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util.py
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util.py
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""" batch processing using luigi """
import luigi
import luigi.contrib.postgres
import pandas as pd
import psycopg2
import logging
import abc
import string
logger = logging.getLogger('luigi-interface')
logger.setLevel(logging.DEBUG)
class QueryPostgres(luigi.Task):
"""
Base class to pull data from postgres and write to csv.
When inheriting, you must implement:
sql
output
"""
host = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='host'),
significant=False)
database = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='database'),
significant=False)
user = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='user'),
significant=False)
password = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='password'),
significant=False)
chunksize = 10000
def run(self):
# create db connection
self.conn = psycopg2.connect(
dbname=self.database,
user=self.user,
host=self.host,
password=self.password)
df_iterator = pd.read_sql_query(self.sql,
self.conn,
chunksize=self.chunksize)
# write to output file
with open(self.output().path, 'a') as f:
for ind, df in enumerate(df_iterator):
# Erase non-standard characters from string fields, like the Unicode character for a checkmark.
string_filter = lambda cell: filter(lambda x: x in string.printable, cell) if type(cell)==str else cell
df = df.applymap(string_filter) # prevents UnicodeDecodeError when trying to write unusual characters to CSV
if ind == 0:
df.to_csv(f, index=None, encoding='utf-8')
else:
df.to_csv(f, index=None, header=None, encoding='utf-8')
lines_written = ind * self.chunksize + len(df)
logger.info(str(lines_written) + " lines written")
self.conn.close()
class LoadPostgres(luigi.contrib.postgres.CopyToTable):
host = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='host'),
significant=False)
database = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='database'),
significant=False)
user = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='user'),
significant=False)
password = luigi.Parameter(config_path=dict(section='QueryPostgres',
name='password'),
significant=False)
null_values = ['']
header = False
seperator = ','
def rows(self):
"""
Return/yield tuples or lists corresponding to each row to be inserted.
"""
with self.input().open('r') as fobj:
for k, line in enumerate(fobj):
if k == 0 and self.header:
continue
row_str = filter(lambda x: x in string.printable, line)
row_str = row_str.strip('\n\r').split(self.seperator)
yield row_str
@abc.abstractproperty
def table(self):
return None