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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024 36

Hey all,

after looking at this again, I've been able to resolve it as follows.

For our sqlalchemy models we created this PydanticJSONType factory:

def pydantic_column_type(pydantic_type):
    class PydanticJSONType(TypeDecorator, Generic[T]):
        impl = JSON()

        def __init__(
            self, json_encoder=json,
        ):
            self.json_encoder = json_encoder
            super(PydanticJSONType, self).__init__()

        def bind_processor(self, dialect):
            impl_processor = self.impl.bind_processor(dialect)
            dumps = self.json_encoder.dumps
            if impl_processor:

                def process(value: T):
                    if value is not None:
                        if isinstance(pydantic_type, ModelMetaclass):
                            # This allows to assign non-InDB models and if they're
                            # compatible, they're directly parsed into the InDB
                            # representation, thus hiding the implementation in the
                            # background. However, the InDB model will still be returned
                            value_to_dump = pydantic_type.from_orm(value)
                        else:
                            value_to_dump = value
                        value = recursive_custom_encoder(value_to_dump)
                    return impl_processor(value)

            else:

                def process(value):
                    if isinstance(pydantic_type, ModelMetaclass):
                        # This allows to assign non-InDB models and if they're
                        # compatible, they're directly parsed into the InDB
                        # representation, thus hiding the implementation in the
                        # background. However, the InDB model will still be returned
                        value_to_dump = pydantic_type.from_orm(value)
                    else:
                        value_to_dump = value
                    value = dumps(recursive_custom_encoder(value_to_dump))
                    return value

            return process

        def result_processor(self, dialect, coltype) -> T:
            impl_processor = self.impl.result_processor(dialect, coltype)
            if impl_processor:

                def process(value):
                    value = impl_processor(value)
                    if value is None:
                        return None

                    data = value
                    # Explicitly use the generic directly, not type(T)
                    full_obj = parse_obj_as(pydantic_type, data)
                    return full_obj

            else:

                def process(value):
                    if value is None:
                        return None

                    # Explicitly use the generic directly, not type(T)
                    full_obj = parse_obj_as(pydantic_type, value)
                    return full_obj

            return process

        def compare_values(self, x, y):
            return x == y

    return PydanticJSONType

where recursive_custom_encoder() is pretty much the fastAPI jsonable_encoder

Using this in SQLModel as follows:

class ConnectionResistances(SQLConnectionModel, table=False):
    very_short: ResistancesInLoadDuration = ResistancesInLoadDuration()
    short: ResistancesInLoadDuration = ResistancesInLoadDuration()
    middle: ResistancesInLoadDuration = ResistancesInLoadDuration()
    long: ResistancesInLoadDuration = ResistancesInLoadDuration()
    constant: ResistancesInLoadDuration = ResistancesInLoadDuration()
    earth_quake: ResistancesInLoadDuration = ResistancesInLoadDuration()

class Connection(SQLConnectionModel, table=True):

    id: Optional[uuid.UUID] = Field(default=None, sa_column=Column(PGUUID(as_uuid=True), default=uuid.uuid4, primary_key=True))
    name: str
    comment: str
    path_to_pdf: Optional[str] = None
    resistance_values: ConnectionResistances = Field(..., sa_column=Column(pydantic_column_type(ConnectionResistances)))

Works perfectly!
That means:

  • In the DB data is stored as JSON
  • whenever the model is read from the DB, data is read into the pydantic class (including validation)
  • whenever the the model is written into DB, the data is transformed into JSON

This could be integrated into an sqlmodel api based on the type hint alone (i.e. creating the sa_column based on the pydantic type automatically). Potentially in get_sqlachemy_type.

What do you think, @tiangolo?

from sqlmodel.

TheJedinator avatar TheJedinator commented on May 23, 2024 21

@OXERY && @scuervo91 - I was able to get something that works Using this:

regions: dict = Field(sa_column=Column(JSON), default={'all': 'true'})

That said: this is a postgresql JSONB column in my database. But it works.

