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1690 lines (1484 loc) · 65.1 KB
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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.
"""Dealing with storage of biopython objects in a BioSQL relational db."""
import configparser
import os
import platform
import tempfile
import time
import unittest
# Hide annoying warnings from things like bonds in GenBank features,
# or PostgreSQL schema rules. TODO - test these warnings are raised!
import warnings
from io import StringIO
from seq_tests_common import SeqRecordTestBaseClass
from Bio import BiopythonWarning
# local stuff
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Seq import MutableSeq
from Bio.Seq import Seq
from Bio.Seq import UndefinedSequenceError
from Bio.SeqFeature import ExactPosition
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import UnknownPosition
from Bio.SeqRecord import SeqRecord
from BioSQL import BioSeqDatabase
if __name__ == "__main__":
raise RuntimeError("Call this via test_BioSQL_*.py not directly")
# Exporting these to the test_BioSQL_XXX.py files which import this file:
# DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA, SQL_FILE, SYSTEM
SYSTEM = platform.system()
DBDRIVER = DBTYPE = DBHOST = DBUSER = DBPASSWD = TESTDB = DBSCHEMA = SQL_FILE = None
def load_biosql_ini(DBTYPE):
"""Load the database settings from INI file."""
if not os.path.isfile("biosql.ini"):
raise MissingExternalDependencyError(
"BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)"
)
config = configparser.ConfigParser()
config.read("biosql.ini")
DBHOST = config.get(DBTYPE, "dbhost")
DBUSER = config.get(DBTYPE, "dbuser")
DBPASSWD = config.get(DBTYPE, "dbpasswd")
TESTDB = config.get(DBTYPE, "testdb")
return DBHOST, DBUSER, DBPASSWD, TESTDB
def temp_db_filename():
"""Generate a temporary filename for SQLite database."""
# In memory SQLite does not work with current test structure since the tests
# expect databases to be retained between individual tests.
# TESTDB = ':memory:'
# Instead, we use (if we can) /dev/shm
try:
h, test_db_fname = tempfile.mkstemp("_BioSQL.db", dir="/dev/shm")
except OSError:
# We can't use /dev/shm
h, test_db_fname = tempfile.mkstemp("_BioSQL.db")
os.close(h)
return test_db_fname
def check_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
"""Verify the database settings work for connecting."""
global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
global SYSTEM, SQL_FILE
DBDRIVER = dbdriver
DBTYPE = dbtype
DBHOST = dbhost
DBUSER = dbuser
DBPASSWD = dbpasswd
TESTDB = testdb
if not DBDRIVER or not DBTYPE or not DBUSER:
# No point going any further...
raise MissingExternalDependencyError("Incomplete BioSQL test settings")
# Check the database driver is installed:
if SYSTEM == "Java":
try:
if DBDRIVER in ["MySQLdb"]:
import com.mysql.jdbc.Driver # noqa: F401
elif DBDRIVER in ["psycopg2", "pgdb"]:
import org.postgresql.Driver # noqa: F401
except ImportError:
message = f"Install the JDBC driver for {DBTYPE} to use BioSQL "
raise MissingExternalDependencyError(message) from None
else:
try:
__import__(DBDRIVER)
except ImportError:
if DBDRIVER in ["MySQLdb"]:
message = (
"Install MySQLdb or mysqlclient if you want to use %s with BioSQL "
% (DBTYPE)
)
else:
message = f"Install {DBDRIVER} if you want to use {DBTYPE} with BioSQL "
raise MissingExternalDependencyError(message) from None
try:
if DBDRIVER in ["sqlite3"]:
server = BioSeqDatabase.open_database(driver=DBDRIVER, db=TESTDB)
else:
server = BioSeqDatabase.open_database(
driver=DBDRIVER, host=DBHOST, user=DBUSER, passwd=DBPASSWD
)
server.close()
del server
except Exception as e:
message = f"Connection failed, check settings if you plan to use BioSQL: {e}"
raise MissingExternalDependencyError(message) from None
DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
SQL_FILE = os.path.join(os.getcwd(), "BioSQL", DBSCHEMA)
if not os.path.isfile(SQL_FILE):
message = f"Missing SQL schema file: {SQL_FILE}"
raise MissingExternalDependencyError(message)
def _do_db_cleanup():
"""Cleanup everything from TESTDB.
