dedupe

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
+

readme.md

@@ -1,2 +0,0 @@
-Some dotfiles for operating a system.
-

spmid.sh

@@ -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
-