For a nested Object you could use a pydantic model as the Type and do it the same way. Hope this helps as I was having a difficult time figuring out a solution as well :)

from sqlmodel.

HenningScheufler avatar HenningScheufler commented on May 23, 2024 19

A hacky method with type checking that work with sqlite is

from sqlalchemy import Column
from typing import List
# from sqlalchemy.dialects.postgresql import JSONB
from sqlmodel import Field
from sqlmodel import Session
from pydantic import validator
from sqlmodel import SQLModel, JSON,create_engine

# from engine import get_sqlalchemy_engine
sqlite_file_name = "test.db"
sqlite_url = f"sqlite:///{sqlite_file_name}"

engine = create_engine(sqlite_url)


class J2(SQLModel):
    test: List[int]

class J(SQLModel):
    j: int
    nested: J2


class A(SQLModel, table=True):
    a: int = Field(primary_key=True)
    b: J = Field(sa_column=Column(JSON))

    @validator('b')
    def val_b(cls, val):
        return val.dict()

SQLModel.metadata.create_all(engine)

with Session(engine) as session:
    a = A(a=1, b=J(j=1,nested=J2(test=[100,100,100])))
    session.add(a)
    session.commit()
    session.refresh(a)

from sqlmodel.

OXERY avatar OXERY commented on May 23, 2024 18

I also got it working, on SQLite and Postgresql:
mygreatfield: Dict[Any, Any] = Field(index=False, sa_column=Column(JSON))
needs from sqlmodel import Field, SQLModel, Column, JSON as well as from typing import Dict, Any

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OXERY avatar OXERY commented on May 23, 2024 8

I also wondered how to store JSON objects without converting to string. SQL Alchemy supports storing these directly

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024 5

Hey all,

thanks for the great advice here. Creating a the object using the classes and writing them to the DB works as expected and writes the data as a dict into a JSON field.

See this example:

class ComplexHeroField(SQLModel, table=False):
    some: str
    other: float
    more: Optional[List[str]]

class Hero(SQLModel, table=True):
    id: Optional[int] = Field(default=None, primary_key=True)
    complex_field: ComplexHeroField = Field(sa_column=Column(JSON))
    name: str
    secret_name: str
    age: Optional[int] = None

    @validator('complex_field')
    def val_complex(cls, val: ComplexHeroField):
        # Used in order to store pydantic models as dicts
        return val.dict()

    class Config:
        arbitrary_types_allowed = True

However, when reading the model from the DB using a select() I would want the JSON field to be read into a ComplexHeroField class using pydantics parse_raw or parse_obj. Because they way it's currently done (with the validator) this happens:

        statement = select(Hero)
        results = session.exec(statement)
        for hero in results:
            print(hero.complex_field.some)

       # AttributeError: 'dict' object has no attribute 'some'

Any hint how that could be achieved? Maybe via the custom-serialiser mentioned by @psarka ?

Thanks already!

from sqlmodel.

Tridagger avatar Tridagger commented on May 23, 2024 4

@tiangolo , @MaximilianFranz

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psarka avatar psarka commented on May 23, 2024 3

@TheJedinator Could you help a bit more with the nested object? I tried to "use the pydantic model as the Type" but I can't get it to work :( Here is my snippet:

from sqlalchemy import Column
from sqlalchemy.dialects.postgresql import JSONB
from sqlmodel import Field
from sqlmodel import Session
from sqlmodel import SQLModel

from engine import get_sqlalchemy_engine


class J(SQLModel):
    j: int


class A(SQLModel, table=True):
    a: int = Field(primary_key=True)
    b: J = Field(sa_column=Column(JSONB))


engine = get_sqlalchemy_engine()
SQLModel.metadata.create_all(engine)

with Session(engine) as session:
    a = A(a=1, b=J(j=1))
    session.add(a)
    session.commit()
    session.refresh(a)

Throws an error

sqlalchemy.exc.StatementError: (builtins.TypeError) Object of type J is not JSON serializable
[SQL: INSERT INTO a (b, a) VALUES (%(b)s, %(a)s)]
[parameters: [{'a': 1, 'b': J(j=1)}]]

from sqlmodel.

