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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.
"""Test storing biopython objects in a BioSQL relational db."""
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
import requires_internet
from common_BioSQL import check_config
from common_BioSQL import create_database
from common_BioSQL import destroy_database
from Bio import BiopythonWarning
from Bio import Entrez
# local stuff
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Seq import MutableSeq
from Bio.Seq import Seq
from Bio.SeqFeature import SeqFeature
from Bio.SeqRecord import SeqRecord
from BioSQL import BioSeq
from BioSQL import BioSeqDatabase
if __name__ == "__main__":
raise RuntimeError("Call this via test_BioSQL_*online.py not directly")
# Sharing these with test_BioSQL_XXX_online.py files which import this file:
# DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA, SQL_FILE, SYSTEM
SYSTEM = platform.system()
def share_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
"""Make sure we can access the DB settings from this file."""
global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
global SYSTEM, SQL_FILE
DBDRIVER = dbdriver
DBTYPE = dbtype
DBHOST = dbhost
DBUSER = dbuser
DBPASSWD = dbpasswd
TESTDB = testdb
class TaxonomyTest(unittest.TestCase):
"""Test proper insertion and retrieval of taxonomy data."""
def setUp(self):
global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
global SYSTEM, SQL_FILE
Entrez.email = "biopython@biopython.org"
# 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_taxon_left_right_values(self):
self.db.load(self.iterator, True)
sql = """SELECT DISTINCT include.ncbi_taxon_id FROM taxon
INNER JOIN taxon AS include ON
(include.left_value BETWEEN taxon.left_value
AND taxon.right_value)
WHERE taxon.taxon_id IN
(SELECT taxon_id FROM taxon_name
WHERE name = 'Brassicales')
AND include.right_value - include.left_value = 1"""
rows = self.db.adaptor.execute_and_fetchall(sql)
self.assertEqual(4, len(rows))
values = [row[0] for row in rows]
self.assertCountEqual([3704, 3711, 3708, 3702], values)
def test_load_database_with_tax_lookup(self):
"""Load SeqRecord objects and fetch the taxonomy information from NCBI."""
handle = Entrez.efetch(db="taxonomy", id=3702, retmode="XML")
taxon_record = Entrez.read(handle)
entrez_tax = []
for t in taxon_record[0]["LineageEx"]:
entrez_tax.append(t["ScientificName"])
entrez_tax.append(taxon_record[0]["ScientificName"])
self.db.load(self.iterator, True)
# 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)
test_record = self.db.lookup(accession="X55053")
# make sure that the ncbi taxonomy id is correct
self.assertEqual(test_record.annotations["ncbi_taxid"], 3702)
# make sure that the taxonomic lineage is the same as reported
# using the Entrez module
self.assertEqual(test_record.annotations["taxonomy"], entrez_tax)
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