def from_mol(self) -> dict:
if self.get('extension') in ('mol', 'sdf', 'mdl'):
mol = Chem.MolFromMolBlock(self.get('block'),
sanitize=True,
removeHs=False,
strictParsing=True)
elif self.get('extension') in ('mol2', ):
mol = Chem.MolFromMol2Block(self.get('block'),
sanitize=True,
removeHs=False)
elif self.get('extension') in ('pdb', ):
mol = Chem.MolFromPDBBlock(self.get('block'),
sanitize=True,
removeHs=False,
proximityBonding=False)
else:
raise exc.HTTPClientError(
f"Format {self.get('extension')} not supported")
if self.get_bool('protons') is True:
mol = AllChem.AddHs(mol)
p = Params.from_mol(mol,
self.name,
generic=self.generic,
atomnames=self.atomnames)
return self.to_dict(p)
def generate_report(request):
"""Generates xlsx report
"""
try:
user_id = request.user
lang = rt.language(user_id)
except KeyError:
raise http_exc.HTTPUnauthorized()
try:
project = rt.get_state(user_id)._project_id
# TODO remove test project
if project is None:
project = request.json_body['data']['project']
rt.update_state(user_id, tool_id='forecast', project_id=project)
wb = rt.get_wb(user_id)
session = request.dbsession
permission_tree = build_permission_tree(session, project_name=project)
scenarios = get_scenarios(session, user_id, None)
for scenario in scenarios:
scenario['details'] = get_scenario_details(session, user_id, scenario['id'])
options = reporting.get_options_data(config=wb.data_config, scenarios=scenarios)
data = reporting.collect_report_data(options=options, permission_tree=permission_tree,
container=wb.default_container, config=wb.data_config,
entities_ids=wb.selection, lang=lang)
reporting.create_report(request.json_body['data']['file_name'], data)
except Exception:
raise http_exc.HTTPClientError()
else:
return Response(json_body=json.dumps('Success'), content_type='application/json')
def name(self) -> str:
if 'name' in self.request.params:
name = self.request.params['name']
name = re.sub('\W', '', name)
if len(name) != 3:
raise exc.HTTPClientError(
f'{self.request.params["name"]} ("{name}") is not three letters long.'
)
else:
return name
else:
return 'LIG'
def ajacean(self) -> dict:
try:
mode = self.request.matchdict['mode']
if mode == 'smiles':
return self.from_smiles()
elif mode == 'mol':
return self.from_mol()
elif mode == 'smiles_pdb':
return self.from_pdb()
else:
raise exc.HTTPClientError(f'Unknown mode `{mode}`')
except exc.HTTPError as error:
self.request.response.status_code = error.status_code
return {'error': f'{error.__class__.__name__}: {error}'}
except Exception as error:
log.exception(f'{error.__class__.__name__}: {error}')
return {'error': f'{error.__class__.__name__}: {error}'}
def get_report_options(request):
"""Returns options for report
"""
try:
user_id = request.user
except KeyError:
raise http_exc.HTTPUnauthorized()
try:
# project = rt.get_state(user_id)._project_id
wb = rt.get_wb(user_id)
session = request.dbsession
# permission_tree = build_permission_tree(session, project_name=project)
# filters = {'authors': ['default_user'], 'period': [], 'criteria': []}
scenarios = get_scenarios(session, user_id, None)
for scenario in scenarios:
scenario['details'] = get_scenario_details(session, user_id, scenario['id'])
data = reporting.get_options_data(config=wb.data_config, scenarios=scenarios)
except Exception:
raise http_exc.HTTPClientError()
else:
return Response(json_body=json.dumps(data), content_type='application/json')
def get(self, key):
if key in self.request.params:
return self.request.params[key]
else:
raise exc.HTTPClientError(
f'Query parameter {key} was not provided.')