400 Error while reading data using pandas to_gbq to create a table in Google BigQuery

5
votes

I'm trying to query data from a MySQL server and write it to Google BigQuery using pandas .to_gbq api.

def production_to_gbq(table_name_prod,prefix,table_name_gbq,dataset,project):
    # Extract data from Production

    q = """
        SELECT *
        FROM
            {}
        """.format(table_name_prod)

    df = pd.read_sql(q, con)

    # Write to gbq    
    df.to_gbq(dataset + table_name_gbq, project, chunksize=1000, verbose=True, reauth=False, if_exists='replace', private_key=None)

    return df

I keep getting a 400 error indicating invalid input.

Load is 100.0% Complete
---------------------------------------------------------------------------
BadRequest                                Traceback (most recent call last)
/usr/local/lib/python3.6/site-packages/pandas_gbq/gbq.py in load_data(self, dataframe, dataset_id, table_id, chunksize, schema)
    569                     self.client, dataframe, dataset_id, table_id,
--> 570                     chunksize=chunksize):
    571                 self._print("\rLoad is {0}% Complete".format(

/usr/local/lib/python3.6/site-packages/pandas_gbq/_load.py in load_chunks(client, dataframe, dataset_id, table_id, chunksize, schema)
     73             destination_table,
---> 74             job_config=job_config).result()

/usr/local/lib/python3.6/site-packages/google/cloud/bigquery/job.py in result(self, timeout)
    527         # TODO: modify PollingFuture so it can pass a retry argument to done().
--> 528         return super(_AsyncJob, self).result(timeout=timeout)
    529 

/usr/local/lib/python3.6/site-packages/google/api_core/future/polling.py in result(self, timeout)
    110             # Pylint doesn't recognize that this is valid in this case.
--> 111             raise self._exception
    112 

BadRequest: 400 Error while reading data, error message: CSV table encountered too many errors, giving up. Rows: 10; errors: 1. Please look into the error stream for more details.

During handling of the above exception, another exception occurred:

GenericGBQException                       Traceback (most recent call last)
<ipython-input-73-ef9c7cec0104> in <module>()
----> 1 departments.to_gbq(dataset + table_name_gbq, project, chunksize=1000, verbose=True, reauth=False, if_exists='replace', private_key=None)
      2 

/usr/local/lib/python3.6/site-packages/pandas/core/frame.py in to_gbq(self, destination_table, project_id, chunksize, verbose, reauth, if_exists, private_key)
   1058         return gbq.to_gbq(self, destination_table, project_id=project_id,
   1059                           chunksize=chunksize, verbose=verbose, reauth=reauth,
-> 1060                           if_exists=if_exists, private_key=private_key)
   1061 
   1062     @classmethod

/usr/local/lib/python3.6/site-packages/pandas/io/gbq.py in to_gbq(dataframe, destination_table, project_id, chunksize, verbose, reauth, if_exists, private_key)
    107                       chunksize=chunksize,
    108                       verbose=verbose, reauth=reauth,
--> 109                       if_exists=if_exists, private_key=private_key)

/usr/local/lib/python3.6/site-packages/pandas_gbq/gbq.py in to_gbq(dataframe, destination_table, project_id, chunksize, verbose, reauth, if_exists, private_key, auth_local_webserver, table_schema)
    980     connector.load_data(
    981         dataframe, dataset_id, table_id, chunksize=chunksize,
--> 982         schema=table_schema)
    983 
    984 

/usr/local/lib/python3.6/site-packages/pandas_gbq/gbq.py in load_data(self, dataframe, dataset_id, table_id, chunksize, schema)
    572                     ((total_rows - remaining_rows) * 100) / total_rows))
    573         except self.http_error as ex:
--> 574             self.process_http_error(ex)
    575 
    576         self._print("\n")

/usr/local/lib/python3.6/site-packages/pandas_gbq/gbq.py in process_http_error(ex)
    453         # <https://cloud.google.com/bigquery/troubleshooting-errors>`__
    454 
--> 455         raise GenericGBQException("Reason: {0}".format(ex))
    456 
    457     def run_query(self, query, **kwargs):

GenericGBQException: Reason: 400 Error while reading data, error message: CSV table encountered too many errors, giving up. Rows: 10; errors: 1. Please look into the error stream for more details.

I've investigated the table schema, 

id  INTEGER NULLABLE    
name    STRING  NULLABLE    
description STRING  NULLABLE    
created_at  INTEGER NULLABLE    
modified_at FLOAT   NULLABLE

and it is the same as the dataframe:

id                        int64
name                     object
description              object
created_at                int64
modified_at             float64

The table is created in GBQ but remains empty.

I read around a little but am not finding much on pandas.to_gbq api, except for this which seemed relevant but has no reply:

bigquery table is empty when using pandas to_gbq

I found one potential solution about numbers in the object datatypes which are being passed into the GBQ table without quotes, something fixed by setting column datatypes as string.

I use to_gbq on pandas for updating Google BigQuery and get GenericGBQException

I tried the fix:

for col in df.columns:
    if df[col].dtypes == object:
        df[col] = df[col].fillna('')
        df[col] = df[col].astype(str)

Unfortunately I still get the same error. Similarly trying to format missing data and setting dtypes for int and float also gives the same error.

Is there something I'm missing?

3
pythonpandasgoogle-bigquery
I would suggest to break down the steps to isolate the problem. For example, saving the dataframe (or a sample) to a csv and try to import it with the UI or try to write some control dataframes using .to_gbq - Guillem Xercavins

3 Answers

2
votes

Found that bigquery cannot properly handle \r (sometimes \n too) Had the same issue, localized the problem and I was really surprised when just replacing \r with space fixed it:

for col in list(df.columns):
    df[col] = df[col].apply(lambda x: x.replace(u'\r', u' ') if isinstance(x, str) or isinstance(x, unicode) else x)
1
votes

I have ended up here several times when I've had a similar issue with importing to bigquery from parquet files on cloud storage. However, each time I've forgotten the way to solve it, so I hope it's not too much of a breach of protocol to leave my findings here!

What I realised was that I have columns that are all NULL, which will look like they have a data type in pandas, but if you use pyarrow.parquet.read_schema(parquet_file), you will see that the data type is null.

After removing the column, the upload will work!

1
votes

I had some invalid characters in string columns (object in pandas). I use @Echochi approach and it worked

for col in list(parsed_data.select_dtypes(include='object').columns):
        parsed_data[col] = parsed_data[col].apply(lambda x:re.sub('[^A-Za-z0-9]+','', str(x)))

It was a little bit to restrictive with the accepted characters, so I used a more general aproach, given that the biquery compatibility with UTF-8 bigquery docs

for col in list(parsed_data.select_dtypes(include='object').columns):
        parsed_data[col] = parsed_data[col].apply(lambda x:re.sub(r"[^\u0900-\u097F]+",,'?', str(x)))

with r"[^\u0900-\u097F]+" you will accept all UTF-8 compatible charset