def test_plugin_validate(self):
fp = join(self.out_dir, 'prefix1.fastq')
with open(fp, 'w') as f:
f.write(READS)
fp2 = join(self.out_dir, 'prefix1_b.fastq')
with open(fp2, 'w') as f:
f.write(BARCODES)
prep_info = {"1.SKB2.640194": {"not_a_run_prefix": "prefix1"}}
files = {'raw_forward_seqs': [fp], 'raw_barcodes': [fp2]}
atype = "FASTQ"
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
template = self.qclient.post('/apitest/prep_template/',
data=data)['prep']
parameters = {
'template': template,
'files': dumps(files),
'artifact_type': atype
}
data = {
'command': dumps(['Target Gene type', '0.1.0', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'
}
job_id = self.qclient.post('/apitest/processing_job/',
data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'success')
def test_plugin_summary(self):
artifact_id = 1
data = {
'command':
dumps(['Target Gene type', '0.1.0', 'Generate HTML summary']),
'parameters':
dumps({'input_data': artifact_id}),
'status':
'running'
}
job_id = self.qclient.post('/apitest/processing_job/',
data=data)['job']
# Qiita will return a filepath, but in the test environment, these
# files do not exist - create them
files = self.qclient.get('/qiita_db/artifacts/%s/' %
artifact_id)['files']
bcds_fp = files['raw_barcodes'][0]
self._clean_up_files.append(bcds_fp)
with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
fh.write(BARCODES)
fwd_fp = files['raw_forward_seqs'][0]
self._clean_up_files.append(fwd_fp)
with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
fh.write(READS)
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'success')
def test_plugin_validate(self):
fp = join(self.out_dir, 'prefix1.fastq')
with open(fp, 'w') as f:
f.write(READS)
fp2 = join(self.out_dir, 'prefix1_b.fastq')
with open(fp2, 'w') as f:
f.write(BARCODES)
prep_info = {"1.SKB2.640194": {"not_a_run_prefix": "prefix1"}}
files = {'raw_forward_seqs': [fp],
'raw_barcodes': [fp2]}
atype = "FASTQ"
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
template = self.qclient.post(
'/apitest/prep_template/', data=data)['prep']
parameters = {'template': template,
'files': dumps(files),
'artifact_type': atype}
data = {'command': dumps(['Target Gene type', '0.1.0', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'}
job_id = self.qclient.post(
'/apitest/processing_job/', data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'success')
def test_plugin_summary(self):
artifact_id = 1
data = {'command': dumps(['Target Gene type', '0.1.0',
'Generate HTML summary']),
'parameters': dumps({'input_data': artifact_id}),
'status': 'running'}
job_id = self.qclient.post(
'/apitest/processing_job/', data=data)['job']
# Qiita will return a filepath, but in the test environment, these
# files do not exist - create them
files = self.qclient.get(
'/qiita_db/artifacts/%s/' % artifact_id)['files']
bcds_fp = files['raw_barcodes'][0]
self._clean_up_files.append(bcds_fp)
with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
fh.write(BARCODES)
fwd_fp = files['raw_forward_seqs'][0]
self._clean_up_files.append(fwd_fp)
with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
fh.write(READS)
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'success')
def test_plugin_error(self):
parameters = {'template': 1,
'files': dumps({'log': ['/path/to/file1.log']}),
'artifact_type': "Demultiplexed"}
data = {'command': dumps(['Target Gene type', '0.1.0', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'}
job_id = self.qclient.post(
'/apitest/processing_job/', data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'error')
def test_plugin_error(self):
parameters = {
'template': 1,
'files': dumps({'log': ['/path/to/file1.log']}),
'artifact_type': "Demultiplexed"
}
data = {
'command': dumps(['Target Gene type', '0.1.0', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'
}
job_id = self.qclient.post('/apitest/processing_job/',
data=data)['job']
plugin("https://localhost:21174", job_id, self.out_dir)
self._wait_job(job_id)
obs = self.qclient.get_job_info(job_id)
self.assertEqual(obs['status'], 'error')