then
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.+doi\.org\/(.+)#\1#")
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.+doi\.org\/(.+)|\1|")
# fi
#
# if [ -z "$doi" ]; then
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi ?" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi ?(.+)#\1#")
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi ?" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|doi ?(.+)|\1|")
# fi
if [ -z "$doi" ]; then
@@ -57,7 +58,7 @@ fi
## TODO: dedupe this with sdoi.sh
uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s|<Id>([0-9]+)</Id>|\1|")
if [ -z "$uid" ]; then
echo "pubmed id not found"
@@ -70,13 +71,13 @@ xsltproc --novalid $styleSheet $uid.xml > $uid.bib
#extract some strings to make a nice filename for the pdf
key="LastName";
author=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
author=$(grep $key --max-count=1 $uid.xml | sed -E "s|\W*<$key>(.+)</$key>\W*|\1|" | tr -d " ")
key="MedlineTA";
journal=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
journal=$(grep $key --max-count=1 $uid.xml | sed -E "s|\W*<$key>(.+)</$key>\W*|\1|" | tr -d " ")
key1="PubDate";
key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s#\W*<$key2>(.+)</$key2>\W*#\1#")
key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s|\W*<$key2>(.+)</$key2>\W*|\1|")
fn2=${author}_${journal}$year-$uid.pdf