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import os
from cogent.util.unit_test import TestCase, main
from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.database import Database
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
Release = 56
if 'ENSEMBL_ACCOUNT' in os.environ:
username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount('127.0.0.1', username, password)
else:
account = get_ensembl_account(release=Release)
class TestDatabase(TestCase):
def test_connect(self):
human = Database(account=account, release=Release,
species='human', db_type='core')
gene = human.getTable('gene')
def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account, release=Release,
species='human', db_type='variation')
tn, tc = 'variation_feature', 'consequence_type'
expected = set((('3PRIME_UTR', 'ESSENTIAL_SPLICE_SITE'),
('3PRIME_UTR', 'SPLICE_SITE'),
('5PRIME_UTR', 'ESSENTIAL_SPLICE_SITE')))
self.assertNotEquals(set(db.getDistinct(tn, tc)) & expected, set())
db = Database(account=account, release=Release,
species='human', db_type='core')
tn, tc = 'gene', 'biotype'
expected = set(['protein_coding', 'pseudogene', 'processed_transcript',
'Mt_tRNA', 'Mt_rRNA', 'IG_V_gene', 'IG_J_gene',
'IG_C_gene', 'IG_D_gene', 'miRNA', 'misc_RNA', 'snoRNA', 'snRNA', 'rRNA'])
got = set(db.getDistinct(tn, tc))
self.assertEquals(len(got&expected), len(expected))
db = Database(account=account, release=Release, db_type='compara')
got = set(db.getDistinct('homology', 'description'))
expected = set(['apparent_ortholog_one2one', 'between_species_paralog',
'ortholog_many2many', 'ortholog_one2many', 'ortholog_one2one',
'within_species_paralog'])
self.assertEquals(len(got&expected), len(expected))
def test_get_table_row_counts(self):
"""should return correct row counts for some tables"""
expect = {'homo_sapiens_core_56_37a.analysis': 57L,
'homo_sapiens_core_56_37a.seq_region': 55604L,
'homo_sapiens_core_56_37a.assembly': 102068L,
'homo_sapiens_core_56_37a.qtl': 0L}
human = Database(account=account, release=Release,
species='human', db_type='core')
table_names = [n.split('.')[1] for n in expect]
got = dict(human.getTablesRowCount(table_names).getRawData())
self.assertEquals(got, expect)
if __name__ == "__main__":
main()
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