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NoRA - Notion Research Assistant

python hydra license

A Notion template to help you keep track of the papers you read 📜, their authors 👤, your notes 📝, and more 🔥

If you ❤️ or simply use this project, don't forget to give the repository a ⭐, it means a lot to us !


📌  Introduction

This project was built as a Notion-based alternative to reference management softwares such as Zotero and Mendeley.

It is composed of the NoRA Notion template for you to build on top of, as well as NoRA-Tools to programmatically:

  • 🔥 upload papers to your NoRA library as easily as with Zotero Connector from a simple URL or an identifier
  • 🔥 move all your already-existing Zotero library to NoRA

🧪  NoRA template

The NoRA template provides you with a structure of interconnected databases to keep track of your research papers and notes. More specifically, the template contains the following databases:

  • 🏗️ Projects
  • 📜 Papers
  • 👤 People
  • 🏢 Affiliations
  • 🤹 Conferences & journals
  • 🧲 Key topics

The inner workings of the template are quite straightforward, the best way to get familiar with it is probably to play with it 😉 !

🛠  NoRA-Tools

The NoRA-Tools provide functionalities to programmatically upload data to your NoRA template. The main functionalities are:

  • uploading a paper and associated metadata to NoRA from a URL or from an identifier (DOI, ISBN, PMID, arXiv ID), exactly like with Zotero Connector
  • uploading your whole Zotero library to NoRA

You can freely modify or extend the NoRA template. However, keep in mind that if you want to use NoRA-Tools after modifying some sensitive page fields, you may need to adjust your Notion configuration accordingly.


🧱  Installation

Requirements

  • npm installed
  • conda installed
  • Notion account

Installing the template in Notion

Simply duplicate the NoRA template to your personal Notion account.

Installing NoRA-Tools on your machine

# clone project
git clone --recurse-submodules [email protected]:drprojects/nora.git
cd nora

# create a 'nora' conda environment with required dependencies
conda env create -f nora.yml

# install the npm server
cd src/translation_server
npm install
cd ../..
Setting up NoRA-Tools for simpler bash commands (optional, Unix machines only)

As you will see below, executing NoRA-Tools requires activating a conda environment and calling a python script following a specific syntax. For more convenience, it is also possible to configure NoRA to be called using a simpler bash syntax on Unix machines.

To set this up on your machine, you simply need to run the following script once and for all:

scripts/add_nora_to_path_unix

Make sure your restart your terminal ro source the .bashrc to apply the changes:

source ~/.bashrc

Notion configuration

Next, you will need to configure your NoRA-Tools to connect to your NoRA databases in Notion. To this end, do the following:

Once you have recovered your API secret token and the database IDs, you must save these in the configs/notion/default.yaml file:

# Adapt to your own Notion library.
# See https://developers.notion.com/docs/create-a-notion-integration
token: "your_api_secret_token"
papers_db_id: "your_papers_database_id"
people_db_id: "your_people_database_id"
affiliations_db_id: "your_affiliations_database_id"
venues_db_id: "your_venues_database_id"
topics_db_id: "your_topics_database_id"
⚠️ Want to modify some field names in NoRA ?️

By default, NoRA-Tools expect the attribute fields (eg column names in Notion) of your papers, people, etc. to have specific values. If you want to adjust those, you will also need to adjust the configs/notion/default.yaml file:

# If you happen to modify your field names in Notion, update the
# following database-specific keys
person_keys:
    name: 'Name'
    affiliations: '🏢 Affiliations'
    papers: '📜 Papers'
    website: 'Website'

paper_keys:
    name: 'Name'
    authors: '👤 Authors'
    abstract:  'Abstract'
    topics: '🧲 Key topics'
    url: 'URL'
    to_read: 'Reading status'
    year: 'Year'
    venue:  '🤹 Venue'

affiliation_keys:
    name: 'Name'

venue_keys:
    name: 'Name'
⚠️ Want to add your own 🤹 Conferences & journals ?️

By default, when parsing a paper from a remote database, NoRA-Tools will try to figure out which 🤹 Conferences & journals to place it under. However, one can hardly account for all possible conference and journal names, nor for all the slight formatting differences used to describe how a paper was published. Yet, we attempt to group the most frequent ones using a predefined VENUES dictionary in src/utils/venues.py.

If many papers from your library are from a conference or journal absent from this dictionary, and you would like them to be grouped under the same 🤹 Conferences & journals item, you can simply append your own entries in VENUES, using the following format:

lowercase_match_to_search_for_in_remote_metadata: 'shorthand_under_which_to_group'

Zotero configuration (optional)

If you intend to move your whole Zotero library to Notion, you will need to configure your NoRA-Tools accordingly. To this end, you will need to:

You can then save your Zotero library ID and API key in the configs/zotero/default.yaml file:

# Adapt to your own Zotero library
library_id: 'your_library_id'
api_token: 'your_api_key'

By default, the collections (eg folders) in your Zotero library will be used to populate the Key Topics field of your papers in NoRA. If you want to exclude some of your collections from this behavior, your can list them in:

ignored_collections: ['collection name 1', 'collection name 2']

Proxy configuration (optional)

If your machine has a proxy, you will need to configure your NoRA-Tools to use it. To this end, specify your $HTTP_PROXY and $HTTPS_PROXY in the configs/proxy/default.yaml file:

http_proxy: 'your_http_proxy'
https_proxy: 'your_https_proxy'

⚡  Using NoRA-Tools

Uploading a paper to NoRA

NoRA-Tools mimics the behavior of the Zotero Connector, which has two mechanisms for uploading a paper.

From a URL:

# In your activated nora conda environment
python nora.py url=https://arxiv.org/abs/2204.07548
If you set up NoRA for simpler Unix commands 
nora url=https://arxiv.org/abs/2204.07548

From an identifier (DOI, ISBN, PMID, arXiv ID):

# In your activated nora conda environment
python nora.py "id='2204.07548'"
If you set up NoRA for simpler Unix commands 
nora "id='2204.07548'"

Note: we use hydra for parsing shell commands and recommend using quotes as shown above when querying id=.... This is to avoid some potential trailing zeros to be ignored when parsing your shell arguments. For more details on this, see the hydra documentation.

Note: NoRA uses psutil.net_connections() which requires sudo privileges on macOS. Unfortunately, there is no workaround this, you will need to run nora as sudo on macOS.

Uploading your entire Zotero library to NoRA

python nora.py zotero.upload=True
If you set up NoRA for simpler Unix commands 
nora zotero.upload=True

License

NoRA is released under the MIT License.

MIT License

Copyright (c) 2023-2024 Damien Robert

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.