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)