This script uses pyzotero and manubot to generate formatted bibliographies, given a search string and Zotero library. In particular, the script:
- Establishes a connection to a user library using the Zotero API.
- Searches the library using a tag or search query.
- Looks for DOI, ISBN, or URL metadata -- in that order -- for each item in the library that matches the query.
- Passes the list of DOI, ISBN, or URL identifiers to
manubotand renders the citations as Markdown.
The following terminal recording demonstrates creating a bibliography of all papers tagged with "cyclodextrin" in my personal library, ordered by date.
Which will generate output that looks like this:
usage: fetch_papers.py [-h] [-t TAG] [-q QUERY] -o OUTPUT
optional arguments:
-h, --help show this help message and exit
-t TAG, --tag TAG Zotero library tag
-q QUERY, --query QUERY
Zotero library query
-o OUTPUT, --output OUTPUT
Formatted output file
The main program will accept either a tag or general search query as input and a file name for the formatted bibliography. It shouldn't be hard to search by other formats accepted by the Zotero.add_parameters() function.
There may limitations on the number of results imposed by the API, as noted in the pyzotero documentation. No attempt is made to work around those limitations.
-
Install
manubotfollowing the instructions at the Manubot repository. -
Install
pyzoterofollowing the instructions, paying attention to the steps necessary to get a personal library ID and API key from Zotero.
There are no tests yet. This was written quickly, as a prototype, to be built upon.
To cite the Manubot project or for more information on its design and history, see:
Open collaborative writing with Manubot Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter (2019-04-22) https://greenelab.github.io/meta-review/