HenningScheufler avatar HenningScheufler commented on May 23, 2024 3

Does this work?

    @validator('adddresses')
    def val_b(cls, value):
        print(value)
        return [v.dict() for v in value]

from sqlmodel.

Zaffer avatar Zaffer commented on May 23, 2024 3

Hoping this gets merged in the near future.

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avatar commented on May 23, 2024 3

Would be great to have this in-built! CC: @tiangolo , @MaximilianFranz

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AAraKKe avatar AAraKKe commented on May 23, 2024 3

I arrived here looking at something that I imagined might not work yet but that seems to be a feature one would expect from a library like this. The use case is simple (the solution I am not sure haha).

If you have a model with a field that is typed as a pedantic model, it seems to me that as long as you specify the column being a JSON type serialization and deserialiation should happen automatically from the database.

class MyOtherModel(BaseModel):
    name: str
    id: int

class MyModel(SQLModel, table=True):
    id = int](id: int | None = Field(default=None, primary_key=True))
    my_field: MyOtherModel = Field(sa_column=Collumn(type_=JSON)


# ...setup session...
model = session.exec(select(MyModel).where(MyModel.id == 1)).first()
print(model.my_field.name) # Should work
model.my_field = MyOtherModel(name="New name", id=123)
session.flush() # Should work

Is this something that is being considered?

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psarka avatar psarka commented on May 23, 2024 1

Thank you! Unfortunately I get the same error :(

I found one workaround - registering a custom_serializer for the sqlalchemy engine, like so:

def custom_serializer(d):
    return json.dumps(d, default=lambda v: v.json())

def get_sqlalchemy_engine():
    return create_engine("postgresql+psycopg2://", creator=get_conn, json_serializer=custom_serializer)

But if there is a cleaner way, I would gladly use that instead.

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TheJedinator avatar TheJedinator commented on May 23, 2024

@psarka

j = J(j=1)
db_j = J.from_orm(j)
a = A(a=1, b=db_j)

This should resolve your issue in preparing the object for the database. What I'm seeing in the error is that the Raw Object is being included in the statement rather than the instance...

If this doesn't help I can definitely put some more time in to looking at what's going on.

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TheJedinator avatar TheJedinator commented on May 23, 2024

Hey @psarka

I just actually tried what I told and sorry have mislead... I did get a working solution though 😄

It was actually the opposite function that you need to use, here's the example you supplied with the amendments to make it work:

with Session(engine) as session:
    j = J(j=1)
    j_dumped = J.json(j)
    a = A(a=1, b=j_dumped)
    session.add(a)
    session.commit()
    session.refresh(a)

from sqlmodel.

psarka avatar psarka commented on May 23, 2024

Hmm, this doesn't (or at least shouldn't) typecheck :)

But I see what you did there, essentially it's the same as registring a custom serializer, but manually.

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TheJedinator avatar TheJedinator commented on May 23, 2024

It does type check when you create the J Object (which it should) So if you tried to supply a string it would fail J(j="foo")

This allows for the type checking of the object, the A class requires a serialized version of J in order for it to be entered in to the database.

It is essentially the same as registering a custom serializer but allows you to be explicit about using it.

from sqlmodel.

hakanoktay avatar hakanoktay commented on May 23, 2024

hi,
I created a "JSON Field" based on what is written here. I am using SQLite.

from sqlmodel import SQLModel,Relationship,Field,JSON
from typing import Optional,List, Dict
from sqlalchemy import Column
from pydantic import validator


#
class J2(SQLModel):
    id: int
    title:str

#
class Companies(SQLModel, table=True):
    id:Optional[int]=Field(default=None,primary_key=True)
    name:str
    adddresses: List['J2'] = Field(sa_column=Column(JSON))


    @validator('adddresses')
    def val_b(cls, val):
        print(val)
        return val.dict()

Given error.

