pydent.models.Operation¶

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.

__init__(operation_type_id=None, operation_type=None, status=None, x=0, y=0)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`([operation_type_id, …])	Initialize self.
`add_data`(data)	Initializes fake attributes that correspond to data.
`add_to_input_array`(name[, sample, item, …])	Creates and adds a new input `FieldValue`.
`add_to_output_array`(name[, sample, item, …])	Creates and adds a new output `FieldValue`.
`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_interface`()	rtype `Union`[`QueryInterface`, `BrowserInterface`]
`dump`([only, include, ignore, …])	Dump (serialize) the Aquarium model instance to JSON.
`field_value`(name, role)	Returns `FieldValue` with name and role.
`field_value_array`(name, role)	Returns `FieldValue` array with name and role.
`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_field_type`(name, role)	Returns a `pydent.models.FieldType` by its name and role from the instance’s metaclass.
`get_field_types`([name, role])	Returns a list of `pydent.models.FieldType` by their name and role from the instance’s metaclass.
`get_field_value`(name[, role])	Returns a `pydent.models.FieldValue` by its name and role.
`get_field_value_array`(name[, role])	Returns a list of `pydent.models.FieldValue` by their name and role.
`get_metatype`()	Returns the instance’s metatype.
`get_relationships`()
`get_routing`()	Returns the routing dictionary for this instance.
`get_server_model_name`()
`get_tableized_name`()
`init_field_values`()	Initialize the `FieldValue` from the `FieldType` of the parent `Operation` type.
`input`(name)	Returns the input `FieldValue` by name.
`input_array`(name)
`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.
`new_field_value`(name[, role, values_dict])	Instantiates a new `pydent.models.FieldValue` from a name and role.
`new_field_value_from_field_type`(field_type)	Instantiates a new `pydent.models.FieldValue` from a.
`no_getter`(*_)	Callback that always returns None.
`one`(session, query, **kwargs)	rtype `ModelBase`
`one_callback`(model_name, args, *kwargs)	rtype `ModelBase`
`output`(name)	Returns the output `FieldValue` by name.
`output_array`(name)
`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.
`safe_get_field_type`(fv)	Safely returns the field value’s `pydent.models.FieldType` from the model.
`set_field_value`(name, role, values)	Sets a field value name and role using a dictionary, as in the following:
`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:
`set_input`(name[, sample, item, value, …])	Sets a input `FieldValue` to a value.
`set_input_array`(name, values)	Sets input `FieldValue` array using values.
`set_output`(name[, sample, item, value, …])	Sets a output `FieldValue` to a value.
`set_output_array`(name, values)	Sets output `FieldValue` array using values.
`show`([pre])	Print the operation nicely.
`update_field_values`(value_dict[, role])
`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`
`METATYPE`
`PRIMARY_KEY`
`SERVER_MODEL_NAME`
`counter`
`Operation.data_associations`
`Operation.field_values`
`fields`
`id`
`inputs`	Return a list of all input `FieldValues`
`Operation.job_associations`
`Operation.jobs`
`Operation.operation_type`
`outputs`	Return a list of all output `FieldValues`
`plan`
`Operation.plan_associations`
`Operation.plans`
`predecessors`
`rid`	rtype `int`
`Operation.routing`
`session`	The connected session instance.
`Operation.status`
`successors`

_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’.

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

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 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]]