Difficulty serializing Geography column type using sqlalchemy marshmallow

Question

I an trying to use Marshmallow to do do deserialize and serialise SQLAlchemy objects but run into a problem when dealing with Geography fields in the ORM.

Firstly the model:

class Address(db.Model, TableColumnsBase):
    __tablename__ = 'address'
    addressLine1 = db.Column(String(255), nullable=True, info="Street address, company name, c/o")
    addressLine2 = db.Column(String(255), nullable=True, info="Apartment, suite, unit, building floor, etc")
    countryCode = db.Column(String(255), nullable=True, info="Country code such as AU, US etc")
    suburb = db.Column(String(255), nullable=True, info="Users suburb such as Elizabeth Bay")
    postcode = db.Column(String(32), nullable=True, info="Users postcode such as 2011 for Elizabeth Bay")
    state = db.Column(String(64), info="State for user such as NSW")
    user_presence = one_to_many('UserPresence', backref = 'user', lazy='select', cascade='all, delete-orphan')

    location = Column(Geography(geometry_type='POINT', srid=4326))
    discriminator = Column('type', String(50))
    __mapper_args__ = {'polymorphic_on': discriminator}

    def as_physical(self):
        pa = {   # TODO - stub, make it proper
            "latitude": 2.1,
            "longitude": 1.1,
            "unitNumber": '1',
            "streetNumber": self.addressLine1,
            "streetName": self.addressLine2,
            "streetType": 'street',
            "suburb": self.suburb,
            "postcode": self.postcode
        }
        return pa

Secondly the marshmallow schema:

class AddressSchema(ModelSchema):
    class Meta:
        model = Address
        sqla_session 

Then the error when trying to run:

/Users/james/.virtualenvs/trustmile-api-p2710/bin/python /Users/james/Documents/workspace/trustmile-backend/trustmile/tests/postgis_scratch.py
Traceback (most recent call last):
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/tests/postgis_scratch.py", line 1, in <module>
    from app import db
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/__init__.py", line 54, in <module>
    from app.api.consumer_v1 import bp as blueprint
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/api/__init__.py", line 4, in <module>
    import courier_v1
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/api/courier_v1/__init__.py", line 5, in <module>
    from .routes import routes
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/api/courier_v1/routes.py", line 10, in <module>
    from .api.nearestNeighbours_latitude_longitude import NearestneighboursLatitudeLongitude
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/api/courier_v1/api/__init__.py", line 5, in <module>
    from app.ops import requesthandler
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/ops/requesthandler.py", line 1, in <module>
    from app.ops.consumer_operations import cons_ops, ConsumerOperationsFactory
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/ops/consumer_operations.py", line 19, in <module>
    from app.users.serialize import ApplicationInstallationSchema, UserAddressSchema, ConsumerUserSchema, CourierUserSchema
  File "/Users/james/Documents/workspace/trustmile-backend/trustmile/app/users/serialize.py", line 40, in <module>
    class AddressSchema(ModelSchema):
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow/schema.py", line 116, in __new__
    dict_cls=dict_cls
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/schema.py", line 57, in get_declared_fields
    declared_fields = mcs.get_fields(converter, opts)
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/schema.py", line 90, in get_fields
    include_fk=opts.include_fk,
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/convert.py", line 77, in fields_for_model
    field = self.property2field(prop)
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/convert.py", line 95, in property2field
    field_class = self._get_field_class_for_property(prop)
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/convert.py", line 153, in _get_field_class_for_property
    field_cls = self._get_field_class_for_column(column)
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/convert.py", line 123, in _get_field_class_for_column
    return self._get_field_class_for_data_type(column.type)
  File "/Users/james/.virtualenvs/trustmile-api-p2710/lib/python2.7/site-packages/marshmallow_sqlalchemy/convert.py", line 145, in _get_field_class_for_data_type
    'Could not find field column of type {0}.'.format(types[0]))
marshmallow_sqlalchemy.exceptions.ModelConversionError: Could not find field column of type <class 'geoalchemy2.types.Geography'>.

I've tried a few overrides on the location field however to no avail. Any help much appreciated.

Updated Jan 24 2016

This is my code as it stands as the moment with a simpler model:

The SQLAlchemyModel:

class Location(db.Model, TableColumnsBase):
    __tablename__ = "location"
    loc = db.Column(Geography(geometry_type='POINT', srid=4326))

The marshmallow_sqlalchemy schema object

class LocationSchema(ModelSchema):
    loc = GeographySerializationField(attribute='loc')
    class Meta:
        model = Location
        sqla_session = db.session
        model_converter = GeoConverter

Other plumbing as per suggestions:

class GeoConverter(ModelConverter):
    SQLA_TYPE_MAPPING = ModelConverter.SQLA_TYPE_MAPPING.copy()
    SQLA_TYPE_MAPPING.update({
        Geography: fields.Str
    })


class GeographySerializationField(fields.Field):
    def _serialize(self, value, attr, obj):
        if value is None:
            return value
        else:
            if isinstance(value, Geography):
                return json.dumps({'latitude': db.session.scalar(geo_funcs.ST_X(value)), 'longitude': db.session.scalar(geo_funcs.ST_Y(value))})
            else:
                return None

    def _deserialize(self, value, attr, data):
        """Deserialize value. Concrete :class:`Field` classes should implement this method.

        :param value: The value to be deserialized.
        :param str attr: The attribute/key in `data` to be deserialized.
        :param dict data: The raw input data passed to the `Schema.load`.
        :raise ValidationError: In case of formatting or validation failure.
        :return: The deserialized value.

        .. versionchanged:: 2.0.0
            Added ``attr`` and ``data`` parameters.
        """
        if value is None:
            return value
        else:
            if isinstance(value, Geography):
                return {'latitude': db.session.scalar(geo_funcs.ST_X(value)), 'longitude': db.session.scalar(geo_funcs.ST_Y(value))}
            else:
                return None

In running the code:

from app.users.serialize import *
from app.model.meta.schema import Location
l = LocationSchema()
loc = Location(27.685994, 85.317815)
r = l.load(loc)
print r

The result I get is:

UnmarshalResult(data={}, errors={u'_schema': [u'Invalid input type.']})

Answer 1

You can override ModelConverter class and specify custom mapping for your geography field. See Jair Perrut's answer here How to use marshmallow to serialize a custom sqlalchemy field?

from marshmallow_sqlalchemy import ModelConverter
from marshmallow import fields

class GeoConverter(ModelConverter):
    SQLA_TYPE_MAPPING = ModelConverter.SQLA_TYPE_MAPPING.copy()
    SQLA_TYPE_MAPPING.update({
        Geography: fields.Str
    })

class Meta:
    model = Address
    sqla_session = session
    model_converter = GeoConverter