Models (`pydent.models`)¶

This module contains classes for various Aquarium objects.

Models are loaded and initialized from a AqSession instance.

sample = session.Sample.one()
last50 = session.Item.last(50)
first10 = session.SampleType.first(10)
mysamples = session.Sample.last(10, query={'user_id': 66})

Note

If using an interactive developer, type session. and hit [TAB] to view possible models. Most models have standard method interfaces, such as find, where, one, first, last, all.

From a model instance, attributes can be accessed directly from the model.

print(sample.name)
print(sample.id)
# "LJk12345"
# 3

Calling some attributes will automatically make a new request. For example, calling sample_type from sample will initialize a request for information about that sample’s sample_type:

print(sample.sample_type.name)
# "Plasmid Stock"

If we call sample_type again, a new request will not be made, rather the model will return the previously returned data. If a new request is desired, we can reset the field using the reset_field method:

assert sample.is_deserialized('sample_type')
sample.reset_field('sample_type')
assert not sample.is_deserialized('sample_type')


# now calling 'sample_type' again will initialize a new request
# which will be cached. This can be checked using `is_deserialized`
sample.sample_type
assert sample.is_deserialized('sample_type')

New in version 0.1.5a7: reset_field method added to reset fields.

New in version 0.1.5a7: is_deserialized can be called to check if a relation has already been deserialized

Models can be dumped to their JSON data or loaded from data

# dump the data
data = sample.dump()

# load from the data
sample2 = session.Sample.load(data)

Warning

Most model methods require an attached Session instance. Importing models from pydent.models will result in orphaned models. Preferrably, if you need to initialize or load new models, use session.<ModelName>(*args, **kwargs), replacing <ModelName> with the name of the model class. Alternatively, you can attach a Session instance using model.connect_to_session(session)

Model Classes¶

Operations¶

`Operation`([operation_type_id, …])	A Operation model.
`OperationType`(**data)	Represents an OperationType, which is the definition of a protocol in Aquarium.
`Code`(**data)	A Code model.
`Library`(**data)	A Library model.
`Job`(**data)	A Job model.
`JobAssociation`(**data)	A JobAssociation model.

Plans¶

`Plan`([name, status])	A Plan model.
`PlanAssociation`([plan_id, operation_id])	A PlanAssociation model.
`Wire`([source, destination])	A Wire model.

Inventory¶

`Item`([sample_id, sample, object_type, …])	A physical object in the lab, which a location and unique id.
`Collection`([object_type, location, …])	A Collection model, such as a 96-well plate, which contains many parts, each of which can be associated with a different sample.
`ObjectType`(**data)	A ObjectType model that represents the type of container an item is.
`Sample`([name, project, description, …])	A Sample model.
`SampleType`(**data)	A SampleType model.
`PartAssociation`([part_id, collection_id, …])	Represents a PartAssociation linking a part to a collection.

Data and IO¶

`DataAssociation`(**data)	A DataAssociation model.
`FieldValue`([name, role, parent_class, …])	A FieldValue model.
`FieldType`([name, ftype, array, choices, …])	A FieldType model.
`AllowableFieldType`([field_type, …])	A AllowableFieldType model.

User¶

`Account`(**data)	An Account model.
`Budget`(**data)	A Budget model.
`Group`(**data)	A Group model.
`Invoice`(**data)	A Invoice model.
`Membership`(**data)	The model initializer.
`User`()	A User model.
`UserBudgetAssociation`()	An association model between a User and a Budget.

Model Mixins¶

These classes provide some models with common methods such as saving or deleting models from the server or associating data.

`crud_mixin.CreateMixin`
`crud_mixin.DeleteMixin`
`crud_mixin.JSONDeleteMixin`
`crud_mixin.JSONSaveMixin`
`crud_mixin.SaveMixin`
`crud_mixin.UpdateMixin`
`data_associations.DataAssociatorMixin`	Mixin for handling data associations.
`field_value_mixins.FieldMixin`	Mixin for finding FieldType and FieldValue relationships.
`field_value_mixins.FieldTypeInterface`	An interface for things that have field types (i.e.
`field_value_mixins.FieldValueInterface`	A common interface for things (i.e.

Field Relationships¶

Field relationships are attribute descriptors that may call information from the Aquarium server if necesssary.

`BaseRelationship`(nested, callback, ref, attr)	Base class for relationships.
`BaseRelationshipAccessor`(name, field, …[, …])	Python descriptor that is returned by a field during attribute access.
`Function`(callback[, callback_args, …])	Calls a specified function upon attribute access.
`HasMany`(nested[, ref_model, attr, ref, …])	A relationship that establishes a One-to-Many relationship with another model.
`HasManyGeneric`(nested[, additional_args, …])	Establishes a One-to-Many relationship using ‘parent_id’ as the attribute to find other models.
`HasManyThrough`(nested, through[, attr, ref, …])	A relationship using an intermediate association model.
`HasOne`(nested[, attr, ref, callback, …])	HasOne initializer.
`HasOneFromMany`(nested[, ref_model, attr, …])	Returns a single model from a Many relationship.
`JSON`([many, data_key, allow_none, default])	Automatically serializes/deserializes JSON objects.
`Many`(nested[, ref, attr, callback, …])	Defines a many relationship with another model.
`One`(nested[, ref, attr, callback, …])	Defines a single relationship with another model.
`Raw`([many, data_key, allow_none, default])	Field that performs no serialization/deserialization.

