def connect_rethink(self, **kwargs):
if self.database not in ['tdb', 'test_tdb', 'test']:
raise Exception("Cant download to this database: " + self.database)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host, self.auth_key)
self.rethink_io.check_table_exists(self.database, self.virus)
def connect_rethink(self, **kwargs):
if self.database not in ['tdb', 'test_tdb']:
raise Exception("Cant download to this database: " + self.database)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host, self.auth_key)
self.rethink_io.check_table_exists(self.database, self.virus)
def connect(self, **kwargs):
if self.database not in self.uploadable_databases:
raise Exception("Cant upload to this database: " + self.database, "add to list of databases allowed", self.uploadable_databases)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host, self.auth_key)
self.rethink_io.check_table_exists(self.database, self.viruses_table)
self.rethink_io.check_table_exists(self.database, self.sequences_table)
def connect_rethink(self, **kwargs):
if self.database not in ["vdb", "test_vdb", "test"]:
raise Exception("Can't download from this database: " + self.database)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host, self.auth_key)
self.rethink_io.check_table_exists(self.database, self.viruses_table)
self.rethink_io.check_table_exists(self.database, self.sequences_table)
def __init__(self, database, **kwargs):
self.upload_hour = 3
self.database = database.lower()
if 'database' in kwargs:
kwargs['database'] = self.database
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host, self.auth_key)
self.rethink_interact = rethink_interact()
def connect(self, **kwargs):
if self.database not in self.uploadable_databases:
raise Exception("Can't upload to this database: " + self.database,
"add to list of databases allowed",
self.uploadable_databases)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(
**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host,
self.auth_key)
self.rethink_io.check_table_exists(self.database, self.viruses_table)
self.rethink_io.check_table_exists(self.database, self.sequences_table)
def __init__(self, **kwargs):
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(
**kwargs)
self.rethink_interact = rethink_interact()
def __init__(self, **kwargs):
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(**kwargs)
self.rethink_interact = rethink_interact()
def __init__(self, database, virus, subtype, **kwargs):
parse.__init__(self, **kwargs)
flu_upload.__init__(self, database=database, virus=virus)
self.virus = virus.lower()
self.table = self.virus
if subtype is not None:
self.subtype = subtype.lower()
self.database = database.lower()
self.uploadable_databases = [
'tdb', 'test_tdb', 'test_tdb_2', 'cdc_tdb', 'test_cdc',
'vidrl_tdb', 'test_vidrl', 'crick_tdb', 'test_crick', 'niid_tdb',
'test_niid'
]
if self.database not in self.uploadable_databases:
raise Exception("Can't upload to this database: " + self.database,
"add to list of databases allowed",
self.uploadable_databases)
self.flu_upload = flu_upload(database=self.database, virus=self.virus)
self.rethink_io = rethink_io()
self.rethink_host, self.auth_key = self.rethink_io.assign_rethink(
**kwargs)
self.rethink_io.connect_rethink(self.database, self.rethink_host,
self.auth_key)
self.rethink_io.check_table_exists(self.database, self.virus)
self.strain_fix_fname = "source-data/flu_strain_name_fix.tsv"
self.HI_ref_name_abbrev_fname = "source-data/HI_ref_name_abbreviations.tsv"
# fields that are needed to upload
self.upload_fields = [
'virus_strain', 'serum_strain', 'serum_id', 'assay_type',
'assay_date', 'titer', 'timestamp'
]
self.optional_fields = [
'date', 'ref', 'virus_cdc_id', 'virus_passage',
'virus_passage_category', 'subtype', 'serum_host', 'serum_passage',
'serum_passage_category'
]
self.overwritable_fields = ['titer', 'date', 'ref']
self.index_fields = [
'virus_strain', 'serum_strain', 'serum_id', 'source',
'virus_passage_category', 'serum_passage_category', 'assay_type',
'assay_date'
]
self.ref_virus_strains = set()
self.ref_serum_strains = set()
self.test_virus_strains = set()
self.indexes = set()
self.virus_passage = set()
self.serum_passage = set()
self.strain_names = set()
self.assay_type = set()
self.different_date_format = [
'NIMR-REPORT-FEB2010_03.CSV', 'NIMR-REPORT-FEB2010_06.CSV',
'NIMR-REPORT-FEB2010_05.CSV', 'NIMR_Feb2010_15.csv',
'NIMR-REPORT-SEP2009_03.CSV', 'NIMR-REPORT-FEB2010_04.CSV',
'NIMR_FEB2010_15.CSV', 'NIMR_FEB2010_16.CSV',
'NIMR_Feb2010_16.csv', 'NIMR-report-Feb2010_03.csv',
'NIMR-report-Feb2010_06.csv', 'NIMR-report-Feb2010_05.csv',
'NIMR-report-Sep2009_03.csv', 'NIMR-report-Feb2010_04.csv'
]
self.new_different_date_format = set()
self.fix = set()
def __init__(self, **kwargs):
self.rethink_io = rethink_io()
def __init__(self, **kwargs):
self.rethink_io = rethink_io()