def test_vamps_status(self):
ppd = PreprocessedData(1)
# verifying current value
self.assertEqual(ppd.submitted_to_vamps_status(), 'not submitted')
# changing value and then verifying new value
ppd.update_vamps_status('failed')
self.assertEqual(ppd.submitted_to_vamps_status(), 'failed')
# checking failure
with self.assertRaises(ValueError):
ppd.update_vamps_status('not a valid status')
def test_vamps_status(self):
ppd = PreprocessedData(1)
# verifying current value
self.assertEqual(ppd.submitted_to_vamps_status(), 'not submitted')
# changing value and then verifying new value
ppd.update_vamps_status('failed')
self.assertEqual(ppd.submitted_to_vamps_status(), 'failed')
# checking failure
with self.assertRaises(ValueError):
ppd.update_vamps_status('not a valid status')
def submit_VAMPS(preprocessed_data_id):
"""Submit preprocessed data to VAMPS
Parameters
----------
preprocessed_data_id : int
The preprocesssed data id
"""
preprocessed_data = PreprocessedData(preprocessed_data_id)
study = Study(preprocessed_data.study)
sample_template = SampleTemplate(study.sample_template)
prep_template = PrepTemplate(preprocessed_data.prep_template)
status = preprocessed_data.submitted_to_vamps_status()
if status in ('submitting', 'success'):
raise ValueError("Cannot resubmit! Current status is: %s" % status)
preprocessed_data.update_vamps_status('submitting')
# Generating a tgz
targz_folder = mkdtemp(prefix=qiita_config.working_dir)
targz_fp = join(targz_folder, '%d_%d_%d.tgz' % (study.id,
prep_template.id,
preprocessed_data.id))
targz = taropen(targz_fp, mode='w:gz')
# adding sample/prep
samp_fp = join(targz_folder, 'sample_metadata.txt')
sample_template.to_file(samp_fp)
targz.add(samp_fp, arcname='sample_metadata.txt')
prep_fp = join(targz_folder, 'prep_metadata.txt')
prep_template.to_file(prep_fp)
targz.add(prep_fp, arcname='prep_metadata.txt')
# adding preprocessed data
for _, fp, fp_type in preprocessed_data.get_filepaths():
if fp_type == 'preprocessed_fasta':
targz.add(fp, arcname='preprocessed_fasta.fna')
targz.close()
# submitting
cmd = ("curl -F user=%s -F pass='******' -F uploadFile=@%s -F "
"press=UploadFile %s" % (qiita_config.vamps_user,
qiita_config.vamps_pass,
targz_fp,
qiita_config.vamps_url))
obs, _, _ = system_call(cmd)
exp = ("<html>\n<head>\n<title>Process Uploaded File</title>\n</head>\n"
"<body>\n</body>\n</html>")
if obs != exp:
preprocessed_data.update_vamps_status('failure')
return False
else:
preprocessed_data.update_vamps_status('success')
return True
def submit_VAMPS(preprocessed_data_id):
"""Submit preprocessed data to VAMPS
Parameters
----------
preprocessed_data_id : int
The preprocesssed data id
"""
preprocessed_data = PreprocessedData(preprocessed_data_id)
study = Study(preprocessed_data.study)
sample_template = SampleTemplate(study.sample_template)
prep_template = PrepTemplate(preprocessed_data.prep_template)
status = preprocessed_data.submitted_to_vamps_status()
if status in ('submitting', 'success'):
raise ValueError("Cannot resubmit! Current status is: %s" % status)
preprocessed_data.update_vamps_status('submitting')
# Generating a tgz
targz_folder = mkdtemp(prefix=qiita_config.working_dir)
targz_fp = join(
targz_folder,
'%d_%d_%d.tgz' % (study.id, prep_template.id, preprocessed_data.id))
targz = taropen(targz_fp, mode='w:gz')
# adding sample/prep
samp_fp = join(targz_folder, 'sample_metadata.txt')
sample_template.to_file(samp_fp)
targz.add(samp_fp, arcname='sample_metadata.txt')
prep_fp = join(targz_folder, 'prep_metadata.txt')
prep_template.to_file(prep_fp)
targz.add(prep_fp, arcname='prep_metadata.txt')
# adding preprocessed data
for _, fp, fp_type in preprocessed_data.get_filepaths():
if fp_type == 'preprocessed_fasta':
targz.add(fp, arcname='preprocessed_fasta.fna')
targz.close()
# submitting
cmd = ("curl -F user=%s -F pass='******' -F uploadFile=@%s -F "
"press=UploadFile %s" %
(qiita_config.vamps_user, qiita_config.vamps_pass, targz_fp,
qiita_config.vamps_url))
obs, _, _ = system_call(cmd)
exp = ("<html>\n<head>\n<title>Process Uploaded File</title>\n</head>\n"
"<body>\n</body>\n</html>")
if obs != exp:
preprocessed_data.update_vamps_status('failure')
return False
else:
preprocessed_data.update_vamps_status('success')
return True
