Background

In order to visualize an internal database entry using local instance of Mol* 3D viewer, you need to host a local instance of server API. Local instance of Mol* 3D viewer then will be able to send dynamic queries to the local instance of server API, and visualize their results.

Hosting Server API

Make changes in server/cellstar_server/app/settings.py file. DB_PATH constant (line 8 in the code block below) should point to the path to your internal database that was built using Preprocessor, e.g.:

from pathlib import Path
from pydantic import BaseSettings

class _Settings(BaseSettings):
    HOST: str = "0.0.0.0"
    PORT: int = 9000
    DEV_MODE: bool = False
    DB_PATH: Path = Path('preprocessor/temp/test_db')
    GIT_TAG: str = ''
    GIT_SHA: str = ''

settings = _Settings()

Optionally, you can change the HOST and PORT constants to deploy server API at a local address other than localhost 127.0.0.1 (0.0.0.0) and port other than 9000.

From the root repository directory, run server/cellstar_server/serve.py script to deploy the server API:

python server/cellstar_server/serve.py

It will deploy server API at http://localhost:9000/ with API documentation available at http://localhost:9000/docs.

In order for Mol* Volumes & Segmentations extension of Mol* 3D viewer to be able to load entries, http://localhost:9000/v1 should be specified as Server Url parameter: