def test_validate_representative_set(self):
sample_ids = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=1)
fd, fasta_fp = mkstemp(suffix=".fna")
close(fd)
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n>O2\nATGC\n")
self._clean_up_files.append(fasta_fp)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
with open(exp_index_fp, 'w') as f:
f.write("my html")
mkdir(exp_viz_fp)
parameters = {'template': parameters['template'],
'files': dumps({'biom': [biom_fp],
'preprocessed_fasta': [fasta_fp]}),
'artifact_type': 'BIOM'}
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertTrue(obs_success)
files = [(biom_fp, 'biom'), (fasta_fp, 'preprocessed_fasta'),
(exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'),
(exp_qza_fp, 'qza')]
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', files)])
self.assertEqual(obs_error, "")
# Extra ids
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n>O2\nATGC\n>O3\nATGC\n")
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error,
"The representative set sequence file includes observations not "
"found in the BIOM table: O3")
# Missing ids
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n")
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error,
"The representative set sequence file is missing observation ids "
"found in the BIOM tabe: O2")
def test_validate_representative_set(self):
sample_ids = [
'1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195', '1.SKB6.640176',
'1.SKD6.640190', '1.SKM6.640187', '1.SKD9.640182', '1.SKM8.640201',
'1.SKM2.640199'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
template=1)
fd, fasta_fp = mkstemp(suffix=".fna")
close(fd)
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n>O2\nATGC\n")
self._clean_up_files.append(fasta_fp)
parameters = {
'template': parameters['template'],
'files': dumps({
'biom': [biom_fp],
'preprocessed_fasta': [fasta_fp]
}),
'artifact_type': 'BIOM'
}
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertTrue(obs_success)
files = [(biom_fp, 'biom'), (fasta_fp, 'preprocessed_fasta')]
self.assertEqual(obs_ainfo, [ArtifactInfo(None, 'BIOM', files)])
self.assertEqual(obs_error, "")
# Extra ids
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n>O2\nATGC\n>O3\nATGC\n")
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error,
"The representative set sequence file includes observations not "
"found in the BIOM table: O3")
# Missing ids
with open(fasta_fp, 'w') as f:
f.write(">O1 something\nACTG\n")
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertIsNone(obs_ainfo)
self.assertEqual(
obs_error,
"The representative set sequence file is missing observation ids "
"found in the BIOM tabe: O2")
def test_validate_phylogeny(self):
# Create a new job
fp_support_files = join('qtp_biom', 'support_files')
filepaths = {
'biom': [join(fp_support_files, 'sepp.biom')],
'preprocessed_fasta': [join(fp_support_files, 'sepp.fa')],
'plain_text': [join(fp_support_files, 'sepp.tre')]
}
parameters = {
'template': 1,
'files': dumps(filepaths),
'artifact_type': 'BIOM',
'analysis': 1
}
data = {
'command': dumps(['BIOM type', '2.1.4 - Qiime2', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'
}
res = self.qclient.post('/apitest/processing_job/', data=data)
job_id = res['job']
# test validation on valid data
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertTrue(obs_success)
for ft, fp in filepaths.items():
self.assertTrue((fp[0], ft) in obs_ainfo[0].files)
self.assertEqual(obs_error, '')
# test that validation failes if tree is no Newick file, i.e. not
# parsable by skbio
filepaths['plain_text'] = [join(fp_support_files, 'sepp.fa')]
parameters = {
'template': 1,
'files': dumps(filepaths),
'artifact_type': 'BIOM',
'analysis': 1
}
data = {
'command': dumps(['BIOM type', '2.1.4 - Qiime2', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'
}
res = self.qclient.post('/apitest/processing_job/', data=data)
job_id = res['job']
# test validation on valid data
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertEqual(obs_ainfo, None)
self.assertEqual(obs_error,
'Phylogenetic tree cannot be parsed via scikit-biom')
def test_validate_prefix(self):
prep_info = {
'SKB8.640193': {'col': 'val1'},
'SKD8.640184': {'col': 'val2'}}
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['SKB8.640193', 'SKD8.640184']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_biom_fp = exp_fp(basename(biom_fp))
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', [
(exp_biom_fp, 'biom'), (exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'), (exp_qza_fp, 'qza')])])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertCountEqual(obs_t.ids(), ['1.SKB8.640193', '1.SKD8.640184'])
def test_validate_prefix(self):
prep_info = {
'SKB8.640193': {
'col': 'val1'
},
'SKD8.640184': {
'col': 'val2'
}
}
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['SKB8.640193', 'SKD8.640184']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
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,
