brain-app

Used to view brain data using node.js/express.js sever and postgres database

create postgres database from .nii file:

install postgress sql client

install postgres sql client UBUNTU: sudo apt-get update sudo apt-get install postgresql-client

Install python libraries nibabel and sqlalchemy, and pandas, along with their own dependencies.

pip install nibabel pip install sqlalchemy pip install pandas

Run Python file

run the python file brain_to_postgresql.py to load data into postgres table 'braintbl' brain_to_postgresql.py

create readonly user

Some helpful navigation hints in postgres

First change user to postgres sudo su - postgres

starts sql: psql

creates database 'brain': CREATE DATABASE brain

connects to brain: \c brain

shows tables: \dt

simple test command: SELECT * FROM braintbl LIMIT 10;

dumps to file from bash: pg_dump -h localhost --no-acl -U postgres --format=plain --no-owner brain > brain.sql

install postgres sql client UBUNTU: sudo apt-get update sudo apt-get install postgresql-client

MAC: ???

use this to grant priveleges to readonly on brain db.

First change user to postgres sudo su - postgres

create readonly user

CREATE USER readonly WITH ENCRYPTED PASSWORD 'readonly'; GRANT USAGE ON SCHEMA public to readonly; ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT SELECT ON TABLES TO readonly; -- repeat code below for each database: GRANT CONNECT ON DATABASE brain to readonly; \c brain ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT ALL ON TABLES TO readonly; --- this grants privileges on new tables generated in new database "brain" GRANT USAGE ON SCHEMA public to readonly; GRANT SELECT ON ALL SEQUENCES IN SCHEMA public TO readonly; GRANT SELECT ON ALL TABLES IN SCHEMA public TO readonly;