Psycopg2 can't write numpy nans to postgresql table: invalid input syntax for type double precision: ""

Question

I have a small pyhton code that build a dataframe with one (or more) nans and then write it to a postgres database with psycopg2 module using copy_from function. Here it is:

table_name = "test"
df = pd.DataFrame([[1.0, 2.0], [3.0, np.nan]], columns=["VALUE0", "VALUE1"], index=pd.date_range("2000-01-01", "2000-01-02"))
database = "xxxx"
user = "xxxxxxx"
password = "xxxxxx"
host = "127.0.0.1"
port = "xxxxx"
def nan_to_null(f,
                _NULL=psycopg2.extensions.AsIs('NULL'),
                _NaN=np.NaN,
                _Float=psycopg2.extensions.Float):
    if f != f:
        return _NULL
    else:
        return _Float(f)
psycopg2.extensions.register_adapter(float, nan_to_null)
psycopg2.extensions.register_adapter(np.float, nan_to_null)
psycopg2.extensions.register_adapter(np.float64, nan_to_null)
with psycopg2.connect(database=database,
                      user=user,
                      password=password,
                      host=host,
                      port=port) as conn:
    try:
        with conn.cursor() as cur:
            cmd = "CREATE TABLE {} (TIMESTAMP timestamp PRIMARY KEY NOT NULL, VALUE0 FLOAT, VALUE1 FLOAT)"
            cur.execute(sql.SQL(cmd).format(sql.Identifier(table_name)))
            buffer = StringIO()
            df.to_csv(buffer, index_label='TIMESTAMP', header=False)
            buffer.seek(0)
            cur.copy_from(buffer, table_name, sep=",")
        conn.commit()
    except Exception as e:
        conn.rollback()
        logging.error(traceback.format_exc())
        raise e

The problème is that psycopg2 fail to transform nan into posgres NULL, although I have used this trick: How do I convert numpy NaN objects to SQL nulls? (the nan_to_null function). I cannot make it work, it throws the following exception:

psycopg2.errors.InvalidTextRepresentation: invalid input syntax for type double precision: ""
CONTEXT:  COPY test, line 2, column value1: ""

I am using python 3.8 on windows 10 with anaconda 3, psycopg2 v2.8.5 and postgres v12.3. Thanks!

score 2 · Answer 1 · answered Oct 01 '20 at 09:32

I put here the same code with the solution updated of Adrian Klaver. The line that changed is:

df.to_csv(buffer, index_label='TIMESTAMP', header=False, na_rep='NaN')

We've added na_rep='NaN' in to_csv function. No need to replace nans with another line of code. replacing with 'NULL' does not work.

import psycopg2, logging, numpy as np, pandas as pd
from psycopg2 import sql
import traceback
from io import StringIO


if __name__ == '__main__':
    table_name = "test"
    df = pd.DataFrame([[1.0, 2.0], [3.0, np.nan]], columns=["VALUE0", "VALUE1"], index=pd.date_range("2000-01-01", "2000-01-02"))

    database = "xxxxxx"
    user = "xxxxx"
    password = "xxxxxx"
    host = "127.0.0.1"
    port = "xxxxxx"

    with psycopg2.connect(database=database,
                          user=user,
                          password=password,
                          host=host,
                          port=port) as conn:
        try:
            with conn.cursor() as cur:
                #Creating a new table test
                cmd = "CREATE TABLE {} (TIMESTAMP timestamp PRIMARY KEY NOT NULL, VALUE0 FLOAT, VALUE1 FLOAT);"
                cur.execute(sql.SQL(cmd).format(sql.Identifier(table_name)))
                #Writting content
                buffer = StringIO()
                df.to_csv(buffer, index_label='TIMESTAMP', header=False, na_rep='NaN')
                buffer.seek(0)
                cur.copy_from(buffer, table_name, sep=",")

                #Reading the table content
                cmd = "SELECT * FROM {};"
                cur.execute(sql.SQL(cmd).format(sql.Identifier(table_name)))
                test_data = pd.DataFrame(cur.fetchall())
                print(test_data)
                print(type(test_data.loc[1, 2]))

                #Deleting the test table
                cmd = "DROP TABLE {};"
                cur.execute(sql.SQL(cmd).format(sql.Identifier(table_name)))
            conn.commit()
        except Exception as e:
            conn.rollback()
            logging.error(traceback.format_exc())
            raise e

The prints shows that nan is well interpreted and stored in the DB.

Adrian Klaver · Accepted Answer · 2020-09-30T14:40:45.523

1

The issue is the use of copy_from. From the docs:

Currently no adaptation is provided between Python and PostgreSQL types on COPY: ...

So your adapter does not come into play.

UPDATE A possible solution:

Pandas Changing the format of NaN values when saving to CSV

See @cs95 answer.

edited Sep 30 '20 at 14:40

answered Sep 30 '20 at 14:16

Adrian Klaver

15,886
2
17
28

That's very sweet, even more efficient. Thanks! – Cunningham Oct 01 '20 at 09:27

jlandercy · Answer 3 · 2020-09-30T14:10:43.447

It seems you are inserting empty string instead of NULL value, you can easily reproduce you error with the following SQL code:

CREATE TABLE test(
   x FLOAT
);
INSERT INTO test(x) VALUES ('');
-- ERROR: invalid input syntax for type double precision: "" Position: 29

On the other hand, NaN can be safely inserted into PostgreSQL:

INSERT INTO test(x) VALUES ('NaN');

Notice PostgreSQL float support slightly differs from IEEE 754 standards because PostresSQL needs all value to be orderable to consistently build index. Therefore NaN is greater or equal to any other number including itself in PostgreSQL.

score 0 · Answer 4 · answered Sep 30 '20 at 14:36

0

Thanks to Adrian Klaver and jlandercy answer, the solution is simple... replace np.nan by 'NaN' manually with the following line that replace the nan_to_null function: ''' df.replace(np.nan, "NaN", inplace=True) ''' And it works fine. Thank you guys!

answered Sep 30 '20 at 14:36

Cunningham

178
2
10

score 0 · Answer 5 · answered Aug 16 '22 at 19:42

Add na_rep='NaN' when you write your csv file.

If you are using this in conjunction with psycopg2's copy_expert method, you may need to also add the null = "NaN" param to your postgres syntax so that the null representations match up.

Here's an example:

df.to_csv(csv_filename, index=False, na_rep='NaN')

string = sql.SQL("""
        copy {} 
        from stdin (
            format csv,
            null "NaN",
            delimiter ',',
            header
        )
""").format(sql.Identifier(table_name))

Psycopg2 can't write numpy nans to postgresql table: invalid input syntax for type double precision: ""

5 Answers5