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.
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
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;
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
sudo pip install setuptools --upgrade
sudo pip install -r conf/dependencies.cfg
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)
To run this project:
#ingest knowledge objects from CancerDataExpo into database
python manage.py ingestorgans
python manage.py ingestpublications
python manage.py ingestpersons
python manage.py runserver 0.0.0.0:8000
You can now visit the following URLS:
Run the test suite:
python manage.py test ksdb