def init(file_path, url, engine_options={}, create_tables=False):
"""Connect mappings to the database"""
# Load the appropriate db module
load_egg_for_url(url)
# Create the database engine
engine = create_engine(url, **engine_options)
# Connect the metadata to the database.
metadata.bind = engine
# Clear any existing contextual sessions and reconfigure
Session.remove()
Session.configure(bind=engine)
# Create tables if needed
if create_tables:
metadata.create_all()
# Pack everything into a bunch
result = Bunch(**globals())
result.engine = engine
result.session = Session
result.create_tables = create_tables
# Load local tool shed security policy
result.security_agent = CommunityRBACAgent(result)
result.shed_counter = shed_statistics.ShedCounter(result)
result.hgweb_config_manager = galaxy.webapps.community.util.hgweb_config.HgWebConfigManager(
)
return result
def init( file_path, url, engine_options={}, create_tables=False ):
"""Connect mappings to the database"""
# Load the appropriate db module
load_egg_for_url( url )
# Create the database engine
engine = create_engine( url, **engine_options )
# Connect the metadata to the database.
metadata.bind = engine
# Clear any existing contextual sessions and reconfigure
Session.remove()
Session.configure( bind=engine )
# Create tables if needed
if create_tables:
metadata.create_all()
# Pack everything into a bunch
result = Bunch( **globals() )
result.engine = engine
result.session = Session
result.create_tables = create_tables
#load local galaxy security policy
result.security_agent = CommunityRBACAgent( result )
result.shed_counter = ShedCounter( result )
return result
import sys
sys.path.insert(1,'/galaxy-central')
sys.path.insert(1,'/galaxy-central/lib')
from scripts.db_shell import *
from galaxy.util.bunch import Bunch
from galaxy.security import GalaxyRBACAgent
from sqlalchemy.orm import sessionmaker
from sqlalchemy import *
import argparse
bunch = Bunch( **globals() )
engine = create_engine('postgres://*****:*****@localhost:5432/galaxy')
bunch.session = sessionmaker(bind=engine)
# For backward compatibility with "model.context.current"
bunch.context = sessionmaker(bind=engine)
security_agent = GalaxyRBACAgent( bunch )
security_agent.sa_session = sa_session
def add_user(email, password, key=None):
"""
Add Galaxy User.
From John https://gist.github.com/jmchilton/4475646
"""
query = sa_session.query( User ).filter_by( email=email )
if query.count() > 0:
return query.first()
else:
User.use_pbkdf2 = False
user = User(email)
# FROM https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/create_galaxy_user.py
from scripts.db_shell import *
from galaxy.util.bunch import Bunch
from galaxy.security import GalaxyRBACAgent
from sqlalchemy.orm import sessionmaker
from sqlalchemy import *
import argparse
bunch = Bunch(**globals())
#engine = create_engine('postgres://*****:*****@localhost:5432/galaxy')
engine = create_engine(
'sqlite:///home/vagrant/galaxy/database/universe.sqlite')
bunch.session = sessionmaker(bind=engine)
# For backward compatibility with "model.context.current"
bunch.context = sessionmaker(bind=engine)
security_agent = GalaxyRBACAgent(bunch)
security_agent.sa_session = sa_session
def add_user(email, password, key=None):
"""
Add Galaxy User.
From John https://gist.github.com/jmchilton/4475646
"""
query = sa_session.query(User).filter_by(email=email)
if query.count() > 0:
return query.first()
else:
user = User(email)
user.set_password_cleartext(password)
sa_session.add(user)
