papers

Command-line tool to manage bibliography (pdfs + bibtex)

WARNING: This tool requires further development and testing, and is not production-ready as such (contributors welcome).

Motivation

This project is an attempt to create a light-weight, command-line bibliography managenent tool. Aims:

maintain a PDF library (with appropriate naming)
maintain one or several bibtex-compatible collections, linked to PDFs
enough PDF-parsing capability to fetch metadata from the internet (i.e. crossref or google-scholar)

Dependencies

python 2 or 3
popper-utils (only:pdftotext): convert PDF to text for parsing
bibtexparser (1.0.1) : parse bibtex files
crossrefapi (1.2.0) : make polite requests to crossref API
scholarly (0.2.2) : interface for google scholar
fuzzywuzzy (0.15.1) : calculate score to sort crossref requests
unidecode (0.04.21) : replace unicode with ascii equivalent
six: python 2-3 compatibility

Install

clone this project
pip install unidecode crossrefapi bibtexparser scholarly fuzzywuzzy six
install third-party dependencies (Ubuntu: sudo apt install popper-utils)
python setup.py install

Getting started

This tool's interface is built like git, with main command papers and a range of subcommands.

Start with PDF of your choice (modern enough to have a DOI, e.g. anything from the Copernicus publications). For the sake of the example, one of my owns: https://www.earth-syst-dynam.net/4/11/2013/esd-4-11-2013.pdf

extract pdf metadata (doi-based if available, otherwise crossref, or google scholar if so specified)

  $> papers extract esd-4-11-2013.pdf
  @article{Perrette_2013,
      doi = {10.5194/esd-4-11-2013},
      url = {https://doi.org/10.5194%2Fesd-4-11-2013},
      year = 2013,
      month = {jan},
      publisher = {Copernicus {GmbH}},
      volume = {4},
      number = {1},   
      pages = {11--29},
      author = {M. Perrette and F. Landerer and R. Riva and K. Frieler and M. Meinshausen},
      title = {A scaling approach to project regional sea level rise and its uncertainties},
      journal = {Earth System Dynamics}
  }

add pdf to papers.bib library, and rename a copy of it in a files directory files.

  $> papers add --rename --copy --bibtex papers.bib --filesdir files esd-4-11-2013.pdf --info
  INFO:papers:found doi:10.5194/esd-4-11-2013
  INFO:papers:new entry: perrette_2013
  INFO:papers:create directory: files/2013
  INFO:papers:mv /home/perrette/playground/papers/esd-4-11-2013.pdf files/2013/Perrette_2013.pdf
  INFO:papers:renamed file(s): 1

(the --info argument asks for the above output information to be printed out to the terminal)

In the common case where the bibtex (--bibtex) and files directory (--filesdir) do not change, it is convenient to install papers. Install comes with the option to git-track any change to the bibtex file (--git) options.

setup git-tracked library (optional)

  $> papers install --bibtex papers.bib --filesdir files --git --gitdir ./
  papers configuration
  * configuration file: /home/perrette/.config/papersconfig.json
  * cache directory:    /home/perrette/.cache/papers
  * git-tracked:        True
  * git directory :     ./
  * files directory:    files (1 files, 5.8 MB)
  * bibtex:            papers.bib (1 entries)

Note the existing bibtex file was detected but untouched. The configuration file is global (unless --local is specified), so from now on, any papers command will be know about these settings. Type papers status -v to check your configuration. You also notice that crossref requests are saved in the cache directory. This happens regardless of whether papers is installed or not. From now on, no needs to specify bibtex file or files directory.

list entries (and edit etc...)

