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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
131 lines
4.4 KiB
Python
131 lines
4.4 KiB
Python
# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Test storing biopython objects in a BioSQL relational db."""
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import os
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import platform
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import tempfile
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import time
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import unittest
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# Hide annoying warnings from things like bonds in GenBank features,
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# or PostgreSQL schema rules. TODO - test these warnings are raised!
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import warnings
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from io import StringIO
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import requires_internet
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from common_BioSQL import check_config
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from common_BioSQL import create_database
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from common_BioSQL import destroy_database
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from Bio import BiopythonWarning
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from Bio import Entrez
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# local stuff
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from Bio import MissingExternalDependencyError
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from Bio import SeqIO
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from Bio.Seq import MutableSeq
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from Bio.Seq import Seq
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from Bio.SeqFeature import SeqFeature
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from Bio.SeqRecord import SeqRecord
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from BioSQL import BioSeq
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from BioSQL import BioSeqDatabase
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if __name__ == "__main__":
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raise RuntimeError("Call this via test_BioSQL_*online.py not directly")
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# Sharing these with test_BioSQL_XXX_online.py files which import this file:
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# DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA, SQL_FILE, SYSTEM
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SYSTEM = platform.system()
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def share_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
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"""Make sure we can access the DB settings from this file."""
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global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
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global SYSTEM, SQL_FILE
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DBDRIVER = dbdriver
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DBTYPE = dbtype
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DBHOST = dbhost
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DBUSER = dbuser
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DBPASSWD = dbpasswd
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TESTDB = testdb
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class TaxonomyTest(unittest.TestCase):
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"""Test proper insertion and retrieval of taxonomy data."""
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def setUp(self):
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global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
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global SYSTEM, SQL_FILE
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Entrez.email = "biopython@biopython.org"
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# create TESTDB
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TESTDB = create_database()
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# load the database
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db_name = "biosql-test"
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self.server = BioSeqDatabase.open_database(
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driver=DBDRIVER, user=DBUSER, passwd=DBPASSWD, host=DBHOST, db=TESTDB
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)
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# remove the database if it already exists
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try:
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self.server[db_name]
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self.server.remove_database(db_name)
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except KeyError:
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pass
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self.db = self.server.new_database(db_name)
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# get the GenBank file we are going to put into it
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self.iterator = SeqIO.parse("GenBank/cor6_6.gb", "gb")
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def tearDown(self):
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self.server.close()
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destroy_database()
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del self.db
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del self.server
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def test_taxon_left_right_values(self):
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self.db.load(self.iterator, True)
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sql = """SELECT DISTINCT include.ncbi_taxon_id FROM taxon
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INNER JOIN taxon AS include ON
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(include.left_value BETWEEN taxon.left_value
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AND taxon.right_value)
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WHERE taxon.taxon_id IN
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(SELECT taxon_id FROM taxon_name
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WHERE name = 'Brassicales')
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AND include.right_value - include.left_value = 1"""
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rows = self.db.adaptor.execute_and_fetchall(sql)
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self.assertEqual(4, len(rows))
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values = [row[0] for row in rows]
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self.assertCountEqual([3704, 3711, 3708, 3702], values)
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def test_load_database_with_tax_lookup(self):
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"""Load SeqRecord objects and fetch the taxonomy information from NCBI."""
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handle = Entrez.efetch(db="taxonomy", id=3702, retmode="XML")
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taxon_record = Entrez.read(handle)
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entrez_tax = []
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for t in taxon_record[0]["LineageEx"]:
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entrez_tax.append(t["ScientificName"])
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entrez_tax.append(taxon_record[0]["ScientificName"])
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self.db.load(self.iterator, True)
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# do some simple tests to make sure we actually loaded the right
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# thing. More advanced tests in a different module.
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items = list(self.db.values())
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self.assertEqual(len(items), 6)
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self.assertEqual(len(self.db), 6)
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test_record = self.db.lookup(accession="X55053")
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# make sure that the ncbi taxonomy id is correct
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self.assertEqual(test_record.annotations["ncbi_taxid"], 3702)
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# make sure that the taxonomic lineage is the same as reported
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# using the Entrez module
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self.assertEqual(test_record.annotations["taxonomy"], entrez_tax)
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