Exceptions¶

FieldValidationError

Utilities¶

add_schema(cls)

Decorator that dynamically attaches a schema to a model.

class pydent.models.Account(**data)[source]

Bases: pydent.base.ModelBase

An Account model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.AccountSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

This specific usecase is that when copying whole plans, that the integrity of the inventory used in the operations is maintained. These are the items that refer to physical inventory in the laboratory and are referred to by their rids, and so it is important to that any of these inventory are always maintain their rids. Meaning in the lab, their is only ONE instance of the inventory. In Trident and Aquarium, there is only ONE instance of inventory that is referred to by its rid.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.AccountSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return a URI for this model using the attached session url and tableized model name. For example, http://aquarium.org/samples/. If no session is attached, use the ModelBase.DEFAULT_NAMESPACE key for the url.

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.AllowableFieldType(field_type=None, object_type=None, sample_type=None)[source]

Bases: pydent.base.ModelBase

A AllowableFieldType model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.AllowableFieldTypeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.AllowableFieldTypeSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Budget(**data)[source]

Bases: pydent.base.ModelBase

A Budget model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.BudgetSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.BudgetSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Code(**data)[source]

Bases: pydent.base.ModelBase

A Code model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.CodeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.CodeSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Collection(object_type=None, location=None, data_associations=None, parts=None, part_associations=None, **kwargs)[source]

Bases: pydent.models.inventory.ItemLocationMixin, pydent.models.data_associations.DataAssociatorMixin, pydent.models.crud_mixin.SaveMixin, pydent.models.controller_mixin.ControllerMixin, pydent.base.ModelBase

A Collection model, such as a 96-well plate, which contains many parts, each of which can be associated with a different sample.

Initialize a new Collection.

Changed in version 0.1.5a10: Advanced indexing added for setting and getting samples and data associations

Setting samples using new advanced indexing

object_type = session.ObjectType.one(query='rows > 2 AND columns > 2')
collection = session.Collection.new(object_type=object_type)

# assign sample '1' to (0, 0) row=0, column=0
collection[0, 0] = 1

# assign sample '2' to (1, 2) row=1, column=2
collection[1, 2] = 2

# assign sample '3234' to row 3
collection[3] = 3234

# assign sample '444' to column 1
collection[:, 1] = 444

# assign sample '6' to the whole collection
collection[:, :] = 6

# assign sample using Sample instance
collection[2, 2] = session.Sample.one()

Getting samples using new advanced indexing

# get 2d matrix of sample ids
print(collection.matrix)  # or collection.sample_id_matrix

# get 2d matrix of Samples assigned at each location
print(collection.sample_matrix)

# get 2d matrix of Parts assigned at each location
print(collection.part_matrix)

# get 2d matrix of PartAssociations assigned at each location
collection.part_associations_matrix

# get 2d matrix of values of DataAssociations at each location
collection.data_matrix

# get 2d matrix of DataAssociations at each location
collection.data_association_matrix

Assigning data to locations

To assign data, you can use the advanced indexing on the data_matrix

collection.data_matrix[0, 0] = {'key': 'value'}

collection.data_matrix[1] = {'key': 'value2'}

collection.associate_to('key', 'value3', 3, 3)

You can delete associations using the following:

# delete 3, 3
collection.delete_association_at('key', 3, 3)

# delete first three rows at column 3
collection.delete_association_at('key', slice(None, 3, None), 3)

# delete all of the 'key' associations
collection.delete_association_at('key', slice(None, None, None), slice(None, None, None))

Parameters

object_type (Optional[ObjectType]) –
location (Optional[str]) –
data_associations (Optional[List]) –
parts (Optional[List]) –
part_associations (Optional[List]) –
kwargs –

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.CollectionSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

as_item()[source]: Returns the Item object with the ID of this Collection.

assign_sample(sample_id, pairs)[source]

Assign sample id to the (row, column) pairs for the collection.

Parameters

sample_id (int) – the sample id to assign
pairs (List[Tuple[int, int]]) – list of (row, column) tuples

Returns

self

associate(key, value, upload=None, create_new=False, save=None)

Adds a data association with the key and value to this object.

Parameters

key (str) – Key of the association
value (dict | str | int | float) – a json serializable object
upload (File) – optional file to upload
create_new – if True (default) will create a new association instead of updating the existing association.

Tuype create_new

bool

Returns

newly created or updated data association

Return type

DataAssociation

associate_file(key, value, file, job_id=None)

Associate a file.

