diff --git a/f b/f index d26e934..fbce109 100755 --- a/f +++ b/f @@ -8,9 +8,10 @@ if [ "$1" == "-h" ] ; then depends: fzf + bat grep, git-grep, or ripgrep zathura (or other fast pdf viewer) - pdf2bib.sh - handles saving to your bib db + spdf.sh - handles saving to your bib db " exit 0 fi @@ -33,6 +34,8 @@ if [ -z "$1" ]; then else # rg $1 | fzf --delimiter : --preview 'less {1}' \ - rg $1 | fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {}' \ + # todo: replace this with a series elif blocks mapping selective previews and downstream application bindings to a set of desired filetypes + ls *.$1 | fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {}' \ --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" fi + diff --git a/readme.md b/readme.md deleted file mode 100644 index 4340901..0000000 --- a/readme.md +++ /dev/null @@ -1,2 +0,0 @@ -Some dotfiles for operating a system. - diff --git a/spmid.sh b/spmid.sh deleted file mode 100755 index f73190b..0000000 --- a/spmid.sh +++ /dev/null @@ -1,103 +0,0 @@ -#!/bin/bash -if [ "$1" == "-h" ] ; then - echo " - spmid - search for pubmed guid and append bibtex entry to bibtex db. Optionally import an associated pdf. - usage: - spmid.sh '12345678' - spmid.sh '12345678' download.pdf - - " - exit 0 -fi - -#TODO: deprecate this function, add pmid logic into sdoi - -set -e #exit if an error -# set -v -x -e #debugging - -#Setup defaults -uid=$1 -fn=$2 -styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl} -bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib} -pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers} -relPath=$(basename $pdfPathOut) - -#define functions -import_bib() { - #decide whether to process and move an associated pdf or just exit - if [ -z "$fn" ]; then - append_bibfile - clean_up - else - extract_name - append_pdf - append_bibfile - clean_up - fi -} - -fetchBib_pubmed() { - #request pubmed xml and transform into bibtex - curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $tmpBib.xml - xsltproc --novalid $styleSheet $tmpBib.xml > $tmpBib -} - -fetchBib_doiDotOrg() { - echo "pubmed id not found, trying doi.org.." - curl -LH 'Accept: application/x-bibtex' "https//dx.doi.org/"$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)" $tmpBib.xml | tr -d ' ') - - key="MedlineTA"; - journal=$(xmllint --xpath "string(//$key)" $tmpBib.xml | tr -d ' ') - - key="Year"; - year=$(xmllint --xpath "string(//$key)" $tmpBib.xml) -} - -append_bibfile() { - #import bibtex - #first grep for a uid (doi) in case its already in db - if [[ -z $(rg $doi $bibdFileOut) ]]; then - echo "importing $tmpBib" - cat $tmpBib >> $bibdFileOut - else - echo "$doi already found in $bibdFileOut, exiting" - fi -} - - -append_pdf() { - fn2=${author}_${journal}$year-$uid.pdf - #move pdf file to papers repository, add file name to bibtex url field - mv $fn $pdfPathOut/$fn2 - echo "moved to $pdfPathOut/$fn2" - sed -i -E "s|(\W*url = \{).*(\}.*)|\1$relPath/$fn2\2|" $tmpBib -} - - -clean_up() { - #clean up - rm -f $tmpBib $tmpBib.xml - exit 1 -} - - -#main -tmpBib=$(mktemp -p ./ --suffix=.bib) - -fetchBib_pubmed - -if [ -s "$tmpBib" ]; then - import_bib -else - echo "sorry, doi not found.." - clean_up -fi -