[ArtifactInfo(None, 'BIOM', [(exp_biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertCountEqual(obs_t.ids(), ['1.SKB8.640193', '1.SKD8.640184'])
def test_validate_unknown_samples(self):
prep_info = {
'SKB8.640193': {
'col': 'val1'
},
'SKD8.640184': {
'col': 'val2'
}
}
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2', 'Sample3']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
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):
prep_info = {
'SKB8.640193': {
'col': 'val1',
'run_prefix': 'Sample1'
},
'SKD8.640184': {
'col': 'val2',
'run_prefix': 'Sample2'
}
}
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_biom_fp = exp_fp(basename(biom_fp))
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
self._clean_up_files.append(exp_biom_fp)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [
ArtifactInfo(None, 'BIOM', [(exp_biom_fp, 'biom'),
(exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'),
(exp_qza_fp, 'qza')])
])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertCountEqual(obs_t.ids(), ["1.SKB8.640193", "1.SKD8.640184"])
def test_validate_analysis(self):
sample_ids = ['1.SKM4.640180', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM9.640192', '1.SKB7.640196']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, analysis=1)
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
def test_validate_no_changes(self):
sample_ids = [
'1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195', '1.SKB6.640176',
'1.SKD6.640190', '1.SKM6.640187', '1.SKD9.640182', '1.SKM8.640201',
'1.SKM2.640199', '1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186', '1.SKB1.640202',
'1.SKM1.640183', '1.SKD1.640179', '1.SKD3.640198', '1.SKB5.640181',
'1.SKB4.640189', '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
template=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [
ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom'),
(exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'),
(exp_qza_fp, 'qza')])
])
self.assertEqual(obs_error, "")
def test_validate_no_changes(self):
sample_ids = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
'1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
'1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
'1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
'1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=1)
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
self.assertTrue(obs_success)
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', [
(biom_fp, 'biom'), (exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'), (exp_qza_fp, 'qza')])])
self.assertEqual(obs_error, "")
def test_validate_missing_samples(self):
prep_info = {
'SKB8.640193': {
'col': 'val1',
'run_prefix': 'Sample1'
},
'SKD8.640184': {
'col': 'val2',
'run_prefix': 'Sample2'
}
}
data = {'prep_info': dumps(prep_info), 'study': 1, 'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2', 'New.Sample']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
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: New.Sample')
self.assertEqual(obs_error, exp)
def test_validate_unknown_type(self):
parameters = {'template': 1, 'files': dumps({'BIOM': ['ignored']}),
'artifact_type': 'UNKNOWN'}
obs_success, obs_ainfo, obs_error = validate(
self.qclient, 'job-id', 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_analysis(self):
sample_ids = [
'1.SKM4.640180', '1.SKB8.640193', '1.SKD8.640184', '1.SKM9.640192',
'1.SKB7.640196'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
analysis=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
def test_validate_phylogeny(self):
# Create a new job
fp_support_files = join('qtp_biom', 'support_files')
filepaths = {'biom': [join(fp_support_files, 'sepp.biom')],
'preprocessed_fasta': [join(fp_support_files, 'sepp.fa')],
'plain_text': [join(fp_support_files, 'sepp.tre')]}
parameters = {'template': 1,
'files': dumps(filepaths),
'artifact_type': 'BIOM',
'analysis': 1}
data = {'command': dumps(['BIOM type', '2.1.4 - Qiime2', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'}
res = self.qclient.post('/apitest/processing_job/', data=data)
job_id = res['job']
# test validation on valid data
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertTrue(obs_success)
for ft, fp in filepaths.items():
self.assertTrue((fp[0], ft) in obs_ainfo[0].files)
self.assertEqual(obs_error, '')
# test that validation failes if tree is no Newick file, i.e. not
# parsable by skbio
filepaths['plain_text'] = [join(fp_support_files, 'sepp.fa')]
parameters = {'template': 1,
'files': dumps(filepaths),
'artifact_type': 'BIOM',
'analysis': 1}
data = {'command': dumps(['BIOM type', '2.1.4 - Qiime2', 'Validate']),
'parameters': dumps(parameters),
'status': 'running'}
res = self.qclient.post('/apitest/processing_job/', data=data)
job_id = res['job']
# test validation on valid data
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertFalse(obs_success)
self.assertEqual(obs_ainfo, None)
self.assertEqual(
