def main(
dbfile,
start_id=1,
write_reaction=True,
write_ase=True,
write_publication=True,
write_reaction_system=True,
block_size=1000,
start_block=0,
db_user='******',
db_password=None,
):
stdout.write('Starting db2server\n')
db = CathubPostgreSQL(user=db_user, password=db_password)
stdout.write('Established SQL Server connection.\n')
db.transfer(dbfile,
start_id=start_id,
write_reaction=write_reaction,
write_ase=write_ase,
write_publication=write_publication,
write_reaction_system=write_reaction_system,
block_size=block_size,
start_block=start_block)
def delete():
if auth_required(f, session=flask.session):
params = flask.request.get_json()
endorser = params.get('userInfo', {}).get('username', '')
endorser_email = params.get('userInfo', {}).get('email', '')
pub_id = params.get('dataset', {}).get('pubId', '')
cathub_db = CathubPostgreSQL(
user='******',
password=os.environ.get('UPLOAD_ADMIN_PASSWORD'))
userhandle = cathub_db.get_pub_id_owner(pub_id)
if not userhandle == endorser_email:
return flask.jsonify({
'status':
'Failed',
'message':
"You don't have permission to delete this dataset"
})
cathub_db.delete_publication(pub_id)
return flask.jsonify({
'status':
'ok',
'message':
"The dataset '{}' was succesfully deleted".format(pub_id)
})
def test2_cli_db2server(self):
from cathub.postgresql import CathubPostgreSQL
from cathub.cli import db2server
db = CathubPostgreSQL(user='******')
con = db._connect()
db._initialize(con)
db.truncate_schema()
runner = CliRunner()
runner.invoke(db2server,
['--dbuser=postgres', 'aayush/MontoyaChallenge2015.db'])
def test7_modify_reaction(self):
db = CathubPostgreSQL(user='******')
id = db.check(pub_id='MontoyaChallenge2015',
chemical_composition='Pt16',
reactants=json.dumps({
'N2gas': 0.5,
'star': 1.0
}),
products=json.dumps({'Nstar': 1.0}))
db.update_reaction(id, reaction_energy=10)
db.delete_reaction(id)
def __init__(self, user='******', filename=None):
if filename is not None:
sql_url = 'sqlite:///' + str(filename)
self.backend = 'sqlite'
else:
sql_url = CathubPostgreSQL(user).server_name
self.backend = 'postgres'
self.sql_url = sql_url
self.connection = None
def test3_upload(self):
"""Ensure postgres database is empty"""
db = CathubPostgreSQL(user='******')
con = db._connect()
db._initialize(con)
db.truncate_schema()
con.commit()
con.close()
db2server.main(
'{path}/aayush/MontoyaChallenge2015.db'.format(path=path),
user='******')
if os.path.exists(
'{path}/aayush/MontoyaChallenge2015.db'.format(path=path)):
os.remove(
'{path}/aayush/MontoyaChallenge2015.db'.format(path=path))
def main():
server_name = CathubPostgreSQL().server_name
db = ase.db.connect(server_name)
return db
def test6_delete_user(self):
db = CathubPostgreSQL(user='******')
db.delete_user('viggo')
def test5_release(self):
with CathubPostgreSQL(user='******') as db:
db.release(['MontoyaChallenge2015'],
from_schema='public',
to_schema='viggo')
def test4_create_user(self):
with CathubPostgreSQL(user='******') as db:
db.create_user('viggo', row_limit=None)
def get_ase_db():
server_name = CathubPostgreSQL().server_name
return ase.db.connect(server_name)