A tool for annotating research papers (and more) and sharing those annotations (via git for starters)
Fermat's Last Theorem was captioned "I have a truly marvelous demonstration of this proposition which this margin is too narrow to contain."
This tool intends to be an infinite margin.
Do you read many research papers or PhD theses? If yes, you might want to use this tool!
I like to write in the margins of my books and printed research papers. I want to read what other people have to say about a paper after I write down my own notes. I want to be able to search my notes. I want to be able to share my notes! I want to be able to remember why I downloaded a paper years later.
Distributing PDFs will get you sued for lots of money ( https://en.wikipedia.org/wiki/Sci-Hub#United_States ). I don't want to get sued.
- install poppler-utils, or more specifically, make sure the pdftocairo binary from poppler-utils is in your
$PATH - git clone this repository
- run this from cabal
cabal run(optionally:nix-shell --run "cabal run") - point your web browser to
localhost:3000All of the annotations are saved in a local directory~/.fermatslastmargin/localuserand your friend's annotations are saved in~/.fermatslastmargin/friends/<github_name_of_friend>
- add paper info
- read/write annotations
- load page images
- render 'uploaded' PDF to page images
- push to github repo
- pull from friends' github repo
- switch notes view to see github friends' notes
- setup new user (ask for github OAuth and username, set git remote correctly)
- search crossref.org by title to get DOI
- update PDF when viewing paper
- plugin system to download paper (as PDF) when given unique ID (DOI for now)
- search arxiv by title to get DOI
- swap to github v4 graphql API so pulling friend repos doesn't get rate limited
- git
- poppler-utils (apt install poppler-utils)
- zlib (apt install zlib1g-dev)
- cabal 2.4 - if you get "cabal: fermatslastmargin.cabal:14: Parse of field 'build-depends' failed." you need to upgrade with "cabal install Cabal"
- GHC 8.6 (at least, that's all I've tried)
- brew install poppler
- brew install zlib
Scotty is used to handle a bunch of HTTP endpoints.
All state is saved in ~/.fermatslastmargin/. For the user viewing the papers, their state will be in ~/.fermatslastmargin/localuser.
The notes for each paper will be in ~/.fermatslastmargin/localuser/$DOI/paper.json.
For example, Conor McBride's paper "Everybody's Got to be Somewhere" has a DOI of 10.4204/EPTCS.275.6.
Once that paper is added, the notes will be saved into ~/.fermatslastmargin/localuser/10.4204/EPTCS.275.6/paper.json
Notes written by users followed by this user will be in ~/.fermatslastmargin/friends/<github_name_of_friend>
When a PDF is uploaded to create a new paper, the PDF is saved into ~/.fermatslastmargin/pageimages/$DOI/paper.pdf.
Next, page images are generated by poppler-utils into ~/.fermatslastmargin/pageimages/$DOI/page-1.png up to however many pages in the PDF.
The front end uses jquery in a thoroughly haphazard manner.
The state is mostly passed around as GET parameters for DOI, page number, and friend name.
For example, http://localhost:3000/index.html?pagenum=1&uid=10.2168/LMCS-10(3:19)2014&friendview=chazzam
The front end javascript calls HTTP endpoints defined in Main.hs.
- page images are fetched from the filesystem via a static endpoint
- local and friend notes are fetched by GET'ing from
/getannotate - a new or updated note is saved by posting to
/annotate - friends are found by GET'ing the DOI from
/friends?paperuid=DOI - pushing local notes to github GETs
/gitpush - pulling remote notes from github GETs
/gitpull - creating a new paper POSTs to
/paper - creating a new user will hit
/newuser
If you created a local repository and annotated papers before January 2020, you'll need to do cabal run migrate to get your repository in the new format!