33import os
44import tempfile
55
6+ import pandas as pd
67
78os .environ ["PY4CYTOSCAPE_DETAIL_LOGGER_DIR" ] = str (tempfile .gettempdir ())
89
910from pathlib import Path # noqa: E402
10- from typing import Any , Union # noqa: E402
11+ from typing import Any , Union , Optional # noqa: E402
1112
13+ import libsbml
1214import py4cytoscape as p4c # type: ignore # noqa: E402
1315from requests .exceptions import RequestException # noqa: E402
1416
@@ -30,19 +32,91 @@ def visualize_antimony(source: Union[Path, str], delete_session: bool = False) -
3032 visualize_sbml (Path (f_tmp .name ), delete_session = delete_session )
3133
3234
33- def visualize_sbml (sbml_path : Path , delete_session : bool = False ) -> None :
34- """Visualize SBML networks in cytoscape."""
35+ def visualize_sbml (sbml_path : Path , delete_session : bool = False ) -> Optional [int ]:
36+ """Visualize SBML networks in cytoscape.
37+
38+ Returns dictionary with "networks" and "views".
39+ """
40+ if sbml_path .suffix != ".xml" :
41+ console .error (f"SBML path { sbml_path } )
3542
3643 try :
3744 console .print (p4c .cytoscape_version_info ())
3845
3946 if delete_session :
4047 p4c .session .close_session (save_before_closing = False )
4148
42- p4c .networks .import_network_from_file (str (sbml_path ))
49+ networks_views = p4c .networks .import_network_from_file (str (sbml_path ))
50+ console .print (f"{ networks_views } )
51+ network = networks_views ["networks" ][1 ]
52+ p4c .set_current_view (network = network ) # set the base network
53+ return network
54+
55+ return networks_views
4356
4457 except RequestException :
4558 logger .error (
4659 "Could not connect to a running Cytoscape instance. "
4760 "Start Cytoscape before running the python script."
4861 )
62+ return None
63+
64+
65+
66+
67+
68+
69+
70+ def read_layout_xml (sbml_path : Path , xml_path : Path ) -> pd .DataFrame :
71+ """Read own xml layout information form cytoscape."""
72+ # read positions
73+ df : pd .DataFrame = pd .read_xml (xml_path , xpath = "//boundingBox" )
74+ df = df [['id' , 'xpos' , 'ypos' ]]
75+ df .rename (columns = {"xpos" : "x" , "ypos" : "y" }, inplace = True )
76+ df .set_index ("id" , inplace = True )
77+ return df
78+
79+ def apply_layout (network , layout : pd .DataFrame ) -> None :
80+ """Apply layout information from Cytoscape to SBML networks."""
81+
82+ # get SUIDs, sbml_id from node table;
83+ df_nodes = p4c .get_table_columns (table = "node" , columns = ["sbml id" ], network = network )
84+ console .print (df_nodes )
85+ sid2suid = {row ["sbml id" ]: suid for suid , row in df_nodes .iterrows ()}
86+ console .print (sid2suid )
87+
88+ # FIXME: necessary to check that all sids exist
89+ suids = [sid2suid [sid ] for sid in layout .index .values ]
90+ x_values = layout ["x" ].values .tolist ()
91+ y_values = layout ["y" ].values .tolist ()
92+
93+ # set positions
94+ # see: https://github.com/cytoscape/py4cytoscape/issues/144
95+ p4c .set_node_position_bypass (suids , new_x_locations = x_values , new_y_locations = y_values , network = network )
96+ # p4c.set_node_property_bypass(suids, new_values=x_values, visual_property='NODE_X_LOCATION', network=network)
97+ # p4c.set_node_property_bypass(suids, new_values=y_values, visual_property='NODE_Y_LOCATION', network=network)
98+ p4c .set_current_view (network = network )
99+
100+ # remove bypass
101+ # p4c.clear_node_property_bypass(suids, visual_property='NODE_X_LOCATION', network=network)
102+ # p4c.clear_node_property_bypass(suids, visual_property='NODE_Y_LOCATION', network=network)
103+
104+ # fit content
105+ p4c .fit_content ()
106+
107+
108+
109+ if __name__ == "__main__" :
110+ pass
111+ # # visual style
112+ # p4c.set_visual_style('Marquee')
113+ #
114+ # # fit the content
115+ # p4c.fit_content()
116+
117+ # p4c.load_table_data
118+
119+ # annotations!
120+
121+ # network_views.export_image
122+
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