Parameters

key (str or json) – association key
value (str or json) – association value
file (file object) – file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

associate_file_from_path(key, value, filepath, job_id=None)

Associate a file from a filepath.

Parameters

key (str or json) – association key
value (str or json) – association value
filepath (str) – path to file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

controller_method(controller_method, table, model_id, data, params=None)

Method for create, updating, and deleting models.

Parameters

controller_method (str) – Name of the controller method
table (str) – Table name of model (e.g. ‘samples’ or ‘data_associations’)
model_id (Union[str, int, None]) – Optional model_id (not required for ‘post’)
data (Optional[dict]) – data
params – controller parameters

Returns

json formatted server response

Return type

dict

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

create()[source]: Create a new empty collection on the server.

property data_association_matrix

Return a view of.

DataAssociation

New in version 0.1.5a9.

Return type: MatrixMapping[DataAssociation]
Returns: collection as a view of DataAssociations

property data_matrix

Return a view of values from the.

DataAssociation

New in version 0.1.5a9.

Return type: MatrixMapping[Any]
Returns: collection as a view of DataAssociation values

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

make()

Makes the Item on the Aquarium server.

Requires this Item to be connected to a session.

property matrix

Returns the matrix of Samples for this Collection.

(Consider using samples of parts directly.)

Changed in version 0.1.5a9: Refactored using MatrixMapping

model_schema: alias of pydent.marshaller.base.CollectionSchema

no_getter(*_): Callback that always returns None.

part(row, col)[source]

Returns the part Item at (row, col) of this Collection (zero- based).

Return type: Item

property part_association_matrix

Return a view of part associations.

New in version 0.1.5a9.

Return type: MatrixMapping[PartAssociation]
Returns: collection as a view of PartAssociations

property part_matrix

Return a view of Item

New in version 0.1.5a9.

Return type: MatrixMapping[Item]
Returns: collection as a view of Items (Parts)

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

remove_sample(pairs)[source]

Clear the sample_id assigment in the (row, column) pairs for the collection.

Parameters: pairs (List[Tuple[int, int]]) – list of (row, column) tuples
Returns: self

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property sample_id_matrix

Return a view of sample_ids Sample

New in version 0.1.5a9.

Return type: MatrixMapping[int]
Returns: collection as a view of Sample.ids

property sample_matrix

Return a view of Sample

New in version 0.1.5a9.

Return type: MatrixMapping[Sample]
Returns: collection as a view of Samples

property session: The connected session instance.

update()[source]

Updates the item.

Will update the data associations and its location.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.DataAssociation(**data)[source]

Bases: pydent.models.crud_mixin.JSONDeleteMixin, pydent.models.crud_mixin.JSONSaveMixin, pydent.base.ModelBase

A DataAssociation model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.DataAssociationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.DataAssociationSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.FieldType(name=None, ftype=None, array=None, choices=None, operation_type=None, preferred_field_type_id=None, preferred_operation_type_id=None, required=None, routing=None, role=None, parent_class=None, parent_id=None, sample_type=None, aft_stype_and_objtype=(), allowable_field_types=None)[source]

Bases: pydent.models.field_value_mixins.FieldMixin, pydent.base.ModelBase

A FieldType model.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.FieldTypeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

find_field_parent(model_name, model_id)

Callback for finding operation_type or sample_type.

If parent_class does not match the expected nested model name (OperationType or SampleType), callback will return None

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

initialize_field_value(field_value=None, parent=None)[source]

Updates or initializes a new FieldValue from this FieldType.

Parameters: field_value (FieldValue) – optional FieldValue to update with this FieldType
Returns: updated FieldValue
Return type: FieldValue

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.FieldTypeSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.FieldValue(name=None, role=None, parent_class=None, parent_id=None, field_type=None, sample=None, value=None, item=None, container=None)[source]

Bases: pydent.models.field_value_mixins.FieldMixin, pydent.models.crud_mixin.JSONSaveMixin, pydent.models.crud_mixin.JSONDeleteMixin, pydent.base.ModelBase

A FieldValue model. One of the more complex models.

Changed in version 0.1.2: FieldValues no longer

have’wires_as_source’ or ‘wires_as_dest’ fields. Wires may only be accessed via plans only or via the FieldValue instance method ‘get_wires,’ which accesses the FieldValues operation and its Plan to obtain wires.

Parameters

value –
sample –
container –
item –

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.FieldValueSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

choose_item(first=True)[source]: Set the item associated with the field value.

compatible_items()[source]: Find items compatible with the field value.

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

find_field_parent(model_name, model_id)

Callback for finding operation_type or sample_type.

If parent_class does not match the expected nested model name (OperationType or SampleType), callback will return None

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

get_sid()[source]: The FieldValues sample identifier.

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.FieldValueSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset()[source]: Resets the inputs of the field_value.

