Bib integration in dendron

Messing around with pandoc citer and trying to integrate bibliography management in dendron

The markender extension (https://github.com/mjwsteenbergen/markender) is causing conflict with pandoc citer for the autocompletion. Deactivate Markender

Conflict thrown projects.tramadol

Error: Command failed: pandoc --from=markdown-raw_tex+tex_math_single_backslash --to=html --katex --filter pandoc-citeproc Error reading bibliography /Users/pma/Documents/library_formatted.bib (line 60541, column 1): unexpected end of input expecting "}", "\" or "{" Error running filter pandoc-citeproc: Filter returned error status 1

Now trying to troubleshoot the file using bibdesk

Bib file formatting

Bib file formatting is required to avoid the previous error. This error is somehow misleading because it indicates that the error comes from the end of the file ... and it's not the case, rather a curly brace somewhere which is not closed.

From the automatically sync .bib of Mendeley, make a copy and ctrl+F replace all { by \'{ and all all } by \'} This should make the trick.

See cli.sed_bash for the recipee.

And here goes a Note reference

From cli.sed_bash

Go to text →

TODO automate with a sed script ? the bib cleaning

Some sed black magic

echo "\{" | sed "s|\\\{|\\\'{|"

Double \ to escape the \

And repeat

echo "\{jhdgjshgjhfsjdhgf\}" | sed "s|\\\{|\\\'{|g; s|\\\}|\\\'}|g;"

Now add input and outputs

sed "s|\\\{|\\\'{|g; s|\\\}|\\\'}|g" library.bib > library_formatted.bib

We'll try to automatize the process using https://stackoverflow.com/a/13807906 fswatch and alternative to inotifywatch on linux https://linux.die.net/man/1/inotifywatch

So here is the small bash script. It will take the command line arg 1 and add the _formatted prefix to it. Could be cleaner and directly extract the filename to accomodate for various type of extension. Not the point here. If any body has an idea, please contribute ! :point_down:

#!/bin/bash
sed "s|\\\{|\\\'{|g; s|\\\}|\\\'}|g" "$1" > "${1%.bib}_formatted.bib"

#!/bin/bash

# fullfilename="$(basename $1)"
# extension="${fullfilename##*.}"
# filename="${fullfilename%.*}"

# echo $fullfilename
# echo $extension
# echo $filename

#echo "File added: " "$(basename $1)" "$(basename $1)"
sed "s|\\\{|\\\'{|g; s|\\\}|\\\'}|g" "$1" > "./formatted_bib/${filename}_formatted.bib"

fswatch has been somehow a nightmare to understand ...

to trouble shoot use the follwoing line to be sure of what exactly you take as input

fswatch -0 ./mendeley_output/ | xargs -0 -n1 -I{} echo "{}"

TODO check Amoeba splitting of notes (here is a typical application case ... Automatization and sed lines should go in separate notes as these can be used for other purposes than just the .bib reformating) 2021-01-02 17:30 checking .... and just splitted the above sed commands

TODO understand the way to have the bibliography display on the published version of dendron. Not the case at the moment see projects.tramadol

TODO set bibliography globally