def create(self, params):
body = self.getBodyJson()
user = self.getCurrentUser()
public = body.get('public', True)
gen3d = body.get('generate3D', True)
gen3d_forcefield = body.get('gen3dForcefield', 'mmff94')
gen3d_steps = body.get('gen3dSteps', 100)
provenance = body.get('provenance', 'uploaded by user')
mol = None
if 'fileId' in body:
file_id = body['fileId']
file = ModelImporter.model('file').load(file_id, user=user)
parts = file['name'].split('.')
input_format = parts[-1]
name = '.'.join(parts[:-1])
if input_format not in Molecule.input_formats:
raise RestException('Input format not supported.', code=400)
with File().open(file) as f:
data_str = f.read().decode()
mol = create_molecule(data_str, input_format, user, public, gen3d,
provenance, gen3d_forcefield, gen3d_steps,
body)
elif 'inchi' in body:
input_format = 'inchi'
data = body['inchi']
if not data.startswith('InChI='):
data = 'InChI=' + data
mol = create_molecule(data, input_format, user, public, gen3d,
provenance, gen3d_forcefield, gen3d_steps,
body)
for key in body:
if key in Molecule.input_formats:
input_format = key
data = body[input_format]
# Convert to str if necessary
if isinstance(data, dict):
data = json.dumps(data)
mol = create_molecule(data, input_format, user, public, gen3d,
provenance, gen3d_forcefield,
gen3d_steps, body)
break
if not mol:
raise RestException('Invalid request', code=400)
return self._clean(mol)
def search(self, params):
limit, offset, sort = parse_pagination_params(params)
query_string = params.get('q')
formula = params.get('formula')
cactus = params.get('cactus')
if query_string is None and formula is None and cactus is None:
raise RestException(
'Either \'q\', \'formula\' or \'cactus\' is required.')
if query_string is not None:
try:
mongo_query = query.to_mongo_query(query_string)
except query.InvalidQuery:
raise RestException('Invalid query', 400)
fields = ['inchikey', 'smiles', 'properties', 'name']
cursor = MoleculeModel().find(query=mongo_query,
fields=fields,
limit=limit,
offset=offset,
sort=sort)
mols = [x for x in cursor]
num_matches = cursor.collection.count_documents(mongo_query)
return search_results_dict(mols, num_matches, limit, offset, sort)
elif formula:
# Search using formula
return MoleculeModel().findmol(params)
elif cactus:
if getCurrentUser() is None:
raise RestException('Must be logged in to search with cactus.')
# Disable cert verification for now
# TODO Ensure we have the right root certs so this just works.
r = requests.get(
'https://cactus.nci.nih.gov/chemical/structure/%s/file?format=sdf'
% cactus,
verify=False)
if r.status_code == 404:
return []
else:
r.raise_for_status()
sdf_data = r.content.decode('utf8')
provenance = 'cactus: ' + cactus
mol = create_molecule(sdf_data,
'sdf',
getCurrentUser(),
True,
provenance=provenance)
return search_results_dict([mol], 1, limit, offset, sort)
def create_calc(self, params):
body = getBodyJson()
if 'cjson' not in body and ('fileId' not in body
or 'format' not in body):
raise RestException('Either cjson or fileId is required.')
user = getCurrentUser()
cjson = body.get('cjson')
props = body.get('properties', {})
molecule_id = body.get('moleculeId', None)
geometry_id = body.get('geometryId', None)
public = body.get('public', True)
notebooks = body.get('notebooks', [])
image = body.get('image')
input_parameters = body.get('input', {}).get('parameters')
if input_parameters is None:
input_parameters = body.get('inputParameters', {})
file_id = None
file_format = body.get('format', 'cjson')
if 'fileId' in body:
file = File().load(body['fileId'], user=getCurrentUser())
file_id = file['_id']
cjson = self._file_to_cjson(file, file_format)
if molecule_id is None:
mol = create_molecule(json.dumps(cjson),
'cjson',
user,
public,
parameters=input_parameters)
molecule_id = mol['_id']
calc = CalculationModel().create_cjson(
user,
cjson,
props,
molecule_id,
geometry_id=geometry_id,
image=image,
input_parameters=input_parameters,
file_id=file_id,
notebooks=notebooks,
public=public)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] \
= '/calculations/%s' % (str(calc['_id']))
return CalculationModel().filter(calc, user)