Scripture Reference Fixer for Obsidian

pre-commit

#!/usr/bin/env bash
# This turns natural references into wiki link references like this:
#   Genesis 12:3   -> [[Genesis 12#12:3]]
#   Psalm 119:9-11 -> [[Psalm 119#119:9-11]]
#   1 John 3       -> [[1 John 3]]
#   First John 1   -> [[1 John 1]]

# Put this file into .git/hooks/ and it will run every time you
# commit into your repository. Make sure it is executable, you can run
#   chmod +x .git/hooks/pre-commit

# Requires the gsed utility on Mac. For Linux, change `gsed` to `sed` below (line 63).

### BEGIN USER CONFIG ###

# You need to fill in the path to your git-backed Obsidian vault.
PATHTOVAULT=

# Where are your markdown files? Uncomment the option you want
#MARKDOWNFILES="*/*.md" # look 1 directory deep
#MARKDOWNFILES="resources/notes/*.md" # only look in the notes directory

### END USER CONFIG ###

cd "$PATHTOVAULT"

GREPREGEX='[0-9][0-9]*[ ,;.:?)]'
SEDVSREGEX='\([0-9]*\)\(:[0-9]*[-0-9]*\)/\[\[\1 \2#\2\3\]\]/g'
SEDCPREGEX='\([0-9]*\)\([ ,;.]\)/\[\[\1 \2\]\]\3/g'

