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def getDatabase(self):
import operator
clusterSize = self.clusterSize
import pymysql
ensemblDb = pymysql.connect(host='ensembldb.ensembl.org',
user='anonymous',
password='',
db='ensembl_website_88',
charset='utf8mb4',
cursorclass=pymysql.cursors.DictCursor)
ensemblConnection = ensemblDb.cursor()
query = "SELECT\
display_label, gene_autocomplete.stable_id, location, homo_sapiens_core_88_38.gene.biotype\
FROM\
gene_autocomplete, homo_sapiens_core_88_38.gene\
WHERE\
species = 'homo_sapiens' and gene_autocomplete.stable_id = homo_sapiens_core_88_38.gene.stable_id"
ensemblConnection.execute(query)
rawConversionTable = ensemblConnection.fetchall()
conversionTable = {}
for item in rawConversionTable:
locus = item["location"]
contig, position = locus.split(":")
start, end = position.split("-")
start = int(start)
end = int(end)
def load_import_request():
import pymysql.cursors
# Connect to the database
connection = pymysql.connect(host='localhost',
user=os.environ.get('DB_USER'),
passwd=os.environ.get('DB_PWD'),
db='labspy',
cursorclass=pymysql.cursors.DictCursor)
try:
# connection is not autocommit by default. So you must commit to save
# your changes.
# connection.commit()
with connection.cursor() as cursor:
# Read a single record
# sql = "SELECT `id`, `password` FROM `users` WHERE `email`=%s"
# cursor.execute(sql, ('webmaster@python.org',))
sql = '''SELECT * FROM importer_importrequest'''
cursor.execute(sql)
result = cursor.fetchone()
runs = result['runlist_blob']
expid = result['repository_identifier']
def __init__(self, user, pw, db, host='127.0.0.1'):
self._conn = pymysql.connect(host=host, user=user, passwd=pw, db=db)
self._conn.autocommit(1)
self._conn.ping(True)
self._cur = self._conn.cursor(pymysql.cursors.DictCursor)
def sql_rb(user, password, host, port, sequence, backup_dbname): ## 查询回滚语句的表格
port_a = int(port)
connection = pymysql.connect(host=host, port=port_a, user=user, password=password, db=backup_dbname, charset="utf8",
cursorclass=pymysql.cursors.DictCursor)
connection1 = pymysql.connect(host=host, port=port_a, user=user, password=password, db=backup_dbname,
charset="utf8",
cursorclass=pymysql.cursors.DictCursor)
try:
with connection.cursor() as cursor:
sql = " select tablename from {0}.{1} where opid_time ='{2}' ;".format(backup_dbname, '$_$inception_backup_information$_$',sequence)
cursor.execute(sql)
result = cursor.fetchone()
connection.commit()
connection.close()
table = result['tablename']
try:
with connection1.cursor() as cursor1:
sql = " select rollback_statement from {0}.{1} where opid_time = '{2}' ;".format(backup_dbname, table,sequence)
cursor1.execute(sql)
result1 = cursor1.fetchone()
def from_settings(cls, settings):
db_params = dict(
host=settings['MYSQL_HOST'],
database=settings['MYSQL_database'],
user=settings['MYSQL_USER'],
passwd=settings['MYSQL_PASSWORD'],
port=settings['MYSQL_PORT'],
charset='utf8mb4',
use_unicode=True,
cursorclass=pymysql.cursors.DictCursor
)
dbpool = adbapi.ConnectionPool('pymysql', **db_params)
return cls(dbpool)
def get_mysql_connection(host_name, port=3306, user="", password=""):
if (connection_pools.get(host_name) == None):
pool = PooledDB(creator=pymysql, mincached=2, maxcached=4, maxconnections=5,
host=host_name, port=port, user=user, passwd=password,
use_unicode=False, charset="utf8", cursorclass=pymysql.cursors.DictCursor, reset=False, autocommit=True)
connection_pools[host_name] = pool
return connection_pools[host_name].connection()
# check if connection already exists
try:
if self.inquisitionDbHandle:
self.inquisitionDbHandle.close()
except AttributeError:
# sometimes the above statement does fail properly when inquisitionDbHandle == None
# this is harmless; see Issue #66
pass
# regenerate conn
self.inquisitionDbHandle = pymysql.connect(host=self.cfg['mysql_database']['db_host'],
port=int(self.cfg['mysql_database']['db_port']),
user=self.cfg['mysql_database']['db_user'],
password=self.cfg['mysql_database']['db_pass'],
db=self.cfg['mysql_database']['db_name'],
charset='utf8mb4', cursorclass=pymysql.cursors.DictCursor)
if self.inquisitionDbHandle:
self.lgr.debug('database connection established [ SUCCESSFULLY ] for main inquisition database :: [ '
+ self.cfg['mysql_database']['db_host'] + ':' + self.cfg['mysql_database']['db_port'] + ' ]')
return True
else:
return False
def insert_recording(hw):
"""Insert recording `hw` into database."""
mysql = utils.get_mysql_cfg()
connection = pymysql.connect(
host=mysql["host"],
user=mysql["user"],
passwd=mysql["passwd"],
db=mysql["db"],
charset="utf8mb4",
cursorclass=pymysql.cursors.DictCursor,
)
try:
cursor = connection.cursor()
sql = (
"INSERT INTO `wm_raw_draw_data` ("
"`user_id`, "
"`data`, "
"`md5data`, "
"`creation_date`, "
"`device_type`, "
"`accepted_formula_id`, "
"`secret`, "
"`ip`, "
"`segmentation`, "
"`internal_id`, "
"`description` "
def main():
connection = pymysql.connect(host='localhost',
user='root',
password='',
db='testdb',
charset='utf8mb4',
cursorclass=pymysql.cursors.DictCursor)
start = int(time.time())
insert_to_mysql(connection, 10000, start)