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

set_field_type(field_type)[source]: Sets properties from a field_type.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Group(**data)[source]

Bases: pydent.base.ModelBase

A Group model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.GroupSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.GroupSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Invoice(**data)[source]

Bases: pydent.base.ModelBase

A Invoice model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.InvoiceSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.InvoiceSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Item(sample_id=None, sample=None, object_type=None, object_type_id=None, location=None)[source]

Bases: pydent.models.data_associations.DataAssociatorMixin, pydent.models.inventory.ItemLocationMixin, pydent.base.ModelBase

A physical object in the lab, which a location and unique id.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.ItemSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

as_collection()[source]

Returns the Collection object with the ID of this Item, which must be a collection.

Returns None if this Item is not a collection.

associate(key, value, upload=None, create_new=False, save=None)

Adds a data association with the key and value to this object.

Parameters

key (str) – Key of the association
value (dict | str | int | float) – a json serializable object
upload (File) – optional file to upload
create_new – if True (default) will create a new association instead of updating the existing association.

Tuype create_new

bool

Returns

newly created or updated data association

Return type

DataAssociation

associate_file(key, value, file, job_id=None)

Associate a file.

Parameters

key (str or json) – association key
value (str or json) – association value
file (file object) – file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

associate_file_from_path(key, value, filepath, job_id=None)

Associate a file from a filepath.

Parameters

key (str or json) – association key
value (str or json) – association value
filepath (str) – path to file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

property containing_collection

Returns the collection of which this Item is a part.

Returns the collection object if the Item is a part, otherwise returns None.

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

property is_collection

Returns True if this Item is a collection in a PartAssociation.

Note: this is not how Aquarium does this test in the collection? method.

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

make()

Makes the Item on the Aquarium server.

Requires this Item to be connected to a session.

model_schema: alias of pydent.marshaller.base.ItemSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

update()

Updates the item.

Will update the data associations and its location.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Job(**data)[source]

Bases: pydent.base.ModelBase

A Job model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.JobSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.JobSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.JobAssociation(**data)[source]

Bases: pydent.base.ModelBase

A JobAssociation model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.JobAssociationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.JobAssociationSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Library(**data)[source]

Bases: pydent.base.ModelBase

A Library model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.LibrarySchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

code(accessor)[source]: Reminant from previous API.

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.LibrarySchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Membership(**data)[source]

Bases: pydent.base.ModelBase

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.MembershipSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.MembershipSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.ObjectType(**data)[source]

Bases: pydent.models.crud_mixin.SaveMixin, pydent.base.ModelBase

A ObjectType model that represents the type of container an item is.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.ObjectTypeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.ObjectTypeSchema

new_item(sample)[source]

Create a new item.

New in version 0.1.5a13.

Parameters: sample (Union[int, Sample]) – the sample id
Returns: the new item

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Operation(operation_type_id=None, operation_type=None, status=None, x=0, y=0)[source]

Bases: pydent.models.field_value_mixins.FieldValueInterface, pydent.models.data_associations.DataAssociatorMixin, pydent.base.ModelBase

A Operation model.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.OperationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

add_to_input_array(name, sample=None, item=None, value=None, container=None)[source]

Creates and adds a new input FieldValue. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldType/FieldValue
sample (Sample) – an existing Sample
item (Item) – an existing Item
value (string|integer) – a string or number value
container (ObjectType) – an existing ObjectType

Returns

the newly created FieldValue

Return type

FieldValue

add_to_output_array(name, sample=None, item=None, value=None, container=None)[source]

Creates and adds a new output FieldValue. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldType/FieldValue
sample (Sample) – an existing Sample
item (Item) – an existing Item
value (string|integer) – a string or number value
container (ObjectType) – an existing ObjectType

Returns

the newly created FieldValue

Return type

FieldValue

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

associate(key, value, upload=None, create_new=False, save=None)

Adds a data association with the key and value to this object.

Parameters

key (str) – Key of the association
value (dict | str | int | float) – a json serializable object
upload (File) – optional file to upload
create_new – if True (default) will create a new association instead of updating the existing association.

Tuype create_new

bool

Returns

newly created or updated data association

Return type

DataAssociation

associate_file(key, value, file, job_id=None)

Associate a file.

Parameters

key (str or json) – association key
value (str or json) – association value
file (file object) – file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

associate_file_from_path(key, value, filepath, job_id=None)

Associate a file from a filepath.

Parameters

key (str or json) – association key
value (str or json) – association value
filepath (str) – path to file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

field_value(name, role)[source]

Returns FieldValue with name and role.

Return None if not found.

field_value_array(name, role)[source]: Returns FieldValue array with name and role.

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

get_field_type(name, role)

Returns a pydent.models.FieldType by its name and role from the instance’s metaclass.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

metatypes field type or None if not found

Return type

FieldType | None

get_field_types(name=None, role=None)

Returns a list of pydent.models.FieldType by their name and role from the instance’s metaclass.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

list of field types

Return type

list

get_field_value(name, role=None)

Returns a pydent.models.FieldValue by its name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

the field value or None if not found

Return type

FieldValue | None

get_field_value_array(name, role=None)

Returns a list of pydent.models.FieldValue by their name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

list of field values

Return type

list

get_metatype()

Returns the instance’s metatype.