TypeError: Type is not JSON serializable: J2

when i print it, it returns

[J2(id=1, title='address1'), J2(id=2, title='address2')]

how can i handle that? Why is this J2 added, how can I get rid of it, i can't turn it to .dict(), i cannot serialise it... can you give an idea?

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hakanoktay avatar hakanoktay commented on May 23, 2024

Does this work?

    @validator('adddresses')
    def val_b(cls, value):
        print(value)
        return [v.dict() for v in value]

@HenningScheufler thank you for your help, it worked perfect.

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

Something like this works, but obviously doesn't scale if we have mulitple nested models, instead of just the ComplexHeroField:


def custom_serializer(d):
    return json.dumps(d, default=lambda v: v.json())

def custom_deserialiser(d):
    return ComplexHeroField.parse_raw(d)

engine = create_engine(url_string, echo=True, json_serializer=custom_serializer, json_deserializer=custom_deserialiser)

complex_value = ComplexHeroField(some="value", other=5, more=["dd", "sdf"])
hero_1 = Hero(name="Deadpond", secret_name="Dive Wilson", complex_field=complex_value)
session.add(hero_1)
session.commit()

statement = select(Hero)
results = session.exec(statement)
for hero in results:
    print(hero.complex_field.some)
    # value

Instead, we would need more context in the deserialiser (i.e. access to the type-hint of the field we're trying to deserialise so that we can use UseType.parse_raw().

Any hint where and how I could achieve that kind of access to the deserialisation process?

Thanks :)

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tchaton avatar tchaton commented on May 23, 2024

@tiangolo Any updates ?

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tchaton avatar tchaton commented on May 23, 2024

Hey @MaximilianFranz Would you mind sharing your entire solution, I am quite interested in trying it out, but it is missing some code pieces.

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

Hey @MaximilianFranz Would you mind sharing your entire solution, I am quite interested in trying it out, but it is missing some code pieces.

What exactly are you missing? Happy to provide more context!

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tchaton avatar tchaton commented on May 23, 2024

The recursive_custom_encoder is missing. Ideally, a fully working example I can simply copy/paste and adapt to my use case ;)

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

You can use jsonable_encode like such, instead of the recursive_custom_encoder

from fastapi.encoders import jsonable_encoder

also I would start with a simpler model like:

class NestedModel(SQLModel):
    some_value: str

class OuterModel(SQLModel, table=True):
    guid: str = Field(
        default=None,
        sa_column=Column(PGUUID(as_uuid=True), default=uuid.uuid4, primary_key=True),
    )
    nested: NestedModel = Field(..., sa_column=Column(pydantic_column_type(NestedModel)))

That should work!

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tchaton avatar tchaton commented on May 23, 2024

Thanks, @MaximilianFranz Let me try. My code is here: https://github.com/Lightning-AI/lightning-hpo/blob/master/lightning_hpo/commands/sweep.py#L36. Trying to store the Sweep distributions.
Do you think it would work with the recursion?
Missing parse_obj_as and ModelMetaclass.

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tchaton avatar tchaton commented on May 23, 2024

Hey @MaximilianFranz

I have made a draft PR there: https://github.com/Lightning-AI/lightning-hpo/pull/19/files. I tried but it is raising an error. Would you mind having a look?

Best,
T.C

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

Thanks, @MaximilianFranz Let me try. My code is here: https://github.com/Lightning-AI/lightning-hpo/blob/master/lightning_hpo/commands/sweep.py#L36. Trying to store the Sweep distributions. Do you think it would work with the recursion? Missing parse_obj_as and ModelMetaclass.

Both parse_obj_as and ModelMetaClass can be imported from pydantic:

from pydantic import parse_obj_as
from pydantic.main import ModelMetaclass

As for the error, would you mind pointing me to the action that fails or post a traceback somewhere?

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MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

It makes sense that it doesn't work yet. You'll have to use the ModelMetaclass as is done in my snippet above for the isinstance check. Also the import for parse_obj_as is missing, so it can't work as it is :)

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tchaton avatar tchaton commented on May 23, 2024

Hey @MaximilianFranz, I updated the code with your inputs, but it is still failing. I pushed the updated code.

