Base (pydent.base)¶
Aquarium model baseclass
This module contains the base classes for Trident models.
Trident models load from JSON and dump to JSON.
This is accomplished by adding the @add_schema decorator to classes
inherited by the Base class.
Using @add_schema dynamically creates a model schema that handles dumping
and loading.
Features of Trident models:
load - models can be loaded from JSON data. Hierarchical JSON is loaded intelligently.
Sample.load({"name": "MyPrimer", "sample_type": {"name": "Primer", ...} })
# => <Sample(name="MyPrimer", sample_type=<SampleType(name="Primer")>)>
- dump - models can be dumped to JSON. Dependent models and relationships can be
dumped as well.
s.dump(include=("sample_type"))
relationships - models relationships are stored
s = Sample.load(
{"name": "MyPrimer",
"sample_type_id": 1}
)
primer_type = s.sample_type
-
class
pydent.base.ModelBase(**data)[source]¶ Bases:
pydent.marshaller.base.SchemaModelBase class for Aquarium models. Subclass of.
pydent.marshaller.MarshallerBasecreates instances from JSON using load
contains a reference to the
pydent.session.aqsession.AqSessioninstance that loaded this model
The model initializer.
- Parameters
data (dict) – data to add to the model
-
_check_for_session()[source]¶ Raises error if model is not connected to a session.
:raises NoSessionError
-
classmethod
_flatten_deserialized_data(models, memo)[source]¶ 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.
-
property
_primary_key¶ Returns the primary key (e.g. ‘id’) or the rid if id does not exist or is None.
-
add_data(data)¶ Initializes fake attributes that correspond to data.
-
anonymize()[source]¶ Resets the primary key of the model and assigns a new rid.
Metatypes cannot be annonymized.
- Returns
self
-
append_to_many(name, model)[source]¶ 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)[source]¶ Connect model to a session.
- Parameters
session (
SessionABC) – theAqSession- Returns
None
- Raises
SessionAlreadySet – if session is already set
NoSessionError – if session is not a SessionABC type
-
copy(keep=None)[source]¶ 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
- Returns
copied model
-
dump(only=None, include=None, ignore=None, include_model_type=False, include_uri=False)[source]¶ Dump (serialize) the Aquarium model instance to JSON.
- Parameters
only (
Union[str,List[str],Tuple[str],Dict[str,Any],None]) – dump only the provided keysinclude (
Union[str,List[str],Tuple[str],Dict[str,Any],None]) – include the provided nested dump keysignore (
Union[str,List[str],Tuple[str],Dict[str,Any],None]) – ignore the provided keysinclude_model_type (
bool) – if True, include the model class type for each entry using the __model__ keyinclude_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
-
find_callback(model_name, model_id)[source]¶ Finds a model using the model interface and model_id.
Used to find models in model relationships.
- Return type
-
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.
- 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)[source]¶ Deserialize the data to a model.
- Parameters
data (dict) – data to deserialize
- Returns
the deserialized model
- Return type
-
classmethod
load_from(data, owner=None)[source]¶ Create a new model instance from loaded attributes.
‘obj’ should have a o
-
reload(data)[source]¶ Reload model attributes from new data.
- Parameters
data (dict) – data to update model instance
- Returns
model instance
- Return type
-
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