def invoke_migrate_main():
# Migrate has its own args, so cannot use argparse
config = get_config(sys.argv, use_argparse=False)
db_url = config['db_url']
repo = config['repo']
main(repository=repo, url=db_url)
def invoke_migrate_main():
# Migrate has its own args, so cannot use argparse
config = get_config(sys.argv, use_argparse=False)
db_url = config['db_url']
repo = config['repo']
main(repository=repo, url=db_url)
def invoke_create():
config = get_config(sys.argv)
if config['database'] == 'galaxy':
create_db(config['db_url'], config['config_file'])
elif config['database'] == 'tool_shed':
create_tool_shed_db(config['db_url'])
elif config['database'] == 'install':
create_install_db(config['db_url'])
def invoke_create():
config = get_config(sys.argv)
if config['database'] == 'galaxy':
create_db(config['db_url'], config['config_file'])
elif config['database'] == 'tool_shed':
create_tool_shed_db(config['db_url'])
elif config['database'] == 'install':
create_install_db(config['db_url'])
def invoke_create():
config = get_config(sys.argv)
if config["database"] == "galaxy":
create_db(config["db_url"], config["config_file"])
elif config["database"] == "tool_shed":
create_tool_shed_db(config["db_url"])
elif config["database"] == "install":
create_install_db(config["db_url"])
def delete_galaxy_user():
db_url = get_config(sys.argv, use_argparse=False)['db_url']
options = cli_options()
mapping = init('/tmp/', db_url)
sa_session = mapping.context
security_agent = mapping.security_agent
delete_user(sa_session, security_agent, options.user)
def main():
ini_file = sys.argv.pop(1)
config = get_config(ini_file)
model = mapping.init( ini_file, config['db_url'], create_tables = False )
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()
def main():
ini_file = sys.argv.pop(1)
config = get_config(ini_file)
model = mapping.init(ini_file, config['db_url'], create_tables=False)
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()
def manage_galaxy_bootstrap_user():
db_url = get_config(sys.argv, use_argparse=False)['db_url']
options = cli_options()
mapping = init('/tmp/', db_url)
sa_session = mapping.context
security_agent = mapping.security_agent
if options.action == "create":
add_user(sa_session,
security_agent,
options.user,
options.password,
key=options.key,
username=options.username)
elif options.action == "delete":
delete_user(sa_session, security_agent, options.user)
def main():
if len(sys.argv) != 2 or sys.argv == "-h" or sys.argv == "--help":
usage(sys.argv[0])
sys.exit()
ini_file = sys.argv.pop(1)
config = get_config(ini_file)
model = mapping.init( ini_file, config['db_url'], create_tables=False )
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()
def main():
if len(sys.argv) != 2 or sys.argv == "-h" or sys.argv == "--help":
usage(sys.argv[0])
sys.exit()
ini_file = sys.argv.pop(1)
config = get_config(ini_file)
model = mapping.init( ini_file, config['db_url'], create_tables=False )
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()
def find_missing_indexes():
def load_indexes(metadata):
indexes = {}
for t in metadata.tables.values():
for index in t.indexes:
index_tuple = tuple_from_index(index)
indexes[index_tuple] = index.name
return indexes
# load metadata from mapping.py
metadata = mapping.metadata
mapping_indexes = load_indexes(metadata)
# create EMPTY metadata, then load from database
db_url = get_config(sys.argv)['db_url']
metadata = MetaData(bind=create_engine(db_url))
metadata.reflect()
indexes_in_db = load_indexes(metadata)
missing_indexes = set(mapping_indexes.keys()) - set(indexes_in_db.keys())
if missing_indexes:
return [(mapping_indexes[index], index.table, index.column_names)
for index in missing_indexes]
def invoke_migrate_main():
config = get_config(sys.argv)
db_url = config['db_url']
repo = config['repo']
main(repository=repo, url=db_url)
def invoke_migrate_main():
config = get_config( sys.argv )
db_url = config['db_url']
repo = config['repo']
main( repository=repo, url=db_url )
if not user.default_permissions:
security_agent.user_set_default_permissions(user,
history=True,
dataset=True)
if key is not None:
api_key = APIKeys()
api_key.user_id = user.id
api_key.key = key
sa_session.add(api_key)
sa_session.flush()
return user
if __name__ == "__main__":
db_url = get_config(sys.argv, use_argparse=False)['db_url']
parser = argparse.ArgumentParser(description='Create Galaxy Admin User.')
parser.add_argument("--user",
required=True,
help="Username, it should be an email address.")
parser.add_argument("--password", required=True, help="Password.")
parser.add_argument("--key", help="API-Key.")
parser.add_argument(
"--username",
default="admin",
help=
"The public username. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the '-' character."
