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