new things

bibview

@@ -0,0 +1,30 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+    bibview - search for citekey in a bibjson.json and preview pdf
+         usage:
+          bibview
+
+         depends: 
+          fzf
+          zathura (or other fast pdf viewer)
+
+         defaults:
+          Set the required default file locations (csl file, bib file)
+ 
+    "
+    exit 0
+fi
+#Setup defaults
+bibdFile=${2:-$HOME/projects/bibd/OMEGA.json}
+#pandoc-citeproc --bib2json ~/projects/bibd/OMEGA.bib > OMEGA.json
+cd $(dirname $bibdFile)
+set -e #exit if an error
+
+# export citeKey=$1
+# doiStr=$(jq -r '.[] | select(.id==env.citeKey).DOI' $bibdFile)
+# urlStr=$(jq -r '.[] | select(.id==env.citeKey).URL' $bibdFile)
+
+#actually this is the good one, opens pdfs quickly
+jq -r '.[] | [.id, .title, .abstract, .keyword, .DOI, .PMID, .author[]?.family, .issued[]?[0]?[0], .["container-title"], .URL] | join("  ")' $bibdFile | fzf --preview 'echo {}' --preview-window=:up:70%:wrap --bind "enter:execute-silent(zathura {-1} &)"
+

cp2figs.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+          cp2figs.sh - copy and convert image to figure assets folder and put html figure string containing relative link to the asset on system clipboard
+               - converts to a smaller asset size for html presentation
+               - default figure assets set as HOME/figures
+    
+              Usage: cp2figs.sh img.jpg 
+                     cp2figs.sh img.jpg ~/myproject/assets
+    "
+    exit 0
+fi
+
+set -e
+
+# fn=$(basename $1)
+fn=$1
+#default image location
+# blobFolder=$HOME/figures
+blobFolder=${2:-$HOME/figures}
+
+#TODO: add xorg-x11 vs wayland logic here
+# wayland: use "wl-copy"
+#xorg-x11: use "xclip -selection clipboard"
+
+origHash=$(md5sum $fn | cut -d ' ' -f 1 | cut -c -7)
+
+newName=$blobFolder/$(basename -s .jpg $fn)_$origHash.jpg
+cp $fn $newName 
+convert -resize 1280x1280 -quality 90 $newName $newName
+
+echo "<figure><img src=\""$(basename $blobFolder)/$(basename $newName)"\" width=\"500px\"><figcaption></figcaption></figure>" | wl-copy 

f

@@ -0,0 +1,43 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+    f - fuzzy preview and open text files or pdfs
+         usage:
+          f 
+          f p
+
+         depends: 
+          fzf
+          grep, git-grep, or ripgrep
+          zathura (or other fast pdf viewer)
+          pdf2bib.sh - handles saving to your bib db
+    "
+    exit 0
+fi
+
+#Setup defaults
+# cslFile=${2:-$HOME/projects/bibd/bibd-md.csl}
+# bibdFile=${3:-$HOME/projects/bibd/OMEGA.bib}
+# cd $(dirname $bibdFile)
+set -e #exit if an error
+inFlag=${1:-"-i --files"}
+
+
+if [ "$1" == "p" ]; then
+
+    ls *.pdf | fzf --preview 'pdftotext -l 2 -nopgbrk -q {1} -' \
+        --preview-window=up:70% --bind "enter:execute-silent(zathura {} &)" \
+        --bind "ctrl-s:execute(pdf2bib.sh {})+reload(ls *.pdf)"
+    exit 1
+fi
+
+if [ -z "$1" ]; then
+    #FZF_DEFAULT_COMMAND=rg -i --files --glob "!.git/*"
+    fzf --delimiter : --preview 'less {1}' \
+        --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
+
+else
+
+    rg $1 | fzf --delimiter : --preview 'less {1}' \
+        --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
+fi

pdf2bib.sh

@@ -31,13 +31,25 @@ 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#")
+
 
 #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 -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 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.+doi\.org\/(.+)#\1#")
+# fi
+# 
+# if [ -z "$doi" ]; then
+# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi ?" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi ?(.+)#\1#")
+# fi
+
 if [ -z "$doi" ]; then
   echo "doi not found"
   exit 1

pdfsplit

@@ -0,0 +1,31 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+        pdfsplit - extract a range of pdf pages with ghostscript
+
+         usage:
+          pdfsplit firstPage lastPage inputFile.pdf
+
+        output file will be named inputfile_pXX-pYY.pdf
+
+         depends:
+          gs - ghostscript 
+
+          "
+    exit 0
+fi
+
+# the following is from a stackoverflow answer
+# function pdfsplit()
+# {
+    # this function uses 3 arguments:
+    #     $1 is the first page of the range to extract
+    #     $2 is the last page of the range to extract
+    #     $3 is the input file
+    gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dSAFER \
+       -dFirstPage=${1} \
+       -dLastPage=${2} \
+       -sOutputFile=${3%.pdf}_p${1}-p${2}.pdf \
+       ${3}
+# }
+

reveal.sh

@@ -5,7 +5,7 @@ if [ "$1" == "-h" ] ; then
               Useful for serving markdown text files locally with reveal.js
               
