def init():
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
object_store = build_object_store_from_config(config)
model = init_models_from_config(config, object_store=object_store)
return model, object_store
def __init__(self, config):
self.object_store = build_object_store_from_config(config)
# Setup the database engine and ORM
self.model = init_models_from_config(config,
object_store=self.object_store)
registry = Registry()
registry.load_datatypes()
galaxy.model.set_datatypes_registry(registry)
def init():
if args.username == 'all':
args.username = None
if args.email == 'all':
args.email = None
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
object_store = build_object_store_from_config(config)
engine = config.database_connection.split(":")[0]
return init_models_from_config(config, object_store=object_store), object_store, engine
def _init(args):
properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**properties)
object_store = build_object_store_from_config(config)
if not config.database_connection:
logging.warning("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
model = init_models_from_config(config, object_store=object_store)
return (
model,
object_store,
config,
)
def main(argv):
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-k',
'--secret-key',
help='Key to convert pages with',
default='')
parser.add_argument('-d',
'--dry-run',
help='No changes, just test it.',
action='store_true')
populate_config_args(parser)
args = parser.parse_args()
properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**properties)
secret = args.secret_key or config.id_secret
security_helper = IdEncodingHelper(id_secret=secret)
object_store = build_object_store_from_config(config)
if not config.database_connection:
print(
"The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml"
)
model = init_models_from_config(config, object_store=object_store)
session = model.context.current
pagerevs = session.query(model.PageRevision).all()
mock_trans = Bunch(app=Bunch(security=security_helper),
model=model,
user_is_admin=lambda: True,
sa_session=session)
for p in pagerevs:
try:
processor = PageContentProcessor(mock_trans,
placeholderRenderForSave)
processor.feed(p.content)
newcontent = unicodify(processor.output(), 'utf-8')
if p.content != newcontent:
if not args.dry_run:
p.content = unicodify(processor.output(), 'utf-8')
session.add(p)
session.flush()
else:
print("Modifying revision %s." % p.id)
print(difflib.unified_diff(p.content, newcontent))
except Exception:
logging.exception(
"Error parsing page, rolling changes back and skipping revision %s. Please report this error."
% p.id)
session.rollback()
def _configure_models(self,
check_migrate_databases=False,
config_file=None):
"""Preconditions: object_store must be set on self."""
db_url = self.config.database_connection
install_db_url = self.config.install_database_connection
# TODO: Consider more aggressive check here that this is not the same
# database file under the hood.
combined_install_database = not (install_db_url
and install_db_url != db_url)
install_db_url = install_db_url or db_url
install_database_options = self.config.database_engine_options if combined_install_database else self.config.install_database_engine_options
if self.config.database_wait:
self._wait_for_database(db_url)
if getattr(self.config, "max_metadata_value_size", None):
custom_types.MAX_METADATA_VALUE_SIZE = self.config.max_metadata_value_size
if check_migrate_databases:
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
create_or_verify_database(
db_url,
config_file,
self.config.database_engine_options,
app=self,
map_install_models=combined_install_database)
if not combined_install_database:
tsi_create_or_verify_database(install_db_url,
install_database_options,
app=self)
self.model = init_models_from_config(
self.config,
map_install_models=combined_install_database,
object_store=self.object_store,
trace_logger=getattr(self, "trace_logger", None))
if combined_install_database:
log.info(
"Install database targetting Galaxy's database configuration.")
self.install_model = self.model
else:
install_db_url = self.config.install_database_connection
log.info(
f"Install database using its own connection {install_db_url}")
self.install_model = install_mapping.init(
install_db_url, install_database_options)
def main():
parser = argparse.ArgumentParser(DESCRIPTION)
populate_config_args(parser)
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
model = init_models_from_config(config)
for row in model.context.query(model.Dataset):
if row.uuid is None:
row.uuid = uuid.uuid4()
print("Setting dataset:", row.id, " UUID to ", row.uuid)
model.context.flush()
for row in model.context.query(model.Workflow):
if row.uuid is None:
row.uuid = uuid.uuid4()
print("Setting Workflow:", row.id, " UUID to ", row.uuid)
model.context.flush()
print("Complete")
from galaxy.model.mapping import init_models_from_config
from galaxy.security import idencoding
from galaxy.util.script import app_properties_from_args, populate_config_args
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-e', '--encode-id', dest='encode_id', help='Encode an ID')
parser.add_argument('-d', '--decode-id', dest='decode_id', help='Decode an ID')
parser.add_argument('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
parser.add_argument('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
model = init_models_from_config(config)
if args.encode_id:
print(f'Encoded "{args.encode_id}": {helper.encode_id(args.encode_id)}')
if args.decode_id:
print(f'Decoded "{args.decode_id}": {helper.decode_id(args.decode_id)}')
if args.hda_id:
try:
hda_id = int(args.hda_id)
except Exception:
hda_id = int(helper.decode_id(args.hda_id))
hda = model.context.current.query(model.HistoryDatasetAssociation).get(hda_id)
print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.file_name}')