Relevant for MySQL and PostgreSQL.
"""
if DBDRIVER in ["psycopg2", "pgdb"]:
# first open a connection the database
# notice that postgres doesn't have createdb privileges, so
# the TESTDB must exist
server = BioSeqDatabase.open_database(
driver=DBDRIVER, host=DBHOST, user=DBUSER, passwd=DBPASSWD, db=TESTDB
)
# The pgdb postgres driver does not support autocommit, so here we
# commit the current transaction so that 'drop database' query will
# be outside a transaction block
server.adaptor.cursor.execute("COMMIT")
# drop anything in the database
# with Postgres, can get errors about database still being used.
# Wait briefly to be sure previous tests are done with it.
time.sleep(1)
# drop anything in the database
sql = r"DROP OWNED BY " + DBUSER
server.adaptor.cursor.execute(sql, ())
server.close()
else:
# first open a connection to create the database
server = BioSeqDatabase.open_database(
driver=DBDRIVER, host=DBHOST, user=DBUSER, passwd=DBPASSWD
)
# Auto-commit
try:
server.adaptor.autocommit()
except AttributeError:
pass
# drop the database
try:
sql = r"DROP DATABASE " + TESTDB
server.adaptor.cursor.execute(sql, ())
except (
server.module.OperationalError,
server.module.Error,
server.module.DatabaseError,
): # the database doesn't exist
pass
except (
server.module.IntegrityError,
server.module.ProgrammingError,
) as e: # ditto--perhaps
if str(e).find(f'database "{TESTDB}" does not exist') == -1:
server.close()
raise
# create a new database
sql = r"CREATE DATABASE " + TESTDB
server.adaptor.execute(sql, ())
server.close()
def create_database():
"""Delete any existing BioSQL test DB, then (re)create an empty BioSQL DB.
Returns TESTDB name which will change for for SQLite.
"""
if DBDRIVER in ["sqlite3"]:
global TESTDB
if os.path.exists(TESTDB):
try:
os.remove(TESTDB)
except Exception:
time.sleep(1)
try:
os.remove(TESTDB)
except Exception:
# Seen this with PyPy 2.1 (and older) on Windows -
# which suggests an open handle still exists?
print(f"Could not remove {TESTDB!r}")
# Now pick a new filename - just in case there is a stale handle
# (which might be happening under Windows...)
TESTDB = temp_db_filename()
else:
_do_db_cleanup()
# now open a connection to load the database
server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
try:
server.load_database_sql(SQL_FILE)
server.commit()
server.close()
except Exception:
# Failed, but must close the handle...
server.close()
raise
return TESTDB
def destroy_database():
"""Delete any temporary BioSQL sqlite3 database files."""
if DBDRIVER in ["sqlite3"]:
if os.path.exists(TESTDB):
os.remove(TESTDB)
def load_database(gb_filename_or_handle):
"""Load a GenBank file into a new BioSQL database.
This is useful for running tests against a newly created database.
"""
TESTDB = create_database()
# now open a connection to load the database
db_name = "biosql-test"
server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
db = server.new_database(db_name)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle, "gb")
records = []
for record in iterator:
if record.annotations.get("molecule_type") == "mRNA":
record.annotations["molecule_type"] = "DNA"
records.append(record)
# finally put it in the database
count = db.load(records)
server.commit()
server.close()
return count
def load_multi_database(gb_filename_or_handle, gb_filename_or_handle2):
"""Load two GenBank files into a new BioSQL database as different subdatabases.
This is useful for running tests against a newly created database.
