Sync pdf attachments to zotero
This is a collection of python scripts that scans the files in a folder and checks whether there are any pdf files with filenames that begin with a citation key of an zotero bibliography item. If there are then the scripts add the files as an attachment to corresponding zotero item. At the moment the scripts assume that they are scanning files that are contained in the Zotero base directory and the files are attached as linked files, that is, the files are not uploaded to the zotero cloud storage.
WARNING: These scripts could potentially delete attachments from your zotero libary if not properly configured.
To run clone the repository and install peewee and requests using
$ pip install peewee requests
Then create a file keys.py with the following contents
API_KEY = "Zotero API KEY with Write Access"
USER_ID = "Your Zotero user Id"
PDF_DIRECTORY = 'absoulte path of the directory you want to search'
ZOTERO_ROOT = 'Your zotero base directory with trailing forward slash, eg: /home/user/zotero_base/'
SEARCH_EXCLUDE = 'attachments:References' #this is a parameter that ignores any references that you don't want to mess with. For example, if you store all your actual pdfs in zotero_base/Refernces and you don't want these scripts to interfere with these. Just set this to a 'null' (a string) empty string if you don't want to use this feature.The reccomended setup for this is to have a Zotero base directory where you have a folder structure as follows
base_directory:
References:
Zotero managed pdf references
NotePDFs:
Folder of pdfs that begin with citation keys
Settings for this setup would be, if the base directory is /home/user/base_directory
PDF_DIRECTORY = '/home/user/base_directory/NotePDFs'
ZOTERO_ROOT = '/home/user/base_directory/'
SEARCH_EXCLUDE = 'attachments:References'
and the scripts will check whether there are pdfs in NotePDFs that start with a citation key and if so then add a linked file to the zotero item.
To use this with zotero, each item needs to have it's citation key in the extra tag such that the extra field contains text of the form
some info...
Citation Key: theCitationKey
some other info...
This can be achived automatically using better bibtex and setting it to automatically pin the citation keys in the better bibtex settings.
There are four scripts in the repository.
sync_db.py and sync_attachments.py use the Zotero API to access your library items and stores all items for which it can find a citation key in the items extra field. They use the Zotero version information and so can be called fairly often with out causing any networm or api request issues. For example, you may want to set these to run every 5 minutes. These scripts update a zotero_cache.db sqlite database which stores the details of all the zotero items and the relevant attachments. The file upload_attachment.py reads all the pdfs in the specified folder and then adds the corresponding linked file to the zotero item if the citation key is contained in the file path. This means that you can either just create a note with the citation key in the title, or make a folder and then all the items will in the folder will be added to the zotero item. The final script, update_attachments.py checks whether there have been any changes to the attachment folder (eg deletions) and then updates the zotero items.
These scripts can be combined into a script bash script, for example:
#!/bin/bash
cd /path/to/zotero_pdf_sync/directory
python sync_db.py
python sync_attachments.py
python upload_attachment.py
python update_attachments.pyand then you can schedule this script to run at set intervals using, for example, cron on linux.