               Usage: reveal.sh neuroanatomy1.md
-
+                     reveal.sh neuroanatomy1.md 8001
     "
     echo "$(tput setaf 6)$EDITOR $(tput setaf 7)is currently set as editor"
     exit 0
@@ -13,8 +13,9 @@ fi
 
 set -e
 
-
-appPath="$HOME/projects/dev/reveal.js"
+# appPath="$HOME/projects/dev/reveal.js"
+appPath="$HOME/projects/archive/external/reveal.js"
+portNumber=${2:-8000}
 
 if [[ ! -d $appPath ]]; then
     echo "reveal.js not found"
@@ -30,5 +31,5 @@ fi
 
 #add markdown filename to reveal placeholder start file
 sed -i -E "s|(<section data-markdown=\")[A-Za-z0-9\.-]*(\" )|\1$fn\2|" index.html
-npm start
-
+npm start -- --port=$portNumber
+# npm start 

sbib

@@ -0,0 +1,68 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+    sbib - search for citekey in a bibtex.bib (or maybe eventually bibjson.json) file and return a bibliography entry in markdown or possibly other format
+         usage:
+          sbib
+          # use 'a' flag to search all 
+          sbib a
+          # pass a custom citation style and database
+          sbib a citeprocStyle.csl bibdFile.json
+
+         depends: 
+          fzf
+          git grep
+          pandoc
+          pandoc-citeproc
+          wl-copy
+
+         defaults:
+          Set the required default file locations (csl file, bib file)
+ 
+    "
+    exit 0
+fi
+
+#Setup defaults
+cslFile=${2:-$HOME/projects/bibd/bibd-md.csl}
+bibdFile=${3:-$HOME/projects/bibd/OMEGA.bib}
+cd $(dirname $bibdFile)
+set -e #exit if an error
+
+#set pattern to the null character '\0' for search all, else search only cite keys
+if [ "$1" == "a" ]; then
+    sPattern='\0'
+else
+    sPattern="@[a-zA-Z_-]+\{"
+fi
+
+# Use fzf to search citation
+# Initial scroll offset is set to the line number of each line
+# of git grep output *minus* 5 lines (-5)
+# str=$(cat $fn | fzf)
+
+# str=$(git grep -E --line-number $sPattern $bibdFile | fzf --delimiter : --preview 'nl {1} --body-numbering=a' --preview-window=:up:70%:+{2}-5)
+str=$(git grep -E --line-number $sPattern $bibdFile | fzf --delimiter : --preview 'less {1}' --preview-window=:up:70%:+{2}-5)
+
+
+# extract citation key from the fzf string
+citeKey=$(echo $str | sed -E "s|$(basename $bibdFile):[0-9]+:@[a-zA-Z]+\{(.+),|\1|")
+
+#method1
+#todo: use json with jq
+# outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $bibdFile --citeproc --csl $cslFile | tail -n +3)
+
+#method2
+#need to use a temporary bib file as input to pandoc because parsing a large bib file is too slow, but json input would be faster
+#and because pandoc expects a file input for bibliography
+tmpName=$(mktemp --suffix=.bib)
+str3=$(grep -A 30 $citeKey $bibdFile)
+echo $str3 | sed -E "s|(.+\} ?\}).+|\1|" > $tmpName
+outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $tmpName --citeproc --csl $cslFile | tail -n +3)
+rm $tmpName
+
+#tail -n +61 $fn | sed -E "s#(.+\}\})#\1#"
+# fzf --preview="head {}" --preview-window=up:30%
+# fzf --preview="file {}" --preview-window=down:1
+echo $outCitation
+echo $outCitation | wl-copy

woola

@@ -8,7 +8,7 @@ if [ "$1" == "-h" ] ; then
 
               By default this app will serve files from the current directory by default using woola.
              
-              Takes an optional flags listed below. For example '--build' to build website files instead of serving.
+              Takes an optional flag of those listed below. For example '--build' to build website files instead of serving.
 
               Optional arguments passed to woola/lib/index.js:
                 .option('-b, --build', 'Build and write html to path {site.options.dstPath}')  
@@ -24,7 +24,7 @@ if [ "$1" == "-h" ] ; then
                 .option('-x, --x', 'Don\'t open browser on run.')
                 .option('-v, --verbose', 'verbose output')
 
-              Installation: place in home directory and make this file executable chmod: u=rwX,go= woola
+              Installation: place in home bin directory and make this file executable chmod: u=rwX,go= woola
     "
     exit 0
 fi
@@ -34,8 +34,7 @@ set -e
 #helper startup script for woola
 appPath="$HOME/projects/dev/woola"
 configFile=$HOME/.config/woola/config.js
-# optFlag=${1:-serve}
-optFlag=$1
+optFlag=$@
 
 if [[ -e $configFile ]] && [[ ! -e config.js ]]; then
     ln -s $configFile config.js
@@ -58,9 +57,11 @@ fi
     # node $appPath/lib/index.js 
 # fi
 
-if [[ "$optFlag" ]]; then
-    node $appPath/lib/index $optFlag
-else
-    node $appPath/lib/index.js 
-fi
+# if [[ "$optFlag" ]]; then
+    # node $appPath/lib/index $optFlag
+# else
+    # node $appPath/lib/index.js 
+# fi
+
+node $appPath/lib/index $optFlag