def get_bioc_relations(self, docid, relations):
# <relation id="5618#7534">
# <infon key="Gene1">5618</infon>
# <infon key="Gene2">7534</infon>
# <infon key="relation">PPIm</infon>
# </relation>
biocDoc=BioCDocument()
biocDoc.id = docid
biocDoc.relations=[]
for rel in relations:
bioc_rel = BioCRelation()
rel_list = list(rel)
infon = {}
infon["relation"] = "PPIm"
infon["Gene1"] = rel_list[0]
infon["Gene2"] = rel_list[0]
if len(rel_list) == 2:
infon["Gene2"] = rel_list[1]
bioc_rel.id="{}#{}".format(infon["Gene1"], infon["Gene2"])
bioc_rel.infons=infon
biocDoc.relations.append(bioc_rel)
return biocDoc
def __parse_relation(self, tree):
relation = BioCRelation()
if 'id' in tree.attrib:
relation.id = tree.attrib['id']
relation.infons = self.__parse_infons(tree)
for child in tree.findall('node'):
relation.add_node(BioCNode(child.attrib['refid'], child.attrib['role']))
return relation
def test_is_valid(self, relations_infons, gene1, gene2, expected):
# arrange
sut = BiocRelation()
doc = BioCDocument()
for dict in relations_infons:
dict["relation"] = "PPIm"
relation = BioCRelation()
relation.infons = dict
doc.add_relation(relation)
# Act
actual = sut.is_valid(doc, gene1, gene2)
# Assert
self.assertEqual(expected, actual)