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, 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, username=None, password=None, server=None, authSource='admin', database='datanator', max_entries=float('inf'), verbose=True, collection_str='sabio_compound', readPreference='nearest', replicaSet=None): super().__init__(MongoDB=server, db=database, verbose=verbose, max_entries=max_entries, username=username, password=password, authSource=authSource, readPreference=readPreference, replicaSet=replicaSet) self.file_manager = file_util.FileUtil() self.max_entries = max_entries self.verbose = verbose self.db = self.db_obj self.collection = self.db[collection_str] self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY) self.collection_str = collection_str
def setUpClass(cls): cls.cache_dirname = tempfile.mkdtemp() cls.db = 'datanator' conf = config.TestConfig() username = conf.USERNAME password = conf.PASSWORD MongoDB = conf.SERVER cls.MongoDB = MongoDB cls.username = username cls.password = password cls.src = query_kegg_orthology.QueryKO(server=cls.MongoDB, database=cls.db, verbose=True, max_entries=20, username=cls.username, password=cls.password) cls.file_manager = file_util.FileUtil()
def __init__(self, username=None, password=None, server=None, authSource='admin', src_database='datanator', max_entries=float('inf'), verbose=True, collection='sabio_reaction_entries', destination_database='datanator', cache_dir=None): ''' Args: src_database (:obj: `str`): name of database in which source collections reside destination_database (:obj: `str`): name of database to put the aggregated collection ''' super().__init__(MongoDB=server, db=destination_database, username=username, password=password, authSource=authSource) self.col = self.db_obj[collection] self.query_manager = query_sabiork_old.QuerySabioOld(MongoDB=server, password=password, authSource=authSource, username=username) self.metabolites_meta_manager = self.client[src_database]['metabolites_meta'] self.file_manager = file_util.FileUtil() self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY) self.verbose = verbose self.max_entries = max_entries
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, username=None, password=None, server=None, authSource='admin', database='datanator', max_entries=float('inf'), verbose=True, collection_str='uniprot', readPreference='nearest', replicaSet=None): super().__init__(MongoDB=server, username=username, password=password, authSource=authSource, db=database, readPreference=readPreference, replicaSet=replicaSet) self.taxon_manager = query_taxon_tree.QueryTaxonTree( MongoDB=server, username=username, password=password, authSource=authSource, db=database, replicaSet=replicaSet) self.taxon_col = self.db_obj['taxon_tree'] self.kegg_manager = query_kegg_orthology.QueryKO(username=username, password=password, server=server, authSource=authSource, replicaSet=replicaSet) self.file_manager = file_util.FileUtil() self.max_entries = max_entries self.verbose = verbose self.collection = self.db_obj[collection_str] self.paxdb_collection = self.db_obj['pax'] self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY) self.collection_str = collection_str
def __init__(self, MongoDB=None, db=None, collection_str=None, username=None, password=None, authSource='admin', readPreference='nearest', verbose=True, replicaSet=None): super().__init__(MongoDB=MongoDB, db=db, verbose=verbose, username=username, password=password, authSource=authSource, readPreference=readPreference, replicaSet=replicaSet) self.file_manager = file_util.FileUtil() self._collection = self.db_obj[collection_str] self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY)
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 = file_util.FileUtil()