def __is_complete__(self,configs,mockdb,*args,**kwargs):
"""
Since concordance search is an optional sub-process, this function checks for
both the completeness of the self concordance program and the necessity,
and if necessary the completeness, of the concordance search. Then, once
complete, relevant statistics are stored.
"""
if GenericProcess.__is_complete__(self,*args,**kwargs):
return True
elif not os.path.isfile(self.complete_file):
return False
store_snp_stats_in_db(self)
if self.percentage_concordance > configs['pipeline'].get('Concordance','threshold'):
self.__finish__(*args,**kwargs)
return True
#If the concordance is below the threshold, we need to conduct a concordance search against the database
#First we split the search across processors
if self.search_key is None:
sample = mockdb['Sample'].objects[self.sample_key]
concord_search = mockdb['ConcordanceSearch'].__new__(configs['system'],sample=sample,snp_stats=self)
self.search_key = concord_search.key
concord_search.__launch_split_searches__(configs)
return False
concord_search = mockdb['ConcordanceSearch'].objects[self.search_key]
if concord_search.__is_complete__(configs['system'],*args,**kwargs):
self.__finish__(*args,**kwargs)
return True
#Now we gather
if concord_search.__are_split_searches_complete__(configs['pipeline']):
if os.path.isfile(concord_search.qsub_file):
return False
concord_search.__fill_qsub_file__(configs)
concord_search.__launch__(configs['system'])
return False
return False
def things_to_do_if_snp_stats_complete(configs,mockdb,pipeline,snp_stats):
store_snp_stats_in_db(snp_stats)
snp_stats.__finish__()
if snp_stats.search_key is None:
return 1
search = mockdb['ConcordanceSearch'].__get__(configs['system'],snp_stats.search_key)
store_search_stats_in_db(search)
search.state = "Complete"
return 1
