def setUpClass(cls): cls.cache_dirname = tempfile.mkdtemp() cls.db = 'test' conf = config.TestConfig() cls.username = conf.USERNAME cls.password = conf.PASSWORD cls.MongoDB = conf.SERVER cls.src = query_taxon_tree.QueryTaxonTree( cache_dirname=cls.cache_dirname, MongoDB=cls.MongoDB, db=cls.db, collection_str='test_taxon_tree', verbose=True, max_entries=20, username = cls.username, password = cls.password, readPreference='primary') dic_0 = {'tax_id': 0, 'tax_name': 's0', 'anc_id': [5,4,3,2,1], 'anc_name': ['s5', 's4', 's3', 's2', 's1']} dic_1 = {'tax_id': 1, 'tax_name': 's1', 'anc_id': [5,4,3,2], 'anc_name': ['s5', 's4', 's3', 's2']} dic_2 = {'tax_id': 2, 'tax_name': 's2', 'anc_id': [5,4,3], 'anc_name': ['s5', 's4', 's3']} dic_3 = {'tax_id': 3, 'tax_name': 's3', 'anc_id': [5,4], 'anc_name': ['s5', 's4']} dic_4 = {'tax_id': 4, 'tax_name': 's4', 'anc_id': [5], 'anc_name': ['s5']} dic_5 = {'tax_id': 5, 'tax_name': 's5', 'anc_id': [], 'anc_name': []} dic_6 = {'tax_id': 6, 'tax_name': 's6', 'anc_id': [5,4,3,2], 'anc_name': ['s5', 's4', 's3', 's2']} dic_7 = {'tax_id': 7, 'tax_name': 's7', 'anc_id': [5,4,3,2,6], 'anc_name': ['s5', 's4', 's3', 's2', 's6']} dic_8 = {'tax_id': 8, 'tax_name': 's8', 'anc_id': [5,4,3,2,6,7], 'anc_name': ['s5', 's4', 's3', 's2', 's6', 's7']} dic_9 = {'tax_id': 9, 'tax_name': 's9', 'anc_id': [5,4,3], 'anc_name': ['s5', 's4', 's3']} dic_10 = {'tax_id': 10, 'tax_name': 's10', 'anc_id': [5,4,3,9], 'anc_name': ['s5', 's4', 's3', 's9']} dic_11 = {'tax_id': 11, 'tax_name': 's11', 'anc_id': [5,4,3,2,1,0], 'anc_name': ['s5', 's4', 's3', 's2', 's1', 's0']} dic_12 = {'tax_id': 12, 'tax_name': 's12', 'anc_id': [5,4,3,2,1,0], 'anc_name': ['s5', 's4', 's3', 's2', 's1', 's0']} dic_13 = {'tax_id': 13, 'tax_name': 's13', 'anc_id': [5,4,3,2,1], 'anc_name': ['s5', 's4', 's3', 's2', 's1']} cls.src.collection.insert_many([dic_0,dic_1,dic_2,dic_3,dic_4, dic_5,dic_6,dic_7,dic_8,dic_9,dic_10,dic_11,dic_12,dic_13])
def txn_manager(self): return query_taxon_tree.QueryTaxonTree( username=config.AtlasConfig.USERNAME, password=config.AtlasConfig.PASSWORD, MongoDB=config.AtlasConfig.SERVER, authSource=config.AtlasConfig.AUTHDB, readPreference=config.AtlasConfig.READ_PREFERENCE, replicaSet=config.AtlasConfig.REPLSET)
def setUpClass(cls): cls.cache_dirname = tempfile.mkdtemp() cls.db = 'datanator' conf = config.TestConfig() cls.username = conf.USERNAME cls.password = conf.PASSWORD cls.MongoDB = conf.SERVER cls.src = query_taxon_tree.QueryTaxonTree( cache_dirname=cls.cache_dirname, MongoDB=cls.MongoDB, db=cls.db, verbose=True, max_entries=20, username = cls.username, password = cls.password, readPreference='nearest')
def __init__(self, MongoDB=None, db=None, max_entries=float('inf'), verbose=False, username=None, password=None, authSource='admin', replicaSet=None, collection_str='uniprot'): self.url = 'http://www.uniprot.org/uniprot/?fil=reviewed:yes' self.query_url = 'https://www.uniprot.org/uniprot/?query=' self.MongoDB = MongoDB self.db = db self.max_entries = max_entries self.collection_str = collection_str super(UniprotNoSQL, self).__init__(MongoDB=MongoDB, db=db, username=username, password=password, authSource=authSource, replicaSet=replicaSet, verbose=verbose, max_entries=max_entries) self.taxon_manager = query_taxon_tree.QueryTaxonTree(username=username, MongoDB=MongoDB, password=password, authSource=authSource) self.ko_manager = query_kegg_orthology.QueryKO(username=username, password=password, server=MongoDB, authSource=authSource, verbose=verbose, max_entries=max_entries) self.sabio_manager = query_sabiork.QuerySabio(MongoDB=MongoDB, username=username, password=password, authSource=authSource) self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY) self.collection = self.db_obj[collection_str] self.verbose = verbose
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, 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 __init__(self, username=None, password=None, server=None, authSource='admin', src_database='datanator', max_entries=float('inf'), verbose=True, collection='protein', 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 ''' self.max_entries = max_entries self.verbose = verbose self.cache_dir = cache_dir self.mongo_manager = mongo_util.MongoUtil(MongoDB=server, username=username, password=password, authSource=authSource, db=src_database) self.pax_manager = query_pax.QueryPax(MongoDB=server, db=src_database, collection_str='pax', verbose=verbose, max_entries=max_entries, username=username, password=password, authSource=authSource) self.kegg_manager = query_kegg_orthology.QueryKO( server=server, database=src_database, verbose=verbose, max_entries=max_entries, username=username, password=password, authSource=authSource) self.taxon_manager = query_taxon_tree.QueryTaxonTree( collection_str='taxon_tree', verbose=verbose, max_entries=max_entries, username=username, MongoDB=server, password=password, db=src_database, authSource=authSource) self.protein_manager = query_protein.QueryProtein( username=username, password=password, server=server, collection_str='protein', max_entries=max_entries, database=src_database) self.client, self.db, self.col = mongo_util.MongoUtil( MongoDB=server, username=username, password=password, authSource=authSource, db=destination_database).con_db(collection) self.bad_kinlawid = [ 24416, 24417, 24418, 24419, 24420, 24421, 24422, 24423 ] self.collation = Collation(locale='en', strength=CollationStrength.SECONDARY)