def test_delete_analysis(self):
# as samples have been submitted to EBI, this will fail
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 test_copy_artifact(self):
# Failure test
job = self._create_job('copy_artifact', {
'artifact': 1,
'prep_template': 1
})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("Prep template 1 already has an artifact associated",
job.log.msg)
# Success test
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)
prep = PrepTemplate.create(metadata, Study(1), "16S")
job = self._create_job('copy_artifact', {
'artifact': 1,
'prep_template': prep.id
})
private_task(job.id)
self.assertEqual(job.status, 'success')
def test_create_sample_template(self):
# Test error
job = self._create_job('create_sample_template', {
'fp': self.fp, 'study_id': 1, 'is_mapping_file': False,
'data_type': None})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("The 'SampleTemplate' object with attributes (id: 1) "
"already exists.", job.log.msg)
# Test success with a warning
info = {"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"study_alias": "TDST",
"study_description": "Test create sample template",
"study_abstract": "Test create sample template",
"principal_investigator_id": StudyPerson(1)}
study = Study.create(User('*****@*****.**'),
"Create Sample Template test", info)
job = self._create_job('create_sample_template',
{'fp': self.fp, 'study_id': study.id,
'is_mapping_file': False, 'data_type': None})
private_task(job.id)
self.assertEqual(job.status, 'success')
obs = r_client.get("sample_template_%d" % study.id)
self.assertIsNotNone(obs)
obs = loads(obs)
self.assertCountEqual(obs, ['job_id', 'alert_type', 'alert_msg'])
self.assertEqual(obs['job_id'], job.id)
self.assertEqual(obs['alert_type'], 'warning')
self.assertIn(
'Some functionality will be disabled due to missing columns:',
obs['alert_msg'])
def test_delete_study(self):
# as samples have been submitted to EBI, this will fail
job = self._create_job('delete_study', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
"Cannot delete artifact 2: Artifact 2 has been "
"submitted to EBI", job.log.msg)
# making sure the analysis, first thing to delete, still exists
self.assertTrue(Analysis.exists(1))
# delete everything from the EBI submissions and the processing job so
# we can try again: test success (with tags)
with TRN:
sql = """DELETE FROM qiita.ebi_run_accession"""
TRN.add(sql)
sql = """DELETE FROM qiita.artifact_processing_job"""
TRN.add(sql)
TRN.execute()
# adding tags
Study(1).update_tags(self.user, ['my new tag!'])
job = self._create_job('delete_study', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Study(1)
def test_update_sample_template(self):
fd, fp = mkstemp(suffix=".txt")
close(fd)
with open(fp, 'w') as f:
f.write("sample_name\tnew_col\n1.SKD6.640190\tnew_value")
self._clean_up_files.append(fp)
job = self._create_job('update_sample_template', {
'study': 1,
'template_fp': fp
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(
SampleTemplate(1)['1.SKD6.640190']['new_col'], 'new_value')
obs = r_client.get("sample_template_1")
self.assertIsNotNone(obs)
obs = loads(obs)
self.assertCountEqual(obs, ['job_id', 'alert_type', 'alert_msg'])
self.assertEqual(obs['job_id'], job.id)
self.assertEqual(obs['alert_type'], 'warning')
self.assertIn(
'The following columns have been added to the existing '
'template: new_col', obs['alert_msg'])
# making sure that the error name is not in the messages
self.assertNotIn('QiitaDBWarning', obs['alert_msg'])
def test_delete_study_empty_study(self):
info = {
"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"emp_person_id": StudyPerson(2),
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)
}
new_study = Study.create(User('*****@*****.**'),
"Fried Chicken Microbiome %s" % time(), info)
job = self._create_job('delete_study', {'study': new_study.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
# making sure the study doesn't exist
with self.assertRaises(QiitaDBUnknownIDError):
Study(new_study.id)
def test_delete_analysis(self):
# as samples have been submitted to EBI, this will fail
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 test_delete_study(self):
# as samples have been submitted to EBI, this will fail
job = self._create_job('delete_study', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("Cannot delete artifact 2: it has been "
"submitted to EBI", job.log.msg)
# delete everything from the EBI submissions and the processing job so
# we can try again: test success (with tags)
with TRN:
sql = """DELETE FROM qiita.ebi_run_accession"""
TRN.add(sql)
sql = """DELETE FROM qiita.artifact_processing_job"""
TRN.add(sql)
TRN.execute()
# adding tags
Study(1).update_tags(self.user, ['my new tag!'])
