def test_validate_error(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/",
body='{"success": true, "error": ""}'
)
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": "", "success": false, "error": "Some error"}')
with self.assertRaises(ValueError):
validate(self.qclient, 'job-id', self.parameters, self.out_dir)
def test_validate_prefix(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S1": {"orig_name": "S1"}, "1.S2": '
'{"orig_name": "S2"}, "1.S3": {"orig_name": "S3"}}}')
fd, biom_fp = mkstemp(suffix=".biom")
close(fd)
data = np.asarray([[0, 0, 1], [1, 3, 42]])
table = Table(data, ['O1', 'O2'], ['S1', 'S2', 'S3'])
with biom_open(biom_fp, 'w') as f:
table.to_hdf5(f, "Test")
self._clean_up_files.append(biom_fp)
self.parameters['files'] = '{"BIOM": ["%s"]}' % biom_fp
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
exp_biom_fp = join(self.out_dir, basename(biom_fp))
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [exp_biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertItemsEqual(obs_t.ids(), ["1.S1", "1.S2", "1.S3"])
def test_validate_unknown_type(self):
self.parameters['artifact_type'] = 'UNKNOWN'
obs = validate(self.qclient, 'job-id', self.parameters, self.out_dir)
exp = {'success': False,
'error': 'Unknown artifact type UNKNOWN. Supported types: BIOM',
'artifacts': None}
self.assertEqual(obs, exp)
def test_validate_prefix(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S1": {"orig_name": "S1"}, "1.S2": '
'{"orig_name": "S2"}, "1.S3": {"orig_name": "S3"}}}')
fd, biom_fp = mkstemp(suffix=".biom")
close(fd)
data = np.asarray([[0, 0, 1], [1, 3, 42]])
table = Table(data, ['O1', 'O2'], ['S1', 'S2', 'S3'])
with biom_open(biom_fp, 'w') as f:
table.to_hdf5(f, "Test")
self._clean_up_files.append(biom_fp)
self.parameters['files'] = '{"BIOM": ["%s"]}' % biom_fp
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
exp_biom_fp = join(self.out_dir, basename(biom_fp))
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [exp_biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertItemsEqual(obs_t.ids(), ["1.S1", "1.S2", "1.S3"])
def test_validate_unknown_type(self):
self.parameters['artifact_type'] = 'UNKNOWN'
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = 'Unknown artifact type UNKNOWN. Supported types: BIOM'
self.assertEqual(obs_error, exp)
def test_validate_unknown_type(self):
self.parameters['artifact_type'] = 'UNKNOWN'
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = 'Unknown artifact type UNKNOWN. Supported types: BIOM'
self.assertEqual(obs_error, exp)
def test_validate_no_changes(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S1": {"run_prefix": "S1"}, "1.S2": '
'{"run_prefix": "S2"}, "1.S3": {"run_prefix": "S3"}}}')
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [self.biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
def test_validate_missing_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}}}')
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = ('Your prep information is missing samples that are present in '
'your BIOM table: 1.S3')
self.assertEqual(obs_error, exp)
def test_validate_no_changes(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S1": {"run_prefix": "S1"}, "1.S2": '
'{"run_prefix": "S2"}, "1.S3": {"run_prefix": "S3"}}}')
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [self.biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
def test_validate_missing_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}}}')
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = ('Your prep information is missing samples that are present in '
'your BIOM table: 1.S3')
self.assertEqual(obs_error, exp)
def test_validate_missing_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/",
body='{"success": true, "error": ""}'
)
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}}, "success": true, "error": ""}')
obs = validate(self.qclient, 'job-id', self.parameters, self.out_dir)
exp = {'success': False,
'error': 'Your prep information is missing samples that are '
'present in your BIOM table: 1.S3',
'artifacts': None}
self.assertEqual(obs, exp)
def test_validate_no_changes(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/",
body='{"success": true, "error": ""}'
)
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S1": {"run_prefix": "S1"}, "1.S2": '
'{"run_prefix": "S2"}, "1.S3": {"run_prefix": "S3"}}, '
'"success": true, "error": ""}')
obs = validate(self.qclient, 'job-id', self.parameters, self.out_dir)
exp = {'success': True,
'error': '',
'artifacts': {None: {'artifact_type': 'BIOM',
'filepaths': [self.biom_fp, 'biom']}}}
self.assertEqual(obs, exp)
def test_validate_unknown_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"orig_name": "S1"}, "1.S22": '
'{"orig_name": "S2"}, "1.S33": {"orig_name": "S3"}}, '
'"success": true, "error": ""}')
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = ('The sample ids in the BIOM table do not match the ones in the '
'prep information. Please, provide the column "run_prefix" in '
'the prep information to map the existing sample ids to the '
'prep information sample ids.')
self.assertEqual(obs_error, exp)
def test_validate_run_prefix(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}, "1.S33": {"run_prefix": "1.S3"}}}')
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', self.parameters, self.out_dir)
exp_biom_fp = join(self.out_dir, basename(self.biom_fp))
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [exp_biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertItemsEqual(obs_t.ids(), ["1.S11", "1.S22", "1.S33"])
def test_validate_run_prefix(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}, "1.S33": {"run_prefix": "1.S3"}}}')
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
exp_biom_fp = join(self.out_dir, basename(self.biom_fp))
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [[None, 'BIOM', [exp_biom_fp, 'biom']]])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertItemsEqual(obs_t.ids(), ["1.S11", "1.S22", "1.S33"])
def test_validate_unknown_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/")
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"orig_name": "S1"}, "1.S22": '
'{"orig_name": "S2"}, "1.S33": {"orig_name": "S3"}}, '
'"success": true, "error": ""}')
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
self.parameters,
self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
exp = ('The sample ids in the BIOM table do not match the ones in the '
'prep information. Please, provide the column "run_prefix" in '
'the prep information to map the existing sample ids to the '
'prep information sample ids.')
self.assertEqual(obs_error, exp)
def test_validate_unknown_samples(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/",
body='{"success": true, "error": ""}'
)
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"orig_name": "S1"}, "1.S22": '
'{"orig_name": "S2"}, "1.S33": {"orig_name": "S3"}}, '
'"success": true, "error": ""}')
obs = validate(self.qclient, 'job-id', self.parameters, self.out_dir)
exp = {'success': False,
'error': 'The sample ids in the BIOM table do not match the '
'ones in the prep information. Please, provide the '
'column "run_prefix" in the prep information to map '
'the existing sample ids to the prep information '
'sample ids.',
'artifacts': None}
self.assertEqual(obs, exp)
def test_validate_run_prefix(self):
httpretty.register_uri(
httpretty.POST,
"https://test_server.com/qiita_db/jobs/job-id/step/",
body='{"success": true, "error": ""}'
)
httpretty.register_uri(
httpretty.GET,
"https://test_server.com/qiita_db/prep_template/1/data",
body='{"data": {"1.S11": {"run_prefix": "1.S1"}, "1.S22": '
'{"run_prefix": "1.S2"}, "1.S33": {"run_prefix": "1.S3"}}, '
'"success": true, "error": ""}')
obs = validate(self.qclient, 'job-id', self.parameters, self.out_dir)
exp_biom_fp = join(self.out_dir, basename(self.biom_fp))
self._clean_up_files.append(exp_biom_fp)
exp = {'success': True,
'error': '',
'artifacts': {None: {'artifact_type': 'BIOM',
'filepaths': [exp_biom_fp, 'biom']}}}
self.assertEqual(obs, exp)
obs_t = load_table(exp_biom_fp)
self.assertItemsEqual(obs_t.ids(), ["1.S11", "1.S22", "1.S33"])