def test_submit_EBI_step_2_failure(self):
ppd = self.write_demux_files(PrepTemplate(1), True)
pid = ppd.id
with self.assertRaises(ComputeError):
submit_EBI(pid, 'VALIDATE', True)
rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
def test_submit_EBI_step_2_failure(self):
ppd = self.write_demux_files(PrepTemplate(1), True)
pid = ppd.id
with self.assertRaises(ComputeError):
submit_EBI(pid, 'VALIDATE', True)
rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
def test_full_submission(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(artifact.study.ebi_submission_status, 'not submitted')
aid = artifact.id
submit_EBI(aid, 'VALIDATE', True, test=True)
self.assertEqual(artifact.study.ebi_submission_status, 'submitted')
rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
def test_full_submission(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(
artifact.study.ebi_submission_status, 'not submitted')
aid = artifact.id
submit_EBI(aid, 'VALIDATE', True, test=True)
self.assertEqual(artifact.study.ebi_submission_status, 'submitted')
rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
def test_max_ebiena_curl_error(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(artifact.study.ebi_submission_status, 'not submitted')
aid = artifact.id
with self.assertRaises(ComputeError) as error:
submit_EBI(aid, 'VALIDATE', True, test_size=True)
error = str(error.exception)
self.assertIn('is too large. Before cleaning:', error)
rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
with self.assertRaises(ComputeError) as error:
submit_EBI(ppd.id, 'VALIDATE', True)
error = str(error.exception)
self.assertIn('EBI Submission failed! Log id:', error)
self.assertIn('The EBI submission failed:', error)
self.assertIn('Failed to validate run xml, error: Expected element',
error)
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
pid = ppd.id
with self.assertRaises(ComputeError) as error:
submit_EBI(pid, 'VALIDATE', True)
error = str(error.exception)
self.assertIn('EBI Submission failed! Log id:', error)
self.assertIn('The EBI submission failed:', error)
rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
pid = ppd.id
with self.assertRaises(ComputeError) as error:
submit_EBI(pid, 'VALIDATE', True)
error = str(error.exception)
self.assertIn('EBI Submission failed! Log id:', error)
self.assertIn('The EBI submission failed:', error)
rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
def test_max_ebiena_curl_error(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(
artifact.study.ebi_submission_status, 'not submitted')
aid = artifact.id
with self.assertRaises(ComputeError) as error:
submit_EBI(aid, 'VALIDATE', True, test_size=True)
error = str(error.exception)
self.assertIn('is too large. Before cleaning:', error)
rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
def submit_to_EBI(job):
"""Submit a study to EBI
Parameters
----------
job : qiita_db.processing_job.ProcessingJob
The processing job performing the task
"""
with qdb.sql_connection.TRN:
param_vals = job.parameters.values
artifact_id = int(param_vals['artifact'])
submission_type = param_vals['submission_type']
submit_EBI(artifact_id, submission_type, True)
job._set_status('success')
def submit_to_EBI(job):
"""Submit a study to EBI
Parameters
----------
job : qiita_db.processing_job.ProcessingJob
The processing job performing the task
"""
with qdb.sql_connection.TRN:
param_vals = job.parameters.values
artifact_id = int(param_vals['artifact'])
submission_type = param_vals['submission_type']
submit_EBI(artifact_id, submission_type, True)
job._set_status('success')
def submit_to_ebi(preprocessed_data_id, submission_type):
"""Submit a study to EBI"""
study_acc, submission_acc = submit_EBI(preprocessed_data_id,
submission_type,
True)
return study_acc, submission_acc
def submit_to_EBI(job):
"""Submit a study to EBI
Parameters
----------
job : qiita_db.processing_job.ProcessingJob
The processing job performing the task
"""
with qdb.sql_connection.TRN:
param_vals = job.parameters.values
artifact_id = int(param_vals['artifact'])
submission_type = param_vals['submission_type']
artifact = qdb.artifact.Artifact(artifact_id)
for info in artifact.study._ebi_submission_jobs():
jid, aid, js, cbste, era = info
if js in ('running', 'queued') and jid != job.id:
error_msg = ("Cannot perform parallel EBI submission for "
"the same study. Current job running: %s" % js)
raise EBISubmissionError(error_msg)
submit_EBI(artifact_id, submission_type, True)
job._set_status('success')
def submit_to_EBI(job):
"""Submit a study to EBI
Parameters
----------
job : qiita_db.processing_job.ProcessingJob
The processing job performing the task
"""
with qdb.sql_connection.TRN:
param_vals = job.parameters.values
artifact_id = int(param_vals['artifact'])
submission_type = param_vals['submission_type']
artifact = qdb.artifact.Artifact(artifact_id)
for info in artifact.study._ebi_submission_jobs():
jid, aid, js, cbste, era = info
if js in ('running', 'queued') and jid != job.id:
error_msg = ("Cannot perform parallel EBI submission for "
"the same study. Current job running: %s" % js)
raise EBISubmissionError(error_msg)
submit_EBI(artifact_id, submission_type, True)
job._set_status('success')
def test_full_submission(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(artifact.study.ebi_submission_status, 'not submitted')
submit_EBI(artifact.id, 'VALIDATE', True, test=True)
self.assertEqual(artifact.study.ebi_submission_status, 'submitted')
def test_submit_EBI_step_2_failure(self):
ppd = self.write_demux_files(PrepTemplate(1), False)
with self.assertRaises(EBISubmissionError):
submit_EBI(ppd.id, 'VALIDATE', True)
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
with self.assertRaises(ComputeError):
submit_EBI(ppd.id, 'ADD', True)
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
with self.assertRaises(ComputeError):
submit_EBI(ppd.id, 'ADD', True)