pd.read_json() leads to a segmentation fault

[gambingo]

Code Sample

The following code leads to either a segmentation fault or a bus error:

def load_dataframe(name):
    ...
    df_json = db.dataframes.find_one({"_id": name})["df"]
    df = pd.read_json(df_json)
    return df

But the following workaround fixes it:

def load_dataframe(name):
    ...
    df_json = db.dataframes.find_one({"_id": name})["df"]
    df = pd.DataFrame().from_dict(json.loads(df_json))
    return df

Problem description

I am storing several jsonified dataframes in MongoDB. Trying to go straight from the json to the dataframe leads to either a segmentation fault or a bus error. I am storying several dataframes, but confusingly it only happens with one dataframe and not the others. The problem dataframe is identical in nature to other dataframes (same column names and data types). Unfortunately, it's not shareable but happy to answer any questions I can.

Output of pd.show_versions()

Note: I am using the latest pandas, 1.0.1. I downgraded to pandas 0.25.3 and had the same issue.

INSTALLED VERSIONS ------------------ commit : None python : 3.7.0.final.0 python-bits : 64 OS : Darwin OS-release : 17.7.0 machine : x86_64 processor : i386 byteorder : little LC_ALL : None LANG : en_US.UTF-8 LOCALE : en_US.UTF-8

pandas : 1.0.1
numpy : 1.18.1
pytz : 2019.3
dateutil : 2.8.1
pip : 20.0.2
setuptools : 45.1.0
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.11.1
IPython : 7.11.1
pandas_datareader: None
bs4 : None
bottleneck : None
fastparquet : None
gcsfs : None
lxml.etree : None
matplotlib : 3.1.3
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pytables : None
pytest : None
pyxlsb : None
s3fs : None
scipy : 1.4.1
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlwt : None
xlsxwriter : None
numba : None

[jbrockmendel]

Can you post a copy/paste-able example (https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)?

[gambingo]

Yes I can! Apologies for not doing so sooner. Thanks for the helpful MCVE post.

This leads to a segmentation fault on my machine:

import pandas as pd

df = pd.DataFrame(
        {'_id': {'0': '0'},
        'category': {'0': 'Goods'},
        'recommender_id': {'0': '3'},
        'recommender_name_jp': {'0': '浦田'},
        'recommender_name_en': {'0': 'Urata'},
        'name_jp': {'0': '博多人形（松尾吉将まつお よしまさ）'},
        'name_en': {'0': 'Hakata Dolls Matsuo'}
        })

df_json = df.to_json()
pd.read_json(df_json)

But this does not:

import json
import pandas as pd

df = pd.DataFrame(
        {'_id': {'0': '0'},
        'category': {'0': 'Goods'},
        'recommender_id': {'0': '3'},
        'recommender_name_jp': {'0': '浦田'},
        'recommender_name_en': {'0': 'Urata'},
        'name_jp': {'0': '博多人形（松尾吉将まつお よしまさ）'},
        'name_en': {'0': 'Hakata Dolls Matsuo'}
        })

df_json = df.to_json()
df_dict = json.loads(df_json)
pd.DataFrame().from_dict(df_dict)

And, unfortunately, there is no helpful traceback. All I get is a Segmentation fault: 11 or sometimes a Bus error: 10.

[jbrockmendel]

Hmm i cant reproduce this locally, so let's try to narrow down the example. Do you need all of the entries in that dict to get the segfault, or can you remove some? (id speculate that the ASCII entries can be removed)

[TomAugspurger]

I also can't reproduce using the code in #32383 (comment) (using pandas master).

[TomAugspurger]

@gambingo can you try on pandas master?

[mroeschke]

Cant produce this either on master with OSX. Something possible might have been fixed on master in the meantime. Suppose it could use a test