def __init__(self, test_directory, mock_model=True):
# The following line is needed in order to create
# HistoryDatasetAssociations - ideally the model classes would be
# usable without the ORM infrastructure in place.
in_memomry_model = mapping.init("/tmp",
"sqlite:///:memory:",
create_tables=True)
self.datatypes_registry = Bunch(
integrated_datatypes_configs=
'/galaxy/integrated_datatypes_configs.xml',
get_datatype_by_extension=lambda ext: Bunch(),
)
self.config = Bunch(
outputs_to_working_directory=False,
commands_in_new_shell=True,
new_file_path=os.path.join(test_directory, "new_files"),
tool_data_path=os.path.join(test_directory, "tools"),
root=os.path.join(test_directory, "galaxy"),
admin_users="*****@*****.**",
len_file_path=os.path.join('tool-data', 'shared', 'ucsc', 'chrom'),
builds_file_path=os.path.join('tool-data', 'shared', 'ucsc',
'builds.txt.sample'),
migrated_tools_config=os.path.join(test_directory,
"migrated_tools_conf.xml"),
)
# Setup some attributes for downstream extension by specific tests.
self.job_config = Bunch(dynamic_params=None, )
# Two ways to handle model layer, one is to stub out some objects that
# have an interface similar to real model (mock_model) and can keep
# track of 'persisted' objects in a map. The other is to use a real
# sqlalchemy layer but target an in memory database. Depending on what
# is being tested.
if mock_model:
# Create self.model to mimic app.model.
self.model = Bunch(context=MockContext())
for module_member_name in dir(galaxy.model):
module_member = getattr(galaxy.model, module_member_name)
if type(module_member) == type:
self.model[module_member_name] = module_member
else:
self.model = in_memomry_model
self.genome_builds = GenomeBuilds(self)
self.toolbox = None
self.object_store = None
self.security = SecurityHelper(id_secret="testing")
from galaxy.security import GalaxyRBACAgent
self.job_queue = NoopQueue()
self.security_agent = GalaxyRBACAgent(self.model)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self.name = "galaxy"
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)
user.set_password_cleartext(password)
# 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)