for object_key, object in collection.objects.iteritems():
try:
if object.sample_key == orig_sample_key:
object.sample_key = new_sample_key
count += 1
except AttributeError:
pass
return count
def rename_sample_key(config,mockdb,orig_sample_key,new_sample_key):
collection_clses = child_classes(Sample,config=config) + [Sample]
for cls in collection_clses:
collection = mockdb[cls.__name__]
for object_key, object in collection.objects.iteritems():
if object.key == orig_sample_key:
object.key = new_sample_key
return 1
if __name__ == '__main__':
#Handle arguments
parser = argparse.ArgumentParser(description='Puts the project-summary.csv info into the bcbio database')
parser.add_argument('sample_key', type=str, help='The sample name as it currently is in the database')
parser.add_argument('new_key', type=str, help='The sample name to which the sample_key will be renamed')
args = parser.parse_args()
config = ConfigParser.ConfigParser()
config.read('/home/sequencing/src/pipeline_project/pipeline/config/qc_on_ihg.cfg')
mockdb = initiate_mockdb(config)
rename_all_sample_keys(mockdb,args.sample_key,args.new_key)
rename_sample_key(config,mockdb,args.sample_key,args.new_key)
save_mockdb(config,mockdb)
configs.update({'system':system_config})
config_instance = MyConfigParser()
configs.update({"seq_run":config_instance})
config_instance.read(system_config.get('Pipeline',"seq_run"))
pipelines = system_config.get('Pipeline','opts').split(',')
pipeline_config = {}
for pipeline_name in pipelines:
config_instance = MyConfigParser()
pipeline_config.update({pipeline_name:config_instance})
pipeline_config[pipeline_name].read(system_config.get('Pipeline',pipeline_name))
#Initialize and load mockdb
if system_config.get("Logging","debug") is "True":
print "Initializing mockdb"
mockdb=initiate_mockdb(system_config)
#Grab storage devices to keep track of storage
storage_devices = initiate_storage_devices(system_config)
if system_config.get("Logging","debug") is "True":
print "Add waiting storage"
for pipeline_name in pipeline_config.keys():
add_waiting_storage(pipeline_config[pipeline_name],storage_devices,mockdb,pipeline_name)
#Maintain sequencing run through new directory identification
if system_config.get("Logging","debug") is "True":
print "Analyzing sequencing dir"
maintain_sequencing_run_objects(system_config,mockdb)
if system_config.get("Logging","debug") is "True":
print "Continuing sequencing runs "
continue_seq_run(configs,storage_devices,mockdb)
from mockdb.initiate_mockdb import initiate_mockdb print initiate_mockdb().keys()
