def create_cjson(self,
user,
cjson,
props,
molecule_id=None,
image=None,
input_parameters=None,
file_id=None,
public=False,
notebooks=None):
if notebooks is None:
notebooks = []
calc = {'cjson': cjson, 'properties': props, 'notebooks': notebooks}
if molecule_id:
calc['moleculeId'] = molecule_id
if file_id:
calc['fileId'] = file_id
if image is not None:
calc['image'] = image
if input_parameters is not None:
calc.setdefault('input', {})['parameters'] = input_parameters
calc.setdefault(
'input',
{})['parametersHash'] = oc.hash_object(input_parameters)
calc['creatorId'] = user['_id']
self.setUserAccess(calc, user=user, level=AccessType.ADMIN)
if public:
self.setPublic(calc, True)
return self.save(calc)
def create_cjson(self, user, cjson, props, molecule_id= None,
image=None, input_parameters=None,
file_id = None, public=False, notebooks=None):
if notebooks is None:
notebooks = []
calc = {
'cjson': cjson,
'properties': props,
'notebooks': notebooks
}
if molecule_id:
calc['moleculeId'] = molecule_id
if file_id:
calc['fileId'] = file_id
if image is not None:
calc['image'] = image
if input_parameters is not None:
calc.setdefault('input', {})['parameters'] = input_parameters
calc.setdefault('input', {})['parametersHash'] = oc.hash_object(input_parameters)
self.setUserAccess(calc, user=user, level=AccessType.ADMIN)
if public:
self.setPublic(calc, True)
return self.save(calc)
def findcal(self, molecule_id=None, geometry_id=None, image_name=None,
input_parameters=None, input_geometry_hash=None,
name=None, inchi=None, inchikey=None, smiles=None,
formula=None, creator_id=None, pending=None, limit=None,
offset=None, sort=None, user=None):
# Set these to their defaults if they are not already set
limit, offset, sort = default_pagination_params(limit, offset, sort)
query = {}
# If a molecule id is specified it has higher priority
if molecule_id:
query['moleculeId'] = ObjectId(molecule_id)
# Otherwise, if query parameters for the molecules are
# specified, search for matching molecules first
elif any((name, inchi, inchikey, smiles, formula)):
params = {'offset': 0, 'limit': sys.maxsize}
if name:
params['name'] = name
if inchi:
params['inchi'] = inchi
if inchikey:
params['inchikey'] = inchikey
if smiles:
params['smiles'] = smiles
if formula:
params['formula'] = formula
molecules = MoleculeModel().find_molecule(params)['results']
molecule_ids = [molecule['_id'] for molecule in molecules]
query['moleculeId'] = {'$in': molecule_ids}
if geometry_id:
# This is currently not being stored as an ObjectId
query['geometryId'] = geometry_id
if image_name:
repository, tag = oc.parse_image_name(image_name)
query['image.repository'] = repository
query['image.tag'] = tag
if input_parameters:
input_json = json.loads(urllib.parse.unquote(input_parameters))
query['input.parametersHash'] = oc.hash_object(input_json)
if input_geometry_hash:
query['input.geometryHash'] = input_geometry_hash
if creator_id:
query['creatorId'] = ObjectId(creator_id)
if pending is not None:
pending = toBool(pending)
query['properties.pending'] = pending
# The absence of the field mean the calculation is not pending ...
if not pending:
query['properties.pending'] = {
'$ne': True
}
fields = ['image', 'input', 'code',
'cjson', 'cjson.vibrations.modes', 'cjson.vibrations.intensities',
'cjson.vibrations.frequencies', 'properties', 'fileId', 'access',
'moleculeId', 'public']
calcs = self.find(query, fields=fields, limit=limit,
offset=offset, sort=sort)
num_matches = calcs.collection.count_documents(query)
calcs = self.filterResultsByPermission(calcs, user,
AccessType.READ, limit=limit)
calcs = [self.filter(x, user) for x in calcs]
return search_results_dict(calcs, num_matches, limit, offset, sort)