pydent.models.Item¶

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.

__init__(sample_id=None, sample=None, object_type=None, object_type_id=None, location=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`([sample_id, sample, object_type, …])	Initialize self.
`add_data`(data)	Initializes fake attributes that correspond to data.
`anonymize`()	Resets the primary key of the model and assigns a new rid.
`append_to_many`(name, model)	Appends a model to the many relationship.
`as_collection`()	Returns the Collection object with the ID of this Item, which must be a collection.
`associate`(key, value[, upload, create_new, save])	Adds a data association with the key and value to this object.
`associate_file`(key, value, file[, job_id])	Associate a file.
`associate_file_from_path`(key, value, filepath)	Associate a file from a filepath.
`connect_to_session`(session)	Connect model to a session.
`copy`([keep])	Provides a deepcopy of the model, but annonymizes the primary and global keys unless class is a metatype (e.g.
`create`()
`create_interface`()	rtype `Union`[`QueryInterface`, `BrowserInterface`]
`dump`([only, include, ignore, …])	Dump (serialize) the Aquarium model instance to JSON.
`find`(session, model_id)	Finds a model instance by its model_id.
`find_callback`(model_name, model_id)	Finds a model using the model interface and model_id.
`get`(key)
`get_data_associations`(key)
`get_deserialized`(name)	Get deserialized data by name.
`get_relationships`()
`get_server_model_name`()
`get_tableized_name`()
`interface`(session)	Creates a model interface from this class and a session.
`is_deleted`()
`is_deserialized`(name)	Check if a given key has already been deserialized.
`load`(args, *kwargs)	Deserialize the data to a model.
`load_from`(data[, owner])	Create a new model instance from loaded attributes.
`make`()	Makes the Item on the Aquarium server.
`no_getter`(*_)	Callback that always returns None.
`one`(session, query, **kwargs)	rtype `ModelBase`
`one_callback`(model_name, args, *kwargs)	rtype `ModelBase`
`print`()
`refresh`()	Refresh this model from data from the server.
`reload`(data)	Reload model attributes from new data.
`reset_field`(name)	Reset the field descriptor to its placeholder value, returning the behavior.
`save`()
`update`()	Updates the item.
`where`(session, params)	Finds a list of models by some parameters.
`where_callback`(model_name, args, *kwargs)	Finds models using a model interface and a set of parameters.

Attributes

`DEFAULT_COPY_KEEP_UNANONYMOUS`
`GLOBAL_KEY`
`PRIMARY_KEY`
`SERVER_MODEL_NAME`
`collection`
`Item.collections`
`containing_collection`	Returns the collection of which this Item is a part.
`counter`
`Item.data`
`Item.data_associations`
`fields`
`id`
`is_collection`	Returns True if this Item is a collection in a PartAssociation.
`Item.object_type`
`part_association`
`Item.part_associations`
`query_hook`
`rid`	rtype `int`
`Item.sample`
`session`	The connected session instance.

_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’.

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]

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 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]]