entity_management.base¶

Base simulation entities

Functions

`attributes`([attr_dict, repr])	decorator to simplify creation of classes that have args and kwargs
`custom_getattr`(obj, name)	Overload of __getattribute__ to trigger instantiation of Nexus object if the attribute is NotInstantiated

Classes

`BlankNode`()	Blank node.
`BrainLocation`(*, brainRegion)	Brain location.
`Derivation`(*, entity)	Derivation.
`Frozen`()	Utility class making derived classed immutable.
`Identifiable`()	Represents collapsed/lazy loaded entity having type and id.
`OntologyTerm`(*, url[, label])	Ontology term such as brain region or species
`QuantitativeValue`(*, value[, unitText, unitCode])	External resource representations, this can be a file or a folder on gpfs
`Subject`(*[, species, strain])	Subject.
`Unconstrained`(*, json)	Shapeless data.

class entity_management.base.BlankNode¶

Bases: Frozen

Blank node.

class entity_management.base.BrainLocation(*, brainRegion)¶

Bases: BlankNode

Brain location.

Parameters:: brainRegion (OntologyTerm) – Brain region ontology term.

class entity_management.base.Derivation(*, entity)¶

Bases: BlankNode

Derivation.

class entity_management.base.Frozen¶

Bases: object

Utility class making derived classed immutable. Use evolve method to introduce changes.

evolve(**changes)¶

Create new instance of the frozen(immutable) object with changes applied.

Parameters:: changes – Keyword changes in the new copy, should be a subset of class constructor(__init__) keyword arguments.
Returns:: New instance of the same class with changes applied.

class entity_management.base.Identifiable¶

Bases: Frozen

Represents collapsed/lazy loaded entity having type and id. Access to any attributes will load the actual entity from nexus and forward property requests to that entity.

as_json_ld(include_rev=False)¶: Get json-ld representation of the Entity Return json with added json-ld properties such as @context and @type

clone(**changes)¶

Create new instance of the frozen(immutable) object with changes applied.

Note: A clone is stripped of its id if present.

Parameters:: changes – Keyword changes in the new copy, should be a subset of class constructor(__init__) keyword arguments.
Returns:: New instance of the same class with changes applied.

deprecate(sync_index=False, use_auth=None)¶

Mark entity as deprecated. Deprecated entities are not possible to retrieve by name.

Parameters:: use_auth (str) – OAuth token in case access is restricted. Token should be in the format for the authorization header: Bearer VALUE.

evolve(**changes)¶

Create new instance of the frozen(immutable) object with changes applied.

Parameters:: changes – Keyword changes in the new copy, should be a subset of class constructor(__init__) keyword arguments.
Returns:: New instance of the same class with changes applied.

classmethod from_id(resource_id, *, on_no_result=None, cross_bucket=False, resolve_context=False, base=None, org=None, proj=None, use_auth=None, **kwargs)¶

Load entity from resource id.

Parameters:

resource_id (str) – id of the entity to load.
on_no_result (Callable) – A function to be called when no result found. It will receive resource_id as a first argument.
cross_bucket (bool) – Use the resolvers instead of the resources endpoint. Default False.
resolve_context (bool) – Resolve ontological term curies using the resource’s context. Default False.
kwargs – Keyword arguments which will be forwarded to on_no_result function.
use_auth (str) – OAuth token in case access is restricted. Token should be in the format for the authorization header: Bearer VALUE.

classmethod from_url(url, *, resolve_context=False, base=None, org=None, proj=None, use_auth=None)¶

Load entity from url.

Parameters:

url (str) – Full url to the entity in nexus. _self content is a valid full URL.
resolve_context (bool) – Resolve ontological term curies using the resource’s context. Default False.
use_auth (str) – OAuth token in case access is restricted. Token should be in the format for the authorization header: Bearer VALUE.

classmethod get_constrained_url(base=None, org=None, proj=None)¶: Get schema constrained url.

get_id()¶: Retrieve _id property.

get_rev()¶: Retrieve _rev property.

get_url()¶

Retrieve URL of the nexus entity.

Returns:: Content of the _self property.

classmethod list_by_schema(**kwargs)¶

List all instances belonging to the schema this type defines.

Parameters:: changes – Keyword changes in the new copy, should be a subset of class constructor(__init__) keyword arguments.
Returns:: New instance of the same class with changes applied.

publish(*, resource_id=None, sync_index=False, base=None, org=None, proj=None, use_auth=None, include_rev=False)¶

Create or update entity in nexus. Makes a remote call to nexus instance to persist entity attributes.

Parameters:

resource_id (str) – Resource identifier. If not provided nexus will generate one.
use_auth (str) – OAuth token in case access is restricted. Token should be in the format for the authorization header: Bearer VALUE.
include_rev (bool) – Whether to include _rev in the linked entities or not.

Returns:

New instance of the same class with revision updated.

class entity_management.base.OntologyTerm(*, url, label=None)¶

Bases: Frozen

Ontology term such as brain region or species

Parameters:

url (str) – Ontology term url identifier.
label (str) – Label for the ontology term.

class entity_management.base.QuantitativeValue(*, value, unitText=None, unitCode=None)¶

Bases: Frozen

External resource representations, this can be a file or a folder on gpfs

Parameters:

value (str) – Value.
unitText (str) – Unit text.
unitCode (str) – The unit of measurement given using the UN/CEFACT Common Code (3 characters) or a URL. Other codes than the UN/CEFACT Common Code may be used with a prefix followed by a colon.

class entity_management.base.Subject(*, species=None, strain=None)¶

Bases: BlankNode

Subject.

Parameters:

name (str) – Subject name.
species (OntologyTerm) – Species ontology term.
strain (OntologyTerm) – Strain ontology term.

class entity_management.base.Unconstrained(*, json)¶

Bases: Identifiable

Shapeless data.

Parameters:: json (dict) – python dictionary which will be seralized into json.

entity_management.base.attributes(attr_dict=None, repr=True)¶: decorator to simplify creation of classes that have args and kwargs

entity_management.base.custom_getattr(obj, name)¶: Overload of __getattribute__ to trigger instantiation of Nexus object if the attribute is NotInstantiated