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Fix BUG: read_sql tries to convert blob/varbinary to string with pyarrow backend#60105
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The most recent change on main seems to also have 17 failing tasks so Ithink these failures are unrelated to the change in my PR but please let me know if that's wrong! |
# Try and greedily convert to string | ||
# Will fail if the object is bytes | ||
arr = arr_cls._from_sequence(arr, dtype=new_dtype) |
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Shouldn't this ideally returnpandas.ArrowDtype(pyarrow.binary())
type?
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that makes sense thanks! so looks like the previous logic was not taking into account pyarrow types when doing this conversation so I've added logic similar to my initial change where we try to convert to a pyarrow string but then fall back to binary if we run into an invalid error (i.e. we tried to parse but it failed due to an encoding error). Please let me know what you think! Was also considering trying to type check the contents ofarr
to see if it has string or bytes data but seems like greedily trying to convert ends up being better performance in most cases (since we might have to search the whole arr to see if one of the elements is a bytes sequence that can't be converted to a string)
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I definitely appreciate what we are trying to do here although I'm wary about trying to infer "non-first class" types at runtime.
Have you tried using an ADBC driver instead? That should be Arrow-native and yield the proper dtypes
@@ -968,9 +972,31 @@ def convert(arr): | |||
# i.e. maybe_convert_objects didn't convert | |||
arr = maybe_infer_to_datetimelike(arr) | |||
if dtype_backend != "numpy" and arr.dtype == np.dtype("O"): |
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I think this is the wrong place to be doing this; in the sql.py module can't we read in the type of the database and only try to convert BINARY types to Arrow binary types?
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Based on some local testing using the ADBC driver I can confirm that it yields apandas.core.arrays.arrow.array.ArrowExtensionArray
with ._dtype
ofpandas.ArrowDtype
. When the query returns a bytes type column we get a.type
ofbytes
, and likewise a.type
ofstring
is returned for a string type column. Seems like we don't need to do any conversions when using the ADBC driver as you've stated if I'm understanding correctly here!
Wondering if it makes sense to remove the code here trying to convert based on adtype_backend != 'numpy'
since this will fix the cause of the exception in the issue? and maybe raise an exception when trying to use apyarrow
dtype_backend
with theSQLiteDatabase
connection type here:https://github.com/pandas-dev/pandas/blob/main/pandas/io/sql.py#L695 ?
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I think the general problem is that pandas does not have a first class "binary" data type, so I'm not sure how to solve this for anything but the pyarrow backend.
With the pyarrow backend, I think you can still move this logic tosql.py
and check the type of the column coming back from the database. If it is a binary type in the database, using the PyArrow binary type with that backend makes sense.
Not sure if@mroeschke has other thoughts to the general issue. This is likely another good use case to track in PDEP-13#58455
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I agree that this is the incorrect place to handle this conversion logic and this should only be a valid conversion for the pyarrow backend (ArrowExtensionArray._from_sequence
should be able to return a binary type with binary data.)
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insql.py
it looks like the result of this conversion is being overwritten when thedtype_backend
ispyarrow
:https://github.com/pandas-dev/pandas/blob/main/pandas/io/sql.py#L181 and the dtype returned by the current logic isArrowDtype(pa.binary())
for the example in the issue, so maybe just removing the conversion logic is all that's needed to resolve this issue? I've removed the block doing the conversion and added a test case showing that the resulting df has a dtype ofArrowDtype(pa.binary())
when thedtype_backend='pyarrow'
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Very nice - simplification is always good and I think this implementation looks reasonable :-)
Just need a few tweaks to the test case
pandas/tests/io/test_sql.py Outdated
select cast(x'0123456789abcdef0123456789abcdef' as blob) a | ||
""" | ||
df = pd.read_sql(query, sqlite_buildin, dtype_backend=dtype_backend) | ||
assert df.a.values[0] == b"\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" |
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Can you use our built-in test helpers instead? I think you can just do:
result=pd.read_sql(...)expected=pd.DataFrame({"a": ...},dtype=pd.ArrowDtype(pa.binary()))tm.assert_frame_equal(result,expected)
What data type does this produce currently with thenumpy_nullable
backend - object?
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for sure, changed the testing logic over to using this! fornumpy_nullable
andlib.no_default
the dtype returned is an object
pandas/tests/io/test_sql.py Outdated
@pytest.mark.parametrize("dtype_backend", ["pyarrow", "numpy_nullable", lib.no_default]) | ||
def test_bytes_column(sqlite_buildin, dtype_backend): |
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deftest_bytes_column(sqlite_buildin,dtype_backend): | |
deftest_bytes_column(all_connectable,dtype_backend): |
Should test this against all databases
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sure thing! I was trying to pass in the cartesian product of theall_connectable
anddtype_backend
arrays usingitertools.product
to@pytest.mark.parametrize
but was running into issues with the connections getting passed. I instead made it so the connectables are being passed in theparametrize
and then we loop through the dtypes in the test. Would love to know if there's a better way to do this so we're testing eachdtype_backend
/connection
combination independently
pandas/tests/io/test_sql.py Outdated
@pytest.mark.parametrize("dtype_backend", ["pyarrow", "numpy_nullable", lib.no_default]) | ||
def test_bytes_column(sqlite_buildin, dtype_backend): | ||
pa = pytest.importorskip("pyarrow") | ||
""" |
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This is well intentioned but can you remove the docstring? We don't use them in tests.
