def test_delete_analysis(self):
# adding extra filepaths to make sure the delete works as expected, we
# basically want 8 -> 9 -> 10 -> 12 -> 14
# -> 11 -> 13
fd, fp10 = mkstemp(suffix='_table.biom')
close(fd)
fd, fp11 = mkstemp(suffix='_table.biom')
close(fd)
fd, fp12 = mkstemp(suffix='_table.biom')
close(fd)
fd, fp13 = mkstemp(suffix='_table.biom')
close(fd)
fd, fp14 = mkstemp(suffix='_table.biom')
close(fd)
with biom_open(fp10, 'w') as f:
et.to_hdf5(f, "test")
with biom_open(fp11, 'w') as f:
et.to_hdf5(f, "test")
with biom_open(fp12, 'w') as f:
et.to_hdf5(f, "test")
with biom_open(fp13, 'w') as f:
et.to_hdf5(f, "test")
with biom_open(fp14, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.extend([fp10, fp11, fp12, fp13, fp14])
# copying some processing parameters
a9 = Artifact(9)
pp = a9.processing_parameters
# 7: BIOM
a10 = Artifact.create([(fp10, 7)],
"BIOM",
parents=[a9],
processing_parameters=pp)
a11 = Artifact.create([(fp11, 7)],
"BIOM",
parents=[a9],
processing_parameters=pp)
a12 = Artifact.create([(fp12, 7)],
"BIOM",
parents=[a10],
processing_parameters=pp)
Artifact.create([(fp13, 7)],
"BIOM",
parents=[a11],
processing_parameters=pp)
Artifact.create([(fp14, 7)],
"BIOM",
parents=[a12],
processing_parameters=pp)
job = self._create_job('delete_analysis', {'analysis_id': 1})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Analysis(1)
def setUp(self):
# Generate some files for a root artifact
fd, self.fp1 = mkstemp(suffix='_seqs.fastq')
close(fd)
with open(self.fp1, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
"+\n"
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
fd, self.fp2 = mkstemp(suffix='_barcodes.fastq')
close(fd)
with open(self.fp2, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n"
"NNNCNNNNNNNNN\n"
"+\n"
"#############\n")
self.filepaths_root = [(self.fp1, 1), (self.fp2, 3)]
# Generate some files for a processed artifact
fd, self.fp3 = mkstemp(suffix='_seqs.fna')
close(fd)
with open(self.fp3, 'w') as f:
f.write(">1.sid_r4_0 M02034:17:000000000-A5U18:1:1101:15370:1394 "
"1:N:0:1 orig_bc=CATGAGCT new_bc=CATGAGCT bc_diffs=0\n"
"GTGTGCCAGCAGCCGCGGTAATACGTAGGG\n")
self.filepaths_processed = [(self.fp3, 4)]
# Generate some file for a BIOM
fd, self.fp4 = mkstemp(suffix='_table.biom')
with biom_open(self.fp4, 'w') as f:
et.to_hdf5(f, "test")
self.filepaths_biom = [(self.fp4, 7)]
# Create a new prep template
metadata_dict = {
'SKB8.640193': {
'center_name': 'ANL',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'
}
}
metadata = pd.DataFrame.from_dict(metadata_dict,
orient='index',
dtype=str)
self.prep_template = \
qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(1), "16S")
self._clean_up_files = [self.fp1, self.fp2, self.fp3, self.fp4]
def setUp(self):
# Generate some files for a root artifact
fd, self.fp1 = mkstemp(suffix='_seqs.fastq')
close(fd)
with open(self.fp1, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
"NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
"+\n"
"#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
fd, self.fp2 = mkstemp(suffix='_barcodes.fastq')
close(fd)
with open(self.fp2, 'w') as f:
f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n"
"NNNCNNNNNNNNN\n"
"+\n"
"#############\n")
self.filepaths_root = [(self.fp1, 1), (self.fp2, 3)]
# Generate some files for a processed artifact
fd, self.fp3 = mkstemp(suffix='_seqs.fna')
close(fd)
with open(self.fp3, 'w') as f:
f.write(">1.sid_r4_0 M02034:17:000000000-A5U18:1:1101:15370:1394 "
"1:N:0:1 orig_bc=CATGAGCT new_bc=CATGAGCT bc_diffs=0\n"
"GTGTGCCAGCAGCCGCGGTAATACGTAGGG\n")
self.filepaths_processed = [(self.fp3, 4)]
# Generate some file for a BIOM
fd, self.fp4 = mkstemp(suffix='_table.biom')
with biom_open(self.fp4, 'w') as f:
et.to_hdf5(f, "test")
self.filepaths_biom = [(self.fp4, 7)]
# Create a new prep template
metadata_dict = {
'SKB8.640193': {'center_name': 'ANL',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'}}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
dtype=str)
self.prep_template = \
qdb.metadata_template.prep_template.PrepTemplate.create(
metadata, qdb.study.Study(1), "16S")
self._clean_up_files = [self.fp1, self.fp2, self.fp3, self.fp4]
def test_post_analysis(self):
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with biom_open(fp, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.append(fp)
data = {'filepaths': dumps([(fp, 'biom')]),
'type': "BIOM",
'name': "New biom artifact",
'analysis': 1,
'data_type': '16S'}
obs = self.post('/apitest/artifact/', headers=self.header, data=data)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertEqual(obs.keys(), ['artifact'])
a = qdb.artifact.Artifact(obs['artifact'])
self._clean_up_files.extend([afp for _, afp, _ in a.filepaths])
self.assertEqual(a.name, "New biom artifact")
def test_post_analysis(self):
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with biom_open(fp, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.append(fp)
data = {'filepaths': dumps([(fp, 'biom')]),
'type': "BIOM",
'name': "New biom artifact",
'analysis': 1,
'data_type': '16S'}
obs = self.post('/apitest/artifact/', headers=self.header, data=data)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertEqual(obs.keys(), ['artifact'])
a = qdb.artifact.Artifact(obs['artifact'])
self._clean_up_files.extend([afp for _, afp, _ in a.filepaths])
self.assertEqual(a.name, "New biom artifact")
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
next(Command(3).default_parameter_sets), {'input_data': 1})
a = Artifact.create(files_biom,
"BIOM",
parents=[Artifact(2)],
processing_parameters=params)
for x in a.filepaths:
self._clean_up_files.append(x['fp'])
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = ('- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_[0-9]*-[0-9]*.txt '