IFS=$'\n'
for x in `/usr/bin/grep -l -i \
  -e "[123] [JPTCSKjptcsk][a-z]* $GREPREGEX" \
  -e "[Ff]irst [JPTCSKjptcsk][a-z]* $GREPREGEX" \
  -e "[Ss]econd [JPTCSKjptcsk][a-z]* $GREPREGEX" \
  -e "[Tt]hird [JPTCSKjptcsk][a-z]* $GREPREGEX" \
  -e "[123][snr][td] [JPTCSKjptcsk][a-z]* $GREPREGEX" \
  -e "Genesis $GREPREGEX" -e "Exodus $GREPREGEX" \
  -e "Leviticus $GREPREGEX" -e "Numbers $GREPREGEX" \
  -e "Deuteronomy $GREPREGEX" -e "Joshua $GREPREGEX" \
  -e "Judges $GREPREGEX" -e "Ruth $GREPREGEX" \
  -e "Ezra $GREPREGEX" -e "Nehemiah $GREPREGEX" \
  -e "Esther $GREPREGEX" -e "Job $GREPREGEX" \
  -e "Psalms* $GREPREGEX" -e "Proverbs $GREPREGEX" \
  -e "Ecclesiastes $GREPREGEX" -e "Song of Solomon $GREPREGEX" \
  -e "Isaiah $GREPREGEX" -e "Jeremiah $GREPREGEX" \
  -e "Lamentations $GREPREGEX" -e "Ezekiel $GREPREGEX" \
  -e "Daniel $GREPREGEX" -e "Hosea $GREPREGEX" \
  -e "Joel $GREPREGEX" -e "Amos $GREPREGEX" \
  -e "Obadiah $GREPREGEX" -e "Jonah $GREPREGEX" \
  -e "Micah $GREPREGEX" -e "Nahum $GREPREGEX" \
  -e "Habakkuk $GREPREGEX" -e "Zephaniah $GREPREGEX" \
  -e "Haggai $GREPREGEX" -e "Zechariah $GREPREGEX" \
  -e "Malachi $GREPREGEX" -e "Matthew $GREPREGEX" \
  -e "Mark $GREPREGEX" -e "Luke $GREPREGEX" \
  -e "John $GREPREGEX" -e "Acts $GREPREGEX" \
  -e "Romans $GREPREGEX" -e "Galatians $GREPREGEX" \
  -e "Ephesians $GREPREGEX" -e "Philippians $GREPREGEX" \
  -e "Colossians $GREPREGEX" -e "Titus $GREPREGEX" \
  -e "Philemon $GREPREGEX" -e "Hebrews $GREPREGEX" \
  -e "James $GREPREGEX" -e "Jude $GREPREGEX" -e "Revelation $GREPREGEX" \
  ${MARKDOWNFILES}`; do
    gsed -i \
      -e "s/\([123] [JPTCSKjptcsk][a-z]*\) $SEDVSREGEX" \
      -e "s/[Ff]irst \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\(:[0-9]*[-0-9]*\)/\[\[1 \1 \2#\2\3\]\]/g" \
      -e "s/[Ss]econd \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\(:[0-9]*[-0-9]*\)/\[\[2 \1 \2#\2\3\]\]/g" \
      -e "s/[Tt]hird \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\(:[0-9]*[-0-9]*\)/\[\[3 \1 \2#\2\3\]\]/g" \
      -e "s/\([123]\)[snr][td] \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\(:[0-9]*[-0-9]*\)/\[\[\1 \2 \3#\3\4\]\]/g" \
      -e "s/\(Genesis\) $SEDVSREGEX" -e "s/\(Exodus\) $SEDVSREGEX" \
      -e "s/\(Leviticus\) $SEDVSREGEX" -e "s/\(Numbers\) $SEDVSREGEX" \
      -e "s/\(Deuteronomy\) $SEDVSREGEX" -e "s/\(Joshua\) $SEDVSREGEX" \
      -e "s/\(Judges\) $SEDVSREGEX" -e "s/\(Ruth\) $SEDVSREGEX" \
      -e "s/\(Ezra\) $SEDVSREGEX" -e "s/\(Nehemiah\) $SEDVSREGEX" \
      -e "s/\(Esther\) $SEDVSREGEX" -e "s/\(Job\) $SEDVSREGEX" \
      -e "s/\(Psalms*\) $SEDVSREGEX" -e "s/\(Proverbs\) $SEDVSREGEX" \
      -e "s/\(Ecclesiastes\) $SEDVSREGEX" -e "s/\(Song of Solomon\) $SEDVSREGEX" \
      -e "s/\(Isaiah\) $SEDVSREGEX" -e "s/\(Jeremiah\) $SEDVSREGEX" \
      -e "s/\(Lamentations\) $SEDVSREGEX" -e "s/\(Ezekiel\) $SEDVSREGEX" \
      -e "s/\(Daniel\) $SEDVSREGEX" -e "s/\(Hosea\) $SEDVSREGEX" \
      -e "s/\(Joel\) $SEDVSREGEX" -e "s/\(Amos\) $SEDVSREGEX" \
      -e "s/\(Obadiah\) $SEDVSREGEX" -e "s/\(Jonah\) $SEDVSREGEX" \
      -e "s/\(Micah\) $SEDVSREGEX" -e "s/\(Nahum\) $SEDVSREGEX" \
      -e "s/\(Habakkuk\) $SEDVSREGEX" -e "s/\(Zephaniah\) $SEDVSREGEX" \
      -e "s/\(Haggai\) $SEDVSREGEX" -e "s/\(Zechariah\) $SEDVSREGEX" \
      -e "s/\(Malachi\) $SEDVSREGEX" -e "s/\(Matthew\) $SEDVSREGEX" \
      -e "s/\(Mark\) $SEDVSREGEX" -e "s/\(Luke\) $SEDVSREGEX" \
      -e "s/\(John\) $SEDVSREGEX" -e "s/\(Acts\) $SEDVSREGEX" \
      -e "s/\(Romans\) $SEDVSREGEX" -e "s/\(Galatians\) $SEDVSREGEX" \
      -e "s/\(Ephesians\) $SEDVSREGEX" -e "s/\(Philippians\) $SEDVSREGEX" \
      -e "s/\(Colossians\) $SEDVSREGEX" -e "s/\(Titus\) $SEDVSREGEX" \