The metatype is either pydent.models.SampleType or pydent.models.OperationType). The metatype class name is stored as METATYPE in the class definition.

Returns: the metatype
Return type: ModelBase

get_routing()[source]

Returns the routing dictionary for this instance.

Returns: routing dictionary
Return type: dict

init_field_values()[source]: Initialize the FieldValue from the FieldType of the parent Operation type.

input(name)[source]: Returns the input FieldValue by name.

property inputs: Return a list of all input FieldValues

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.OperationSchema

new_field_value(name, role=None, values_dict=None)

Instantiates a new pydent.models.FieldValue from a name and role. The should be a field type with the name and role in the metatype. Optionally, a values dictionary may be provided with the following format:

values_dict = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

Parameters

name (basestring) – its name
role (basestring) – its role
values_dict (dict) – values to set the new field value

Returns

the new field value

Return type

FieldValue

new_field_value_from_field_type(field_type, values_dict=None)

Instantiates a new pydent.models.FieldValue from a.

pydent.models.FieldType instance. Optionally, a values dictionary may be provided with the following format:

values_dict = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

Parameters

field_type (FieldType) – field type to instantiate the field value
values_dict (dict) – values to set the new field value

Returns

the new field value

Return type

FieldValue

no_getter(*_): Callback that always returns None.

output(name)[source]: Returns the output FieldValue by name.

property outputs: Return a list of all output FieldValues

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

safe_get_field_type(fv)

Safely returns the field value’s pydent.models.FieldType from the model.

If the field value has no reference to the field type, its metatype (e.g. pydent.models.SampleType or pydent.models.OperationType) is used to recover the field type.

property session: The connected session instance.

set_field_value(name, role, values)

Sets a field value name and role using a dictionary, as in the following:

values = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

set_field_value_array(name, role, values_array)

Sets an array of field values by name and role using an array of dictionaries, as in the following:

values_array = [{
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}]

set_input(name, sample=None, item=None, value=None, container=None, object_type=None)[source]

Sets a input FieldValue to a value. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldValue/FieldType
sample (Sample) – an existing Sample
item (Item) – an existing Item
value (string|integer) – a string or number value
container (ObjectType) – an existing ObjectType

Returns

the existing FieldValue modified

Return type

FieldValue

set_input_array(name, values)[source]

Sets input FieldValue array using values. Values should be a list of dictionaries containing sample, item, container, or values keys. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldType/FieldValues being modified
values (list) – list of dictionary of values to set (e.g. [{“sample”: mysample}, {“item”: myitem}])

Returns

the list of modified FieldValues

Return type

list

set_output(name, sample=None, item=None, value=None, container=None, object_type=None)[source]

Sets a output FieldValue to a value. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldValue/FieldType
sample (Sample) – an existing Sample
item (Item) – an existing Item
value (string|integer) – a string or number value
container (ObjectType) – an existing ObjectType

Returns

the existing FieldValue modified

Return type

FieldValue

set_output_array(name, values)[source]

Sets output FieldValue array using values. Values should be a list of dictionaries containing sample, item, container, or values keys. When setting values to items/samples/containers, the item/sample/container must be saved.

Parameters

name (string) – name of the FieldType/FieldValues being modified
values (list) – list of dictionary of values to set (e.g. [{“sample”: mysample}, {“item”: myitem}])

Returns

the list of modified FieldValues

Return type

list

show(pre='')[source]: Print the operation nicely.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.OperationType(**data)[source]

Bases: pydent.models.field_value_mixins.FieldTypeInterface, pydent.models.crud_mixin.SaveMixin, pydent.base.ModelBase

Represents an OperationType, which is the definition of a protocol in Aquarium.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.OperationTypeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

field_type(name, role)[source]

Returns a pydent.models.FieldType by its name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

the field type or None if not found

Return type

FieldType | None

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.OperationTypeSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

save()[source]

Saves the Operation Type to the Aquarium server.

Requires this Operation Type to be connected to a session.

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.PartAssociation(part_id=None, collection_id=None, row=None, column=None)[source]

Bases: pydent.models.crud_mixin.JSONSaveMixin, pydent.base.ModelBase

Represents a PartAssociation linking a part to a collection.

Collections contain many parts, each of which can refer to a different sample.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.PartAssociationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.PartAssociationSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Plan(name='MyPlan', status='planning')[source]

Bases: pydent.models.data_associations.DataAssociatorMixin, pydent.models.crud_mixin.SaveMixin, pydent.models.crud_mixin.DeleteMixin, pydent.base.ModelBase

A Plan model.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_get_wire_dict(wires)[source]: Return all wires in the plan grouped by the wire identifier.

_model_schema: alias of pydent.marshaller.base.PlanSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

add_operation(operation)[source]

Adds an operation to the Plan.

