REST API

The Plant-Imager3 project provides a REST API for interacting with the system programmatically. This API is used by the web UI and can also be used by custom scripts and applications.

API Endpoints

The REST API is provided by the FSDB (File System Database) REST API server, which is part of the plantdb.server package. The Plant-Imager3 project uses this API to store and retrieve scan data.

Starting the API Server

To start the API server for testing purposes, you can use the following command:

fsdb_rest_api --test

For production use, you should configure the API server to use a specific database directory:

fsdb_rest_api --db-path /path/to/database

Authentication

The API server supports basic authentication. You can configure users in the server configuration file.

API Documentation

The complete API documentation is available in the plantdb documentation.

Key Endpoints

Here are some of the key endpoints provided by the API:

Scans

• GET /scans: List all scans
• GET /scans/{scan_id}: Get information about a specific scan
• POST /scans: Create a new scan
• DELETE /scans/{scan_id}: Delete a scan

Files

• GET /scans/{scan_id}/files: List all files in a scan
• GET /scans/{scan_id}/files/{file_id}: Get a specific file
• POST /scans/{scan_id}/files: Upload a file to a scan
• DELETE /scans/{scan_id}/files/{file_id}: Delete a file from a scan

Metadata

• GET /scans/{scan_id}/metadata: Get metadata for a scan
• PUT /scans/{scan_id}/metadata: Update metadata for a scan

Using the API

Here's an example of how to use the API with Python:

import requests
import json

# Base URL for the API
base_url = "http://localhost:5000"

# List all scans
response = requests.get(f"{base_url}/scans")
scans = response.json()
print(f"Found {len(scans)} scans")

# Create a new scan
scan_data = {
    "id": "my_scan",
    "metadata": {
        "plant": "Arabidopsis",
        "date": "2023-01-01"
    }
}
response = requests.post(f"{base_url}/scans", json=scan_data)
print(f"Created scan: {response.json()}")

# Upload a file to the scan
with open("image.jpg", "rb") as f:
    files = {"file": f}
    response = requests.post(f"{base_url}/scans/my_scan/files", files=files)
print(f"Uploaded file: {response.json()}")

Integration with Plant-Imager3

The Plant-Imager3 project uses the REST API to store and retrieve scan data. The plantimager.webui package provides a web interface for interacting with the API, and the plantimager.controller package uses the API to store scan data.

For more information on how to use the API with Plant-Imager3, see the developer documentation.