job = self._create_job('delete_study', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Study(1)
def test_copy_artifact(self):
# Failure test
job = self._create_job('copy_artifact',
{'artifact': 1, 'prep_template': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("Prep template 1 already has an artifact associated",
job.log.msg)
# Success test
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)
prep = PrepTemplate.create(metadata, Study(1), "16S")
job = self._create_job('copy_artifact', {'artifact': 1,
'prep_template': prep.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
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 test_create_sample_template_nonutf8(self):
fp = join(dirname(abspath(__file__)), 'test_data',
'sample_info_utf8_error.txt')
job = self._create_job('create_sample_template', {
'fp': fp, 'study_id': 1, 'is_mapping_file': False,
'data_type': None})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("The 'SampleTemplate' object with attributes (id: 1) "
"already exists.", job.log.msg)
def test_delete_artifact(self):
job = self._create_job('delete_artifact', {'artifact': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
'Cannot delete artifact 1: it has children: 2, 3', job.log.msg)
job = self._create_job('delete_artifact', {'artifact': 3})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Artifact(3)
def test_delete_artifact(self):
job = self._create_job('delete_artifact', {'artifact': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
obs = job.log.msg
exp = 'Cannot delete artifact 1: Artifact 2 has been submitted to EBI'
self.assertIn(exp, obs)
job = self._create_job('delete_artifact', {'artifact': 3})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Artifact(3)
def test_delete_artifact(self):
job = self._create_job('delete_artifact', {'artifact': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
obs = job.log.msg
exp = ('Cannot delete artifact 1: it or one of its children has '
'been analyzed by')
self.assertIn(exp, obs)
job = self._create_job('delete_artifact', {'artifact': 3})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Artifact(3)
def test_create_sample_template_nonutf8(self):
fp = join(dirname(abspath(__file__)), 'test_data',
'sample_info_utf8_error.txt')
job = self._create_job('create_sample_template', {
'fp': fp,
'study_id': 1,
'is_mapping_file': False,
'data_type': None
})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
"The 'SampleTemplate' object with attributes (id: 1) "
"already exists.", job.log.msg)
def test_delete_artifact(self):
job = self._create_job('delete_artifact', {'artifact': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
obs = job.log.msg
exp = ('Cannot delete artifact 1: it or one of its children has '
'been analyzed by')
self.assertIn(exp, obs)
job = self._create_job('delete_artifact', {'artifact': 3})
private_task(job.id)
self.assertEqual(job.status, 'success')
with self.assertRaises(QiitaDBUnknownIDError):
Artifact(3)
def test_create_sample_template_nonutf8(self):
fp = join(dirname(abspath(__file__)), 'test_data',
'sample_info_utf8_error.txt')
job = self._create_job('create_sample_template', {
'fp': fp, 'study_id': 1, 'is_mapping_file': False,
'data_type': None})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
'There are invalid (non UTF-8) characters in your information '
'file. The offending fields and their location (row, column) are '
'listed below, invalid characters are represented using '
'🐾: "🐾collection_timestamp" = (0, 13)',
job.log.msg)
def test_delete_sample_template(self):
# Error case
job = self._create_job('delete_sample_template', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
"Sample template cannot be erased because there are "
"prep templates associated", job.log.msg)
# Success case
info = {
"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "TDST",
"study_description": "Test delete sample template",
"study_abstract": "Test delete sample template",
"principal_investigator_id": StudyPerson(1)
}
study = Study.create(User('*****@*****.**'),