'mapping_files/4_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_[0-9]*-[0-9]*.txt '
'mapping_files/5_mapping_file.txt\n'
'- 1256812 /protected/processed_data/1_study_1001_'
'closed_reference_otu_table_Silva.biom processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- [0-9]* /protected/templates/1_prep_1_[0-9]*-[0-9]*.txt '
'mapping_files/6_mapping_file.txt\n'
'- 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n'
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/10/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- [0-9]* /protected/templates/1_prep_1_[0-9]*-[0-9]*.txt '
'mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegex(response.body.decode('ascii'), exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
# returning visibility
a.visibility = 'private'
self.assertEqual(response.code, 200)
# we should have the same files than the previous test, except artifact
# and mapping file 7: position 6 and 7; thus removing 6 twice
exp = exp.split('\n')
exp.pop(6)
exp.pop(6)
exp = '\n'.join(exp)
self.assertRegex(response.body.decode('ascii'), exp)
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
Command(3).default_parameter_sets.next(), {'input_data': 1})
a = Artifact.create(files_biom,
"BIOM",
parents=[Artifact(2)],
processing_parameters=params)
for _, fp, _ in a.filepaths:
self._clean_up_files.append(fp)
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'- 36615 /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'- 39752 /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = ('- 39752 /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
Command(3).default_parameter_sets.next(), {'input_data': 1})
a = Artifact.create(files_biom, "BIOM", parents=[Artifact(2)],
processing_parameters=params)
for _, fp, _ in a.filepaths:
self._clean_up_files.append(fp)
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'- 36615 /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
next(Command(3).default_parameter_sets), {'input_data': 1})
a = Artifact.create(files_biom, "BIOM", parents=[Artifact(2)],
processing_parameters=params)
for x in a.filepaths:
self._clean_up_files.append(x['fp'])
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'1579715020 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'[0-9]* [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegex(response.body.decode('ascii'), exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
# returning visibility
a.visibility = 'private'
self.assertEqual(response.code, 200)
# we should have the same files than the previous test, except artifact
# and mapping file 7: position 6 and 7; thus removing 6 twice
exp = exp.split('\n')
exp.pop(6)
exp.pop(6)
exp = '\n'.join(exp)
self.assertRegex(response.body.decode('ascii'), exp)
def test_post(self):
# no header
obs = self.post('/qiita_db/artifact/', data={})
self.assertEqual(obs.code, 400)
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
# renaming samples
et.update_ids(
{
'S1': '1.SKB1.640202',
'S2': '1.SKD3.640198',
'S3': '1.SKM4.640180'
},
inplace=True)
with biom_open(fp, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.append(fp)
# no job_id or prep_id
data = {
'user_email': '*****@*****.**',
'artifact_type': 'BIOM',
'command_artifact_name': 'OTU table',
'files': dumps({'biom': [fp]})
}
obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
self.assertEqual(obs.code, 400)
self.assertIn('You need to specify a job_id or a prep_id',
str(obs.error))
# both job_id and prep_id defined
data['job_id'] = 'e5609746-a985-41a1-babf-6b3ebe9eb5a9'
data['prep_id'] = 'prep_id'
obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
self.assertEqual(obs.code, 400)
self.assertIn('You need to specify only a job_id or a prep_id',
str(obs.error))
# make sure that all the plugins are on
qdb.util.activate_or_update_plugins(update=True)
# tests success by inserting a new artifact into an existing job
original_job = qdb.processing_job.ProcessingJob(data['job_id'])
input_artifact = original_job.input_artifacts[0]
original_children = input_artifact.children
self.assertEqual(len(original_children), 3)
# send the new data
del data['prep_id']
obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
jid = obs.body.decode("utf-8")
job = qdb.processing_job.ProcessingJob(jid)
while job.status not in ('error', 'success'):
sleep(0.5)
# now the original job should have 4 children and make sure they have
# the same parent and parameters
children = input_artifact.children
new_children = list(set(children) - set(original_children))[0]
self.assertEqual(len(children), 4)
for c in children[1:]:
self.assertCountEqual(children[0].processing_parameters.values,
c.processing_parameters.values)
self.assertEqual(children[0].parents, c.parents)
# making sure the new artifact is part of the descendants, which is a
# different method and usage than children method
self.assertIn(new_children, input_artifact.descendants.nodes)
# now let's test adding an artifact directly to a new prep
new_prep = qdb.metadata_template.prep_template.PrepTemplate.create(
pd.DataFrame({
'new_col': {
'1.SKB1.640202': 1,
'1.SKD3.640198': 2,
'1.SKM4.640180': 3
}
}), qdb.study.Study(1), '16S')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with biom_open(fp, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.append(fp)
data = {
'user_email': '*****@*****.**',
'artifact_type': 'BIOM',
'prep_id': new_prep.id,
'files': dumps({'biom': [fp]})
}
obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
jid = obs.body.decode("utf-8")
job = qdb.processing_job.ProcessingJob(jid)
while job.status not in ('error', 'success'):
sleep(0.5)
self.assertIsNotNone(new_prep.artifact)
