The dbBact paper has been published: Nucleic Acids Research 2023

dbBact-server

This is the REST-API server code for the dbBact open microbiome knowledge-base.

The main dbBact server is running at: dbbact.org.

The dbBact API is available at: api.dbbact.org

API documentation is available at: api.dbbact.org/docs

Example notebooks for using the dbBact REST-API are available at: github.com/amnona/dbbact-examples

dbBact is used by the Calour microbiome analysis tool

The dbBact message forum is now live at: dbbact.boards.net

Installation:

However, you may want to locally install dbBact in order to test new functions, or to run local queries.

1. dbBact server interfaces with a postgres SQL database containing the actual data. dbBact requires postgres 9.3 or higher. postgres can be obtained here.

2. Create the dbBact conda environment:

   conda create -n dbbact python=3.6 numpy matplotlib scipy jupyter statsmodels psycopg2 flask requests
   
   source activate dbbact

3. install additional needed packages:

   
   pip install flask-selfdoc

(or alternatively pip install git+https://github.com/amnona/flask-autodoc)

pip install flask-login

4. for gunicorn (alternatively can run using flask but not for production):

pip install gunicorn

pip install setproctitle

5. Clone the dbbact github repository
  git clone https://github.com/amnona/dbbact-server.git

6. change to the dbbact-server directory and install locally

cd dbbact-server

pip install -e .

7. install the database template to postgres

psql -U postgres < database/setup.psql

psql -U postgres -d dbbact < database/extensions.psql

pg_restore -U dbbact -d dbbact database/dbbact-export.psql

(Password for dbbact is magNiv)

Alternatively, to erase current dbbact database, use:

pg_restore -U postgres -d postgres --clean --create database/dbbact-export.psql

Also prepare the users private data table (which is not exported in the database export due to privacy concerns):

psql -U dbbact -d dbbact < database/data_users_private.txt

dbBact database snapshots are available [here](https://dbbact.org/download)

8. Set the dbbact server environment flag to specify running environment (production/develop/local)
production:

export DBBACT_SERVER_TYPE="production"

develop:

export DBBACT_SERVER_TYPE="develop"

local:

export DBBACT_SERVER_TYPE="local"

9. run locally:
NOTE: the default port for dbbact-server should be 5001

gunicorn 'dbbact_server.Server_Main:gunicorn(debug_level=5)' -b 127.0.0.1:5001 --workers 4 --name=dbbact-rest-api --timeout 300 --reload