def test_isolated_upgrade(self):
lines = to_bel_lines(self.isolated_graph)
with mock_bel_resources:
reconstituted = from_lines(lines, manager=self.manager)
self.bel_isolated_reconstituted(reconstituted)
def cx_to_bel(file, output):
"""Convert a CX document from STDIN and write a BEL Script to STDOUT."""
try:
graph = from_cx_file(file)
except Exception:
log.exception('error occurred while loading CX.')
sys.exit(1)
try:
for line in to_bel_lines(graph):
click.echo(line, file=file)
except Exception:
log.exception('error occurred in conversion to BEL.')
sys.exit(2)
sys.exit(0)
def export_graph(graph, format=None):
"""Convert PyBEL graph to a different format.
:param PyBEL graph graph: graph
:param format: desire format
:return: graph representation in different format
"""
if format is None or format == 'json':
data = to_json_custom(graph)
return jsonify(data)
elif format == 'bytes':
data = BytesIO(to_bytes(graph))
return send_file(data,
mimetype='application/octet-stream',
as_attachment=True,
attachment_filename='graph.gpickle')
elif format == 'bel':
serialize_authors(graph)
data = '\n'.join(to_bel_lines(graph))
return Response(data, mimetype='text/plain')
elif format == 'graphml':
bio = BytesIO()
to_graphml(graph, bio)
bio.seek(0)
return send_file(bio,
mimetype='text/xml',
attachment_filename='graph.graphml',
as_attachment=True)
elif format == 'csv':
bio = StringIO()
to_csv(graph, bio)
bio.seek(0)
data = BytesIO(bio.read().encode('utf-8'))
return send_file(data,
mimetype="text/tab-separated-values",
attachment_filename="graph.tsv",
as_attachment=True)
abort(500, '{} is not a valid format'.format(format))
def serve_network(graph, serve_format=None):
"""A helper function to serialize a graph and download as a file"""
if serve_format is None or serve_format == 'json':
data = to_json_custom(graph)
return jsonify(data)
if serve_format == 'cx':
data = to_cx(graph)
return jsonify(data)
if serve_format == 'bytes':
data = to_bytes(graph)
return send_file(data,
mimetype='application/octet-stream',
as_attachment=True,
attachment_filename='graph.gpickle')
if serve_format == 'bel':
serialize_authors(graph)
data = '\n'.join(to_bel_lines(graph))
return Response(data, mimetype='text/plain')
if serve_format == 'graphml':
bio = BytesIO()
to_graphml(graph, bio)
bio.seek(0)
data = StringIO(bio.read().decode('utf-8'))
return send_file(data,
mimetype='text/xml',
attachment_filename='graph.graphml',
as_attachment=True)
if serve_format == 'csv':
bio = BytesIO()
to_csv(graph, bio)
bio.seek(0)
data = StringIO(bio.read().decode('utf-8'))
return send_file(data,
attachment_filename="graph.tsv",
as_attachment=True)
raise TypeError('{} is not a valid format'.format(serve_format))
def test_isolated_upgrade(self, mock):
lines = to_bel_lines(self.isolated_graph)
reconstituted = from_lines(lines, manager=self.manager)
self.bel_isolated_reconstituted(reconstituted)
def test_thorough_upgrade(self):
lines = to_bel_lines(self.thorough_graph)
reconstituted = from_lines(lines, manager=self.manager)
self.bel_thorough_reconstituted(reconstituted,
check_citation_name=False)