def get_cobra_model(self):
if self.kegg_org is not None:
model = BiomodelMongo.objects(organism=self.kegg_org).first()
else:
model = BiomodelMongo.objects(name=self.name).first()
# try to load the cobra model
cobra_model = None
try:
cobra_model = cobra.io._from_dict(model.cobra_model)
except Exception as e:
logging.error(e)
return cobra_model
def insert_model(xml_model):
import cobra.io
import json
sbml_model = cobra.io.read_sbml_model(xml_model)
# cobra.io.save_json_model(sbml_model, 'test.json')
# d = json.loads(open('test.json').read().encode('utf-8'))
d = cobra.io._to_dict(sbml_model)
infos = retrieve_kegg_org_id(xml_model)
if infos is None:
logging.warn('No infos found')
return False
kegg_org_id, model_name = infos['kegg_org_id'], infos['model_name']
if kegg_org_id is None or model_name is None:
return False
biomodel = BiomodelMongo(name=model_name, organism=kegg_org_id, cobra_model=d)
biomodel.save()
return True
def test_read_models():
m = BiomodelMongo.objects(organism='sse').first()
import cobra.io
import json
try:
# s = json.dumps(m.cobra_model).encode('utf-8')
# with open('test.json', 'w') as f:
# f.write(s)
sbml_model = cobra.io._from_dict(m.cobra_model)
#sbml_model = cobra.io.load_json_model('test.json')
except Exception as e:
print "Got an exception:", e
return None
print "NOTES:", sbml_model.reactions[1].notes
return sbml_model
