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 brat2bioc_event(bratevent: BratEvent) -> BioCRelation:
rel = BioCRelation()
rel.id = bratevent.id
rel.infons['type'] = bratevent.type
rel.infons['trigger_id'] = bratevent.trigger_id
rel.add_node(BioCNode(bratevent.trigger_id, bratevent.type))
for role, refid in bratevent.arguments.items():
rel.add_node(BioCNode(refid, role))
return rel
def __read_relation(self, start_elem):
rel = BioCRelation()
rel.id = start_elem.get('id')
while self.__has_next():
event, elem = self.__next_event()
if event == 'start':
pass
elif event == 'end':
if elem.tag == 'infon':
rel.infons[elem.get('key')] = elem.text
elif elem.tag == 'node':
rel.add_node(BioCNode(elem.get('refid'), elem.get('role')))
if elem.tag == 'relation':
return rel
raise RuntimeError("should not reach here") # pragma: no cover
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)
def brat2bioc_equiv(brat_equiv: BratEquivRelation) -> BioCRelation:
rel = BioCRelation()
rel.id = brat_equiv.id
rel.infons['type'] = brat_equiv.type
for argid in brat_equiv.argids:
rel.add_node(BioCNode(argid, 'Arg'))
return rel
def brat2bioc_relation(bratrelation: BratRelation) -> BioCRelation:
rel = BioCRelation()
rel.id = bratrelation.id
rel.infons['type'] = bratrelation.type
for role, refid in bratrelation.arguments.items():
rel.add_node(BioCNode(refid, role))
return rel
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 to_bioc(self):
relation_bioc = BioCRelation()
relation_bioc.id = str(self.id)
relation_bioc.add_node(BioCNode(str(self.entity1.id), 'annotation 1'))
relation_bioc.add_node(BioCNode(str(self.entity2.id), 'annotation 2'))
relation_bioc.infons['type'] = self.type
return relation_bioc