Parameters: operation (Operation) – Operation to add
Returns: None
Return type: None

add_operations(operations)[source]

Adds multiple operations to the Plan.

Parameters: operations (list) – list of Operations
Returns: None
Return type: None

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

associate(key, value, upload=None, create_new=False, save=None)

Adds a data association with the key and value to this object.

Parameters

key (str) – Key of the association
value (dict | str | int | float) – a json serializable object
upload (File) – optional file to upload
create_new – if True (default) will create a new association instead of updating the existing association.

Tuype create_new

bool

Returns

newly created or updated data association

Return type

DataAssociation

associate_file(key, value, file, job_id=None)

Associate a file.

Parameters

key (str or json) – association key
value (str or json) – association value
file (file object) – file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

associate_file_from_path(key, value, filepath, job_id=None)

Associate a file from a filepath.

Parameters

key (str or json) – association key
value (str or json) – association value
filepath (str) – path to file to create Upload
job_id (int) – optional job_id to associate the Upload

Returns

new data association

Return type

DataAssociation

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

download_files(outdir=None, overwrite=True)[source]

Downloads all uploads associated with the plan. Downloads happen ansynchrounously.

Parameters

outdir – output directory for downloaded files
overwrite – whether to overwrite files if they exist

Returns

None

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

estimate_cost()[source]

Estimates the cost of the plan on the Aquarium server. This is necessary before plan submission.

Returns: cost
Return type: dict

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

find_wires(src, dest)[source]

Retrieves the wire between a source and destination FieldValues.

Parameters

src (FieldValue) – source FieldValue
dest (FieldValue) – destination FieldValue

Returns

array of wires between src and dest FieldValues (determined by rid)

Return type

array of wires

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)[source]

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.PlanSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

replan()[source]

Copies or replans the plan.

Returns a plan copy

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

show()[source]: Print the plan nicely.

step()[source]: Steps a plan.

submit(user, budget)[source]

Submits the Plan to the Aquarium server.

Parameters

user (User) – User to submit the Plan
budget (Budget) – Budget to use for the Plan

Returns

JSON

Return type

dict

to_save_json()[source]

Returns the json representation of the plan for saving and creating Plans on the Aquarium server.

Returns: JSON
Return type: dict

property uri

Return type: str
Returns: the instance URI

validate(raise_error=True)[source]

Validates the plan.

Parameters: raise_error (boolean) – If True, raises an AquariumModelException. If false, returns the error messages.
Returns: list of error messages
Return type: array

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

wire(src, dest)[source]

Creates a new wire between src and dest FieldValues. Returns the new wire if it does not exist in the plan. If the wire already exists and error_if_exists is True, then the existing wire is returned. Else an exception is raised.

Parameters

src (FieldValue) – source field value (the input of the wire)
dest (FieldValue) – destination field value (the output of the wire)
error_if_exists (boolean) – Raise an error if the Wire already exists in the plan.

Returns

Newly created wire or existing wire (if exists and error_if_exists == False)

Return type

Wire

class pydent.models.PlanAssociation(plan_id=None, operation_id=None)[source]

Bases: pydent.base.ModelBase

A PlanAssociation model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.PlanAssociationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.PlanAssociationSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Sample(name=None, project=None, description=None, sample_type=None, sample_type_id=None, properties=None, field_values=None)[source]

Bases: pydent.models.field_value_mixins.FieldValueInterface, pydent.base.ModelBase

A Sample model.

Parameters

name –
project –
description –
sample_type_id –
properties –

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.SampleSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy()[source]: Return a copy of this sample.

create()[source]

Creates this sample in the Aquarium instance if the sample has all fields required by the sample type. Uses is_savable to check for missing fields.

Changed in version 0.1.5a17: Raises AquariumModelError if sample is missing required properties

Return type: List[Sample]
Returns: the list of saved samples
Raises: AquariumModelError – if required FieldValues are missing.

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

field_value(name)[source]

Returns the FieldValue associated with the sample by its name. If the there is more than one FieldValue with the same name (as in field_value arrays), it will return the first FieldValue. See the.

Sample.field_value_array() method.

Parameters: name (str) – name of the field value
Returns: the field value
Return type: FieldValue

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

get_field_type(name, role)

Returns a pydent.models.FieldType by its name and role from the instance’s metaclass.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

metatypes field type or None if not found

Return type

FieldType | None

get_field_types(name=None, role=None)

Returns a list of pydent.models.FieldType by their name and role from the instance’s metaclass.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

list of field types

Return type

list

get_field_value(name, role=None)

Returns a pydent.models.FieldValue by its name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

the field value or None if not found

Return type

FieldValue | None

get_field_value_array(name, role=None)

Returns a list of pydent.models.FieldValue by their name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

list of field values

Return type

list

get_metatype()

Returns the instance’s metatype.

The metatype is either pydent.models.SampleType or pydent.models.OperationType). The metatype class name is stored as METATYPE in the class definition.

Returns: the metatype
Return type: ModelBase

get_routing()

Returns the routing dictionary for this instance.

