sbol2.object

Module Contents

Classes

SBOLObject

An SBOLObject converts a Python data structure into an RDF triple store

Functions

_compare_properties(obj1, obj2)

_compare_owned_objects(obj1, obj2)

sbol2.object._compare_properties(obj1, obj2)
sbol2.object._compare_owned_objects(obj1, obj2)
class sbol2.object.SBOLObject(type_uri=rdflib.URIRef(UNDEFINED), uri=rdflib.URIRef('example'))

An SBOLObject converts a Python data structure into an RDF triple store and contains methods for serializing and parsing RDF triples.

abstract _serialize()
abstract _nest()
abstract _makeQName(uri)
property logger
__uri__() → rdflib.URIRef

Returns a URIRef representing this object.

Returns

The identity of this object as an rdflib.URIRef

Return type

rdflib.URIRef

property type
property this
getTypeURI()
Returns

The uniform resource identifier that describes

the RDF-type of this SBOL Object.

getClassName(rdf_type)

Parses a local class name from the RDF-type of this SBOL Object.

cast(cls)
find(uri)

Search this object recursively to see if an object or any child object with URI already exists.

Parameters

uri – The URI to search for.

Returns

The SBOLObject associated with this URI if it exists,

None otherwise.

abstract cacheObjects(objectCache)

TODO document

Parameters

objectCache – a dictionary mapping strings to SBOLObjects

Returns

None

find_property(uri)

Search this object recursively to see if it contains a member property with the given RDF type.

Parameters

uri – The RDF type of the property to search for.

Returns

The SBOLObject that contains a member property

with the specified RDF type, None otherwise

find_property_value(uri, value, matches=None)

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters

  • uri – The RDF type of the property to search for.

  • value – The property value to match.

  • matches –

Returns

A vector containing all objects found that contain

a member property with the specified RDF type

find_reference(uri)

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters

uri – A URI, either an ontology term or an object reference,

to search for. :return: A vector containing all objects found that contain the URI in a property value.

compare(other)

Compare two SBOLObjects. The behavior is currently undefined for objects with custom annotations or extension classes.

Parameters

other – The object being compared to this one.

Returns

True if the objects are identical, False if they are different.

getPropertyValue(property_uri: str) → str

Get the value of a custom annotation property by its URI.

Parameters

property_uri (str) – The URI for the property.

Returns

The value of the property.

Return type

str

Raises

SBOLError(SBOL_ERROR_NOT_FOUND) if property does not exist

getPropertyValues(property_uri: str) → List[str]

Get all values of a custom annotation property by its URI.

Parameters

property_uri (str) – The URI for the property.

Returns

A vector of property values.

Return type

list of strings

Raises

SBOLError(SBOL_ERROR_NOT_FOUND) if property does not exist

getProperties()

Gets URIs for all properties contained by this object. This includes SBOL core properties as well as custom annotations. Use this to find custom extension data in an SBOL file.

Returns

A vector of URIs that identify the properties contained in this object.

setPropertyValue(property_uri, val)

Set and overwrite the value for a user-defined annotation property.

Parameters

  • property_uri –

  • val – A string

Returns

None

abstract addPropertyValue(property_uri, val)

Append a value to a user-defined annotation property.

Parameters

  • property_uri –

  • val – Either a literal or URI value.

Returns

None

abstract setAnnotation(property_uri, val)

Set the value for a user-defined annotation property. Synonymous with setPropertyValue.

Parameters

  • property_uri –

  • val – If the value is a URI,

it should be surrounded by angle brackets, else it will be interpreted as a literal value. :return: None

abstract getAnnotation(property_uri)

Get the value of a custom annotation property by its URI. Synonymous with getPropertyValue.

Parameters

property_uri – The URI for the property.

Returns

The value of the property or SBOL_ERROR_NOT_FOUND.

abstract apply(callback, user_data)

Recursively call this callback function on the user_data provided :param callback: the callback function :param user_data: the input to the callback :return: None

abstract update_uri()

Recursively generates SBOL compliant ids for an object and all its owned objects, then checks to make sure that these ids are unique. :return: None

build_graph(graph)
__str__()

Return str(self).

is_top_level()
__getattribute__(name)

Return getattr(self, name).

_is_transparent_attribute(name)
_set_transparent_attribute(name, value)
__setattr__(name, value)

Implement setattr(self, name, value).

_added_to_document(doc)

Classes can override this method to do extra work when being added to a document.