def advance_running_qc_pipeline(configs,pipeline,mockdb,*args,**kwargs):
"""
Determines which stage the pipeline currently is running, determines
if that stage is complete, and then passes the relevant
objects to subfunctions that handle the next step.
This needs to be combined with the other advance the pipeline function... A more general framework
where the process are stored.
"""
if pipeline.zcat_key is None: #zcat hasn't begun, which should not be the case.
pipeline.state = 'Initialized'
raise FormattingError("The pipeline somehow began running before zcatting.")
if pipeline.bcbio_key is None: #bcbio hasn't begun
zcat = mockdb['Zcat'].__get__(configs['system'],key=int(pipeline.zcat_key))
#print pipeline.zcat_key
#print zcat.__is_complete__(config)
if zcat.__is_complete__(configs):
things_to_do_if_zcat_complete(configs,mockdb,pipeline,zcat)
return 1
if pipeline.snp_stats_key is None: #snp_stats hasn't begun
bcbio = mockdb['Bcbio'].__get__(configs['system'],int(pipeline.bcbio_key))
if bcbio.__snps_called__():
things_to_do_if_snps_called(configs,mockdb,pipeline,bcbio)
return 1
if pipeline.cleaning_key is None: #cleaning hasn't begun
bcbio = mockdb['Bcbio'].__get__(configs['system'],int(pipeline.bcbio_key))
snp_stats = mockdb['SnpStats'].__get__(configs['system'],int(pipeline.snp_stats_key))
if configs["system"].get("Logging","debug") is "True":
print pipeline.key
print bcbio.__is_complete__(configs)
print snp_stats.__is_complete__(configs,mockdb)
if bcbio.__is_complete__(configs) and snp_stats.__is_complete__(configs,mockdb):
things_to_do_if_bcbio_complete(configs,mockdb,pipeline,bcbio)
things_to_do_if_snp_stats_complete(configs,mockdb,pipeline,snp_stats)
return 1
clean_bcbio = mockdb['CleanBcbio'].__get__(configs['system'],int(pipeline.cleaning_key))
if configs["system"].get("Logging","debug") is "True":
sys.stderr.write(pipeline.sample_key+"\n");
sys.stderr.write(clean_bcbio.key+"\n")
if clean_bcbio.__is_complete__():
things_to_do_if_bcbio_cleaning_complete(mockdb,pipeline,clean_bcbio,*args,**kwargs)
return 1
def advance_running_std_pipeline(configs,pipeline,mockdb,*args,**kwargs):
"""
Same as the advance_running_qc_pipeline function, except for any completely linear pipeline.
"""
if pipeline.zcat_key == None: #zcat hasn't begun, which should not be the case.
pipeline.state = 'Initialized'
raise FormattingError("The pipeline somehow began running before zcatting.")
if pipeline.bcbio_key == None: #bcbio hasn't begun
zcat = mockdb['Zcat'].__get__(configs['system'],key=int(pipeline.zcat_key))
if zcat.__is_complete__():
things_to_do_if_zcat_complete(configs,mockdb,pipeline,zcat)
return 1
if pipeline.cleaning_key is None: #cleaning hasn't begun
bcbio = mockdb['Bcbio'].__get__(configs['system'],int(pipeline.bcbio_key))
if bcbio.__is_complete__(configs):
things_to_do_if_bcbio_complete(configs,mockdb,pipeline,bcbio)
return 1
clean_bcbio = mockdb['CleanBcbio'].__get__(configs['system'],int(pipeline.cleaning_key))
if clean_bcbio.__is_complete__():
things_to_do_if_bcbio_cleaning_complete(mockdb,pipeline,clean_bcbio,*args,**kwargs)
return 1