"Delete Sample Template test", info)
metadata = pd.DataFrame.from_dict(
{
'Sample1': {
'physical_specimen_location': 'location1',
'physical_specimen_remaining': 'true',
'dna_extracted': 'true',
'sample_type': 'type1',
'collection_timestamp': '2014-05-29 12:24:15',
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'latitude': '42.42',
'longitude': '41.41',
'taxon_id': '9606',
'scientific_name': 'h**o sapiens'
}
},
orient='index',
dtype=str)
SampleTemplate.create(metadata, study)
job = self._create_job('delete_sample_template', {'study': study.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertFalse(SampleTemplate.exists(study.id))
def test_create_sample_template(self):
# Test error
job = self._create_job(
'create_sample_template', {
'fp': self.fp,
'study_id': 1,
'is_mapping_file': False,
'data_type': None
})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
"The 'SampleTemplate' object with attributes (id: 1) "
"already exists.", job.log.msg)
# Test success with a warning
info = {
"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"study_alias": "TDST",
"study_description": "Test create sample template",
"study_abstract": "Test create sample template",
"principal_investigator_id": StudyPerson(1)
}
study = Study.create(User('*****@*****.**'),
"Create Sample Template test", info)
job = self._create_job(
'create_sample_template', {
'fp': self.fp,
'study_id': study.id,
'is_mapping_file': False,
'data_type': None
})
private_task(job.id)
self.assertEqual(job.status, 'success')
obs = r_client.get("sample_template_%d" % study.id)
self.assertIsNotNone(obs)
obs = loads(obs)
self.assertCountEqual(obs, ['job_id', 'alert_type', 'alert_msg'])
self.assertEqual(obs['job_id'], job.id)
self.assertEqual(obs['alert_type'], 'warning')
self.assertIn(
'Some functionality will be disabled due to missing columns:',
obs['alert_msg'])
# making sure that the error name is not in the messages
self.assertNotIn('QiitaDBWarning', obs['alert_msg'])
def test_update_prep_template(self):
fd, fp = mkstemp(suffix=".txt")
close(fd)
with open(fp, 'w') as f:
f.write("sample_name\tnew_col\n1.SKD6.640190\tnew_value")
job = self._create_job('update_prep_template', {'prep_template': 1,
'template_fp': fp})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(PrepTemplate(1)['1.SKD6.640190']['new_col'],
'new_value')
obs = r_client.get("prep_template_1")
self.assertIsNotNone(obs)
obs = loads(obs)
self.assertItemsEqual(obs, ['job_id', 'alert_type', 'alert_msg'])
self.assertEqual(obs['job_id'], job.id)
self.assertEqual(obs['alert_type'], 'warning')
self.assertIn('The following columns have been added to the existing '
'template: new_col', obs['alert_msg'])
def test_delete_study_empty_study(self):
info = {
"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)}
new_study = Study.create(User('*****@*****.**'),
"Fried Chicken Microbiome %s" % time(), info)
job = self._create_job('delete_study', {'study': new_study.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
# making sure the study doesn't exist
with self.assertRaises(QiitaDBUnknownIDError):
Study(new_study.id)
def test_delete_sample_template(self):
# Error case
job = self._create_job('delete_sample_template', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("Sample template cannot be erased because there are "
"prep templates associated", job.log.msg)
# Success case
info = {"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "TDST",
"study_description": "Test delete sample template",
"study_abstract": "Test delete sample template",
"principal_investigator_id": StudyPerson(1)}
study = Study.create(User('*****@*****.**'),
"Delete Sample Template test", info)
metadata = pd.DataFrame.from_dict(
{'Sample1': {'physical_specimen_location': 'location1',
'physical_specimen_remaining': 'true',
'dna_extracted': 'true',
'sample_type': 'type1',
'collection_timestamp': '2014-05-29 12:24:15',
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'latitude': '42.42',
'longitude': '41.41',
'taxon_id': '9606',
'scientific_name': 'h**o sapiens'}},
