def setUp(self): super(PmProductionTest, self).setUp() if os.path.exists(delivery_dir): flist = walk(os.path.join(delivery_dir)) for x in flist: os.unlink(x) shutil.rmtree(delivery_dir)
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)
def rm(self): if not self._check_pargs(["project", "analysis_id"]): return indir = os.path.join(self.app.controller._meta.project_root, self.app.controller._meta.path_id, self.pargs.analysis_id) assert os.path.exists(indir), "No such analysis {} for project {}".format(self.pargs.analysis_id, self.pargs.project) try: flist = walk(indir) except IOError as e: self.app.log.warn(str(e)) raise e if len(flist) > 0 and not query_yes_no("Going to remove all contents ({} files) of analysis {} for project {}... Are you sure you want to continue?".format(len(flist), self.pargs.analysis_id, self.pargs.project), force=self.pargs.force): return for f in flist: self.app.cmd.safe_unlink(f) self.app.log.info("removing {}".format(indir)) self.app.cmd.safe_rmdir(indir)