def integrator(request, memory=True, header=False):
main(memory=memory, header=header)
pathToFile = os.path.join(settings.PROJECT_ROOT, 'apps', 'interactions',
'merged.txt')
fields = ('id_a', 'id_b', 'alias_a', 'alias_b', 'system', 'type', 'method',
'modification', 'taxid_a', 'taxid_b', 'pmid', 'source', 'score')
# Raw sql triggered direct insertion of the file:
sql = "load data infile '%s' into table %s_%s columns terminated by '\t'"\
"lines terminated by '\n'(%s);"\
% (pathToFile,'interactions','interaction'"", ", ".join(fields))
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cursor = connection.cursor()
cursor.execute('TRUNCATE TABLE interactions_interaction;')
cursor.execute(sql)
#row = cursor.fetchone()
#print row
print sql
query = Interaction.objects.raw(sql)
# print query
# Reading and inserting via Django ORM (works, but is too slow):
# f = fileinput.input(os.path.join(settings.PROJECT_ROOT, 'apps', 'interactions', 'merged.txt'))
# interactions = []
# for line in f:
# if header:
# header = False
# continue
# values = line.replace('\n', '').split('\t')
# #print values
# input = dict(zip(fields, values))
# interaction = Interaction()
# interaction.__dict__.update(input)
# #interaction.save()
# interactions.append(interaction)
# f.close()
# Interaction.objects.bulk_create(interactions)
# Alternative direct insertion via python-MySQLdb:
# import MySQLdb as mysql
# mydb = mysql.connect(user='******', db='denigma')
# cursor = mydb.cursor()
# handle = cursor.execute(sql)
# print handle
msg = "Successfully integrated interactions"
messages.add_message(request, messages.SUCCESS, msg)
return redirect('/interactions/')
#234567891123456789212345678931234567893
def integrator(request, memory=True, header=False):
main(memory=memory, header=header)
pathToFile = os.path.join(settings.PROJECT_ROOT, 'apps', 'interactions', 'merged.txt')
fields = ('id_a', 'id_b',
'alias_a', 'alias_b',
'system', 'type', 'method', 'modification',
'taxid_a', 'taxid_b',
'pmid', 'source', 'score')
# Raw sql triggered direct insertion of the file:
sql = "load data infile '%s' into table %s_%s columns terminated by '\t'"\
"lines terminated by '\n'(%s);"\
% (pathToFile,'interactions','interaction'"", ", ".join(fields))
#234567891123456789212345678931234567894123456789512345678961234567897123456789
cursor = connection.cursor()
cursor.execute('TRUNCATE TABLE interactions_interaction;')
cursor.execute(sql)
#row = cursor.fetchone()
#print row
print sql
query = Interaction.objects.raw(sql)
# print query
# Reading and inserting via Django ORM (works, but is too slow):
# f = fileinput.input(os.path.join(settings.PROJECT_ROOT, 'apps', 'interactions', 'merged.txt'))
# interactions = []
# for line in f:
# if header:
# header = False
# continue
# values = line.replace('\n', '').split('\t')
# #print values
# input = dict(zip(fields, values))
# interaction = Interaction()
# interaction.__dict__.update(input)
# #interaction.save()
# interactions.append(interaction)
# f.close()
# Interaction.objects.bulk_create(interactions)
# Alternative direct insertion via python-MySQLdb:
# import MySQLdb as mysql
# mydb = mysql.connect(user='******', db='denigma')
# cursor = mydb.cursor()
# handle = cursor.execute(sql)
# print handle
msg = "Successfully integrated interactions"
messages.add_message(request, messages.SUCCESS, msg)
return redirect('/interactions/')
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def update(request, db="BioGRID"):
exec("from %s import main" % db)
main()
return redirect('/interactions/')
def update(request, db="BioGRID"):
exec("from %s import main" % db)
main()
return redirect('/interactions/')
