def test_mutable():
"""
Test mutability of ontology class
"""
ont = Ontology()
ont.add_node('TEST:1', 'foo bar')
ont.add_node('TEST:2', 'bar foo')
ont.add_node('TEST:3', 'foo bar')
ont.add_node('TEST:4', 'wiz')
syn = Synonym('TEST:4', val='bar foo', pred='hasExactSynonym')
ont.add_synonym(syn)
w = GraphRenderer.create('obo')
w.write(ont)
for n in ont.nodes():
meta = ont._meta(n)
print('{} -> {}'.format(n, meta))
assert ont.label('TEST:1') == 'foo bar'
assert ont.synonyms('TEST:1') == []
assert ont.synonyms('TEST:4')[0].val == 'bar foo'
def _get_single_sentence(node_ids: List[str],
ontology: Ontology,
aspect: str,
evidence_group: str,
qualifier: str,
prepostfix_sentences_map: Dict[Tuple[str, str, str],
Tuple[str, str]],
terms_merged: bool = False,
add_others: bool = False,
truncate_others_generic_word: str = "several",
truncate_others_aspect_words: Dict[str, str] = None,
ancestors_with_multiple_children: Set[str] = None,
rename_cell: bool = False,
trimmed: bool = False) -> Union[Sentence, None]:
"""build a sentence object
Args:
node_ids (List[str]): list of ids for the terms to be combined in the sentence
ontology (Ontology): the ontology containing the nodes
aspect (str): aspect
evidence_group (str): evidence group
qualifier (str): qualifier
prepostfix_sentences_map (Dict[Tuple[str, str, str], Tuple[str, str]]): map for prefix and postfix phrases
terms_merged (bool): whether the terms set has been merged to reduce its size
add_others (bool): whether to say that there are other terms which have been omitted from the sentence
truncate_others_generic_word (str): a generic word to indicate that the set of terms reported in the sentence is
only a subset of the original terms, e.g., 'several'
truncate_others_aspect_words (Dict[str, str]): one word for each aspect describing the kind of terms that are
included in the aspect
ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children
term in the original set and which will appear with the label '(multiple)'
rename_cell (bool): whether to rename the term 'cell'
Returns:
Union[Sentence,None]: the combined go sentence
"""
if len(node_ids) > 0:
prefix = prepostfix_sentences_map[(aspect, evidence_group,
qualifier)][0]
additional_prefix = ""
others_word = "entities"
if aspect in truncate_others_aspect_words:
others_word = truncate_others_aspect_words[aspect]
if add_others:
additional_prefix += " " + truncate_others_generic_word + " " + others_word + ", including"
if aspect == "C":
additional_prefix += " the"
postfix = prepostfix_sentences_map[(aspect, evidence_group,
qualifier)][1]
term_labels = [
ontology.label(node_id, id_if_null=True) for node_id in node_ids
]
return Sentence(
prefix=prefix,
terms_ids=node_ids,
postfix=postfix,
text=compose_sentence(prefix=prefix,
term_names=term_labels,
postfix=postfix,
additional_prefix=additional_prefix,
ancestors_with_multiple_children=
ancestors_with_multiple_children,
rename_cell=rename_cell),
aspect=aspect,
evidence_group=evidence_group,
terms_merged=terms_merged,
additional_prefix=additional_prefix,
qualifier=qualifier,
ancestors_covering_multiple_terms=ancestors_with_multiple_children,
trimmed=trimmed)
else:
return None