obs_error, 'Phylogenetic tree cannot be parsed via scikit-biom')
def test_validate_no_changes_superset(self):
sample_ids = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=1)
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
def test_validate_unknown_type(self):
parameters = {
'template': 1,
'files': dumps({'BIOM': ['ignored']}),
'artifact_type': 'UNKNOWN'
}
obs_success, obs_ainfo, obs_error = validate(self.qclient, 'job-id',
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_superset(self):
sample_ids = [
'1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195', '1.SKB6.640176',
'1.SKD6.640190', '1.SKM6.640187', '1.SKD9.640182', '1.SKM8.640201',
'1.SKM2.640199'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
template=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo,
[ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
def test_validate_analysis(self):
sample_ids = ['1.SKM4.640180', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM9.640192', '1.SKB7.640196']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, analysis=1)
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
exp_qza_fp = exp_fp('feature-table.qza')
self.assertTrue(obs_success)
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', [
(biom_fp, 'biom'), (exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir'), (exp_qza_fp, 'qza')])])
self.assertEqual(obs_error, "")
def test_validate_analysis(self):
sample_ids = [
'1.SKM4.640180', '1.SKB8.640193', '1.SKD8.640184', '1.SKM9.640192',
'1.SKB7.640196'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
analysis=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [
ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom'),
(exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir')])
])
self.assertEqual(obs_error, "")
def test_validate_no_changes(self):
sample_ids = [
'1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195', '1.SKB6.640176',
'1.SKD6.640190', '1.SKM6.640187', '1.SKD9.640182', '1.SKM8.640201',
'1.SKM2.640199', '1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186', '1.SKB1.640202',
'1.SKM1.640183', '1.SKD1.640179', '1.SKD3.640198', '1.SKB5.640181',
'1.SKB4.640189', '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
template=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo,
[ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
def test_validate_no_changes(self):
sample_ids = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
'1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
'1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
'1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
'1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=1)
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, parameters, self.out_dir)
self.assertTrue(obs_success)
self.assertEqual(
obs_ainfo, [ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
def test_validate_no_changes_superset(self):
sample_ids = [
'1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195', '1.SKB6.640176',
'1.SKD6.640190', '1.SKM6.640187', '1.SKD9.640182', '1.SKM8.640201',
'1.SKM2.640199'
]
biom_fp, job_id, parameters = self._create_job_and_biom(sample_ids,
template=1)
obs_success, obs_ainfo, obs_error = validate(self.qclient, job_id,
parameters, self.out_dir)
exp_fp = partial(join, self.out_dir)
exp_index_fp = exp_fp('index.html')
exp_viz_fp = exp_fp('support_files')
self.assertTrue(obs_success)
self.assertEqual(obs_ainfo, [
ArtifactInfo(None, 'BIOM', [(biom_fp, 'biom'),
(exp_index_fp, 'html_summary'),
(exp_viz_fp, 'html_summary_dir')])
])
self.assertEqual(obs_error, "")
def test_validate_missing_samples(self):
prep_info = {
'SKB8.640193': {'col': 'val1',
'run_prefix': 'Sample1'},
'SKD8.640184': {'col': 'val2',
'run_prefix': 'Sample2'}}
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2', 'New.Sample']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, 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: New.Sample')
self.assertEqual(obs_error, exp)
def test_validate_unknown_samples(self):
prep_info = {
'SKB8.640193': {'col': 'val1'},
'SKD8.640184': {'col': 'val2'}}
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2', 'Sample3']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, 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):
prep_info = {
'SKB8.640193': {'col': 'val1',
'run_prefix': 'Sample1'},
'SKD8.640184': {'col': 'val2',
'run_prefix': 'Sample2'}}
data = {'prep_info': dumps(prep_info),
'study': 1,
'data_type': '16S'}
res = self.qclient.post('/apitest/prep_template/', data=data)
sample_ids = ['Sample1', 'Sample2']
biom_fp, job_id, parameters = self._create_job_and_biom(
sample_ids, template=res['prep'])
obs_success, obs_ainfo, obs_error = validate(
self.qclient, job_id, 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, [ArtifactInfo(None, 'BIOM', [(exp_biom_fp, 'biom')])])
self.assertEqual(obs_error, "")
obs_t = load_table(exp_biom_fp)
self.assertCountEqual(obs_t.ids(), ["1.SKB8.640193", "1.SKD8.640184"])
