pydent.models.Plan¶

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.

__init__(name='MyPlan', status='planning')[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`([name, status])	Initialize self.
`add_data`(data)	Initializes fake attributes that correspond to data.
`add_operation`(operation)	Adds an operation to the Plan.
`add_operations`(operations)	Adds multiple operations to the Plan.
`all_data_associations`()
`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.
`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`]
`delete`()
`download_files`([outdir, overwrite])	Downloads all uploads associated with the plan.
`dump`([only, include, ignore, …])	Dump (serialize) the Aquarium model instance to JSON.
`estimate_cost`()	Estimates the cost of the plan on the Aquarium server.
`field_values`()
`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.
`find_wires`(src, dest)	Retrieves the wire between a source and destination FieldValues.
`get`(key)
`get_data_associations`(key)
`get_deserialized`(name)	Get deserialized data by name.
`get_relationships`()
`get_server_model_name`()
`get_tableized_name`()
`Plan.has_operation`
`interface`(session)	Creates a model interface from this class and a session.
`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.
`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.
`replan`()	Copies or replans the plan.
`reset_field`(name)	Reset the field descriptor to its placeholder value, returning the behavior.
`save`()
`show`()	Print the plan nicely.
`step`()	Steps a plan.
`submit`(user, budget)	Submits the Plan to the Aquarium server.
`to_save_json`()	Returns the json representation of the plan for saving and creating Plans on the Aquarium server.
`update`()
`validate`([raise_error])	Validates the plan.
`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.
`wire`(src, dest)	Creates a new wire between src and dest FieldValues.

Attributes

`DEFAULT_COPY_KEEP_UNANONYMOUS`
`GLOBAL_KEY`
`PRIMARY_KEY`
`SERVER_MODEL_NAME`
`counter`
`Plan.data_associations`
`fields`
`id`
`Plan.layout`
`Plan.operations`
`Plan.plan_associations`
`query_hook`
`rid`	rtype `int`
`session`	The connected session instance.
`Plan.status`
`Plan.wires`

_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’.

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

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 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

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