"""
TESTDB = create_database()
# now open a connection to load the database
db_name = "biosql-test"
db_name2 = "biosql-test2"
server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
db = server.new_database(db_name)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle, "gb")
count = db.load(iterator)
db = server.new_database(db_name2)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle2, "gb")
# finally put it in the database
count2 = db.load(iterator)
server.commit()
server.close()
return count + count2
class MultiReadTest(unittest.TestCase):
"""Test reading a database with multiple namespaces."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_multi_database("GenBank/cor6_6.gb", "GenBank/NC_000932.gb")
self.server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
self.db = self.server["biosql-test"]
self.db2 = self.server["biosql-test2"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.db2
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertIn("biosql-test2", server)
self.assertEqual(2, len(server))
self.assertEqual(["biosql-test", "biosql-test2"], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
del server["biosql-test2"]
self.assertEqual(0, len(server))
with self.assertRaises(KeyError):
del server["non-existant-name"]
def test_get_db_items(self):
"""Check list, keys, length etc."""
db = self.db
items = list(db.values())
keys = list(db)
length = len(items)
self.assertEqual(length, len(db))
self.assertEqual(length, len(list(db)))
self.assertEqual(length, len(list(db.items())))
self.assertEqual(length, len(list(db.keys())))
self.assertEqual(length, len(list(db.values())))
for (k1, r1), (k2, r2) in zip(zip(keys, items), db.items()):
self.assertEqual(k1, k2)
self.assertEqual(r1.id, r2.id)
for k in keys:
del db[k]
self.assertEqual(0, len(db))
with self.assertRaises(KeyError):
del db["non-existant-name"]
def test_cross_retrieval_of_items(self):
"""Test that valid ids can't be retrieved between namespaces."""
db = self.db
db2 = self.db2
for db2_id in db2.keys():
with self.assertRaises(KeyError):
db[db2_id]
class ReadTest(unittest.TestCase):
"""Test reading a database from an already built database."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
self.db = self.server["biosql-test"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertEqual(1, len(server))
self.assertEqual(["biosql-test"], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
self.assertEqual(0, len(server))
with self.assertRaises(KeyError):
del server["non-existant-name"]
def test_get_db_items(self):
"""Check list, keys, length etc."""
db = self.db
items = list(db.values())
keys = list(db)
length = len(items)
self.assertEqual(length, len(db))
self.assertEqual(length, len(list(db.items())))
self.assertEqual(length, len(list(db)))
self.assertEqual(length, len(list(db.values())))
for (k1, r1), (k2, r2) in zip(zip(keys, items), db.items()):
self.assertEqual(k1, k2)
self.assertEqual(r1.id, r2.id)
for k in keys:
del db[k]
self.assertEqual(0, len(db))
with self.assertRaises(KeyError):
del db["non-existant-name"]
def test_lookup_items(self):
"""Test retrieval of items using various ids."""
self.db.lookup(accession="X62281")
self.assertRaises(IndexError, self.db.lookup, accession="Not real")
self.db.lookup(display_id="ATKIN2")
self.assertRaises(IndexError, self.db.lookup, display_id="Not real")
# primary id retrieval
self.db.lookup(primary_id="16353")
self.assertRaises(IndexError, self.db.lookup, primary_id="Not Real")
class SeqInterfaceTest(unittest.TestCase):
"""Make sure the BioSQL objects implement the expected biopython interface."""
def setUp(self):
"""Load a database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
self.db = self.server["biosql-test"]
self.item = self.db.lookup(accession="X62281")
self.item2 = self.db.lookup(accession="AJ237582")
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.item
del self.server
def test_seq_record(self):
"""Make sure SeqRecords from BioSQL implement the right interface."""
test_record = self.item
self.assertIsInstance(test_record.seq, Seq)
self.assertEqual(test_record.id, "X62281.1", test_record.id)
self.assertEqual(test_record.name, "ATKIN2")
self.assertEqual(test_record.description, "A.thaliana kin2 gene")
self.assertTrue(hasattr(test_record, "annotations"))
# XXX should do something with annotations once they are like
# a dictionary
for feature in test_record.features:
self.assertIsInstance(feature, SeqFeature)
# shouldn't cause any errors!
self.assertIsInstance(str(test_record), str)
# Confirm can delete annotations etc to test these properties
del test_record.annotations
del test_record.dbxrefs
del test_record.features
del test_record.seq
def test_seq(self):
"""Make sure Seqs from BioSQL implement the right interface."""