  File "/Users/thomas/Documents/GitHub/LAI-lightning-hpo-App/lightning_hpo/components/servers/db/server.py", line 42, in insert_sweep
    session.commit()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1451, in commit
    self._transaction.commit(_to_root=self.future)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 829, in commit
    self._prepare_impl()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 808, in _prepare_impl
    self.session.flush()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3383, in flush
    self._flush(objects)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3523, in _flush
    transaction.rollback(_capture_exception=True)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__
    compat.raise_(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 208, in raise_
    raise exception
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3483, in _flush
    flush_context.execute()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 456, in execute
    rec.execute(self)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 630, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj
    _emit_insert_statements(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/persistence.py", line 1238, in _emit_insert_statements
    result = connection._execute_20(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1631, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 332, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1498, in _execute_clauseelement
    ret = self._execute_context(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1862, in _execute_context
    self._handle_dbapi_exception(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2043, in _handle_dbapi_exception
    util.raise_(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 208, in raise_
    raise exception
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1819, in _execute_context
    self.dialect.do_execute(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 732, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.InterfaceError: (sqlite3.InterfaceError) Error binding parameter 5 - probably unsupported type.
[SQL: INSERT INTO sweepconfig (distributions, sweep_id, script_path, n_trials, simultaneous_trials, requirements, script_args, framework, cloud_compute, num_nodes, logger, direction) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]
[parameters: ('{"name": "model.lr", "distribution": "uniform", "params": {"params": {"low": "0.001", "high": "0.1"}}}', 'thomas-5e0dd935', 'train.py', 1, 1, [], [], 'pytorch_lightning', 'cpu', 1, 'wandb', 'maximize')]
(Background on this error at: https://sqlalche.me/e/14/rvf5)

from sqlmodel.

MaximilianFranz avatar MaximilianFranz commented on May 23, 2024

Hey @MaximilianFranz, I updated the code with your inputs, but it is still failing. I pushed the updated code.

  File "/Users/thomas/Documents/GitHub/LAI-lightning-hpo-App/lightning_hpo/components/servers/db/server.py", line 42, in insert_sweep
    session.commit()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1451, in commit
    self._transaction.commit(_to_root=self.future)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 829, in commit
    self._prepare_impl()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 808, in _prepare_impl
    self.session.flush()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3383, in flush
    self._flush(objects)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3523, in _flush
    transaction.rollback(_capture_exception=True)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__
    compat.raise_(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 208, in raise_
    raise exception
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 3483, in _flush
    flush_context.execute()
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 456, in execute
    rec.execute(self)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 630, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj
    _emit_insert_statements(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/orm/persistence.py", line 1238, in _emit_insert_statements
    result = connection._execute_20(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1631, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 332, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1498, in _execute_clauseelement
    ret = self._execute_context(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1862, in _execute_context
    self._handle_dbapi_exception(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2043, in _handle_dbapi_exception
    util.raise_(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 208, in raise_
    raise exception
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1819, in _execute_context
    self.dialect.do_execute(
  File "/Users/thomas/Documents/GitHub/lightning/.venv/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 732, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.InterfaceError: (sqlite3.InterfaceError) Error binding parameter 5 - probably unsupported type.
[SQL: INSERT INTO sweepconfig (distributions, sweep_id, script_path, n_trials, simultaneous_trials, requirements, script_args, framework, cloud_compute, num_nodes, logger, direction) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]
[parameters: ('{"name": "model.lr", "distribution": "uniform", "params": {"params": {"low": "0.001", "high": "0.1"}}}', 'thomas-5e0dd935', 'train.py', 1, 1, [], [], 'pytorch_lightning', 'cpu', 1, 'wandb', 'maximize')]
(Background on this error at: https://sqlalche.me/e/14/rvf5)

To finish this, the problem ended up being a attribute of type List[str] on an SQLModel, which is not natively supported. Using the above pydantic_column_type with List[str] works however and will encode the list as json-string in order to store it to the database.

from sqlmodel.

fahadshery avatar fahadshery commented on May 23, 2024

I was able to setup JSONB column for postgresql database instead of JSON that comes with sqlmodel by:

from sqlalchemy.dialects.postgresql import JSONB
from sqlmodel import Field, SQLModel, Column

class test(SQLModel, table=True):
    result: dict = Field(sa_column=Column(JSONB), default={"message":"hello world"})

from sqlmodel.

