nanobot

Setup

nanobot requires Python version >=3.9. Ensure you have this installed, then set up a virtual environment and install nanobot and its dependencies:

$ python3 -m venv .venv
$ source .venv/bin/activate
$ python3 -m pip install -e .

Finally, you will need to install wiring.py following the directions here

Database

TODO: nanobot requires a database created by cmi_pb_script.load

Usage

To run the server, you'll need to write a small run.py script (or any name you'd like to use). This script should call nanobot.run. For example:

#!/usr/bin/env python3.9
import os

from nanobot import run


if __name__ == '__main__':
    run(
        "my-database.db",     # path to database with tables
        "table.tsv",          # path to "table" table
        base_ontology="mro",  # name of base ontology for project
        title="MRO",          # project title to display in header
    )

Run Options

The run function requires the database path and the table path, but also accepts the following optional parameters:

• base_ontology: the name of the LDTab table for the base ontology of this project
• cgi_path: path to the script to use as SCRIPT_NAME environment variable (setting this will run the app in CGI mode)
  • When running in CGI mode, make sure to change to the correct base directory of the database and table (e.g., os.chdir("../.."))
• default_params: the query parameters to use for the default_table redirection
• default_table: the name of the table to redirect to from base URL (if not specified, an index page will be generated)
• hide_index: if True, hide the table of type index
• flask_host: host to run the Flask app on (default: 127.0.0.1, i.e. localhost)
• flask_port: port to run the Flask app on (default: 5000)
• import_table: name of the import table for an ontology project - this table must have the headers needed for gadget import modules
• log_file: path to a log file - if not provided, logging will output to console
• max_children: max number of child nodes to display in tree view
• synonym: predicate ID for the annotation property to use as synonym in search table (default is IAO:0000118)
• title: project title to display in header bar
• tree_predicates: list of predicate IDs in order that they should be displayed in the tree view - all remaining predicates should be specified with "*"