def get(self):
analysis_id = int(self.get_argument('id'))
analysis = Analysis(analysis_id)
if not analysis.has_access(self.current_user):
raise HTTPError(403, 'User %s does not have permissions to share '
'analysis %s' % (
self.current_user.id, analysis.id))
selected = self.get_argument('selected', None)
deselected = self.get_argument('deselected', None)
if selected is not None:
yield Task(self._share, analysis, selected)
if deselected is not None:
yield Task(self._unshare, analysis, deselected)
users, links = yield Task(self._get_shared_for_study, analysis)
self.write(dumps({'users': users, 'links': links}))
def get(self):
analysis_id = int(self.get_argument('id'))
analysis = Analysis(analysis_id)
if not analysis.has_access(self.current_user):
raise HTTPError(
403, 'User %s does not have permissions to share '
'analysis %s' % (self.current_user.id, analysis.id))
selected = self.get_argument('selected', None)
deselected = self.get_argument('deselected', None)
if selected is not None:
yield Task(self._share, analysis, selected)
if deselected is not None:
yield Task(self._unshare, analysis, deselected)
users, links = yield Task(self._get_shared_for_study, analysis)
self.write(dumps({'users': users, 'links': links}))
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
_, self.fp = get_mountpoint("analysis")[0]
self.biom_fp = join(self.fp, "1_analysis_18S.biom")
self.map_fp = join(self.fp, "1_analysis_mapping.txt")
def tearDown(self):
with open(self.biom_fp, 'w') as f:
f.write("")
with open(self.map_fp, 'w') as f:
f.write("")
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
if exists(fp):
remove(fp)
mp = get_mountpoint("processed_data")[0][1]
study2fp = join(mp, "2_2_study_1001_closed_reference_otu_table.biom")
if exists(study2fp):
move(study2fp,
join(mp, "2_study_1001_closed_reference_otu_table.biom"))
def test_lock_check(self):
for status in ["queued", "running", "public", "completed",
"error"]:
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.status = status
with self.assertRaises(QiitaDBStatusError):
new._lock_check(self.conn_handler)
def test_lock_check_ok(self):
self.analysis.status = "in_construction"
self.analysis._lock_check(self.conn_handler)
def test_status_setter_checks(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.status = "queued"
def test_get_by_status(self):
self.assertEqual(Analysis.get_by_status('public'), set([]))
self.analysis.status = "public"
self.assertEqual(Analysis.get_by_status('public'), {1})
def test_has_access_public(self):
self.conn_handler.execute("UPDATE qiita.analysis SET "
"analysis_status_id = 6")
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_shared(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_no_access(self):
self.assertFalse(self.analysis.has_access(User("*****@*****.**")))
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[1, new_id]])
def test_create_from_default(self):
new_id = get_count("qiita.analysis") + 1
owner = User("*****@*****.**")
new = Analysis.create(owner, "newAnalysis",
"A New Analysis", from_default=True)
self.assertEqual(new.id, new_id)
self.assertEqual(new.step, 3)
# Make sure samples were transfered properly
sql = "SELECT * FROM qiita.analysis_sample WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [owner.default_analysis])
exp = []
self.assertEqual(obs, exp)
sql = "SELECT * FROM qiita.analysis_sample WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
exp = [[new_id, 1, '1.SKD8.640184'],
[new_id, 1, '1.SKB7.640196'],
[new_id, 1, '1.SKM9.640192'],
[new_id, 1, '1.SKM4.640180']]
self.assertEqual(obs, exp)
def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "*****@*****.**")
def test_retrieve_name(self):
self.assertEqual(self.analysis.name, "SomeAnalysis")
def test_retrieve_description(self):
self.assertEqual(self.analysis.description, "A test analysis")
def test_set_description(self):
self.analysis.description = "New description"
self.assertEqual(self.analysis.description, "New description")
def test_retrieve_samples(self):
exp = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196',
'1.SKM9.640192', '1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_retrieve_dropped_samples(self):
# Create and populate second study to do test with
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"portal_type_id": 3,
"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)
}
metadata_dict = {
'SKB8.640193': {'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'str_column': 'Value for sample 1',
'latitude': 42.42,
'longitude': 41.41},
'SKD8.640184': {'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 2',
'str_column': 'Value for sample 2',
'latitude': 4.2,
'longitude': 1.1},
'SKB7.640196': {'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("*****@*****.**"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust", 1, [(study_fp, 6)],
study=Study(2), data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']}
self.analysis._build_biom_tables(samples, 10000,
conn_handler=self.conn_handler)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'},
2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["*****@*****.**"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {12, 13, 14, 15}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, None)
def test_set_step(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 2]])
def test_set_step_twice(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
new.step = 4
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 4]])
def test_retrieve_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
self.assertEqual(new.step, 2)
def test_retrieve_step_new(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
with self.assertRaises(ValueError):
new.step
def test_retrieve_step_locked(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.step = 3
def test_retrieve_jobs(self):
self.assertEqual(self.analysis.jobs, [1, 2])
def test_retrieve_jobs_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.jobs, None)
