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)