def test_execute_job_error(self):
# Create a prep template
prep_info = {'SKB8.640193': {'col': 'val1'},
'SKD8.640184': {'col': 'val2'}}
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
template = self.qclient.post(
'/apitest/prep_template/', data=data)['prep']
# Create a new validate job
fd, biom_fp = mkstemp(suffix=".biom")
close(fd)
data = np.random.randint(100, size=(2, 2))
table = Table(data, ['O1', 'O2'], ['S1', 'S2'])
with biom_open(biom_fp, 'w') as f:
table.to_hdf5(f, "Test")
data = {'command': dumps(['BIOM type', '2.1.4', 'Validate']),
'parameters': dumps(
{'files': dumps({'biom': [biom_fp]}),
'template': template,
'artifact_type': 'BIOM'}),
'artifact_type': 'BIOM',
'status': 'queued'}
job_id = self.qclient.post(
'/apitest/processing_job/', data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
obs = self._wait_job(job_id)
self.assertEqual(obs, 'error')
def test_execute_job_summary(self):
# Create a summary job
data = {'command': dumps(['BIOM type', '2.1.4',
'Generate HTML summary']),
'parameters': dumps({'input_data': 4}),
'status': 'queued'}
job_id = self.qclient.post(
'/apitest/processing_job/', data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
obs = self._wait_job(job_id)
self.assertEqual(obs, 'success')
def test_execute_job_summary(self):
# Create a summary job
data = {
'command': dumps(['BIOM type', '2.1.4', 'Generate HTML summary']),
'parameters': dumps({'input_data': 4}),
'status': 'queued'
}
job_id = self.qclient.post('/apitest/processing_job/',
data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
obs = self._wait_job(job_id)
self.assertEqual(obs, 'success')
def test_execute_job_error(self):
# Create a prep template
prep_info = {
'SKB8.640193': {
'col': 'val1'
},
'SKD8.640184': {
'col': 'val2'
}
}
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
template = self.qclient.post('/apitest/prep_template/',
data=data)['prep']
# Create a new validate job
fd, biom_fp = mkstemp(suffix=".biom")
close(fd)
data = np.random.randint(100, size=(2, 2))
table = Table(data, ['O1', 'O2'], ['S1', 'S2'])
with biom_open(biom_fp, 'w') as f:
table.to_hdf5(f, "Test")
data = {
'command':
dumps(['BIOM type', '2.1.4 - Qiime2', 'Validate']),
'parameters':
dumps({
'files': dumps({'biom': [biom_fp]}),
'template': template,
'artifact_type': 'BIOM'
}),
'artifact_type':
'BIOM',
'status':
'queued'
}
job_id = self.qclient.post('/apitest/processing_job/',
data=data)['job']
plugin("https://localhost:8383", job_id, self.out_dir)
obs = self._wait_job(job_id)
self.assertEqual(obs, 'error')