def create_id():
# TODO: this is wasting an id
cursor = connection.cursor()
cursor.execute("SELECT nextval('reagent_id_seq')")
row = cursor.fetchone();
val = row[0]
new_id = create_substance_id(val)
# logger.info(str(('create_id', val, new_id)))
cursor.execute("SELECT setval('reagent_id_seq', %s)", [val-1])
return new_id
def create_id():
# TODO: There is no way to pass an argument to
# to the default on a model, so this is why we have to grope around for the
# sequence value. The sequence here is used with the model idfield
try:
cursor = connection.cursor()
cursor.execute("SELECT nextval('db_substance_id_seq')")
row = cursor.fetchone();
val = row[0]
new_id = create_substance_id(val)
if(logger.isEnabledFor(logging.DEBUG)):
logger.debug(str(('created_id', val, new_id)))
# if val > 1:
# cursor.execute("SELECT setval('db_substance_id_seq', %s)", [val-1])
return new_id
except Exception, e:
logger.warn(str(('create_substance_id fails', e)))
return None
def create_substance_ids(apps, schema_editor):
connection = schema_editor.connection
cursor = connection.cursor()
count = 0
batch_size = 1000
logger.info('begin create_substance_ids')
cursor.execute(
'create temp table reagent_sub_ids as '
"select nextval('substance_id_seq'), reagent_id "
"from reagent;")
cursor.execute(
'create temp table reagent_sub_ids1 '
'(reagent_id integer, substance_id text )')
cursor1 = connection.cursor()
sql1 = 'insert into reagent_sub_ids1 values (%s, %s)'
cursor.execute('Select * from reagent_sub_ids')
cursor.arraysize = batch_size
try:
while True:
rows = cursor.fetchmany()
if not rows:
break
newrows = []
for row in rows:
newrows.append([row[1], create_substance_id(row[0])])
count += 1
cursor1.executemany(sql1, newrows)
if count % 100000 == 0:
logger.info('processed %d rows', count)
logger.info('processed %d rows, now update reagent table', count)
cursor.execute(
'update reagent '
'set substance_id=a.substance_id '
'from reagent_sub_ids1 a '
'where a.reagent_id=reagent.reagent_id')
except Exception as e:
logger.exception('create substance ids, ex after %d rows',count)
raise
logger.info('create substance ids, done after %d rows',count)
def create_substance_ids(apps, schema_editor):
connection = schema_editor.connection
cursor = connection.cursor()
count = 0
batch_size = 1000
logger.info('begin create_substance_ids')
cursor.execute(
'create temp table reagent_sub_ids as '
"select nextval('substance_id_seq'), reagent_id "
"from reagent;")
cursor.execute(
'create temp table reagent_sub_ids1 '
'(reagent_id integer, substance_id text )')
cursor1 = connection.cursor()
sql1 = 'insert into reagent_sub_ids1 values (%s, %s)'
cursor.execute('Select * from reagent_sub_ids')
cursor.arraysize = batch_size
try:
while True:
rows = cursor.fetchmany()
if not rows:
break
newrows = []
for row in rows:
newrows.append([row[1], create_substance_id(row[0])])
count += 1
cursor1.executemany(sql1, newrows)
if count % 100000 == 0:
logger.info('processed %d rows', count)
logger.info('processed %d rows, now update reagent table', count)
cursor.execute(
'update reagent '
'set substance_id=a.substance_id '
'from reagent_sub_ids1 a '
'where a.reagent_id=reagent.reagent_id')
except Exception as e:
logger.exception('create substance ids, ex after %d rows',count)
raise
logger.info('create substance ids, done after %d rows',count)