def drop_databases(debug, yes, connection):
"""Drop all databases."""
set_debug_param(debug)
if yes or click.confirm(
'Do you really want to delete the databases for {}?'.format(
', '.join(managers))):
for name, Manager in managers.items():
m = Manager(connection=connection)
click.echo('deleting {}'.format(name))
m.drop_all()
def setUp(self):
"""Create temporary file."""
self.fd, self.path = tempfile.mkstemp()
self.connection = 'sqlite:///' + self.path
# create temporary database
self.manager = Manager.from_connection(connection=self.connection)
def drop(debug, yes, connection):
"""Drop ComPath DB."""
set_debug_param(debug)
if yes or click.confirm('Do you really want to delete the ComPath DB'):
m = Manager.from_connection(connection=connection)
click.echo('Deleting ComPath DB')
m.drop_all()
m.create_all()
def populate(debug, connection, delete_first):
"""Populate all registered Bio2BEL pathway packages."""
set_debug_param(debug)
for name, Manager in managers.items():
m = Manager(connection=connection)
log.info('populating %s at %s', name, m.engine.url)
if delete_first:
click.echo('deleting {}'.format(name))
m.drop_all()
m.create_all()
click.echo('populating {}'.format(name))
m.populate()
def load_hierarchy(*, connection=None, curator_email=None):
"""Load the hierarchical relationships for the managers containing them.
:param Optional[str] connection:
:param Optional[str] curator_email: email of the admin
"""
compath_manager = Manager.from_connection(connection)
curator = compath_manager.get_user_by_email(
email=curator_email if curator_email else ADMIN_EMAIL)
if not curator:
raise EnvironmentError(
'There is no user with the email "{}". Please create it with the "make_user" command using '
'the command line interface of Compath')
for pathway_database, ExternalManager in managers.items():
pathway_db_manager = ExternalManager()
if not hasattr(pathway_db_manager, 'has_hierarchy'):
continue
log.info("Loading hierarchies for {}".format(pathway_database))
pathways = pathway_db_manager.get_all_pathways()
if pathway_database == 'reactome':
pathways = _reactome_wrapper(pathways)
log.info("Searching for hierarchical relationships in {} {} pathways".
format(len(pathways), pathway_database))
counter_mappings_created = create_hierarchical_mappings(
pathways, compath_manager, pathway_database, curator)
log.info("{} hierarchical mappings created in {}".format(
counter_mappings_created, pathway_database))
def init_app(self, app):
"""Overwrite init app method."""
super().init_app(app)
self.manager = Manager(engine=self.engine, session=self.session)
def manage(ctx, connection):
"""Manage the database."""
ctx.obj = Manager.from_connection(connection)
Base.metadata.bind = ctx.obj.engine
Base.query = ctx.obj.session.query_property()
ctx.obj.create_all()