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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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