def test_retrieve_pmid(self):
self.assertEqual(self.analysis.pmid, "121112")
def test_retrieve_pmid_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_summary_data(self):
obs = self.analysis.summary_data()
exp = {'studies': 1,
'processed_data': 1,
'samples': 5}
self.assertEqual(obs, exp)
def test_add_samples(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
obs = new.samples
self.assertEqual(obs.keys(), [1])
self.assertItemsEqual(obs[1], ['1.SKB8.640193', '1.SKD5.640186'])
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, ["*****@*****.**",
"*****@*****.**"])
def test_unshare(self):
self.analysis.unshare(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
with open(self.map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', '1.SKB8.640193', '1.SKD8.640184',
'1.SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = ['BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT',
'CGGCCTAAGTTC']
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = ['LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA']
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9',
'1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]
exp = ['tot_org_carb', '5.0', '4.32', '5.0']
self.assertEqual(obs, exp)
obs = [line.split('\t')[-1] for line in mapdata]
exp = ['Description\n'] + ['Cannabis Soil Microbiome\n'] * 3
self.assertEqual(obs, exp)
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(ValueError):
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
def test_build_biom_tables(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100,
conn_handler=self.conn_handler)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': self.biom_fp})
table = load_table(self.biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {'Study':
'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1}
self.assertEqual(obs, exp)
def test_build_files(self):
self.analysis.build_files()
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)
def test_add_file(self):
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
with open(fp, 'w') as f:
f.write('testfile!')
self.analysis._add_file('testfile.txt', 'plain_text', '18S')
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.filepath WHERE filepath_id = 19')
exp = [[19, 'testfile.txt', 9, '3675007573', 1, 1]]
self.assertEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.analysis_filepath WHERE filepath_id = 19')
exp = [[1, 19, 2]]
self.assertEqual(obs, exp)
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
self.portal = qiita_config.portal
_, self.fp = get_mountpoint("analysis")[0]
self.biom_fp = join(self.fp, "1_analysis_18S.biom")
self.map_fp = join(self.fp, "1_analysis_mapping.txt")
def tearDown(self):
qiita_config.portal = self.portal
with open(self.biom_fp, 'w') as f:
f.write("")
with open(self.map_fp, 'w') as f:
f.write("")
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
if exists(fp):
remove(fp)
mp = get_mountpoint("processed_data")[0][1]
study2fp = join(mp, "2_2_study_1001_closed_reference_otu_table.biom")
if exists(study2fp):
move(study2fp,
join(mp, "2_study_1001_closed_reference_otu_table.biom"))
def test_lock_check(self):
for status in ["queued", "running", "public", "completed",
"error"]:
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.status = status
with self.assertRaises(QiitaDBStatusError):
new._lock_check()
def test_lock_check_ok(self):
self.analysis.status = "in_construction"
self.analysis._lock_check()
def test_status_setter_checks(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.status = "queued"
def test_get_by_status(self):
qiita_config.portal = 'QIITA'
self.assertEqual(Analysis.get_by_status('public'), set([]))
qiita_config.portal = 'EMP'
self.assertEqual(Analysis.get_by_status('public'), set([]))
self.analysis.status = "public"
qiita_config.portal = 'QIITA'
self.assertEqual(Analysis.get_by_status('public'), {1})
qiita_config.portal = 'EMP'
self.assertEqual(Analysis.get_by_status('public'), set([]))
def test_has_access_public(self):
self.conn_handler.execute("UPDATE qiita.analysis SET "
"analysis_status_id = 6")
qiita_config.portal = 'QIITA'
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
qiita_config.portal = 'EMP'
self.assertFalse(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_shared(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
qiita_config.portal = 'QIITA'
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
qiita_config.portal = 'EMP'
with self.assertRaises(QiitaDBError):
Analysis(1).has_access(User("*****@*****.**"))
def test_has_access_no_access(self):
self.assertFalse(self.analysis.has_access(User("*****@*****.**")))
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
# make sure portal is associated
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.analysis_portal WHERE analysis_id = %s",
[new_id])
self.assertEqual(obs, [[new_id, 1]])
def test_create_nonqiita_portal(self):
new_id = get_count("qiita.analysis") + 1
qiita_config.portal = "EMP"
Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
# make sure portal is associated
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.analysis_portal WHERE analysis_id = %s",
[new_id])
self.assertEqual(obs, [[new_id, 2], [new_id, 1]])
def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, new_id)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = %s")
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs[0][:-1], [new_id, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[1, new_id]])
def test_create_from_default(self):
new_id = get_count("qiita.analysis") + 1
owner = User("*****@*****.**")
new = Analysis.create(owner, "newAnalysis",
"A New Analysis", from_default=True)
self.assertEqual(new.id, new_id)
self.assertEqual(new.step, 3)
# Make sure samples were transfered properly
sql = "SELECT * FROM qiita.analysis_sample WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [owner.default_analysis])
exp = []
self.assertEqual(obs, exp)
