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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Run BioSQL tests using SQLite."""
import os
import unittest
# Really do want "import *" to get all the test classes:
from common_BioSQL import * # noqa: F403
# Import these explicitly to avoid flake8 F405 below:
from common_BioSQL import check_config
from common_BioSQL import temp_db_filename
from seq_tests_common import SeqRecordTestBaseClass
from Bio import SeqIO
from BioSQL import BioSeqDatabase
# Constants for the database driver
DBDRIVER = "sqlite3"
DBTYPE = "sqlite"
DBHOST = None
DBUSER = "root"
DBPASSWD = None
TESTDB = temp_db_filename()
# This will abort if driver not installed etc:
check_config(DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB)
if False:
# This is how I generated test file Tests/BioSQL/cor6_6.db
# which is test cross-checked with the latest bindings to
# catch any regressions in how we map GenBank entries to
# the database.
assert not os.path.isfile("BioSQL/cor6_6.db")
server = BioSeqDatabase.open_database(driver=DBDRIVER, db="BioSQL/cor6_6.db")
DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
SQL_FILE = os.path.join(os.getcwd(), "BioSQL", DBSCHEMA)
assert os.path.isfile(SQL_FILE), SQL_FILE
server.load_database_sql(SQL_FILE)
server.commit()
db = server.new_database("OLD")
count = db.load(SeqIO.parse("GenBank/cor6_6.gb", "gb"))
assert count == 6
server.commit()
assert len(db) == 6
server.close()
class BackwardsCompatibilityTest(SeqRecordTestBaseClass):
def test_backwards_compatibility(self):
"""Check can reuse an old BioSQL SQLite3 database."""
original_records = []
for record in SeqIO.parse("GenBank/cor6_6.gb", "gb"):
if record.annotations["molecule_type"] == "mRNA":
record.annotations["molecule_type"] = "DNA"
original_records.append(record)
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER, db="BioSQL/cor6_6.db")
db = server["OLD"]
self.assertEqual(len(db), len(original_records))
# Now read them back...
biosql_records = [db.lookup(name=rec.name) for rec in original_records]
# And check they agree
self.compare_records(original_records, biosql_records)
server.close()
if __name__ == "__main__":
# Run the test cases
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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