Using a buffer to write a psycopg3 copy result through pandas

Question

Using psycopg2, I could write large results as CSV using copy_expert and a BytesIO buffer like this with pandas:

copy_sql = "COPY (SELECT * FROM big_table) TO STDOUT CSV"

buffer = BytesIO()
cursor.copy_expert(copy_sql, buffer, size=8192)
buffer.seek(0)
pd.read_csv(buffer, engine="c").to_excel(self.output_file)

However, I can’t figure out how to replace the buffer in copy_expert with psycopg3‘s new copy command. Has anyone figured out a way to do this?

Asked By: FlipperPA

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Source

Answer 1

Data and table setup:

cat test.csv                                                                                                                                                            
1,[email protected],"John Stokes"
2,[email protected],"Emily Ray"

create table test_csv (id integer, mail varchar, name varchar);

import psycopg

with open('test.csv') as f:
    with cur.copy("COPY test_csv FROM STDIN WITH CSV") as copy:
        while data := f.read(1000):
            copy.write(data)
con.commit()

Using a buffer:

buffer = BytesIO()
with cur.copy('copy test_csv to stdout') as copy:
    for data in copy:
        buffer.write(data)
buffer.seek(0)
pd.read_csv(buffer, engine="c").to_excel('test_csv.xlsx')

Since you are using Pandas there is also:


from sqlalchemy import create_engine
engine = create_engine('postgresql://postgres:@localhost:5432/test')
pd.read_sql('select * from test_csv', engine).to_excel('test_csv.xlsx')

Answered By: Adrian Klaver

Answer 2

The key to writing a large query to a file through psycopg3 in this fashion is to use a SpooledTemporaryFile, which will limit the amount of memory usage in Python (see max_size). Then after the CSV is written to disk, convert with pandas.

from tempfile import SpooledTemporaryFile
from pandas import read_csv
from psycopg import connect

cursor = connect([connection]).cursor()
copy_sql = "COPY (SELECT * FROM stocks WHERE price > %s) TO STDOUT"
price = 100

with SpooledTemporaryFile(
    mode="wb",
    max_size=65546,
    buffering=8192,
) as tmpfile:
    with cursor.copy(copy_sql, (price,)) as copy:
        for data in copy:
            tmpfile.write(data)
    tmpfile.seek(0)

    read_csv(tmpfile, engine="c").to_excel("my_spreadsheet.xlsx")

Answered By: FlipperPA

Using a buffer to write a psycopg3 copy result through pandas

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