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dedupe fixes

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ackman678
2021-10-19 00:34:23 -07:00
parent 2c2f3bdf77
commit 0790cf9c4a
3 changed files with 26 additions and 14 deletions
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5
reveal.sh
View File

@@ -29,6 +29,11 @@ if [[ ! -e $basefn ]]; then
ln -s $fn $basefn
fi
#add markdown filename into html title tag
fn2=$(echo $basefn | sed -E 's/[0-9]{2,4}-//g' | sed 's/\.md//') #prep filename
sed -i -E "s|(<title>).+(<\/title>)|\1$fn2\2|" index.html #swap in document title
#add markdown filename to reveal placeholder start file
sed -i -E "s|(<section data-markdown=\")[A-Za-z0-9\.-]*(\" )|\1$basefn\2|" index.html
npm start -- --port=$portNumber

29
sdoi.sh
View File

@@ -1,7 +1,7 @@
#!/bin/bash
if [ "$1" == "-h" ] ; then
echo "
sdoi - search for doi guid on pubmed and append bibtex entry to bibtex db. Optionally import a downloaded pdf.
sdoi - search for a unique identifier (doi or pmid) on doi.org and/or pubmed and append bibtex entry to bibtex db. Optionally import a downloaded pdf.
usage:
sdoi.sh 'doi'
@@ -49,18 +49,19 @@ fetchBib_pubmed() {
}
fetchBib_doiDotOrg() {
#request bibtex from doi.org
echo "pubmed id not found, trying doi.org.."
curl -LH 'Accept: application/x-bibtex' "http//dx.doi.org/"$doi >> $tmpBib
curl -LH 'Accept: application/x-bibtex' "https//dx.doi.org/"$doi >> $tmpBib
echo -e "\n" >> $tmpBib
}
extract_name() {
#extract some strings to make a nice filename for the pdf
key="LastName";
author=$(xmllint --xpath "string(//$key)" $tmpBib.xml)
author=$(xmllint --xpath "string(//$key)" $tmpBib.xml | tr -d ' ')
key="MedlineTA";
journal=$(xmllint --xpath "string(//$key)" $tmpBib.xml)
journal=$(xmllint --xpath "string(//$key)" $tmpBib.xml | tr -d ' ')
key="Year";
year=$(xmllint --xpath "string(//$key)" $tmpBib.xml)
@@ -79,24 +80,31 @@ append_bibfile() {
append_pdf() {
fn2=${author}_${journal}$year-$uid.pdf
echo $fn2
#move pdf file to papers repository, add file name to bibtex url field
fn2=${author}_${journal}$year-$uid.pdf
echo "moving $fn to $pdfPathOut/$fn2"
mv $fn $pdfPathOut/$fn2
echo "moved to $pdfPathOut/$fn2"
#insert local path to pdf into the retrieved bibtex url field
sed -i -E "s|(\W*url = \{).*(\}.*)|\1$relPath/$fn2\2|" $tmpBib
}
clean_up() {
#clean up
rm -f $tmpBib $tmpBib.xml
rm -f $tmpBib.bib $tmpBib.bib.xml
exit 1
}
#main
uid=$(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|")
#main function
##test whether the given unique identifier (doi) is an actual doi, else assume its a pmid
if [[ -z $(echo $doi | grep "^10." -) ]]; then
searchField="pmid"
else
searchField="doi"
fi
uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=$searchField&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s|<Id>([0-9]+)</Id>|\1|")
tmpBib=$(mktemp -p ./ --suffix=.bib)
@@ -110,6 +118,5 @@ if [ -s "$tmpBib" ]; then
import_bib
else
echo "sorry, doi not found.."
clean_up
fi

6
spmid.sh
View File

@@ -45,17 +45,17 @@ fetchBib_pubmed() {
fetchBib_doiDotOrg() {
echo "pubmed id not found, trying doi.org.."
curl -LH 'Accept: application/x-bibtex' "http//dx.doi.org/"$doi >> $tmpBib
curl -LH 'Accept: application/x-bibtex' "https//dx.doi.org/"$doi >> $tmpBib
echo -e "\n" >> $tmpBib
}
extract_name() {
#extract some strings to make a nice filename for the pdf
key="LastName";
author=$(xmllint --xpath "string(//$key)" $tmpBib.xml)
author=$(xmllint --xpath "string(//$key)" $tmpBib.xml | tr -d ' ')
key="MedlineTA";
journal=$(xmllint --xpath "string(//$key)" $tmpBib.xml)
journal=$(xmllint --xpath "string(//$key)" $tmpBib.xml | tr -d ' ')
key="Year";
year=$(xmllint --xpath "string(//$key)" $tmpBib.xml)