def get_kgml(username):
"""
main function to visualize network
return json encoded graph
"""
pathway_id = request.args.get('pathway_id')
if pathway_id is None:
return json.dumps([])
analysis_id = request.args.get('analysis_id')
analysis = Analysis.query.filter(Analysis.id == analysis_id).first_or_404()
# retrieve file data from s3
filename = '{}/{}/{}'.format(username, analysis.project_id, analysis_id)
try:
resp = requests.get(S3_URL + filename)
except ConnectionError:
return render_template('errors/server_error.html', form=LoginForm())
# return error code if request failed
if resp.status_code != 200:
return render_template('errors/server_error.html', form=LoginForm())
# load fba analysis results
results = json.loads(resp.text)
# get the sbml model
model = analysis.model.get_cobra_model()
if model is None:
return render_template('errors/server_error.html')
if pathway_id == 'whole':
# whole drawing requested
cytoscape_formatted = _build_genome_scale_network(model, results)
else:
kegg_model = Kegg.get_kgml_obj(pathway_id)
if model is None or kegg_model is None:
return render_template('errors/page_not_found.html', form=LoginForm())
kegg_model_name = request.args.get('pathway_name')
cytoscape_formatted = build_kegg_network_mixed(kegg_model,
kegg_model_name,
model,
results)
return json.dumps(cytoscape_formatted)