Returns: routing dictionary
Return type: dict

property identifier: Return the identifier used by Aquarium in autocompletes.

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

is_savable(do_raise=True)[source]

Checks whether this sample has fields required by the sample type.: If so, the sample can be saved or updated.

New in version 0.1.5a17.

Parameters: do_raise (bool) – raise an exception when required field values are missing
Return type: Tuple[bool, List[str]]
Returns: a boolean whether there are errors, and list of error messages
Raises: AquariumModelError – if do_raise is True and required fields are missing

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

merge()[source]

Merge sample by name. If a sample with the same name and sample_type_id is found on the server, update that model and save the updated data to the server. Else, create a new sample on the server.

Parameters: sample – sample to merge.
Returns: True if merged, False otherwise

model_schema: alias of pydent.marshaller.base.SampleSchema

new_field_value(name, role=None, values_dict=None)

values_dict = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

Parameters

name (basestring) – its name
role (basestring) – its role
values_dict (dict) – values to set the new field value

Returns

the new field value

Return type

FieldValue

new_field_value_from_field_type(field_type, values_dict=None)

Instantiates a new pydent.models.FieldValue from a.

pydent.models.FieldType instance. Optionally, a values dictionary may be provided with the following format:

values_dict = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

Parameters

field_type (FieldType) – field type to instantiate the field value
values_dict (dict) – values to set the new field value

Returns

the new field value

Return type

FieldValue

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

safe_get_field_type(fv)

Safely returns the field value’s pydent.models.FieldType from the model.

If the field value has no reference to the field type, its metatype (e.g. pydent.models.SampleType or pydent.models.OperationType) is used to recover the field type.

save()[source]

Saves the sample, either by creating a new sample (if id=None) or updating the existing sample on the server.

Changed in version 0.1.5a17: Raises AquariumModelError if sample is missing required properties

Returns

property session: The connected session instance.

set_field_value(name, role, values)

Sets a field value name and role using a dictionary, as in the following:

values = {
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}

set_field_value_array(name, role, values_array)

Sets an array of field values by name and role using an array of dictionaries, as in the following:

values_array = [{
    "value": None,
    "sample": mysample,
    "item": myitem,
    "object_type": None
}]

update()[source]

Updates the sample on the server.

Changed in version 0.1.5a17: Raises AquariumModelError if sample is missing required properties

Return type: Sample
Returns

update_properties(prop_dict)[source]

Update the FieldValues properties for this sample.

Parameters: prop_dict – values to update
Returns: self
Return type: Sample

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.SampleType(**data)[source]

Bases: pydent.models.field_value_mixins.FieldTypeInterface, pydent.models.crud_mixin.JSONSaveMixin, pydent.base.ModelBase

A SampleType model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.SampleTypeSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

field_type(name, role=None)[source]

Returns a pydent.models.FieldType by its name and role.

Parameters

name (basestring) – its name
role (basestring) – its role

Returns

the field type or None if not found

Return type

FieldType | None

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.SampleTypeSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Upload(job_id=None, file=None)[source]

Bases: pydent.base.ModelBase

An Upload model.

Create a new upload.

Parameters

job_id (int) – job id to associate the upload to
file (file object) – file to upload

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

static _download_file_from_url(url, outpath)[source]

Downloads a file from a url.

Parameters

url (str) – url of file
outpath (str) – filepath of out file

Returns

http response

Return type

str

static _download_files(uploads, outdir, overwrite)[source]

Downloads uploaded file from list of Upload models.

Parameters

uploads (list) – list of Uploads
outdir (str) – path to output directory to save downloaded files (defaults to current directory)
overwrite (bool) – if True, will overwrite existing files (default: True)

Returns

list of filepaths

Return type

list

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.UploadSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

static async_download(uploads, outdir=None, overwrite=True)[source]

Asynchronously downloads from list of Upload models.

Parameters

uploads (list) – list of Uploads
outdir (str) – path to output directory to save downloaded files
overwrite (bool) – if True, will overwrite existing files

Returns

list of filepaths

Return type

list

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

create()[source]: Save the upload to the server.

property data: Return the data associated with the upload.

download(outdir=None, filename=None, overwrite=True)[source]

Downloads the uploaded file to the specified output directory. If no output directory is specified, the file will be downloaded to the current directory.

Parameters

outdir (Optional[str]) – path of directory of output file (default is current directory)
outfile – filename of output file (defaults to upload_filename)
overwrite (bool) – whether to overwrite file if it already exists

Returns

filepath of the downloaded file

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

fetch(outdir=None, filename=None, overwrite=True)[source]

Alias for download

Parameters

outdir (Optional[str]) – path of directory of output file (default is current directory)
outfile – filename of output file (defaults to upload_filename)
overwrite (bool) – whether to overwrite file if it already exists

Returns

filepath of the downloaded file

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.UploadSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.User[source]

Bases: pydent.base.ModelBase

A User model.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.UserSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.UserSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.UserBudgetAssociation[source]

Bases: pydent.base.ModelBase

An association model between a User and a Budget.