orient='index', dtype=str)
SampleTemplate.create(metadata, study)
job = self._create_job('delete_sample_template', {'study': study.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertFalse(SampleTemplate.exists(study.id))
def test_delete_sample_or_column(self):
st = SampleTemplate(1)
# Delete a sample template column
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'SampleTemplate',
'obj_id': 1,
'sample_or_col': 'columns',
'name': 'season_environment'
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('season_environment', st.categories())
# Delete a sample template sample - need to add one
# sample that we will remove
npt.assert_warns(
QiitaDBWarning, st.extend,
pd.DataFrame.from_dict({'Sample1': {
'taxon_id': '9606'
}},
orient='index',
dtype=str))
self.assertIn('1.Sample1', st.keys())
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'SampleTemplate',
'obj_id': 1,
'sample_or_col': 'samples',
'name': '1.Sample1'
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('1.Sample1', st.keys())
# Delete a prep template column
pt = PrepTemplate(1)
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'PrepTemplate',
'obj_id': 1,
'sample_or_col': 'columns',
'name': 'target_subfragment'
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('target_subfragment', pt.categories())
# Delete a prep template sample
metadata = pd.DataFrame.from_dict(
{
'1.SKB8.640193': {
'barcode': 'GTCCGCAAGTTA',
'primer': 'GTGCCAGCMGCCGCGGTAA'
},
'1.SKD8.640184': {
'barcode': 'CGTAGAGCTCTC',
'primer': 'GTGCCAGCMGCCGCGGTAA'
}
},
orient='index',
dtype=str)
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata,
Study(1), "16S")
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'PrepTemplate',
'obj_id': pt.id,
'sample_or_col': 'samples',
'name': '1.SKD8.640184'
})
private_task(job.id)
self.assertNotIn('1.SKD8.640184', pt.keys())
# Test exceptions
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'UnknownClass',
'obj_id': 1,
'sample_or_col': 'columns',
'name': 'column'
})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
'Unknown value "UnknownClass". Choose between '
'"SampleTemplate" and "PrepTemplate"', job.log.msg)
job = self._create_job(
'delete_sample_or_column', {
'obj_class': 'SampleTemplate',
'obj_id': 1,
'sample_or_col': 'unknown',
'name': 'column'
})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn(
'Unknown value "unknown". Choose between "samples" '
'and "columns"', job.log.msg)
def test_complete_job(self):
# Complete success
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
exp_artifact_count = get_count('qiita.artifact') + 1
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'success')
self.assertEqual(get_count('qiita.artifact'), exp_artifact_count)
# Complete job error
payload = dumps({'success': False, 'error': 'Job failure'})
job = self._create_job('complete_job', {
'job_id': 'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
c_job = ProcessingJob('bcc7ebcd-39c1-43e4-af2d-822e3589f14d')
self.assertEqual(c_job.status, 'error')
self.assertEqual(c_job.log, LogEntry.newest_records(numrecords=1)[0])
self.assertEqual(c_job.log.msg, 'Job failure')
# Complete internal error
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fp = '/surprised/if/this/path/exists.biom'
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'error')
self.assertIn('No such file or directory', c_job.log.msg)
def test_delete_study(self):
# as samples have been submitted to EBI, this will fail
job = self._create_job('delete_study', {'study': 1})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn("Artifact 2 has been submitted to EBI", job.log.msg)
# making sure the analysis, first thing to delete, still exists
self.assertTrue(Analysis.exists(1))
info = {
"timeseries_type_id": '1',
"metadata_complete": 'true',
"mixs_compliant": 'true',
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)
}
new_study = Study.create(User('*****@*****.**'),
"Fried Chicken Microbiome %s" % time(), info)
# adding tags
new_study.update_tags(User('*****@*****.**'), ['my new tag!'])
