def test_host_comparison(self):
"""instances with same host, account, database, port are equal"""
h1 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5306)
h2 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5306)
self.assertNotEqual(id(h1), id(h2))
self.assertEqual(h1, h2)
# hashes are also equal
self.assertEqual(hash(h1), hash(h2))
h3 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5300)
self.assertNotEqual(h1, h3)
self.assertNotEqual(hash(h1), hash(h3))
def drop(configpath, mysqlcfg, verbose, debug):
"""drop databases from a MySQL server"""
mysql_info = read_mysql_config(mysqlcfg, "mysql")
account = HostAccount(
mysql_info["host"],
mysql_info["user"],
mysql_info["passwd"],
port=mysql_info["port"],
)
server = DbConnection(account, db_name="PARENT", pool_recycle=36000)
cursor = server.cursor()
release, remote_path, local_path, species_dbs = read_config(configpath)
content = get_db_name(account=account, release=str(release))
content = [str(n) for n in content]
dbnames = reduce_dirnames(content, species_dbs)
click.echo("The following databases will be deleted:")
click.echo("\n".join(" %s" % d for d in dbnames))
try:
click.confirm("Confirm you want to delete the databases", abort=True)
except click.exceptions.Abort:
click.echo("EXITING")
exit(0)
for dbname in dbnames:
click.echo(f"Dropping {dbname}")
_drop_db(cursor, dbname)
if verbose:
display_dbs(cursor, release)
cursor.close()
def install(configpath, mysqlcfg, force_overwrite, verbose, debug):
"""install ensembl databases into a MySQL server"""
mysql_info = read_mysql_config(mysqlcfg, "mysql")
account = HostAccount(
mysql_info["host"],
mysql_info["user"],
mysql_info["passwd"],
port=mysql_info["port"],
)
server = DbConnection(account, db_name="PARENT", pool_recycle=36000)
release, remote_path, local_path, species_dbs = read_config(configpath)
content = os.listdir(local_path)
cursor = server.cursor()
sql_for_speed = ["SET FOREIGN_KEY_CHECKS=0;", "SET UNIQUE_CHECKS=0;"]
cursor.execute("\n".join(sql_for_speed))
dbnames = reduce_dirnames(content, species_dbs)
dbnames = sorted_by_size(local_path, dbnames, debug=debug)
for dbname in dbnames:
chk = get_installed_checkpoint_path(local_path, dbname.name)
server.ping(reconnect=True) # reconnect if server not alive
if force_overwrite:
_drop_db(cursor, dbname.name)
if chk.exists():
chk.unlink()
if verbose:
click.echo(f"Creating database {dbname.name}")
# now create dbname
sql = f"CREATE DATABASE IF NOT EXISTS {dbname}"
r = cursor.execute(sql)
install_one_db(
mysqlcfg,
server,
account,
dbname.name,
local_path,
force_overwrite=force_overwrite,
verbose=verbose,
debug=debug,
)
if debug:
display_dbs(cursor, release)
click.echo(server)
undo_sql_for_speed = ["SET FOREIGN_KEY_CHECKS=1;", "SET UNIQUE_CHECKS=1;"]
server.ping(reconnect=True)
cursor.execute("\n".join(undo_sql_for_speed))
cursor.close()
def test_account_str(self):
"""str"""
h1 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5306)
self.assertEqual(str(h1), "user:[email protected]:5306")
self.assertEqual(h1.formatted(),
"anonymous:@ensembldb.ensembl.org:5306")
# default port, actual password
h2 = HostAccount("mysql.host.org", "me", "tricky")
self.assertEqual(str(h2), "user:[email protected]:3306")
self.assertEqual(h2.formatted(), "me:[email protected]:3306")
def show(release, mysqlcfg):
"""shows databases corresponding to release"""
if mysqlcfg.name == _mycfg:
click.secho(f"{show.help}\n")
click.secho("use --help for more options")
exit()
mysql_info = read_mysql_config(mysqlcfg, "mysql")
account = HostAccount(
mysql_info["host"],
mysql_info["user"],
mysql_info["passwd"],
port=mysql_info["port"],
)
names = get_db_name(account=account, release=str(release))
click.echo(f"Databases at host='{account.host}' for release={release}")
if names:
click.echo("\n".join(" %s" % n for n in names))
else:
click.echo(" None")
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2016-, The EnsemblDb Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "BSD"
__version__ = "3.0a1"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
if "ENSEMBL_ACCOUNT" in os.environ:
args = os.environ["ENSEMBL_ACCOUNT"].split()
host, username, password = args[0:3]
kwargs = {}
if len(args) > 3:
kwargs["port"] = int(args[3])
account = HostAccount(host, username, password, **kwargs)
else:
account = get_ensembl_account(release=ENSEMBL_RELEASE)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(species="chicken",
release=ENSEMBL_RELEASE,
account=account)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels("chicken")
chicken_feature_levels = ChickenFeatureLevels(
feature_types=["gene", "cpg", "est"],
core_db=self.chicken.CoreDb,
from ensembldb3.compara import Compara, Genome
from ensembldb3.host import HostAccount, get_ensembl_account
from . import ENSEMBL_GENOMES_RELEASE
__author__ = "Jason Merkin"
__copyright__ = "Copyright 2016-, The EnsemblDb Project"
__credits__ = ["Jason Merkin", "Gavin Huttley", "Hua Ying"]
__license__ = "BSD"
__version__ = "3.0a1"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
account = HostAccount("mysql-eg-publicsql.ebi.ac.uk",
"anonymous",
"",
port=4157)
class MZ_ComparaTestBase(TestCase):
comp = Compara(
["D.grimshawi", "D.melanogaster"],
release=ENSEMBL_GENOMES_RELEASE,
account=account,
division="metazoa",
)
class MZ_TestCompara(MZ_ComparaTestBase):
def test_query_genome(self):
"""compara should attach valid genome attributes by common name"""