def test_slushy_graphml(self):
handle, path = tempfile.mkstemp()
with open(path, 'wb') as f:
to_graphml(self.slushy_graph, f)
os.close(handle)
os.remove(path)
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_slushy_graphml(self):
handle, path = tempfile.mkstemp()
to_graphml(self.slushy_graph, path)
os.close(handle)
os.remove(path)
def get_graph(
self,
directory: Optional[str] = None,
use_cached: bool = True,
use_tqdm: bool = True,
) -> BELGraph:
"""Get the graph from all sources."""
if directory is None:
if self.directory is None:
raise ValueError
directory = self.directory
pickle_path = os.path.join(directory, f'{self.name}.bel.pickle')
if use_cached and os.path.exists(pickle_path):
return pybel.from_pickle(pickle_path)
rv = union(self.get_graphs(use_tqdm=use_tqdm))
self.metadata.update(rv)
pybel.to_pickle(rv, pickle_path)
nodelink_path = os.path.join(directory,
f'{self.name}.bel.nodelink.json')
pybel.to_json_path(rv, nodelink_path)
sif_path = os.path.join(directory, f'{self.name}.bel.sif')
pybel.to_sif_path(rv, sif_path)
gsea_path = os.path.join(directory, f'{self.name}.bel.gmt')
pybel.to_gsea_path(rv, gsea_path)
graphml_path = os.path.join(directory, f'{self.name}.bel.graphml')
pybel.to_graphml(rv, graphml_path)
try:
statements = pybel.to_indra_statements(rv)
except ImportError:
pass
else:
indra_path = os.path.join(directory, f'{self.name}.indra.pickle')
with open(indra_path, 'wb') as file:
pickle.dump(statements, file)
try:
from pybel_cx import to_cx_file
except ImportError:
pass
else:
cx_path = os.path.join(directory, f'{self.name}.bel.cx.json')
with open(cx_path, 'w') as file:
to_cx_file(rv, file)
try:
from pybel_tools.assembler.html import to_html
except ImportError:
pass
else:
html_path = os.path.join(directory, 'index.html')
with open(html_path, 'w') as file:
print(to_html(rv), file=file)
return rv
def serve_network(graph: BELGraph,
serve_format: Optional[str] = None) -> Response: # noqa:C901
"""Help serialize a graph and download as a file."""
if serve_format is None:
return jsonify(to_json_custom(graph))
elif serve_format in {'nl', 'nodelink', 'json'}:
return jsonify(to_nodelink(graph))
elif serve_format == 'nodelink-umbrella':
return jsonify(to_umbrella_nodelink(graph))
elif serve_format == 'graphdati':
return jsonify(to_graphdati(graph))
elif serve_format == 'cx':
return jsonify(to_cx(graph))
elif serve_format == 'jgif':
return jsonify(to_jgif(graph))
elif serve_format == 'indra':
return jsonify(to_indra_statements_json(graph))
elif serve_format == 'bytes':
data = BytesIO(to_bytes(graph))
return send_file(
data,
mimetype='application/octet-stream',
as_attachment=True,
attachment_filename=f'{graph.name}.bel.pickle',
)
elif serve_format == 'bel':
data = '\n'.join(to_bel_script_lines(graph))
return Response(data, mimetype='text/plain')
elif serve_format == 'graphml':
bio = BytesIO()
to_graphml(graph, bio)
bio.seek(0)
return send_file(
bio,
mimetype='text/xml',
attachment_filename=f'{graph.name}.bel.graphml',
as_attachment=True,
)
elif serve_format == 'graphml-umbrella':
bio = BytesIO()
to_graphml(graph, bio, schema='umbrella')
bio.seek(0)
return send_file(
bio,
mimetype='text/xml',
attachment_filename=f'{graph.name}.bel.graphml',
as_attachment=True,
)
elif serve_format == 'sif':
bio = StringIO()
to_sif(graph, bio)
bio.seek(0)
data = BytesIO(bio.read().encode('utf-8'))
return send_file(
data,
attachment_filename=f"{graph.name}.bel.sif",
as_attachment=True,
)
elif serve_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=f"{graph.name}.bel.tsv",
as_attachment=True,
)
elif serve_format == 'gsea':
bio = StringIO()
to_gsea(graph, bio)
bio.seek(0)
data = BytesIO(bio.read().encode('utf-8'))
return send_file(
data,
attachment_filename=f"{graph.name}.grp",
as_attachment=True,
)
elif serve_format == 'citations':
bio = StringIO()
for pubmed_identifier in sorted(get_pubmed_identifiers(graph)):
print(pubmed_identifier, file=bio)
bio.seek(0)
data = BytesIO(bio.read().encode('utf-8'))
return send_file(
data,
mimetype="text/tab-separated-values",
attachment_filename=f"{graph.name}-citations.txt",
as_attachment=True,
)
raise TypeError(f'{serve_format} is not a valid format')