test_seq = self.item.seq
string_rep = str(test_seq)
self.assertEqual(string_rep, str(test_seq)) # check __str__ too
self.assertEqual(type(string_rep), str)
self.assertEqual(len(test_seq), 880)
self.assertEqual(test_seq[879], "A")
self.assertEqual(test_seq[-1], "A")
self.assertEqual(test_seq[0], "A")
self.assertEqual(test_seq[-880], "A")
self.assertRaises(IndexError, test_seq.__getitem__, 880)
self.assertRaises(IndexError, test_seq.__getitem__, -881)
self.assertRaises(TypeError, test_seq.__getitem__, None)
def test_convert(self):
"""Check can turn a Seq object from BioSQL into a Seq or MutableSeq."""
test_seq = self.item.seq
other = Seq(test_seq)
self.assertEqual(test_seq, other)
self.assertIsInstance(other, Seq)
other = MutableSeq(test_seq)
self.assertEqual(test_seq, other)
self.assertIsInstance(other, MutableSeq)
def test_addition(self):
"""Check can add Seq objects from BioSQL together."""
test_seq = self.item.seq
for other in [Seq("ACGT"), MutableSeq("ACGT"), "ACGT", test_seq]:
test = test_seq + other
self.assertEqual(test, str(test_seq) + str(other))
self.assertIsInstance(test, Seq)
test = other + test_seq
self.assertEqual(test, str(other) + str(test_seq))
def test_multiplication(self):
"""Check can multiply Seq objects from BioSQL by integers."""
test_seq = self.item.seq
tripled = test_seq * 3
# Test Seq.__mul__
self.assertIsInstance(tripled, Seq)
self.assertEqual(tripled, str(test_seq) * 3)
# Test Seq.__rmul__
tripled = 3 * test_seq
self.assertIsInstance(tripled, Seq)
self.assertEqual(tripled, str(test_seq) * 3)
# Test Seq.__imul__
original = self.item.seq
tripled = test_seq
tripled *= 3
self.assertIsInstance(tripled, Seq)
self.assertEqual(tripled, str(original) * 3)
def test_seq_slicing(self):
"""Check that slices of sequences are retrieved properly."""
test_seq = self.item.seq
new_seq = test_seq[:10]
self.assertIsInstance(new_seq, Seq)
# simple slicing
self.assertEqual(test_seq[:5], "ATTTG")
self.assertEqual(test_seq[0:5], "ATTTG")
self.assertEqual(test_seq[2:3], "T")
self.assertEqual(test_seq[2:4], "TT")
self.assertEqual(test_seq[870:], "TTGAATTATA")
# getting more fancy
self.assertEqual(test_seq[-1], "A")
self.assertEqual(test_seq[1], "T")
self.assertEqual(test_seq[-10:][5:], "TTATA")
def test_record_slicing(self):
"""Check that slices of DBSeqRecord are retrieved properly."""
new_rec = self.item[400:]
self.assertIsInstance(new_rec, SeqRecord)
self.assertEqual(len(new_rec), 480)
self.assertEqual(len(new_rec.features), 5)
def test_seq_features(self):
"""Check SeqFeatures of a sequence."""
