def setUpClass(self): """ Creates the following directory tree for testing purposes: tmp/ |__ 141124_ST-COMPLETED_01_AFCIDXX | |__ RunInfo.xml | |__ Demultiplexing | | |__ Stats | | |__ DemultiplexingStats.xml | |__ RTAComplete.txt |__ 141124_ST-INPROGRESS_02_AFCIDXX | |__ RunInfo.xml | |__ Demultiplexing | |__ RTAComplete.txt |__ 141124_ST-RUNNING_03_AFCIDXX | |__ RunInfo.xml |__ 141124_ST-TOSTART_04_FCIDXXX |__ RunInfo.xml |__ RTAComplete.txt """ self.tmp_dir = os.path.join(tempfile.mkdtemp(), 'tmp') self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv') running = os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX') to_start = os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX') in_progress = os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX') completed = os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX') finished_runs = [to_start, in_progress, completed] # Create runs directory structure os.makedirs(self.tmp_dir) os.makedirs(running) os.makedirs(to_start) os.makedirs(os.path.join(in_progress, 'Demultiplexing')) os.makedirs(os.path.join(completed, 'Demultiplexing', 'Stats')) # Create files indicating that the run is finished for run in finished_runs: open(os.path.join(run, 'RTAComplete.txt'), 'w').close() # Create files indicating that the preprocessing is done open(os.path.join(completed, 'Demultiplexing', 'Stats', 'DemultiplexingStats.xml'), 'w').close() # Create transfer file and add the completed run with open(self.transfer_file, 'w') as f: tsv_writer = csv.writer(f, delimiter='\t') tsv_writer.writerow([os.path.basename(completed), str(datetime.now())]) # Move sample RunInfo.xml file to every run directory for run in [running, to_start, in_progress, completed]: shutil.copy('data/RunInfo.xml', run) shutil.copy('data/runParameters.xml', run) # Create run objects # Jose : add tests for other sequencers self.running = HiSeqX_Run(os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX'), CONFIG["analysis"]["HiSeqX"]) self.to_start = Run(os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX'), CONFIG["analysis"]["HiSeqX"]) self.in_progress = Run(os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX'), CONFIG["analysis"]["HiSeqX"]) self.completed = Run(os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX'), CONFIG["analysis"]["HiSeqX"]) self.finished_runs = [self.to_start, self.in_progress, self.completed] self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')