def test_get_ensembl_account(self):
"""return an HostAccount with correct port"""
for release in [48, '48', None]:
act_new = get_ensembl_account(release=release)
self.assertEqual(act_new.port, 5306)
for release in [45, '45']:
act_old = get_ensembl_account(release=45)
self.assertEqual(act_old.port, 3306)
def test_get_ensembl_account(self):
"""return an HostAccount with correct port"""
for release in [48, '48', None]:
act_new = get_ensembl_account(release=release)
self.assertEqual(act_new.port, 5306)
for release in [45, '45']:
act_old = get_ensembl_account(release=45)
self.assertEqual(act_old.port, 3306)
def __init__(self, Species, Release, account=None, pool_recycle=None):
super(Genome, self).__init__()
assert Release, 'invalid release specified'
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
# TODO: check Release may not be necessary because: assert Release above
if Release is None:
Release = get_latest_release(account=account)
self._gen_release = None
# TODO make name and release immutable properties
self.Species = _Species.getSpeciesName(Species)
self.Release = str(Release)
# the db connections
self._core_db = None
self._var_db = None
self._other_db = None
self._feature_type_ids = FeatureTypeCache(self)
self._feature_coord_levels = FeatureCoordLevels(self.Species)
def __init__(self, Species, Release, account=None, pool_recycle=None):
super(Genome, self).__init__()
assert Release, 'invalid release specified'
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
# TODO: check Release may not be necessary because: assert Release above
if Release is None:
Release = get_latest_release(account=account)
self._gen_release = None
# TODO make name and release immutable properties
self.Species = _Species.getSpeciesName(Species)
self.Release = str(Release)
# the db connections
self._core_db = None
self._var_db = None
self._other_db = None
self._feature_type_ids = FeatureTypeCache(self)
self._feature_coord_levels = FeatureCoordLevels(self.Species)
def test_active_connections(self):
"""connecting to a database on a specified server should be done once
only, but same database on a different server should be done"""
ensembl_acct = get_ensembl_account(release='46')
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
engine2 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
self.assertEqual(engine1, engine2)
def test_active_connections(self):
"""connecting to a database on a specified server should be done once
only, but same database on a different server should be done"""
ensembl_acct = get_ensembl_account(release='46')
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
engine2 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h")
self.assertEqual(engine1, engine2)
def test_table_has_column(self):
"""return correct values for whether a Table has a column"""
account = get_ensembl_account(release=Release)
var61 = Database(account=account, release=61, species='human',
db_type='variation')
var62 = Database(account=account, release=62, species='human',
db_type='variation')
self.assertTrue(var61.tableHasColumn('transcript_variation',
'peptide_allele_string'))
self.assertFalse(var61.tableHasColumn('transcript_variation',
'pep_allele_string'))
self.assertTrue(var62.tableHasColumn('transcript_variation',
'pep_allele_string'))
self.assertFalse(var62.tableHasColumn('transcript_variation',
'peptide_allele_string'))
def __init__(self, species, Release, account=None, pool_recycle=None, division=None):
assert Release, "invalid release specified"
self.Release = str(Release)
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
self._compara_db = None
sp = sorted([_Species.getSpeciesName(sp) for sp in set(species)])
self.Species = tuple(sp)
self._genomes = {}
self._attach_genomes()
self._species_id_map = None
self._species_db_map = None
self._species_set = None
self._method_species_link = None
self.division = division
def __init__(self,
species,
Release,
account=None,
pool_recycle=None,
division=None):
assert Release, 'invalid release specified'
self.Release = str(Release)
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
self._compara_db = None
sp = sorted([_Species.getSpeciesName(sp) for sp in set(species)])
self.Species = tuple(sp)
self._genomes = {}
self._attach_genomes()
self._species_id_map = None
self._species_db_map = None
self._species_set = None
self._method_species_link = None
self.division = division
def test_table_has_column(self):
"""return correct values for whether a Table has a column"""
account = get_ensembl_account(release=Release)
var61 = Database(account=account,
release=61,
species='human',
db_type='variation')
var62 = Database(account=account,
release=62,
species='human',
db_type='variation')
self.assertTrue(
var61.tableHasColumn('transcript_variation',
'peptide_allele_string'))
self.assertFalse(
var61.tableHasColumn('transcript_variation', 'pep_allele_string'))
self.assertTrue(
var62.tableHasColumn('transcript_variation', 'pep_allele_string'))
self.assertFalse(
var62.tableHasColumn('transcript_variation',
'peptide_allele_string'))
def test_pool_recycle_option(self):
"""excercising ability to specify a pool recycle option"""
ensembl_acct = get_ensembl_account(release='56')
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h", pool_recycle=1000)
__version__ = "1.5.3-dev"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 68
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=Release)
class TestEnsemblDbName(TestCase):
def test_cmp_name(self):
"""should validly compare names by attributes"""
n1 = EnsemblDbName('homo_sapiens_core_46_36h')
n2 = EnsemblDbName('homo_sapiens_core_46_36h')
self.assertEqual(n1, n2)
def test_name_without_build(self):
"""should correctly handle a db name without a build"""
n = EnsemblDbName("pongo_pygmaeus_core_49_1")
self.assertEqual(n.Prefix, "pongo_pygmaeus")
self.assertEqual(n.Type, "core")
self.assertEqual(n.Build, '1')
def test_pool_recycle_option(self):
"""excercising ability to specify a pool recycle option"""
ensembl_acct = get_ensembl_account(release='56')
engine1 = DbConnection(account=ensembl_acct,
db_name="homo_sapiens_core_46_36h",
pool_recycle=1000)
__version__ = "1.5.3-dev"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 76
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=Release)
class TestEnsemblDbName(TestCase):
def test_cmp_name(self):
"""should validly compare names by attributes"""
n1 = EnsemblDbName('homo_sapiens_core_46_36h')
n2 = EnsemblDbName('homo_sapiens_core_46_36h')
self.assertEqual(n1, n2)
def test_name_without_build(self):
"""should correctly handle a db name without a build"""
n = EnsemblDbName("pongo_pygmaeus_core_49_1")
self.assertEqual(n.Prefix, "pongo_pygmaeus")
self.assertEqual(n.Type, "core")
self.assertEqual(n.Build, '1')