test_features = self.item.features
cds_feature = test_features[6]
self.assertEqual(cds_feature.type, "CDS")
self.assertEqual(
str(cds_feature.location), "join{[103:160](+), [319:390](+), [503:579](+)}"
)
self.assertIn("gene", cds_feature.qualifiers)
self.assertIn("protein_id", cds_feature.qualifiers)
self.assertIn("codon_start", cds_feature.qualifiers)
self.assertEqual(cds_feature.qualifiers.get("gene"), ["kin2"])
self.assertEqual(cds_feature.qualifiers.get("protein_id"), ["CAA44171.1"])
self.assertEqual(cds_feature.qualifiers.get("codon_start"), ["1"])
self.assertIn("db_xref", cds_feature.qualifiers)
multi_ann = cds_feature.qualifiers["db_xref"]
self.assertEqual(len(multi_ann), 2)
self.assertIn("GI:16354", multi_ann)
self.assertIn("SWISS-PROT:P31169", multi_ann)
def test_eq(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertEqual(seq1[30:32], seq2[3:5])
self.assertEqual(seq1[30:32], "CA")
self.assertEqual(seq2[3:5], "CA")
self.assertEqual(seq1[30:32], b"CA")
self.assertEqual(seq2[3:5], b"CA")
self.assertEqual(seq1[30:32], Seq("CA"))
self.assertEqual(seq2[3:5], Seq("CA"))
self.assertEqual(seq1[30:32], MutableSeq("CA"))
self.assertEqual(seq2[3:5], MutableSeq("CA"))
self.assertEqual(seq2[3:5], seq1[30:32])
self.assertEqual("CA", seq1[30:32])
self.assertEqual("CA", seq2[3:5])
self.assertEqual(b"CA", seq1[30:32])
self.assertEqual(b"CA", seq2[3:5])
self.assertEqual(Seq("CA"), seq1[30:32])
self.assertEqual(Seq("CA"), seq2[3:5])
self.assertEqual(MutableSeq("CA"), seq1[30:32])
self.assertEqual(MutableSeq("CA"), seq2[3:5])
with self.assertRaises(UndefinedSequenceError):
seq1 == Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 == Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 == Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 == Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq1)) == seq1
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq2)) == seq2
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) == seq1
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) == seq2
def test_ne(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertNotEqual(seq1, seq2)
self.assertNotEqual(seq1, "CA")
self.assertNotEqual(seq2, "CA")
self.assertNotEqual(seq1, b"CA")
self.assertNotEqual(seq2, b"CA")
self.assertNotEqual(seq1, Seq("CA"))
self.assertNotEqual(seq2, Seq("CA"))
self.assertNotEqual(seq1, MutableSeq("CA"))
self.assertNotEqual(seq2, MutableSeq("CA"))
self.assertNotEqual(seq1[30:32], "GG")
self.assertNotEqual(seq2[3:5], "GG")
self.assertNotEqual(seq1[30:32], b"GG")
self.assertNotEqual(seq2[3:5], b"GG")
self.assertNotEqual(seq1[30:32], Seq("GG"))
self.assertNotEqual(seq2[3:5], Seq("GG"))
self.assertNotEqual(seq1[30:32], MutableSeq("GG"))
self.assertNotEqual(seq2[3:5], MutableSeq("GG"))
self.assertNotEqual(seq2, seq1)
self.assertNotEqual("CA", seq1)
self.assertNotEqual("CA", seq2)
self.assertNotEqual(b"CA", seq1)
self.assertNotEqual(b"CA", seq2)
self.assertNotEqual(Seq("CA"), seq1)
self.assertNotEqual(Seq("CA"), seq2)
self.assertNotEqual(MutableSeq("CA"), seq1)
self.assertNotEqual(MutableSeq("CA"), seq2)
self.assertNotEqual("GG", seq1[30:32])
self.assertNotEqual("GG", seq2[3:5])
self.assertNotEqual(b"GG", seq1[30:32])
self.assertNotEqual(b"GG", seq2[3:5])
self.assertNotEqual(Seq("GG"), seq1[30:32])
self.assertNotEqual(Seq("GG"), seq2[3:5])
self.assertNotEqual(MutableSeq("GG"), seq1[30:32])
self.assertNotEqual(MutableSeq("GG"), seq2[3:5])