  $> papers list -l
  Perrette2013: A scaling approach to project regional sea level rise and it... (doi:10.5194/esd-4-11-2013, file:1)

papers list is a useful command, inspired from unix's find and grep. It lets you search in your bibtex in a typical manner (including a number of special flags such as --duplicates, --review-required, --broken-file...), then output the result in a number of formats (one-liner, raw bibtex, keys-only, selected fields) or let you perform actions on it (currently --edit, --delete). For instance, it is possible to manually merge the duplicates with:

    $> papers list --duplicates --edit

other commands:
- papers status ...
- papers check ...
- papers filecheck ...
- papers undo ...
- papers git ...

Consult inline help for more detailed documentation!

Current features

parse PDF to extract DOI
fetch bibtex entry from DOI (using crossref API)
fetch bibtex entry by fulltext search (using crossref API or google scholar)
create and maintain bibtex file
add entry as PDF (papers add ...)
add entry as bibtex (papers add ...)
scan directory for PDFs (papers add ...)
rename PDFs according to bibtex key and year (papers filecheck --rename [--copy])
some support for attachment
merging (papers check --duplicates ...)
fix entries (papers check --format-name --encoding unicode --fix-doi --fix-key ...)
undo command (papers undo)
configuration file with default bibtex and files directory (papers install --bibtex BIB --filesdir DIR ...)
integration with git (papers install --git --gitdir DIR and e.g. papers git ... to setup a remote, push...)
display / search / list entries : format as bibtex or key or whatever (papers list ... [-k | -l])
list + edit or remove entry by key or else (papers list ... [--edit, --delete])
fix broken PDF links (papers filecheck ...):
- remove duplicate file names (always) or file copies (--hash-check)
- remove missing link (--delete-missing)
- fix files name after a Mendeley export (--fix-mendeley):
  - leading '/' missing is added
  - latex characters, e.g. {\_} or {\'{e}} replaced with unicode

Planned features

papers encode: text encoding in bibtex entries (latex, unicode, ascii)
additional checks on entries:
- duplicate-authors and more like here
support collections (distinct bibtex entries, same files directory)
- or maybe more like ´papers update-from OTHER.bib´ to update changes based on DOI / key
- could also use git branches / merge
associate bibtex to existing pdf collection (to move library location)
fetch PDFs for existing entries? Bindings with sopaper
as add-on in separate github: basic flask interface to browse papers & edit entries. E.g. check-out paperhero
lazy loading of modules (optimization)

Tests

Test coverage in progress...

Currently covers:

papers extract
- parse pdf DOI
- fetch bibtex on crossref based on DOI
- fetch bibtex on crossref based fulltext search
- fetch bibtex on google-scholar based fulltext search
papers add
- add entry and manage conflict
- add pdf file, bibtex, directory
- add one pdf file with attachment (beta, API will change)
papers check --duplicates
- conflict resolution
papers install (superficial test)
internals:
- duplicate test with levels EXACT, GOOD, FAIR (the default), PARTIAL

Todo (more bug prone until then !):

papers check (fix DOI etc.)
papers filecheck (especially rename files, including those with attachment)
papers list
papers status
papers install (extend)
papers undo
papers git

Why not JabRef, Zotero or Mendeley (or...) ?

JabRef (2.10) is nice, light-weight, but is not so good at managing PDFs.
Zotero (5.0) features excellent PDF import capability, but it needs to be manually one by one and is a little slow. Not very flexible.
Mendeley (1.17) is perfect at automatically extracting metadata from downloaded PDF and managing your PDF library, but it is not open source, and many issues remain (own experience, Ubuntu 14.04, Desktop Version 1.17):
- very unstable
- PDF automatic naming is too verbose, and sometimes the behaviour is unexpected (some PDFs remain in on obscure Downloaded folder, instead of in the main collection)
- somewhat heavy (it offers functions of online syncing, etc)
- poor seach capability (related to the point above)

Above-mentioned issues will with no doubt be improved in future releases, but they are a starting point for this project. Anyway, a command-line tool is per se a good idea for faster development, as noted here, but so far I could only find zotero clients for their online API (like pyzotero or zotero-cli). Please contact me if you know another interesting project.

kirk86/papers