sbol3.provenance

Module Contents

Classes

Activity	A generated prov:Entity is linked through a prov:wasGeneratedBy
Agent	Examples of agents are a person, organization, or software
Association	An prov:Association is linked to an prov:Agent through the
Plan	The prov:Plan entity can be used as a place holder to describe the
Usage	How different entities are used in an prov:Activity is specified

Functions

build_association(→ sbol3.SBOLObject)
build_usage(→ sbol3.SBOLObject)

class Activity(identity: str, *, types: Optional[str, list[str]] = None, start_time: Union[str, datetime.datetime] = None, end_time: Union[str, datetime.datetime] = None, usage: List[sbol3.Identified] = None, association: List[sbol3.Identified] = None, namespace: str = None, attachments: List[str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, type_uri: str = PROV_ACTIVITY)

Bases: sbol3.CustomTopLevel

A generated prov:Entity is linked through a prov:wasGeneratedBy relationship to an prov:Activity, which is used to describe how different prov:Agents and other entities were used. An prov:Activity is linked through a prov:qualifiedAssociation to prov:Associations, to describe the role of agents, and is linked through prov:qualifiedUsage to prov:Usages to describe the role of other entities used as part of the activity. Moreover, each prov:Activity includes optional prov:startedAtTime and prov:endedAtTime properties. When using prov:Activity to capture how an entity was derived, it is expected that any additional information needed will be attached as annotations. This may include software settings or textual notes. Activities can also be linked together using the prov:wasInformedBy relationship to provide dependency without explicitly specifying start and end times.

accept(visitor: Any) → Any

Invokes visit_activity on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_activity method

Returns

Whatever visitor.visit_activity returns

Return type

Any

class Agent(identity: str, *, namespace: str = None, attachments: List[str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, type_uri: str = PROV_AGENT)

Bases: sbol3.CustomTopLevel

Examples of agents are a person, organization, or software tool. These agents should be annotated with additional information, such as software version, needed to be able to run the same prov:Activity again.

accept(visitor: Any) → Any

Invokes visit_agent on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_agent method

Returns

Whatever visitor.visit_agent returns

Return type

Any

class Association(agent: Union[str, sbol3.Identified], *, roles: Optional[str, list[str]] = None, plan: Union[sbol3.Identified, str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, identity: str = None, type_uri: str = PROV_ASSOCIATION)

Bases: sbol3.CustomIdentified

An prov:Association is linked to an prov:Agent through the prov:agent relationship. The prov:Association includes the prov:hadRole property to qualify the role of the prov:Agent in the prov:Activity.

accept(visitor: Any) → Any

Invokes visit_association on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_association method

Returns

Whatever visitor.visit_association returns

Return type

Any

class Plan(identity: str, *, namespace: str = None, attachments: List[str] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, type_uri: str = PROV_PLAN)

Bases: sbol3.CustomTopLevel

The prov:Plan entity can be used as a place holder to describe the steps (for example scripts or lab protocols) taken when an prov:Agent is used in a particular prov:Activity.

accept(visitor: Any) → Any

Invokes visit_plan on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_plan method

Returns

Whatever visitor.visit_plan returns

Return type

Any

class Usage(entity: str, *, roles: Optional[str, list[str]] = None, name: str = None, description: str = None, derived_from: List[str] = None, generated_by: List[str] = None, measures: List[sbol3.SBOLObject] = None, identity: str = None, type_uri: str = PROV_USAGE)

Bases: sbol3.CustomIdentified

How different entities are used in an prov:Activity is specified with the prov:Usage class, which is linked from an prov:Activity through the prov:Usage relationship. A prov:Usage is then linked to an prov:Entity through the prov:entity property URI and the prov:hadRole property species how the prov:Entity is used. When the prov:wasDerivedFrom property is used together with the full provenance described here, the entity pointed at by the prov:wasDerivedFrom property MUST be included in a prov:Usage.

accept(visitor: Any) → Any

Invokes visit_usage on visitor with self as the only argument.

Parameters

visitor (Any) – The visitor instance

Raises

AttributeError – If visitor lacks a visit_usage method

Returns

Whatever visitor.visit_usage returns

Return type

Any

build_association(identity: str, *, type_uri: str = PROV_USAGE) → sbol3.SBOLObject

build_usage(identity: str, *, type_uri: str = PROV_USAGE) → sbol3.SBOLObject