The model initializer.

Parameters: data (dict) – data to add to the model

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.UserBudgetAssociationSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.UserBudgetAssociationSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

class pydent.models.Wire(source=None, destination=None)[source]

Bases: pydent.models.crud_mixin.DeleteMixin, pydent.base.ModelBase

A Wire model.

_check_for_session()

Raises error if model is not connected to a session.

:raises NoSessionError

classmethod _flatten_deserialized_data(models, memo)

Flattens all of the relationships found in the models, returning a rid: model dictionary.

Return type: dict

_get_data(): Return the model’s data.

_get_deserialized_data(): Return the deserialized model data.

_model_schema: alias of pydent.marshaller.base.WireSchema

property _primary_key: Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.

_rid_dict(): Dictionary of all models attached to this model keyed by their rid.

add_data(data): Initializes fake attributes that correspond to data.

anonymize()

Resets the primary key of the model and assigns a new rid.

Metatypes cannot be annonymized.

Returns: self

append_to_many(name, model)

Appends a model to the many relationship.

Parameters

name (str) – name of the relationship or attribute
model (ModelBase) – model to append

Returns

None

Return type

None

connect_to_session(session)

Connect model to a session.

Parameters

session (SessionABC) – the AqSession

Returns

None

Raises

SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type

copy(keep=None)

Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g. OperationType, SampleType, FieldType) or class name is found in list of ‘keep’.

By default, inventory classes such as Sample, Item, and Collection are ‘kept’.

Similarly, any metatype model must also maintain their rid.

Parameters: keep (Optional[bool]) – list of model classes (as a list of strings) to keep un-anonymous
Return type: ModelBase
Returns: copied model

delete()[source]

Permanently deletes the wire instance on the Aquarium server.

Returns
Return type

does_wire(source, destination)[source]

Checks whether this Wire is a wire between the source and destination FieldValues.

If any of the source or destination FieldValues are None, returns False.

dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)

Dump (serialize) the Aquarium model instance to JSON.

Parameters

only (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – dump only the provided keys
include (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – include the provided nested dump keys
ignore (Union[str, List[str], Tuple[str], Dict[str, Any], None]) – ignore the provided keys
include_model_type (bool) – if True, include the model class type for each entry using the __model__ key
include_uri (bool) – if True, include a URI using the session URL and the tableized model class name using the __uri__ key. If a session is not attached, look for the url namespace in the ModelBase.DEFAULT_NAMESPACE class attribute, as in http://aquarium.org/samples/10.

Return type

dict

Returns

serialized model instance

classmethod find(session, model_id)

Finds a model instance by its model_id.

Return type: ModelBase

find_callback(model_name, model_id)

Finds a model using the model interface and model_id.

Used to find models in model relationships.

Return type: ModelBase

get_deserialized(name)

Get deserialized data by name.

Deprecated since version 0.1.5a7: method will be removed in 0.2. Use self._get_deserialized_data[name] instead.

Parameters: name – name of attribute
Returns

classmethod interface(session)

Creates a model interface from this class and a session.

This method can be overridden in model definitions for special cases.

Return type: Union[QueryInterface, BrowserInterface]

is_deserialized(name)

Check if a given key has already been deserialized.

New in version 0.1.5a7: Method added

Parameters: name (str) – name of the attribute
Return type: bool
Returns: True if key has been deserialized.

classmethod load(*args, **kwargs)

Deserialize the data to a model.

Parameters: data (dict) – data to deserialize
Returns: the deserialized model
Return type: SchemaModel

classmethod load_from(data, owner=None)

Create a new model instance from loaded attributes.

‘obj’ should have a o

Return type: Union[List[ModelBase], ModelBase]

model_schema: alias of pydent.marshaller.base.WireSchema

no_getter(*_): Callback that always returns None.

refresh()

Refresh this model from data from the server.

Returns: self
Return type: self

reload(data)

Reload model attributes from new data.

Parameters: data (dict) – data to update model instance
Returns: model instance
Return type: ModelBase

reset_field(name)

Reset the field descriptor to its placeholder value, returning the behavior.

New in version 0.1.5a7: Method added to reset deserialized attributes

Parameters: name (str) – name of the attribute
Returns: None

property session: The connected session instance.

show(pre='')[source]: Show the wire nicely.

property uri

Return type: str
Returns: the instance URI

classmethod where(session, params)

Finds a list of models by some parameters.

Return type: Optional[List[ModelBase]]

where_callback(model_name, *args, **kwargs)

Finds models using a model interface and a set of parameters.

Used to find models in model relationships.

Return type: Optional[List[ModelBase]]

Models (pydent.models)¶

Model Classes¶

Operations¶

Plans¶

Inventory¶

Data and IO¶

User¶

Model Mixins¶

Field Relationships¶

Exceptions¶

Utilities¶

Models (`pydent.models`)¶