def parse_references(model_node, model=None, progress=None):
reference_list_node = model_node.find(ge_listOfReferences)
if reference_list_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading references...")
progress.setRange(0, len(reference_list_node))
elif progress.wasCanceled():
return
references = []
for i, reference_node in enumerate(
reference_list_node.iterfind(ge_reference)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_reference = Reference(id=reference_node.get("id"),
year=reference_node.get("year"),
title=reference_node.get("title"),
journal=reference_node.get("journal"),
url=reference_node.get("url"))
author_list_node = reference_node.find(ge_listOfAuthors)
if author_list_node is not None:
authors = []
for child in author_list_node.iterfind(ge_author):
authors.append(
Author(firstname=child.get("firstname"),
lastname=child.get("lastname"),
initials=child.get("initials")))
new_reference.authors = authors
annotation = annotate_element_from_xml(reference_node)
if annotation:
for x in annotation:
if x.collection == "pubmed":
new_reference.pmid = x.identifier
elif x.collection == "pmc":
new_reference.pmc = x.identifier
elif x.collection == "doi":
new_reference.doi = x.identifier
if model is None:
references.append(new_reference)
else:
model.add_reference(new_reference)
return references
def test_annotation_property(self):
reference = Reference()
reference.pmc = "1234"
reference.pmid = "54321"
reference.doi = "5555"
assert Annotation("pubmed", reference.pmid) in reference.annotation
assert Annotation("pmc", reference.pmc) in reference.annotation
assert Annotation("doi", reference.doi) in reference.annotation