AAraKKe avatar AAraKKe commented on May 23, 2024

In case this helps anyone, here is how I managed to achieve it, although depending on how many of these fields you have it might impact performance a bit.

I have a model named Meetup that has a field MeetupLocation that I wanted to serialize in the database as JSON.

class Meetup(SQLModel, table=True):
    __tablename__: str = "meetups"  # type: ignore

    # ... some fields definitions ...
    location: MeetupLocation | None = Field(
        default=None,
        sa_column=Column(type_=MeetupLocation.as_mutable(JSON(none_as_null=True)), nullable=True),
    )

I will talk about how MeetupLocation has been defined in a bit.

To serialize and deserialize, I leveraged the engine using the json_serializer and json_deserializer arguments. It looks something like this

    def serialize_pydantic_model(model: BaseModel) -> str:
        return model.model_dump_json()

    def deserialize_pydantic_model(data: str) -> BaseModel | None:
        # Try deserializing with each model until one works.
        # This is a pretty ugly solution but the deserialization seems to only be possible and reliable at an engine level
        # and we need to know the model to deserialize it properly
        # We would need to keep adding more of these if we add more models with JSON fields.
        with suppress(ValidationError):
            return MeetupLocation.model_validate_json(data)
        return None

    engine = create_engine(
        db_config.full_url,
        echo=db_config.engine_echo,
        json_serializer=serialize_pydantic_model,
        json_deserializer=deserialize_pydantic_model,
    )

The key part here is that SQLModel seems to be breaking mutable tracking by SQLAlchemy, so when you later do something like

meetup.location.name = "Other name"
session.add(meetup)
session.commit()

It will not be persisted in the db because, as far as the Session cares, no modification has been made in the model.

To fix this, I have created a MutableModel that takes care of informing the Session through Mutable that the object has been updated.

from pydantic import BaseModel
from sqlalchemy.ext.mutable import Mutable


class MutableModel(BaseModel, Mutable):
    def __setattr__(self, name: str, value: Any) -> None:
        """Allows SQLAlchmey Session to track mutable behavior when updating any field"""
        self.changed()
        return super().__setattr__(name, value)

    @classmethod
    def coerce(cls, key: str, value: Any) -> Self | None:
        """Convert JSON to MeetupLocation object allowing for mutable behavior"""
        if isinstance(value, cls) or value is None:
            return value

        if isinstance(value, str):
            return cls.model_validate_json(value)

        if isinstance(value, dict):
            return cls(**value)

        super().coerce(key, value)

Then, MeetupLocation is created like this

class MeetupLocation(MutableModel):
    name: str | None = None
    location: tuple[float, float] | None = None

And this works as far as I have been able to validate it. It can read json and transform them into the we want and it can update the object in the database if anything changes in the model later on.

I hope this helps.

from sqlmodel.

copdips avatar copdips commented on May 23, 2024 
    def serialize_pydantic_model(model: BaseModel) -> str:
        return model.model_dump_json()

a little question, why not use model.model_dump() ?
and maybe a fix at Pydantic level for the deserializer would be better IMHO.

Otherwise, when I insert data into DB, the nested field is already a dict type.
In fact, during the data preparation, I have an extra step with model_validate() like:

new_row = {"name": "aa", "location": {"address": "bb", "city": "cc"}}
new_row_db = Meetup.model_validate(new_row )
# Here, new_row_db.location is a dict type.
session.add(new_row_db)

The serializer is a must have otherwise I cannot add the new row into DB, but the deserializer is optional for me, as I'm fine with dict instead of MeetupLocation.

from sqlmodel.

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