All UUID created during Model.py/OntologyAnnotation.__init__() are duplicates

[podonnellalidyne]

While parsing isaTab to isaJson, ontologies loaded into the OntologyAnnotation Class have the same @id value

This is because the id method parameter is only evaluated once in python, so it creates a single uuid.uuid4() that is set to all ontologies as the @id param, unless a new id param is passed in. passing in _id = none and then setting the variable to uuid4() if the method param is None fixes this issue. However if then something were passed in in the id value, all future id fields would have that same passed in value, as the optional variable reference would no longer point to None.

Currently:

def __init__(self, term='', term_source=None, term_accession='',
                 comments=None, id_=str(uuid.uuid4())) :
        super().__init__(comments)
        self.__term = term
        self.__term_source = term_source
        self.__term_accession = term_accession
        self.id = id_

This fixes then issue

def __init__(self, term='', term_source=None, term_accession='',
                 comments=None, id_ = None) :
        super().__init__(comments)
        self.__term = term
        self.__term_source = term_source
        self.__term_accession = term_accession
        self.id = str(uuid.uuid4()) if not id_ else id_

Ideally because of the way python evaluates these optional params, maybe the _id param should be required, and evaluates to something every time, or should be removed from init() and can be set after the fact, to ensure there are no inadvertent duplicate values.

[Zigur]

Thanks for noticing this @podonnellalidyne. We'll be fixing the code accordingly and include this bugfix into the next release.