with self.assertRaises(UndefinedSequenceError):
seq1 != Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 != Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 != Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 != Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq1)) != seq1
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq2)) != seq2
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) != seq1
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) != seq2
def test_lt(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertLess(seq1, seq2)
self.assertLess(seq1, "CC")
self.assertLess("CC", seq2)
self.assertLess(seq1, b"CC")
self.assertLess(b"CC", seq2)
self.assertLess(seq1, Seq("CC"))
self.assertLess(Seq("CC"), seq2)
self.assertLess(seq1, MutableSeq("CC"))
self.assertLess(MutableSeq("CC"), seq2)
self.assertLess("AA", seq1)
self.assertLess("AA", seq2)
self.assertLess(b"AA", seq1)
self.assertLess(b"AA", seq2)
self.assertLess(Seq("AA"), seq1)
self.assertLess(Seq("AA"), seq2)
self.assertLess(MutableSeq("AA"), seq1)
self.assertLess(MutableSeq("AA"), seq2)
self.assertLess(seq1, "TT")
self.assertLess(seq2, "TT")
self.assertLess(seq1, b"TT")
self.assertLess(seq2, b"TT")
self.assertLess(seq1, Seq("TT"))
self.assertLess(seq2, Seq("TT"))
self.assertLess(seq1, MutableSeq("TT"))
self.assertLess(seq2, MutableSeq("TT"))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, 10)
self.assertLess("AA", seq1[30:32])
self.assertLess("AA", seq2[3:5])
self.assertLess(b"AA", seq1[30:32])
self.assertLess(b"AA", seq2[3:5])
self.assertLess(seq1[30:32], seq2[3:7])
self.assertLess(Seq("AA"), seq1[30:32])
self.assertLess(Seq("AA"), seq2[3:5])
self.assertLess(MutableSeq("AA"), seq1[30:32])
self.assertLess(MutableSeq("AA"), seq2[3:5])
self.assertLess(seq1[30:32], "TT")
self.assertLess(seq2[3:5], "TT")
self.assertLess(seq1[30:32], b"TT")
self.assertLess(seq2[3:5], b"TT")
self.assertLess(seq1[30:32], Seq("TT"))
self.assertLess(seq2[3:5], Seq("TT"))
self.assertLess(seq1[30:32], MutableSeq("TT"))
self.assertLess(seq2[3:5], MutableSeq("TT"))
def test_le(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertLessEqual(seq1, seq2)
self.assertLessEqual(seq1, "CC")
self.assertLessEqual("CC", seq2)
self.assertLessEqual(seq1, b"CC")
self.assertLessEqual(b"CC", seq2)
self.assertLessEqual(seq1, Seq("CC"))
self.assertLessEqual(Seq("CC"), seq2)
self.assertLessEqual(seq1, MutableSeq("CC"))
self.assertLessEqual(MutableSeq("CC"), seq2)
self.assertLessEqual("AA", seq1)
self.assertLessEqual("AA", seq2)
self.assertLessEqual(b"AA", seq1)
self.assertLessEqual(b"AA", seq2)
self.assertLessEqual(Seq("AA"), seq1)
self.assertLessEqual(Seq("AA"), seq2)
self.assertLessEqual(MutableSeq("AA"), seq1)
self.assertLessEqual(MutableSeq("AA"), seq2)
self.assertLessEqual(seq1, "TT")
self.assertLessEqual(seq2, "TT")
self.assertLessEqual(seq1, b"TT")
self.assertLessEqual(seq2, b"TT")
self.assertLessEqual(seq1, Seq("TT"))
self.assertLessEqual(seq2, Seq("TT"))
self.assertLessEqual(seq1, MutableSeq("TT"))
self.assertLessEqual(seq2, MutableSeq("TT"))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, 10)
self.assertLessEqual("AA", seq1[30:32])
self.assertLessEqual("AA", seq2[3:5])
self.assertLessEqual(b"AA", seq1[30:32])
self.assertLessEqual(b"AA", seq2[3:5])
self.assertLessEqual(seq1[30:32], seq2[3:7])
self.assertLessEqual(Seq("AA"), seq1[30:32])
