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_dump():
collection = _get_collection()
tmp = tempfile.mktemp()
with open(tmp, 'w', encoding='utf8') as fp:
biocxml.dump(collection, fp)
with open(tmp, encoding='utf8') as fp:
collection = biocxml.load(fp)
assert_everything(collection)
def test_dump():
with open(file, encoding='utf8') as fp:
collection = bioc.load(fp, BioCFileType.BIOC_JSON)
tmp = tempfile.mktemp()
with open(tmp, 'w', encoding='utf8') as fp:
bioc.dump(collection, fp, BioCFileType.BIOC_JSON)
with open(tmp, encoding='utf8') as fp:
collection = bioc.load(fp, BioCFileType.BIOC_JSON)
assert_everything(collection)
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_iterwrite_io():
collection = _get_collection()
f = io.BytesIO()
with biocxml.iterwrite(f) as writer:
writer.write_collection_info(collection)
for document in collection.documents:
writer.write_document(document)
collection = biocxml.loads(f.getvalue().decode('utf-8'))
assert_everything(collection)
def test_BioCXMLDocumentWriter_io():
collection = _get_collection()
f = io.BytesIO()
writer = bioc.BioCXMLDocumentWriter(f)
writer.write_collection_info(collection)
for document in collection.documents:
writer.write_document(document)
writer.close()
collection = bioc.loads(f.getvalue().decode('utf-8'))
assert_everything(collection)
def test_iterparse():
with biocxml.iterparse(open(file, 'rb')) as reader:
collection = reader.get_collection_info()
for document in reader:
collection.add_document(document)
assert_everything(collection)
with biocxml.iterparse(str(file)) as reader:
collection = reader.get_collection_info()
for document in reader:
collection.add_document(document)
assert_everything(collection)
def test_BioCXMLDocumentReader():
with open(file, 'rb') as fp:
reader = bioc.BioCXMLDocumentReader(fp)
collection = reader.get_collection_info()
for document in reader:
collection.add_document(document)
assert_everything(collection)
reader = bioc.BioCXMLDocumentReader(str(file))
collection = reader.get_collection_info()
for document in reader:
collection.add_document(document)
assert_everything(collection)
def test_iterwrite_file():
collection = _get_collection()
tmp = tempfile.mktemp()
with biocxml.iterwrite(tmp) as writer:
writer.write_collection_info(collection)
for document in collection.documents:
writer.write_document(document)
with open(tmp, encoding='utf8') as fp:
collection = biocxml.load(fp)
assert_everything(collection)
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 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_dumps():
with open(file, encoding='utf8') as fp:
collection = biocjson.load(fp)
s = biocjson.dumps(collection)
collection = biocjson.loads(s)
assert_everything(collection)
def test_loads():
with open(file, encoding='utf8') as fp:
s = fp.read()
collection = biocxml.loads(s)
assert_everything(collection)
def test_load():
with open(file, encoding='utf8') as fp:
collection = biocxml.load(fp)
assert_everything(collection)
def test_pretty_print():
tmp = tempfile.mktemp()
bioc.pretty_print(file, tmp)
with open(tmp, encoding='utf8') as fp:
collection = bioc.load(fp)
assert_everything(collection)
def test_dumps():
with open(file, encoding='utf8') as fp:
collection = bioc.load(fp, BioCFileType.BIOC_JSON)
s = bioc.dumps(collection, BioCFileType.BIOC_JSON)
collection = bioc.loads(s, BioCFileType.BIOC_JSON)
assert_everything(collection)
def test_dumps():
collection = _get_collection()
s = biocxml.dumps(collection, version=bioc.BioCVersion.V2)
collection = biocxml.loads(s, version=bioc.BioCVersion.V2)
assert_everything(collection)
def test_dumps():
collection = _get_collection()
s = biocxml.dumps(collection)
collection = biocxml.loads(s)
assert_everything(collection)