# creating a sample information file
metadata = pd.DataFrame.from_dict(
{
'Sample1': {
'physical_specimen_location': 'location1',
'taxon_id': '9606',
'scientific_name': 'h**o sapiens'
},
'Sample2': {
'physical_specimen_location': 'location1',
'taxon_id': '9606',
'scientific_name': 'h**o sapiens'
},
'Sample3': {
'physical_specimen_location': 'location1',
'taxon_id': '9606',
'scientific_name': 'h**o sapiens'
}
},
orient='index')
SampleTemplate.create(metadata, new_study)
# creating a preparation information file
metadata = pd.DataFrame.from_dict(
{
'Sample1': {
'center_name': 'ANL',
'target_subfragment': 'V4',
'center_project_name': 'Test Project'
}
},
orient='index',
dtype=str)
PrepTemplate.create(metadata, new_study, '16S')
job = self._create_job('delete_study', {'study': new_study.id})
private_task(job.id)
self.assertEqual(job.status, 'success')
# making sure the study doesn't exist
with self.assertRaises(QiitaDBUnknownIDError):
Study(new_study.id)
def test_delete_sample_or_column(self):
st = SampleTemplate(1)
# Delete a sample template column
job = self._create_job('delete_sample_or_column',
{'obj_class': 'SampleTemplate', 'obj_id': 1,
'sample_or_col': 'columns',
'name': 'season_environment'})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('season_environment', st.categories())
# Delete a sample template sample - need to add one
# sample that we will remove
npt.assert_warns(
QiitaDBWarning, st.extend,
pd.DataFrame.from_dict({'Sample1': {'taxon_id': '9606'}},
orient='index', dtype=str))
self.assertIn('1.Sample1', st.keys())
job = self._create_job('delete_sample_or_column',
{'obj_class': 'SampleTemplate', 'obj_id': 1,
'sample_or_col': 'samples',
'name': '1.Sample1'})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('1.Sample1', st.keys())
# Delete a prep template column
pt = PrepTemplate(1)
job = self._create_job('delete_sample_or_column',
{'obj_class': 'PrepTemplate', 'obj_id': 1,
'sample_or_col': 'columns',
'name': 'target_subfragment'})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertNotIn('target_subfragment', pt.categories())
# Delete a prep template sample
metadata = pd.DataFrame.from_dict(
{'1.SKB8.640193': {'barcode': 'GTCCGCAAGTTA',
'primer': 'GTGCCAGCMGCCGCGGTAA'},
'1.SKD8.640184': {'barcode': 'CGTAGAGCTCTC',
'primer': 'GTGCCAGCMGCCGCGGTAA'}},
orient='index', dtype=str)
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create, metadata,
Study(1), "16S")
job = self._create_job('delete_sample_or_column',
{'obj_class': 'PrepTemplate', 'obj_id': pt.id,
'sample_or_col': 'samples',
'name': '1.SKD8.640184'})
private_task(job.id)
self.assertNotIn('1.SKD8.640184', pt.keys())
# Test exceptions
job = self._create_job('delete_sample_or_column',
{'obj_class': 'UnknownClass', 'obj_id': 1,
'sample_or_col': 'columns', 'name': 'column'})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn('Unknown value "UnknownClass". Choose between '
'"SampleTemplate" and "PrepTemplate"', job.log.msg)
job = self._create_job('delete_sample_or_column',
{'obj_class': 'SampleTemplate', 'obj_id': 1,
'sample_or_col': 'unknown', 'name': 'column'})
private_task(job.id)
self.assertEqual(job.status, 'error')
self.assertIn('Unknown value "unknown". Choose between "samples" '
'and "columns"', job.log.msg)
def test_complete_job(self):
# Complete success
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(
Command.get_validator('BIOM'),
values_dict={'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'}), True)
c_job._set_status('running')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
exp_artifact_count = get_count('qiita.artifact') + 1
payload = dumps(
{'success': True, 'error': '',
'artifacts': {'OTU table': {'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'}}})
job = self._create_job('complete_job', {'job_id': c_job.id,
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'success')
self.assertEqual(get_count('qiita.artifact'), exp_artifact_count)
# Complete job error
payload = dumps({'success': False, 'error': 'Job failure'})
job = self._create_job(
'complete_job', {'job_id': 'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
c_job = ProcessingJob('bcc7ebcd-39c1-43e4-af2d-822e3589f14d')
self.assertEqual(c_job.status, 'error')
self.assertEqual(c_job.log, LogEntry.newest_records(numrecords=1)[0])
self.assertEqual(c_job.log.msg, 'Job failure')
# Complete internal error
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(
Command.get_validator('BIOM'),
values_dict={'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'}), True)
c_job._set_status('running')
fp = '/surprised/if/this/path/exists.biom'
payload = dumps(
{'success': True, 'error': '',
'artifacts': {'OTU table': {'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'}}})
job = self._create_job('complete_job', {'job_id': c_job.id,
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'error')
self.assertIn('No such file or directory', c_job.log.msg)
