def kegg_manager(self):
return query_kegg_orthology.QueryKO(
username=config.AtlasConfig.USERNAME,
password=config.AtlasConfig.PASSWORD,
server=config.AtlasConfig.SERVER,
authSource=config.AtlasConfig.AUTHDB,
readPreference=config.AtlasConfig.READ_PREFERENCE,
verbose=False,
replicaSet=config.AtlasConfig.REPLSET)
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, 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, server, src_db='datanator', des_db='datanator', collection_str='uniprot',
username=None, password=None, readPreference='nearest', authSource='admin', verbose=True,
max_entries=float('inf')):
super().__init__(MongoDB=server, db=des_db, verbose=verbose, max_entries=max_entries,
username=username, password=password, authSource=authSource,
readPreference=readPreference)
self.collection_str = collection_str
self.max_entries = max_entries
self.verbose = verbose
self.des_client, self.des_db, self.des_collection = self.con_db(collection_str)
self.koc_manager = query_kegg_organism_code.QueryKOC(username=username, password=password,
server=server, authSource=authSource, collection_str='kegg_organism_code', readPreference=readPreference,
database=src_db)
self.uniprot_manager = query_uniprot.QueryUniprot(username=username, password=password, server=server,
authSource=authSource, database=src_db, collection_str='uniprot', readPreference=readPreference)
self.kegg_manager = query_kegg_orthology.QueryKO(username=username, password=password, server=server,
authSource=authSource, database=src_db, max_entries=max_entries, verbose=verbose, readPreference=readPreference)
self.protein_manager = query_protein.QueryProtein(username=username, password=password, server=server,
authSource=authSource, database=src_db, max_entries=max_entries, verbose=verbose, readPreference=readPreference)
self.uniprot_nosql_manager = uniprot_nosql.UniprotNoSQL(MongoDB=server, db=des_db, max_entries=max_entries,
verbose=verbose, username=username, password=password, authSource=authSource)
self.endpoint = 'https://www.kegg.jp/ssdb-bin/ssdb_best?org_gene='
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)