def __init__(self,
username=None,
password=None,
server=None,
authSource='admin',
src_database='datanator',
dest_database=None,
max_entries=float('inf'),
verbose=True,
src_collection='sabio_compound',
dest_collection=None,
cache_dir=None):
'''
Args:
src_database (:obj: `str`): name of database in which source collections reside
'''
self.mongo_manager = mongo_util.MongoUtil(MongoDB=server,
username=username,
password=password,
authSource=authSource,
db=src_database)
self.file_manager = file_util.FileUtil()
self.chem_manager = chem_util.ChemUtil()
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
self.verbose = verbose
self.max_entries = max_entries
self.src_collection = src_collection
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db=None,
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
meta_loc=None):
self.cache_dirname = cache_dirname
self.verbose = verbose
self.MongoDB = MongoDB
self.replicaSet = replicaSet
self.max_entries = max_entries
self.username = username
self.password = password
self.authSource = authSource
self.meta_loc = meta_loc
super(MetabolitesMeta, self).__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource)
self.frequency = 50
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.ymdb_query = query_xmdb.QueryXmdb(username=username,
password=password,
server=MongoDB,
authSource=authSource,
database=db,
collection_str='ymdb',
readPreference='nearest')
self.ecmdb_query = query_xmdb.QueryXmdb(username=username,
password=password,
server=MongoDB,
authSource=authSource,
database=db,
collection_str='ecmdb',
readPreference='nearest')
self.collation = Collation('en', strength=CollationStrength.SECONDARY)
self.client, self.db, self.collection = self.con_db('metabolites_meta')
def main():
db = 'datanator'
username = datanator.config.core.get_config()['datanator']['mongodb']['user']
password = datanator.config.core.get_config()['datanator']['mongodb']['password']
server = datanator.config.core.get_config()['datanator']['mongodb']['server']
port = datanator.config.core.get_config()['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config()['datanator']['mongodb']['replSet']
manager = CalcTanimoto(
MongoDB=server, replicaSet=replSet, db=db,
verbose=True, password=password, username=username)
chem_manager = chem_util.ChemUtil()
# manager.many_to_many(field1 = 'inchi', field2 = 'inchi')
# one-time update for adp
inchi = 'InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1'
sorted_coeff, sorted_inchi = manager.one_to_many(inchi)
_, _, collection = manager.con_db('metabolites_meta')
for key, val in zip(sorted_inchi, sorted_coeff):
dic = {key: val}
collection.update_one({'inchi': inchi},
{'$push': {'similar_compounds': dic} })
def __init__(self,
db=None,
MongoDB=None,
cache_directory=None,
verbose=False,
max_entries=float('inf'),
replicaSet=None,
username=None,
password=None,
authSource='admin'):
'''
Attributes:
cache_directory: JSON file (converted from sqlite) directory
db: mongodb database name
MongoDB: MongoDB server address and login e.g. 'mongodb://mongo:27017/'
'''
self.db = db
self.MongoDB = MongoDB
self.cache_directory = cache_directory
self.verbose = verbose
self.max_entries = max_entries
self.collection_str = 'sabio_rk_old'
super(SabioRkNoSQL, self).__init__(cache_dirname=cache_directory,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource)
self.client, self.db_obj, self.collection = self.con_db(
self.collection_str)
self.sabio_reaction_entries = self.db_obj['sabio_reaction_entries']
self.kegg_collection = self.db_obj['kegg_orthology']
self.sabiork_manager = query_sabiork.QuerySabio(
MongoDB=MongoDB,
db=db,
collection_str='sabio_rk',
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource)
self.protein_manager = query_protein.QueryProtein(
username=username,
password=password,
server=MongoDB,
authSource=authSource,
database=db,
max_entries=max_entries,
verbose=verbose,
collection_str='uniprot',
readPreference='nearest')
self.ec = self.db_obj['ec']
self.chem_manager = chem_util.ChemUtil()
self.tax_manager = query_taxon_tree.QueryTaxonTree(username=username,
MongoDB=MongoDB,
password=password)
self.file_manager = file_util.FileUtil()
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.src = chem_util.ChemUtil()