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(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)