Reference management solution using Python and Notion.
The main idea of this app is to allow to furnish a Notion database using a BibTex formatted string or file. It also helps you to organize papers, create a bibliography and give you the opportunity to annotate the publications directly on their Notion's pages.
Example of a database obtained using notion-scholar.
pip install git+https://github.com/thomashirtz/notion-scholar#egg=notion-scholar
You can now call the application using notion-scholar or ns
Never used python nor github before ?
- Install Python 3.7 or above (tutorial available online)
- Install pip (Generally included with Python)
- Run the command
pip install ...above using your machine command line (Maybe need to launch the command prompt as administrator on Windows)
You can either duplicate the page template using the link below, or create a new database with the properties listed in requirements.
Template
Preview images
Requirements
The properties necessary to import publications in a database are the following:
| Property Name | Property Type |
|---|---|
| Title | Title |
| Authors | Text |
| Year | Number |
| Journal | Text |
| Filename | Text |
| URL | URL |
| Abstract | Text |
| DOI | Text |
| Type | Select |
| Bibtex | Text |
| Inbox | Checkbox |
No space should be in the names of the properties.
Create an integration for the notion-scholar database. The integration needs to target the workplace containing the publication database.
Option needed:
- Internal Integration
- Read content
- Update content
- Insert content
Copy the Internal Integration Token for the step 4.
Go to your database in notion => Click on ... (top right) => + Add connections => Select the integration that you just created.
Copy the link of the database (simply the URL on a browser, on the application => Click on ... => Copy Link) for the step 4.
It is the database page and not the dashboard page that needs to be integrated. Moreover, it is also the URL of the database page that needs to be set into notion-scholar.
For the first use, it is recommended to set up the configuration file. The main parameters to save are the token (which will be securely saved using the keyring library) and the database-url.
ns set-config --token <token> --database-id <database_id>
or
ns set-config -t <token> -db <database_id>
The database_id is one part of the URL:
https://www.notion.so/<workspace_name>/<database_id>?v=<view_id>
For example, if the database url is :
https://www.notion.so/thomashirtz/be31bb3f190f46c69e804785cc83c7ce?v=5674957e71e24aeb91d6db65f7978f0c
The command that needs to be used to set the database is :
ns set-config -db be31bb3f190f46c69e804785cc83c7ce
If you want to set the default bib path that will be used when the ns run is called, you can set it by typing:
ns set-config --bib-file-path <bib_file_path>
or
ns set-config -f <bib_file_path>
The bib file needs to exist and the file path needs to be absolute.
There is three main way to use this application:
- Setting up the
bib-file-pathand call therunmode (It will automatically upload the new publications from the bib file into the database):
ns run
- Giving the
bib-file-pathargument:
ns run -f <bib-file-path>
- Giving a
bib-stringargument (/!\ be careful to type three quotes"""before pasting thebib-string) :
ns run -s """<bib-string>"""
The --token (-t) and the --database_url (-db) are also required, however, if they have been set, they don't need to be added again to the argument list.
For getting help it is possible to call:
ns --help
usage: Use "notion-scholar --help" or "ns --help" for more information
notion-scholar
positional arguments:
{run,download,clear-config,inspect-config,set-config}
Selection of the action
run Run notion-scholar.
download Download the bibtex entries present in the database.
clear-config Clear the notion-scholar config.
inspect-config Inspect the notion-scholar config.
set-config Save the default values of notion-scholar.
optional arguments:
-h, --help show this help message and exit
Five main modes exist: run, download, set-config, inspect-config and clear-config. The help can be called this way:
ns <mode> --help
Example:
ns run --help
usage: Use "notion-scholar --help" or "ns --help" for more information run [-h] [-t] [-db] [-f] [-s]
optional arguments:
-h, --help show this help message and exit
-t , --token Token used to connect to Notion. (default: None)
-db , --database-id Database that will be furnished. The database_id can be found in the url of the database:
https://www.notion.so/{workspace_name}/{database_id}?v={view_id} (default: None)
-f , --bib-file-path
Bib file that will be used. This argument is required if the bib file is not saved in the
config and no bib-string is passed. (default: None)
-s , --bib-string Bibtex entries to add (must be in-between three quotes """<bib-string>"""). By default, the
entries will be saved to the bib file from the config. It is possible to disable this behavior
by changing the "save" option: "ns setup -save false".
ns set-config --help
usage: Use "notion-scholar --help" or "ns --help" for more information set [-h] [-f] [-s] [-t] [-db]
optional arguments:
-h, --help show this help message and exit
-f , --bib-file-path
Save the input file path in the user config using "platformdirs". The path must be absolute
and the file need to exist. (current: None)
-s , --save Set whether the entries from "bib-string" will be saved in the bib file. (current: True)
-t , --token Save the Notion token using "keyring". (current: None)
-db , --database-id Save the database-id in the user config using the library "platformdirs". The database_id can
be found in the url of the database:
https://www.notion.so/{workspace_name}/{database_id}?v={view_id} (current: None)```
When uploading a BibTex file into the database, the BibTex citekey will be mapped to the property "filename". This is because it seems convenient to have the same name for the key and the filename. It is therefore advised to change the citekey before uploading to Notion. (If you want to change it manually afterwards you would need to change both the Bibtex and the Filename property, which is not very convinient.)
This is ~ the nomenclature I used for the citekey (source). Feel free to take inspiration:
Nomenclature
Filename:
aaaayyyyxxxx.pdf
Where:
aaaa: Name of the first author (variable length)yyyy: Year of publication (fixed length)xxxx: First word of title, minus articles and other small words (variable length)
For example: Attention Is All You Need, Ashish Vaswani et al., 2017
Would give:
vaswani2017attention.pdf
If an author publish two papers the same year with the same beginning first word, it is possible to add an 1 and 2 depending on which one was the first released.
For example:
- Soft Actor-Critic Algorithms and Applications, Tuomas Haarnoja et al., 2018
haarnoja2018soft1.pdf - Soft Actor-Critic: Off-Policy Maximum Entropy Deep Reinforcement Learning with a Stochastic Actor, Tuomas Haarnoja et al., 2018
haarnoja2018soft2.pdf
It is possible to copy the equation in the table view. Here is a comment to explain how, it can be very useful.
If you want to see a new feature, or you have some feedback to give, feel free to email me at thomashirtz@pm.me.
If this repository helped you or you if you like this project, feel free to support me!
Copyright 2021 Thomas Hirtz
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.