def add_sequencing_run_object(config,mockdb,input_dir,output_dir=None,sample_sheet=None):
"""
Reads in the directories in the hiseq output directory and compares it to what's in the
SequencingRun database. If it is a new directory, a new sequencing run object is created in
the Running state.
"""
[date,machine_key,run_number,side,flowcell_key] = parse_sequencing_run_dir(input_dir)
machine = mockdb['HiSeqMachine'].__get__(config,key=machine_key)
flowcell = mockdb['Flowcell'].__get__(config,key=flowcell_key)
run_type = determine_run_type(input_dir)
seq_run=mockdb['SequencingRun'].__new__(config,input_dir=input_dir,fastq_archive=output_dir,flowcell=flowcell,machine=machine,date=date,run_number=run_number,side=side,run_type=run_type,sample_sheet=sample_sheet)
seq_run.state = 'Running'
return 1
def things_to_do_if_initializing_pipeline_with_input_directory(configs,storage_devices,mockdb,source_dir,pipeline_name=None,base_output_dir=None,combine_projects=True):
if combine_project:
sample_dirs["dummy_project"] = list_sample_dirs(source_dir)
else:
sample_dirs = list_project_sample_dirs(source_dir)
target_config = MyConfigParser()
target_config.read(configs["system"].get("Filenames","target_config"))
for project in sample_dirs:
for sample in sample_dirs[project]:
running_location = identify_running_location_with_most_currently_available(configs,storage_devices)
parsed = parse_sample_sheet(configs['system'],mockdb,sample_dirs[project][sample][0])
if base_output_dir is None:
base_output_dir = configs['pipeline'].get('Common_directories','archive_directory')
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(configs["system"].get("Filenames","automation_config"))
description_dict = parse_description_into_dictionary(parsed['description'])
if 'Pipeline' in description_dict:
pipeline_key = description_dict['Pipeline']
else:
description_pieces = parsed['description'].split('_')
pipeline_key = description_pieces[-1]
pipeline_name_for_sample = automation_parameters_config.safe_get("Pipeline",pipeline_key)
if not pipeline_name_for_sample == pipeline_name:
continue
mockdb[pipeline_name].__new__(configs['system'],input_dir=sample_dirs[project][sample][0],pipeline_config=configs["pipeline"],project=parsed['project_name'],pipeline_key=pipeline_key,**parsed)
flowcell_dict = mockdb['SequencingRun'].__attribute_value_to_object_dict__('flowcell_key')
flowcell_dict = mockdb['SequencingRun'].__attribute_value_to_object_dict__('flowcell_key')
if parsed['flowcell'].key in flowcell_dict:
seq_run = flowcell_dict[parsed['flowcell'].key]
pass
else:
try:
base_dir = get_sequencing_run_base_dir(source_dir)
[date,machine_key,run_number,side,flowcell_key] = parse_sequencing_run_dir(base_dir)
machine = mockdb['HiSeqMachine'].__get__(configs['system'],machine_key)
run_type = determine_run_type(base_dir)
seq_run = mockdb['SequencingRun'].__new__(configs['system'],flowcell,machine,date,run_number,output_dir=base_dir,side=side,run_type=run_type)
fill_demultiplex_stats(configs['system'],mockdb,seq_run.output_dir,flowcell,machine)
except:
pass
return 1
string += "," + machine.key
string += "," + number
print string
return 1
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Places the statistics in Demultiplex_Stats.html into the database')
parser.add_argument('directory', type=str, help='The directory name where the casava results are placed.')
parser.add_argument('--report', dest='report', action='store_true', default=False, help='Prints data insead of inputting into database')
parser.add_argument('--add_seq_run', dest='add_seq_run', action='store_true', default=False, help='Adds a completed sequencing run for the flowcell')
args = parser.parse_args()
config = ConfigParser.ConfigParser()
config.read('/home/sequencing/src/pipeline_project/pipeline/config/ihg_system.cfg')
mockdb = initiate_mockdb(config)
[date,machine_key,run_number,side,flowcell_key] = parse_sequencing_run_dir(args.directory)
flowcell = mockdb['Flowcell'].__get__(config,key=flowcell_key)
machine = mockdb['HiSeqMachine'].__get__(config,key=machine_key)
if args.report is True:
report_demultiplex_stats(config,mockdb,args.directory,flowcell,machine)
else:
if args.add_seq_run is True:
try:
flowcell_seq_run_dict = mockdb['SequencingRun'].__attribute_value_to_object_dict__('flowcell_key')
seq_run = flowcell_seq_run_dict[flowcell.key][0]
except KeyError:
run_type = determine_run_type(args.directory)
seq_run=mockdb['SequencingRun'].__new__(config,flowcell=flowcell,machine=machine,date=date,run_number=run_number,output_dir=args.directory,side=side,run_type=run_type)
seq_run.__finish__()
fill_demultiplex_stats(config,mockdb,args.directory,flowcell,machine)
save_mockdb(config,mockdb)
