Exploring BGCFlow result database using Metabase

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How do I explore and query tabular data from BGCFlow result?

Objectives

• Start a local Metabase server

• Loadi BGCFlow OLAP database (DuckDB) in metabase

Pre-requisite

• Activate the BGCFlow conda environment and make sure you have a clone of BGCFlow installed locally (see Part 1 - Introduction)

  cd <your BGCFlow path>
  conda activate bgcflow
  

• Download and extract a BGCFlow project demo (see Part 7)

Starting Metabase server

• Make sure you are in your bgcflow directory. Metabase can then be started using:

  bgcflow serve --metabase
  

• Metabase will be launched in locally in http://localhost:3000/

Setting a local Metabase account

• Follow the steps to set up your account
• Choose DuckDB as the database type and give the DuckDB Path: /home/<my_user_name>/Lactobacillus_delbrueckii_report/Lactobacillus_delbrueckii/dbt_as_6.1.1/

Key Points

• All of the tabular ouputs from BGCFlow are loaded and transformed into an OLAP database (DuckDB)

• A business intelligence tools such as Metabase, can be used to interactively explore the database and build SQL queries