def test_dump():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
tmp = tempfile.mktemp()
with open(tmp, 'w', encoding='utf8') as fp:
biocjson.dump(collection, fp)
with open(tmp, encoding='utf8') as fp:
collection = biocjson.load(fp)
assert_everything(collection)
def test_dump(tmp_path):
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
filepath = tmp_path / 'foo.json'
with open(filepath, 'w', encoding='utf8') as fp:
biocjson.dump(collection, fp)
with open(filepath, encoding='utf8') as fp:
collection = biocjson.load(fp)
assert_everything(collection)
def test_iterreader_sentence():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = io.StringIO()
with biocjson.iterwriter(s) as writer:
for sen in collection.documents[1].passages[0].sentences:
writer.write(sen)
del collection.documents[1].passages[0].sentences[:]
with pytest.raises(IndexError):
assert_everything(collection)
with biocjson.iterreader(io.StringIO(s.getvalue())) as reader:
for obj in reader:
collection.documents[1].passages[0].add_sentence(obj)
assert_everything(collection)
#
#
# def test_level():
# with pytest.raises(ValueError):
# BioCJsonIterReader(io.StringIO(), level=-1)
def test_toJSON():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
obj = biocjson.toJSON(collection)
assert obj['documents'][0]['id'] == '1'
with pytest.raises(TypeError):
biocjson.toJSON({})
def test_jsoniterwriter(tmp_path):
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
filepath = tmp_path / 'foo.json'
with biocjson.iterwriter(filepath) as writer:
for doc in collection.documents:
writer.write(doc)
del collection.documents[:]
with biocjson.iterreader(filepath) as reader:
for doc in reader:
collection.add_document(doc)
assert_everything(collection)
def __load_collection_json(bioc_json: str, is_file: bool = True):
"""load a json bioc collection .
It will return a bioc collection object.
:param bioc_json: a str path to a bioc file or a bioc input json string
:param is_file: if True bioc_input is a path else it is a string
:returns: a bioc collection object
"""
if is_file:
with open(bioc_json, 'r') as fp:
collection = biocjson.load(fp)
return (collection)
else:
collection = biocjson.loads(bioc_json)
return (collection)
def test_iterreader_passage():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = io.StringIO()
with biocjson.iterwriter(s) as writer:
for p in collection.documents[0].passages:
writer.write(p)
del collection.documents[0].passages[:]
with pytest.raises(IndexError):
assert_everything(collection)
with biocjson.iterreader(io.StringIO(s.getvalue())) as reader:
for obj in reader:
collection.documents[0].add_passage(obj)
assert_everything(collection)
def test_BioCJsonIterReader_sentence():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = io.StringIO()
writer = BioCJsonIterWriter(s, level=bioc.SENTENCE)
for sen in collection.documents[1].passages[0].sentences:
writer.write(sen)
del collection.documents[1].passages[0].sentences[:]
with pytest.raises(IndexError):
assert_everything(collection)
reader = BioCJsonIterReader(io.StringIO(s.getvalue()), level=bioc.SENTENCE)
for obj in reader:
collection.documents[1].passages[0].add_sentence(obj)
assert_everything(collection)
def test_BioCJsonIterReader_document():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = io.StringIO()
writer = BioCJsonIterWriter(s, level=bioc.DOCUMENT)
for doc in collection.documents:
writer.write(doc)
del collection.documents[:]
with pytest.raises(IndexError):
assert_everything(collection)
reader = BioCJsonIterReader(io.StringIO(s.getvalue()), level=bioc.DOCUMENT)
for obj in reader:
collection.add_document(obj)
assert_everything(collection)
def test_level():
with pytest.raises(ValueError):
BioCJsonIterWriter(io.StringIO(), level=-1)
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
with pytest.raises(ValueError):
writer = BioCJsonIterWriter(io.StringIO(), level=bioc.SENTENCE)
writer.write(collection.documents[0])
with pytest.raises(ValueError):
writer = BioCJsonIterWriter(io.StringIO(), level=bioc.PASSAGE)
writer.write(collection.documents[0])
with pytest.raises(ValueError):
writer = BioCJsonIterWriter(io.StringIO(), level=bioc.DOCUMENT)
writer.write(collection.documents[0].passages[0])
def test_load():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
assert_everything(collection)
def test_dumps():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = biocjson.dumps(collection)
collection = biocjson.loads(s)
assert_everything(collection)