      -e "s/\(Philemon\) $SEDVSREGEX" -e "s/\(Hebrews\) $SEDVSREGEX" \
      -e "s/\(James\) $SEDVSREGEX" -e "s/\(Jude\) $SEDVSREGEX" \
      -e "s/\(Revelation\) $SEDVSREGEX" \
      -e "s/\([123] [JPTCSKjptcsk][a-z]*\) $SEDCPREGEX" \
      -e "s/[Ff]irst \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\([ ,;.]\)/\[\[1 \1 \2\]\]/g" \
      -e "s/[Ss]econd \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\([ ,;.]\)/\[\[2 \1 \2\]\]/g" \
      -e "s/[Tt]hird \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\([ ,;.]\)/\[\[3 \1 \2\]\]/g" \
      -e "s/\([123]\)[snr][td] \([JPTCSKjptcsk][a-z]*\) \([0-9]*\)\([ ,;.]\)/\[\[\1 \2 \3\]\]/g" \
      -e "s/\(Genesis\) $SEDCPREGEX" -e "s/\(Exodus\) $SEDCPREGEX" \
      -e "s/\(Leviticus\) $SEDCPREGEX" -e "s/\(Numbers\) $SEDCPREGEX" \
      -e "s/\(Deuteronomy\) $SEDCPREGEX" -e "s/\(Joshua\) $SEDCPREGEX" \
      -e "s/\(Judges\) $SEDCPREGEX" -e "s/\(Ruth\) $SEDCPREGEX" \
      -e "s/\(Ezra\) $SEDCPREGEX" -e "s/\(Nehemiah\) $SEDCPREGEX" \
      -e "s/\(Esther\) $SEDCPREGEX" -e "s/\(Job\) $SEDCPREGEX" \
      -e "s/\(Psalms*\) $SEDCPREGEX" -e "s/\(Proverbs\) $SEDCPREGEX" \
      -e "s/\(Ecclesiastes\) $SEDCPREGEX" -e "s/\(Song of Solomon\) $SEDCPREGEX" \
      -e "s/\(Isaiah\) $SEDCPREGEX" -e "s/\(Jeremiah\) $SEDCPREGEX" \
      -e "s/\(Lamentations\) $SEDCPREGEX" -e "s/\(Ezekiel\) $SEDCPREGEX" \
      -e "s/\(Daniel\) $SEDCPREGEX" -e "s/\(Hosea\) $SEDCPREGEX" \
      -e "s/\(Joel\) $SEDCPREGEX" -e "s/\(Amos\) $SEDCPREGEX" \
      -e "s/\(Obadiah\) $SEDCPREGEX" -e "s/\(Jonah\) $SEDCPREGEX" \
      -e "s/\(Micah\) $SEDCPREGEX" -e "s/\(Nahum\) $SEDCPREGEX" \
      -e "s/\(Habakkuk\) $SEDCPREGEX" -e "s/\(Zephaniah\) $SEDCPREGEX" \
      -e "s/\(Haggai\) $SEDCPREGEX" -e "s/\(Zechariah\) $SEDCPREGEX" \
      -e "s/\(Malachi\) $SEDCPREGEX" -e "s/\(Matthew\) $SEDCPREGEX" \
      -e "s/\(Mark\) $SEDCPREGEX" -e "s/\(Luke\) $SEDCPREGEX" \
      -e "s/\(John\) $SEDCPREGEX" -e "s/\(Acts\) $SEDCPREGEX" \
      -e "s/\(Romans\) $SEDCPREGEX" -e "s/\(Galatians\) $SEDCPREGEX" \
      -e "s/\(Ephesians\) $SEDCPREGEX" -e "s/\(Philippians\) $SEDCPREGEX" \
      -e "s/\(Colossians\) $SEDCPREGEX" -e "s/\(Titus\) $SEDCPREGEX" \
      -e "s/\(Philemon\) $SEDCPREGEX" -e "s/\(Hebrews\) $SEDCPREGEX" \
      -e "s/\(James\) $SEDCPREGEX" -e "s/\(Jude\) $SEDCPREGEX" \
      -e "s/\(Revelation\) $SEDCPREGEX" \
      $x
done
exit 0

When testing this from the terminal with a file Bible Ref link test.md that contains the following content:

This is a link to 1 John 1:5.

This is a link to 1 John 1:7-9.

I get the following error:

grep: [na]*/*.md: No such file or directory

That could depend on how you have your vault folder structure. "PATHTOYOURVAULT" above should go to the root of your vault and then the script assumes 1 layer of directories and markdown folders below that. For example, at the root of my vault I have:

• notes
• archives
• etc.

Below each of those I have my markdown files. You might need to modify that line if your markdown files are in a different location.

Note that the [na] part means that it will only look at directories starting with an a or n -- in my case I only want to run this in my notes and archives directories. You probably will need to change that based on your directory names.

I changed the latest version (revision 6) to only reference */*.md which should make it more usable for others.

I just added support for references like "First John 3:2" or "2nd Samuel 3" to support my speech to text engine which isn't consistent.

Added support for entries like "first chronicles" which were not working previously. Also added a USER CONFIG section to make it easier to define the path to your vault and the search path for Markdown files.