def validate(self):
is_valid = super(Form, self).validate()
analysis = Analysis.query(Analysis.title == self.title.data).first()
if analysis is None:
return is_valid
return False
def launch_fba(username):
data = request.get_json(force=True)
logging.debug(data)
model_name = data['model']
project_id = data['project_id']
title = data['title']
model = Biomodel.query.filter(Biomodel.name == model_name).first_or_404()
# have often exception here du to encoding issues
sbml_model = model.get_cobra_model()
if sbml_model is None:
return render_template('errors/server_error.html', form=LoginForm())
solution = _launch_fba(sbml_model,
data['objective_functions'],
data['constraints'])
# create analysis object
a = Analysis(title=data['title'],
kind=Analysis.KIND[0],
model_id=model.id,
project_id=project_id)
a.results_content = solution.status
a.serialized_properties = json.dumps(data)
# in order to populate its id field
a.save()
# building several path local and s3 path
filename = "{}-{}-{}".format(username, project_id, a.id)
results_url = filename.replace('-', '/')
# dump solution to file
d = {'status': solution.status, 'objective_value': solution.f,
'x_dict': solution.x_dict, 'y_dict': solution.y_dict}
with open(filename, 'w') as f:
f.write(json.dumps(d).encode('utf-8'))
# upload to s3
logging.info('uploading to s3')
s3_upload_from_server(filename, destination_filename=results_url)
# finally save analysis object
logging.info('saving analysis')
a.results_url = results_url
a.save()
# remove created file
logging.info('removing created file...')
try:
os.remove(filename)
logging.warn('Done')
except OSError:
logging.warn('Enable to remove "{}"'.format(filename))
logging.warn('Failed !')
flash('FBA analysis {} saved...'.format(title), 'success')
return json.dumps({'redirect': url_for('user.profile', username=username)})
