def setUp(self): super(CleanTest, self).setUp() ## Setup pre-casava results for k in self.RESULT_FILES.keys(): for f in self.RESULT_FILES[k]: outfile = os.path.join(intermediate, flowcell, f) if not os.path.exists(os.path.dirname(outfile)): safe_makedir(os.path.dirname(outfile)) exit_code = shell.exec_cmd2(['touch', outfile]) for k in self.INPUT_FILES.keys(): for f in self.INPUT_FILES[k]: outfile = os.path.join(data, flowcell, '1_120829_AA001AAAXX_barcode', f) if not os.path.exists(os.path.dirname(outfile)): safe_makedir(os.path.dirname(outfile)) exit_code = shell.exec_cmd2(['touch', outfile]) ## Setup casava results for k in self.RESULT_FILES.keys(): for f in self.RESULT_FILES[k]: outfile = os.path.join(data, k, flowcell, f) if not os.path.exists(os.path.dirname(outfile)): safe_makedir(os.path.dirname(outfile)) exit_code = shell.exec_cmd2(['touch', outfile]) for k in self.INPUT_FILES.keys(): for f in self.INPUT_FILES[k]: outfile = os.path.join(data, k, flowcell, '1_120829_AA001AAAXX_barcode', f) if not os.path.exists(os.path.dirname(outfile)): safe_makedir(os.path.dirname(outfile)) exit_code = shell.exec_cmd2(['touch', outfile])
def setUp(self): super(ProjectTest, self).setUp() ## FIX ME: deliver data first - serves as test data self.app = self.make_app(argv = []) self.app.setup() self.fastq_dir = os.path.join(self.app.config.get("project", "root"), "j_doe_00_01", "data", flowcell) safe_makedir(self.fastq_dir) for f in self.COMPRESS_FILES: m = glob.glob("{}*".format(os.path.join(self.fastq_dir, f))) if not m: exit_code = shell.exec_cmd2(['touch', os.path.join(self.fastq_dir, f)]) flist = walk(j_doe_00_04['data']) for f in flist: os.unlink(f)
def setUp(self): super(ProjectTest, self).setUp() ## FIX ME: deliver data first - serves as test data self.app = self.make_app(argv=[]) self.app.setup() self.fastq_dir = os.path.join(self.app.config.get("project", "root"), "j_doe_00_01", "data", flowcell) safe_makedir(self.fastq_dir) for f in self.COMPRESS_FILES: m = glob.glob("{}*".format(os.path.join(self.fastq_dir, f))) if not m: exit_code = shell.exec_cmd2( ['touch', os.path.join(self.fastq_dir, f)]) flist = walk(j_doe_00_04['data']) for f in flist: os.unlink(f)