MagicStack / MagicStack/asyncpg
set_type_codec encoder to handle numpy/pandas null types not working with copy_records_to_table
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Description
* **asyncpg version**:0.21.0
* **PostgreSQL version**: PostgreSQL 13.1 on x86_64-pc-linux-gnu, compiled by gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44), 64-bit
* **Do you use a PostgreSQL SaaS? If so, which? Can you reproduce
the issue with a local PostgreSQL install?**:
* **Python version**: 3.7
* **Platform**: Ubuntu 18.04
* **Do you use pgbouncer?**: no
* **Did you install asyncpg with pip?**: yes
* **If you built asyncpg locally, which version of Cython did you use?**: -
* **Can the issue be reproduced under both asyncio and
[uvloop](https://github.com/magicstack/uvloop)?**: -
I am trying to set up an asyncpg in order to use ```copy_records_to_table``` method passing pandas data frame, converted to list of lists.
My table is simple:
```sql
create table sg.test("no" int4, dt timestmap)
```
As pandas/numpy have their own Null types for different types (pd.NaT for dates and np.nan for numerics) I tried to set up an appropriate encoder:
```python
import asyncio
import asyncpg
import pandas as pd
import numpy as np
data = [[1, np.datetime64('NaT')]]
df = pd.DataFrame(data=data, columns=["no", "dt"])
def encoder(val):
if isinstance(val, (type(pd.NaT), type(np.nan))):
return None
return bytes(val)
def decoder(val): # we do not need that for this task
return val
async def main(df: pd.DataFrame):
conn: asyncpg.Connection=await asyncpg.connect('postgresql://connection_string')
try:
await conn.set_type_codec(
'timestamp',
encoder=encoder,
decoder=decoder,
schema='pg_catalog',
format='binary'
)
res=await conn.copy_records_to_table('test', records=df.values.tolist(), columns=df.columns.values.tolist(), schema_name='sg')
print(res)
except ValueError as e:
print(e.args)
finally:
await conn.close()
asyncio.get_event_loop().run_until_complete(main(df))
```
I am getting following error:
```log
....
File "asyncpg/protocol/protocol.pyx", line 482, in copy_in
File "asyncpg/protocol/protocol.pyx", line 429, in asyncpg.protocol.protocol.BaseProtocol.copy_in
File "asyncpg/protocol/codecs/base.pyx", line 192, in asyncpg.protocol.protocol.Codec.encode
File "asyncpg/protocol/codecs/base.pyx", line 178, in asyncpg.protocol.protocol.Codec.encode_in_python
File "asyncpg/pgproto/./codecs/bytea.pyx", line 19, in asyncpg.pgproto.pgproto.bytea_encode
TypeError: a bytes-like object is required, not 'NoneType'
```
For me it is unclear what kind of bytes should ```encoder``` return in case of Null value, I have tried to investigate it backwards: select a null value from original table with custom decoder, but it seems that ```asyncpg``` just amends that method in case of null values at all. So it is still unclear what kind of data should be passed.
I have already tried to return following values at ```encoder```:
- ```b''```
- ```b'\x01'```
another error occurs:
```log
insufficient data left in message
````
Contributor guide
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Research direction
Start with the copy_in and Codec.encode stack-trace entries in asyncpg/protocol/protocol.pyx and asyncpg/protocol/codecs/base.pyx, then inspect asyncpg/pgproto/./codecs/bytea.pyx. Reproduce the set_type_codec and copy_records_to_table example with pandas and NumPy null values; done means the expected null behavior is established and covered for this path.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, pandas, postgresql, python
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100