def move_file_to_staging(self):
dir_name = self.gcst
sumstats_file_name = self.gcst + '_build' + str(self.assembly)
ssf = fh.SumStatFile(file_path=self.file_path, callback_id=self.callback_id,
study_id=self.study_id, readme=self.readme, entryUUID=self.entryUUID,
staging_dir_name=dir_name, staging_file_name=sumstats_file_name, raw_ss=self.raw_ss)
return ssf.move_file_to_staging()
def validate_study(self, minrows=None, forcevalid=False):
# Step through the validation
if self.mandatory_metadata_check() is True:
ssf = fh.SumStatFile(file_path=self.file_path, callback_id=self.callback_id, study_id=self.study_id,
md5exp=self.md5, readme=self.readme, entryUUID=self.entryUUID, minrows=minrows, raw_ss=self.raw_ss)
if ssf.retrieve() is True:
self.set_retrieved_status(1)
if not ssf.md5_ok():
self.set_data_valid_status(0)
self.set_error_code(2)
else:
if ssf.check_raw_ss():
validation_status = ssf.validate_file() if forcevalid is False else True
if validation_status is True:
self.set_data_valid_status(1)
ssf.write_readme_file()
ssf.tidy_files()
else:
self.set_data_valid_status(0)
self.set_error_code(ssf.validation_error)
else:
self.set_data_valid_status(0)
self.set_error_code(11)
else:
self.set_retrieved_status(0)
self.set_error_code(1)
def test_validate_false_when_invalid(self):
ssf = fh.SumStatFile(file_path=self.invalid_url, callback_id=self.cid,
study_id=self.sid, md5exp=self.valid_url_md5, minrows=10)
ssf.retrieve()
result = ssf.validate_file()
self.assertFalse(result)
self.assertTrue(os.path.exists(os.path.join(ssf.parent_path, str(self.sid + ".log"))))
def test_md5(self):
ssf = fh.SumStatFile(file_path=self.valid_url, callback_id=self.cid,
study_id=self.sid, md5exp=self.valid_url_md5)
ssf.retrieve()
self.assertEqual(fh.md5_check(os.path.join(ssf.store_path)),self.valid_url_md5)
md5_ok = ssf.md5_ok()
self.assertTrue(md5_ok)
def test_remove_parent_dir(self):
ssf = fh.SumStatFile(callback_id=self.cid, study_id=self.sid)
ssf.set_parent_path()
self.assertFalse(os.path.exists(ssf.parent_path))
ssf.make_parent_dir()
self.assertTrue(os.path.exists(ssf.parent_path))
fh.remove_payload(self.cid)
self.assertFalse(os.path.exists(ssf.parent_path))
def test_retrieve(self):
ssf = fh.SumStatFile(file_path=self.valid_url, callback_id=self.cid, study_id=self.sid)
retrieved = ssf.retrieve()
self.assertTrue(retrieved)