notion

name	notion
description	Search, read, and download from Notion. Use when the user asks about protocols, lab databases, or needs to download files (like vector maps) from Notion.

Notion CLI

Search, read, query, and download files from Notion pages and databases.

CLI Location

scripts/notion_cli.py

Environment

export NOTION_TOKEN="your_token_here"

Commands

Search

python3 scripts/notion_cli.py search "query"
python3 scripts/notion_cli.py search "protocol" --type page
python3 scripts/notion_cli.py search "proteins" --type database

Read Page Content

python3 scripts/notion_cli.py read <page_id> --depth 3

List Databases

python3 scripts/notion_cli.py databases

Query Database

python3 scripts/notion_cli.py query <database_id>
python3 scripts/notion_cli.py query <database_id> --filter '{"property": "Status", "select": {"equals": "Done"}}'

Download Files from Page

python3 scripts/notion_cli.py download <page_id> -o ./output

Download Files by Entry Name

# Download vector file from Series-438 database
python3 scripts/notion_cli.py files <YOUR_SERIES_438_DB_ID> "438-C" -o ./vectors

# Download from specific property
python3 scripts/notion_cli.py files <database_id> "entry name" -o ./output --property "Plasmid maps"

Key Database IDs

Configure your Notion database IDs in .env or note them here:

Database	ID	Contents
Series-438	<YOUR_DB_ID>	438 vector series (.dna files)
Lab Meeting Schedule	<YOUR_DB_ID>	Meeting dates/presenters
Protein purifications	<YOUR_DB_ID>	Active purifications

Example: Download and Parse Vector

# 1. Download 438-C vector from Notion
python3 scripts/notion_cli.py files <YOUR_SERIES_438_DB_ID> "438-C" -o ./vectors

# 2. Parse with SnapGene reader
python3 scripts/snapgene_cli.py ./vectors/438-C.dna --features

# 3. Convert to GenBank
python3 scripts/snapgene_cli.py ./vectors/438-C.dna --export-gb ./vectors/438-C.gb

Output Formats

• Search results: page/database listings with IDs
• Page content: formatted blocks (headings, lists, code)
• Query results: table format with key properties
• File downloads: saved to specified directory