EDRN/KSDB

Name: KSDB

Owner: Early Detection Research Network

Description: Knowledge System DB

Created: 2016-07-05 00:55:45.0

Updated: 2016-07-05 00:58:21.0

Pushed: 2018-01-01 23:31:14.0

Homepage: null

Size: 6047

Language: JavaScript

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README

KSDB

Knowledge System DB: The goal of this system is to maintain generalized project information to be used for any bioinformatics knowledge system that the JPL Informatics Center supports. For example, EDRN or MCL.

DEPENDENCIES

sudo yum install postgresql-server postgresql-devel gcc openldap-devel openssl openssl-devel python3:

curl -O https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tgz
tar xf Python-3.5.0.tgz
cd Python-3.5.0
./configure
make
sudo make altinstall

pip3:

curl -O https://bootstrap.pypa.io/get-pip.py
sudo python3 get-pip.py 

SETUP POSTGRES

setup postgres

sudo service postgresql initdb
sudo chkconfig postgresql on
sudo service postgresql start
modify /var/lib/pgsql/data/pg_hba.conf so that all "ident" methods are changed to "md5"
sudo -i -u postgres createuser -s edrn --password   (set password to edrn)
sudo -i -u postgres psql 
    create database ksdb;
    alter user edrn password 'edrn';
    GRANT ALL ON database ksdb TO edrn;

insert tables

ctrl^D once to exit out of database
sudo service postgresql restart
export PGPASSWORD=edrn
psql -U edrn -h 127.0.0.1 -d ksdb -a -f conf/createtables.sql

SETUP KSDB

Make sure to create a virtual environment

sudo pip install setuptools --upgrade
sudo pip install -r conf/dependencies.cfg

Configure KSDB

modify sitemain/settings.py to update DATABASES parameter. Make sure you updated 'name' to ksdb, 'user' to edrn, 'password' to edrn, and host to localhost.
*You can use support/set_settings.py to automatically apply a local settings file to the template settings file. The script will write a settings.py in the same directory as the template settings file:
**Example: python support/set_settings.py ~/KSDB/settings.tumor.py sitemain/settings.py.in 
python manage.py migrate auth
python manage.py migrate
python manage.py createsuperuser (create the user you will be using to login)

Running the project

To run this project:

#ingest knowledge objects from CancerDataExpo into database
python manage.py ingestorgans
python manage.py ingestpublications
python manage.py ingestpersons

Run the server

python manage.py runserver 0.0.0.0:8000

You can now visit the following URLS:

• http://127.0.0.1:8000/
• http://127.0.0.1:8000/ksdb/view/

Tests

Run the test suite:

python manage.py test ksdb