)
parser.add_argument('args', nargs=argparse.REMAINDER)
1,
os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
from galaxy.datatypes.registry import Registry
from galaxy.model import * # noqa
from galaxy.model import set_datatypes_registry # More explicit than `*` import
from galaxy.model.mapping import init
from galaxy.model.orm.scripts import get_config
if sys.version_info > (3, ):
long = int
registry = Registry()
registry.load_datatypes()
set_datatypes_registry(registry)
db_url = get_config(sys.argv)['db_url']
sa_session = init('/tmp/', db_url).context
# Helper function for debugging sqlalchemy queries...
# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query
def printquery(statement, bind=None):
"""
Print a query, with values filled in
for debugging purposes *only*
for security, you should always separate queries from their values
please also note that this function is quite slow
"""
import sqlalchemy.orm
if isinstance(statement, sqlalchemy.orm.Query):
if bind is None:
from flask import Flask, request, make_response, current_app, send_file
from flask_socketio import SocketIO, emit, disconnect, join_room, leave_room
import flask.ext.login as flask_login
from flask.ext.login import current_user
from datetime import timedelta
from functools import update_wrapper
from galaxy.model.orm.scripts import get_config
from galaxy.model import mapping
from galaxy.util.properties import load_app_properties
from galaxy.web.security import SecurityHelper
from galaxy.util.sanitize_html import sanitize_html
# Get config file and load up SA session
config = get_config( sys.argv )
model = mapping.init( '/tmp/', config['db_url'] )
sa_session = model.context.current
# With the config file we can load the full app properties
app_properties = load_app_properties(ini_file=config['config_file'])
# We need the ID secret for configuring the security helper to decrypt
# galaxysession cookies.
if "id_secret" not in app_properties:
log.warn('No ID_SECRET specified. Please set the "id_secret" in your galaxy.ini.')
id_secret = app_properties.get('id_secret', 'dangerous_default')
security_helper = SecurityHelper(id_secret=id_secret)
# And get access to the models
from sqlalchemy.sql import label # noqa
sys.path.insert(
1,
os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
from galaxy.datatypes.registry import Registry
from galaxy.model import * # noqa
from galaxy.model import set_datatypes_registry # More explicit than `*` import
from galaxy.model.mapping import init
from galaxy.model.orm.scripts import get_config
registry = Registry()
registry.load_datatypes()
set_datatypes_registry(registry)
config = get_config(sys.argv)
db_url = config['db_url']
sa_session = init('/tmp/', db_url).context
# Helper function for debugging sqlalchemy queries...
# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query
def printquery(statement, bind=None):
"""
Print a query, with values filled in
for debugging purposes *only*
for security, you should always separate queries from their values
please also note that this function is quite slow
"""
import sqlalchemy.orm
if isinstance(statement, sqlalchemy.orm.Query):
# # You can also use this script as a library, for instance see https://gist.github.com/1979583 # TODO: This script overlaps a lot with manage_db.py and create_db.py, # these should maybe be refactored to remove duplication. import sys import os.path db_shell_path = __file__ new_path = [ os.path.join( os.path.dirname( db_shell_path ), os.path.pardir, "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path from galaxy.model.orm.scripts import get_config from galaxy import eggs eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) db_url = get_config( sys.argv )['db_url'] # Setup DB scripting environment from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exc import * from galaxy.model.mapping import init sa_session = init( '/tmp/', db_url ).context from galaxy.model import *
# TODO: This script overlaps a lot with manage_db.py and create_db.py,
# these should maybe be refactored to remove duplication.
import datetime
import decimal
import os.path
import sys
db_shell_path = __file__
new_path = [os.path.join(os.path.dirname(db_shell_path), os.pardir, "lib")]
new_path.extend(sys.path[1:]) # remove scripts/ from the path
sys.path = new_path
from galaxy.model.orm.scripts import get_config
db_url = get_config(sys.argv)["db_url"]
# Setup DB scripting environment
from sqlalchemy import * # noqa
from sqlalchemy.orm import * # noqa
from sqlalchemy.exc import * # noqa
from galaxy.model.mapping import init
sa_session = init("/tmp/", db_url).context
from galaxy.model import * # noqa
# Helper function for debugging sqlalchemy queries...
# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query