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app to make managing references/footnotes and tagging notes easier
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Simple app to facilitate tagging and footnotes of markdown notes.

Assumes notes are in the format of:

# Rosset, P. M., & Altieri, M. A. (1997). Agroecology versus input substitution: a fundamental contradiction of sustainable agriculture. Society & Natural Resources, 10(3), 283-295.

Some notes

> A quotation


# Muller, A., Schader, C., Scialabba, N. E. H., Brüggemann, J., Isensee, A., Erb, K. H., ... & Niggli, U. (2017). Strategies for feeding the world more sustainably with organic agriculture. Nature communications, 8(1), 1290.

Some more notes

> Another quotation

That is, documents are separated by ---, followed by the citation starting with # .


Edit the following values in

  • DB_PATH: where the tag database (in CSV format) will be saved.
  • NOTES_DIR: the directory to look for markdown notes in.


Run the server with python, which runs the app at http://localhost:5000.

Opening a note

To open a markdown note, append the path to the app url. E.g. say my NOTES_DIR variable is /home/ftseng/notes/research, I can open the note at /home/ftseng/notes/research/ by visiting http://localhost:5000/

Tagging text and images

To tag highlights in this note, select some text and hit t, then enter your tags (comma-separated). To add tags to an image, CTRL+click the image. Hit ESC to cancel out of the tag input.

Each article has an id generated for it (the base64 encoded data preceding each article title). This id is generated from the article "title" (what follows the #, assumed to be a citation--see above). When you add tags, the tags and highlighted text or image path are associated with that article id in the saved CSV (specified with the DB_PATH configuration variable).

Other items of note

  • To generate markdown-formatted footnotes, click on the Footnotes link.
  • To generate an "outline" (tagged texts/images grouped by tag), click on the Outline link.
  • Highlights are assumed to be unique on an article id and highlighted text or image source basis. So if you tag the text "the cat in the hat" in article abc123 and "the cat in the hat" occurs elsewhere in that article, both instances are treated as identical.
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