def _prepare_pathway_model(pathway_id, database, bel_graph):
"""Prepare dictionary pathway model.
:param str pathway_id: identifier
:param str database: database name
:param pybel.BELGraph bel_graph: graph
:rtype: dict
:return: pathway model in dict
"""
return {
'pathway_id':
pathway_id,
'resource_name':
database,
'name':
bel_graph.name,
'version':
bel_graph.version,
'number_of_nodes':
bel_graph.number_of_nodes(),
'number_of_edges':
bel_graph.number_of_edges(),
'authors':
bel_graph.authors,
'contact':
bel_graph.contact,
'description':
bel_graph.document.get('description') if isinstance(
bel_graph.document.get('description'), str) else '{}'.format(
bel_graph.document.get('description')),
'pybel_version':
bel_graph.pybel_version,
'blob':
to_bytes(bel_graph)
}
def test_import_warning(self):
"""Tests an error is thrown when the version is set wrong"""
graph = BELGraph()
# Much with stuff that would normally be set
graph.graph[GRAPH_PYBEL_VERSION] = '0.0.0'
graph_bytes = to_bytes(graph)
with self.assertRaises(ImportVersionWarning) as cm:
from_bytes(graph_bytes)
self.assertEqual(
import_version_message_fmt.format(
'0.0.0', PYBEL_MINIMUM_IMPORT_VERSION), str(cm.exception))
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_bytes(self):
graph_bytes = to_bytes(self.slushy_graph)
graph = from_bytes(graph_bytes)
self.bel_slushy_reconstituted(graph)
def test_thorough_bytes(self):
graph_bytes = to_bytes(self.thorough_graph)
graph = from_bytes(graph_bytes)
self.bel_thorough_reconstituted(graph)
def test_example_bytes(self):
graph_bytes = to_bytes(sialic_acid_graph)
graph = from_bytes(graph_bytes)
self.help_test_equal(graph)
def test_example_bytes(self):
"""Test the round-trip through bytes."""
graph_bytes = to_bytes(sialic_acid_graph)
graph = from_bytes(graph_bytes)
self._help_test_equal(graph)
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')
