def test_exists(self):
qiita_config.portal = 'QIITA'
self.assertTrue(Analysis.exists(1))
new_id = get_count("qiita.analysis") + 1
self.assertFalse(Analysis.exists(new_id))
qiita_config.portal = 'EMP'
self.assertFalse(Analysis.exists(1))
new_id = get_count("qiita.analysis") + 1
self.assertFalse(Analysis.exists(new_id))
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_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_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_exists(self):
self.assertTrue(Analysis.exists(1))
new_id = get_count("qiita.analysis") + 1
self.assertFalse(Analysis.exists(new_id))
