Embed Skim notes in a collection of PDFs

embed_skim_notes.sh

#!/usr/local/bin/zsh

# In a PDF library with associated Skim notes, automatically embed all
# skim notes in the PDF files.

# I used this to help transition from an OS X + Skim reading environment
# to a Linux reading environment.

# WARNING: This script deletes the Skim files after embedding their contents
# in the PDFs. Make sure you back up your library before using.

ROOT=~/Dropbox/Papers

SKIMNOTES=/Applications/Skim.app/Contents/SharedSupport/skimnotes
SKIMPDF=/Applications/Skim.app/Contents/SharedSupport/skimpdf

############

pushd $ROOT

for skim_file in **/*.skim; do
    pdf_file=`echo "$skim_file" | sed s/\.skim$/\.pdf/`

    # TODO check PDF exists

    # First ensure that the Skim notes are actually stored in the PDF.
    $SKIMNOTES set "$pdf_file" "$skim_file"

    # Now embed.
    $SKIMPDF embed "$pdf_file"

    echo "$skim_file"
    #rm "$skim_file"
done

popd