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Merge pull request #222 from FRED-2/develop
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Change mysql dependency to PyMySQL
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b-schubert authored Nov 13, 2018
2 parents 2a203a4 + 946f27b commit c531b43
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Showing 2 changed files with 3 additions and 3 deletions.
4 changes: 2 additions & 2 deletions Fred2/IO/MartsAdapter.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
import urllib2
import warnings
import logging
import MySQLdb
import pymysql.cursors
from operator import itemgetter

from Fred2.IO.ADBAdapter import ADBAdapter, EAdapterFields, EIdentifierTypes
Expand All @@ -32,7 +32,7 @@ def __init__(self, usr=None, host=None, pwd=None, db=None, biomart=None):
self.sequence_proxy = dict()

if usr and host and pwd and db:
self.connection = MySQLdb.connect(user=usr, host=host, passwd=pwd, db=db)
self.connection = pymysql.connect(user=usr, host=host, password=pwd, db=db)
else:
self.connection = None

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2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,6 @@
#ext_modules=[d2s_module],

# Run-time dependencies. (will be installed by pip when FRED2 is installed)
install_requires=['setuptools>=18.2', 'pandas', 'pyomo>=4.0','svmlight', 'MySQL-python >= 1.2.4', 'biopython', 'pyVCF'],
install_requires=['setuptools>=18.2', 'pandas', 'pyomo>=4.0','svmlight', 'PyMySQL', 'biopython', 'pyVCF'],

)

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