self.assertLessEqual(Seq("AA"), seq2[3:5])
self.assertLessEqual(MutableSeq("AA"), seq1[30:32])
self.assertLessEqual(MutableSeq("AA"), seq2[3:5])
self.assertLessEqual(seq1[30:32], "TT")
self.assertLessEqual(seq2[3:5], "TT")
self.assertLessEqual(seq1[30:32], b"TT")
self.assertLessEqual(seq2[3:5], b"TT")
self.assertLessEqual(seq1[30:32], Seq("TT"))
self.assertLessEqual(seq2[3:5], Seq("TT"))
self.assertLessEqual(seq1[30:32], MutableSeq("TT"))
self.assertLessEqual(seq2[3:5], MutableSeq("TT"))
def test_gt(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertGreater(seq2, seq1)
self.assertGreater("CC", seq1)
self.assertGreater(seq2, "CC")
self.assertGreater(b"CC", seq1)
self.assertGreater(seq2, b"CC")
self.assertGreater(Seq("CC"), seq1)
self.assertGreater(seq2, Seq("CC"))
self.assertGreater(MutableSeq("CC"), seq1)
self.assertGreater(seq2, MutableSeq("CC"))
self.assertGreater(seq1, "AA")
self.assertGreater(seq2, "AA")
self.assertGreater(seq1, b"AA")
self.assertGreater(seq2, b"AA")
self.assertGreater(seq1, Seq("AA"))
self.assertGreater(seq2, Seq("AA"))
self.assertGreater(seq1, MutableSeq("AA"))
self.assertGreater(seq2, MutableSeq("AA"))
self.assertGreater("TT", seq1)
self.assertGreater("TT", seq2)
self.assertGreater(b"TT", seq1)
self.assertGreater(b"TT", seq2)
self.assertGreater(Seq("TT"), seq1)
self.assertGreater(Seq("TT"), seq2)
self.assertGreater(MutableSeq("TT"), seq1)
self.assertGreater(MutableSeq("TT"), seq2)
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, 10)
self.assertGreater(seq1[30:32], "AA")
self.assertGreater(seq2[3:5], "AA")
self.assertGreater(seq1[30:32], b"AA")
self.assertGreater(seq2[3:5], b"AA")
self.assertGreater(seq1[30:34], seq2[3:5])
self.assertGreater(seq1[30:32], Seq("AA"))
self.assertGreater(seq2[3:5], Seq("AA"))
self.assertGreater(seq1[30:32], MutableSeq("AA"))
self.assertGreater(seq2[3:5], MutableSeq("AA"))
self.assertGreater("TT", seq1[30:32])
self.assertGreater("TT", seq2[3:5])
self.assertGreater(b"TT", seq1[30:32])
self.assertGreater(b"TT", seq2[3:5])
self.assertGreater(Seq("TT"), seq1[30:32])
self.assertGreater(Seq("TT"), seq2[3:5])
self.assertGreater(MutableSeq("TT"), seq1[30:32])
self.assertGreater(MutableSeq("TT"), seq2[3:5])
def test_ge(self):
seq1 = self.item.seq
seq2 = self.item2.seq
self.assertGreaterEqual(seq2, seq1)
self.assertGreaterEqual("CC", seq1)
self.assertGreaterEqual(seq2, "CC")
self.assertGreaterEqual(b"CC", seq1)
self.assertGreaterEqual(seq2, b"CC")
self.assertGreaterEqual(Seq("CC"), seq1)
self.assertGreaterEqual(seq2, Seq("CC"))
self.assertGreaterEqual(MutableSeq("CC"), seq1)
self.assertGreaterEqual(seq2, MutableSeq("CC"))
self.assertGreaterEqual(seq1, "AA")
self.assertGreaterEqual(seq2, "AA")
self.assertGreaterEqual(seq1, b"AA")
self.assertGreaterEqual(seq2, b"AA")
self.assertGreaterEqual(seq1, Seq("AA"))
self.assertGreaterEqual(seq2, Seq("AA"))
self.assertGreaterEqual(seq1, MutableSeq("AA"))
self.assertGreaterEqual(seq2, MutableSeq("AA"))
self.assertGreaterEqual("TT", seq1)
self.assertGreaterEqual("TT", seq2)
self.assertGreaterEqual(b"TT", seq1)
self.assertGreaterEqual(b"TT", seq2)
self.assertGreaterEqual(Seq("TT"), seq1)
self.assertGreaterEqual(Seq("TT"), seq2)
self.assertGreaterEqual(MutableSeq("TT"), seq1)
self.assertGreaterEqual(MutableSeq("TT"), seq2)
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, 10)
self.assertGreaterEqual(seq1[30:32], "AA")
self.assertGreaterEqual(seq2[3:5], "AA")
