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_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_file_type():
with pytest.raises(ValueError):
biocxml.load(open(file, encoding='utf8'), None)
with pytest.raises(ValueError):
biocxml.loads('', None)
def test_load():
with open(file, encoding='utf8') as fp:
collection = biocxml.load(fp)
assert_everything(collection)
import copy
from pathlib import Path
import pytest
from bioc import bioc, biocxml
file = Path(__file__).parent / 'everything.xml'
with open(file, encoding='utf8') as fp:
collection = biocxml.load(fp)
def test_BioCLocation():
base = bioc.BioCLocation(1, 10)
assert base != 'foo'
assert base.end == 11
loc = bioc.BioCLocation(1, 10)
assert base == loc
loc = bioc.BioCLocation(2, 9)
assert base != loc
assert loc in base
assert base not in loc
locs = {base, loc}
assert base in locs
assert loc in locs
with pytest.raises(TypeError):
assert 'foo' in base
def collection():
file = Path(__file__).parent / 'everything.xml'
with open(file, encoding='utf8') as fp:
collection = biocxml.load(fp)
return collection
def _get_collection():
file = Path(__file__).parent / 'everything_v2.xml'
with open(file, encoding='utf8') as fp:
return biocxml.load(fp, version=bioc.BioCVersion.V2)