def __init__(self,
cache_dirname=None,
collection_str='taxon_tree',
verbose=False,
max_entries=float('inf'),
username=None,
MongoDB=None,
password=None,
db='datanator-test',
authSource='admin',
readPreference='nearest',
replicaSet=None):
self.collection_str = collection_str
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
replicaSet=replicaSet)
self.pipeline_manager = pipelines.Pipeline()
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[self.collection_str]
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db=None,
collection_str='metabolites_meta',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
self._collection_str = collection_str
self.verbose = verbose
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self._collection = self.client.get_database(
"datanator-test")[collection_str]
self.e_client, self.e_db_obj, self.e_collection = self.con_db('ecmdb')
self.y_client, self.y_db_obj, self.y_collection = self.con_db('ymdb')
self.file_manager = file_util.FileUtil()
self.chem_manager = chem_util.ChemUtil()
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='sabio_rk_old',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
self.max_entries = max_entries
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.u = self.client["datanator-test"]["uniprot"]
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[collection_str]
self.collection_str = collection_str
self.taxon_manager = query_taxon_tree.QueryTaxonTree(
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
MongoDB=MongoDB,
replicaSet=replicaSet)
self.compound_manager = query_sabio_compound.QuerySabioCompound(
server=MongoDB,
database=db,
username=username,
password=password,
readPreference=readPreference,
authSource=authSource,
replicaSet=replicaSet)
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='pax',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
"""Instantiating query_pax
Args:
cache_dirname (str, optional): temparory cache director. Defaults to None.
MongoDB (str, optional): mongodb server address. Defaults to None.
replicaSet (str, optional): name of mongodb replicaset. Defaults to None.
db (str, optional): name of database in which pax collection resides. Defaults to 'datanator'.
collection_str (str, optional): name of collection. Defaults to 'pax'.
verbose (bool, optional): display verbose messages. Defaults to False.
max_entries (float, optional): max number of operations, mainly used for tests. Defaults to float('inf').
username (str, optional): db authentication username. Defaults to None.
password (str, optional): db authentication password. Defaults to None.
authSource (str, optional): authentication database. Defaults to 'admin'.
readPreference (str, optional): mongodb readpreference. Defaults to 'primary'.
"""
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.max_entries = max_entries
self.verbose = verbose
self.collection = self.db_obj[collection_str]
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db=None,
verbose=True,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin',
readPreference='nearest'):
self.verbose = verbose
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.client_ecmdb, self.db_ecmdb, self.collection_ecmdb = self.con_db(
'ecmdb')
self.client_ymdb, self.db_ymdb, self.collection_ymdb = self.con_db(
'ymdb')
self.metabolites_meta_manager = query_metabolites_meta.QueryMetabolitesMeta(
cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
collection_str='metabolites_meta',
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference)
self.chem_manager = chem_util.ChemUtil()
def __init__(self,
cache_dirname=None,
MongoDB=None,
replicaSet=None,
db='datanator',
collection_str='sabio_rk',
verbose=False,
max_entries=float('inf'),
username=None,
password=None,
authSource='admin'):
self.max_entries = max_entries
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
replicaSet=replicaSet,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource)
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[collection_str]
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.src = chem_util.ChemUtil()