self.assertGreaterEqual(seq1[30:32], b"AA")
self.assertGreaterEqual(seq2[3:5], b"AA")
self.assertGreaterEqual(seq1[30:34], seq2[3:5])
self.assertGreaterEqual(seq1[30:32], Seq("AA"))
self.assertGreaterEqual(seq2[3:5], Seq("AA"))
self.assertGreaterEqual(seq1[30:32], MutableSeq("AA"))
self.assertGreaterEqual(seq2[3:5], MutableSeq("AA"))
self.assertGreaterEqual("TT", seq1[30:32])
self.assertGreaterEqual("TT", seq2[3:5])
self.assertGreaterEqual(b"TT", seq1[30:32])
self.assertGreaterEqual(b"TT", seq2[3:5])
self.assertGreaterEqual(Seq("TT"), seq1[30:32])
self.assertGreaterEqual(Seq("TT"), seq2[3:5])
self.assertGreaterEqual(MutableSeq("TT"), seq1[30:32])
self.assertGreaterEqual(MutableSeq("TT"), seq2[3:5])
class LoaderTest(unittest.TestCase):
"""Load a database from a GenBank file."""
def setUp(self):
# create TESTDB
TESTDB = create_database()
# load the database
db_name = "biosql-test"
self.server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
# remove the database if it already exists
try:
self.server[db_name]
self.server.remove_database(db_name)
except KeyError:
pass
self.db = self.server.new_database(db_name)
# get the GenBank file we are going to put into it
self.iterator = SeqIO.parse("GenBank/cor6_6.gb", "gb")
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_load_database(self):
"""Load SeqRecord objects into a BioSQL database."""
self.db.load(self.iterator)
# do some simple tests to make sure we actually loaded the right
# thing. More advanced tests in a different module.
items = list(self.db.values())
self.assertEqual(len(items), 6)
self.assertEqual(len(self.db), 6)
item_names = []
item_ids = []
for item in items:
item_names.append(item.name)
item_ids.append(item.id)
item_names.sort()
item_ids.sort()
self.assertEqual(
item_names,
["AF297471", "ARU237582", "ATCOR66M", "ATKIN2", "BNAKINI", "BRRBIF72"],
)
self.assertEqual(
item_ids,
[
"AF297471.1",
"AJ237582.1",
"L31939.1",
"M81224.1",
"X55053.1",
"X62281.1",
],
)
class DeleteTest(unittest.TestCase):
"""Test proper deletion of entries from a database."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(
driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
)
self.db = self.server["biosql-test"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertEqual(1, len(server))
self.assertEqual(["biosql-test"], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
self.assertEqual(0, len(server))
with self.assertRaises(KeyError):
del server["non-existant-name"]
def test_del_db_items(self):
"""Check all associated data is deleted from an item."""
db = self.db
keys = list(db)
self.assertEqual(len(keys), len(list(db.values())))
for seq_id in keys:
sql = "SELECT seqfeature_id from seqfeature where bioentry_id = '%s'"
# get the original number of seqfeatures associated with the bioentry
seqfeatures = self.db.adaptor.execute_and_fetchall(sql % (seq_id))
del db[seq_id]
# check to see that the entry in the bioentry table is removed
self.assertNotIn(seq_id, db)
# no need to check seqfeature presence if it had none to begin with
if len(seqfeatures):
rows_d = self.db.adaptor.execute_and_fetchall(sql % (seq_id))
# check to see that associated data is removed
self.assertEqual(len(rows_d), 0)
self.assertEqual(0, len(list(db.values())))
class DupLoadTest(unittest.TestCase):
"""Check a few duplicate conditions fail."""
def setUp(self):
You can’t perform that action at this time.