Instead, you can just add a comment pointing to the github issue number in the function body
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trying to figure out why this test is failinghttps://github.com/pandas-dev/pandas/actions/runs/12484030959/job/34840808563?pr=60105 despite passing locally and in the other unit test checks - seems to be due to a library version mismatch between the different unit test CI checks and the |
@kastkeepitjumpinlikekangaroos when running that locally you would need to set an environment variable: PANDAS_FUTURE_INFER_STRING=1 python -m pytest pandas/tests/io/test_sql.py Can you reproduce the error if you do that? |
@WillAyd ah yes thank you!! was able to reproduce and fix the failing test locally. Waiting on CI now but should be passing there too. Please let me know if there's another way to be checking for the |
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pandas/tests/io/test_sql.py Outdated
conn = request.getfixturevalue(con) | ||
pa = pytest.importorskip("pyarrow") | ||
dtype = "O" |
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Hmm why is this defaulting to object out here? That seems like something to avoid for the pyarrow backend.
I think you are doing that in this test anyway, but the structure is confusing. I would just set up the expected data type from the backend up front, so something like:
ifdtype_backend=="pyarrow":exp_dtype= ...else: ...
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makes sense, let me know if the modified structure is less confusing!
pandas/tests/io/test_sql.py Outdated
dtype = ( | ||
pd.ArrowDtype(pa.string()) | ||
if "adbc" not in con | ||
else pd.ArrowDtype(pa.opaque(pa.binary(), "bit", "PostgreSQL")) |
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Why is this an opaque type instead of just binary? That seems like a bug somewhere in this implementation or the driver
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this is coming fromadbc-driver-postgresql
, I guess they've chosenopaque
because this is a bit of a weird type in postgres.https://www.postgresql.org/docs/current/sql-syntax-lexical.html#SQL-SYNTAX-BIT-STRINGS vshttps://www.postgresql.org/docs/current/datatype-binary.html
postgres=# select x'0011'; ?column? ------------------ 0000000000010001(1 row)postgres=# select pg_typeof(x'0011'); pg_typeof ----------- bit(1 row)postgres=# select cast('0011' as bytea); bytea ------------ \x30303131(1 row)postgres=# select pg_typeof(cast('0011' as bytea)); pg_typeof ----------- bytea(1 row)
@@ -2261,7 +2261,9 @@ def type(self): | |||
elif pa.types.is_null(pa_type): | |||
# TODO: None? pd.NA? pa.null? | |||
return type(pa_type) | |||
elif isinstance(pa_type, pa.ExtensionType): | |||
elif isinstance(pa_type, pa.ExtensionType) or isinstance( | |||
pa_type, pa.OpaqueType |
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Hmm AFAIK the OpaqueType is returned when there is no suitable database type, but isn't binary already returned directly? It is a bit unclear what this additionalisinstance
check is for
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I had to add this becauseadbc-driver-postgresql
is returning anOpaqueType
- without this included an exception is thrown
val = b"\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" | ||
if "postgres" in con: | ||
if "adbc" in con: | ||
val = b"\x00\x00\x00\x80\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" |
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Why does postgres have different content than the other databases?
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thex'...'
syntax in sqlite and mysql represents the same data (called a blob literal in sqlite ]) but in postgres this is slighly different in that it's not abytea
type , but instead abit
. Most of the drivers return this as a string representation of the bits (which is whyval = "0000000100100011010001..."
in one of the cases)
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Instead of selecting a literal value can you write and read back the dataframe? I think this PR is missing something about how the different drivers are going to return binary data.
The ADBC driver has maps binary data to the BYTEA type (see alsohttps://github.com/apache/arrow-adbc/blob/c6e529980f1369202adb101f2e1ea03c4e12dcdc/c/driver/postgresql/postgres_type.h#L599) so we should be round tripping that, not bits
pandas/tests/io/test_sql.py Outdated
conn = request.getfixturevalue(con) | ||
pa = pytest.importorskip("pyarrow") | ||
val = b"\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" |
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What does#Eg
represent?
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this is the raw bytes returned from the hex string"0123456789abcdef0123456789abcdef"
- I've changed the test to usebytes.fromhex("0123456789abcdef0123456789abcdef")
to make things more clear here
if "adbc" in con: | ||
val = b"\x00\x00\x00\x80\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" | ||
else: | ||
val = ( |
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Is this supposed to be the binary representation of the bytes? I'm a bit confused why this test has so many different expected values
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yeah exactly and this is due to postgres returning thebit
type which most of the drivers turn into this string
val = b"\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" | ||
if "postgres" in con: | ||
if "adbc" in con: | ||
val = b"\x00\x00\x00\x80\x01#Eg\x89\xab\xcd\xef\x01#Eg\x89\xab\xcd\xef" |
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Instead of selecting a literal value can you write and read back the dataframe? I think this PR is missing something about how the different drivers are going to return binary data.
The ADBC driver has maps binary data to the BYTEA type (see alsohttps://github.com/apache/arrow-adbc/blob/c6e529980f1369202adb101f2e1ea03c4e12dcdc/c/driver/postgresql/postgres_type.h#L599) so we should be round tripping that, not bits
This pull request is stale because it has been open for thirty days with no activity. Pleaseupdate and respond to this comment if you're still interested in working on this. |
doc/source/whatsnew/vX.X.X.rst
file if fixing a bug or adding a new feature.This PR allows for bytes based data to be returned instead of throwing an exception like before