sql = "SELECT * FROM qiita.analysis_sample WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
exp = [[new_id, 1, '1.SKD8.640184'],
[new_id, 1, '1.SKB7.640196'],
[new_id, 1, '1.SKM9.640192'],
[new_id, 1, '1.SKM4.640180']]
self.assertEqual(obs, exp)
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(self):
# successful delete
total_analyses = get_count("qiita.analysis")
Analysis.delete(1)
self.assertEqual(total_analyses - 1, get_count("qiita.analysis"))
# no possible to delete
with self.assertRaises(QiitaDBUnknownIDError):
Analysis.delete(total_analyses + 1)
def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "*****@*****.**")
def test_retrieve_name(self):
self.assertEqual(self.analysis.name, "SomeAnalysis")
def test_retrieve_description(self):
self.assertEqual(self.analysis.description, "A test analysis")
def test_set_description(self):
self.analysis.description = "New description"
self.assertEqual(self.analysis.description, "New description")
def test_retrieve_samples(self):
exp = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196',
'1.SKM9.640192', '1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_retrieve_dropped_samples(self):
# Create and populate second study to do test with
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)
}
metadata_dict = {
'SKB8.640193': {'physical_specimen_location': 'location1',
'physical_specimen_remaining': True,
'dna_extracted': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'str_column': 'Value for sample 1',
'latitude': 42.42,
'longitude': 41.41,
'taxon_id': 9606,
'scientific_name': 'h**o sapiens'},
'SKD8.640184': {'physical_specimen_location': 'location1',
'physical_specimen_remaining': True,
'dna_extracted': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 2',
'str_column': 'Value for sample 2',
'latitude': 4.2,
'longitude': 1.1,
'taxon_id': 9606,
'scientific_name': 'h**o sapiens'},
'SKB7.640196': {'physical_specimen_location': 'location1',
'physical_specimen_remaining': True,
'dna_extracted': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp':
datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41,
'taxon_id': 9606,
'scientific_name': 'h**o sapiens'},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("*****@*****.**"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust", 1, [(study_fp, 6)],
study=Study(2), data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']}
self.analysis._build_biom_tables(samples, 10000)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'},
2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def test_empty_analysis(self):
analysis = Analysis(2)
# These should be empty as the analysis hasn't started
self.assertEqual(analysis.biom_tables, {})
self.assertEqual(analysis.dropped_samples, {})
def test_retrieve_portal(self):
self.assertEqual(self.analysis._portals, ["QIITA"])
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["*****@*****.**"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {10, 11, 12, 13}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_empty(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, {})
def test_set_step(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 2]])
def test_set_step_twice(self):
new_id = get_count("qiita.analysis") + 1
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
new.step = 4
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = %s"
obs = self.conn_handler.execute_fetchall(sql, [new_id])
self.assertEqual(obs, [[new_id, 4]])
def test_retrieve_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
self.assertEqual(new.step, 2)
def test_retrieve_step_new(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
with self.assertRaises(ValueError):
new.step
def test_retrieve_step_locked(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.step = 3
def test_retrieve_jobs(self):
self.assertEqual(self.analysis.jobs, [1, 2])
def test_retrieve_jobs_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.jobs, [])
def test_retrieve_pmid(self):
self.assertEqual(self.analysis.pmid, "121112")
def test_retrieve_pmid_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_summary_data(self):
obs = self.analysis.summary_data()
exp = {'studies': 1,
'processed_data': 1,
'samples': 5}
self.assertEqual(obs, exp)
def test_add_samples(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
obs = new.samples
self.assertEqual(obs.keys(), [1])
self.assertItemsEqual(obs[1], ['1.SKB8.640193', '1.SKD5.640186'])
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, ["*****@*****.**",
"*****@*****.**"])
def test_unshare(self):
self.analysis.unshare(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
new_id = get_count('qiita.filepath') + 1
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
base_dir = get_mountpoint('analysis')[0][1]
obs = pd.read_csv(obs, sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
exp = pd.read_csv(join(base_dir, '1_analysis_mapping_exp.txt'),
sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
assert_frame_equal(obs, exp)
sql = """SELECT * FROM qiita.filepath
WHERE filepath=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(
sql, ("%d_analysis_mapping.txt" % self.analysis.id,))
exp = [[13, '1_analysis_mapping.txt', 9, '852952723', 1, 1],
[new_id, '1_analysis_mapping.txt', 9, '1606265094', 1, 1]]
self.assertEqual(obs, exp)
sql = """SELECT * FROM qiita.analysis_filepath
WHERE analysis_id=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(QiitaDBError):
self.analysis._build_mapping_file(samples)
def test_build_biom_tables(self):
new_id = get_count('qiita.filepath') + 1
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': self.biom_fp})
table = load_table(self.biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {'Study':
'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1}
self.assertEqual(obs, exp)
sql = """SELECT EXISTS(SELECT * FROM qiita.filepath
WHERE filepath_id=%s)"""
obs = self.conn_handler.execute_fetchone(sql, (new_id,))[0]
self.assertTrue(obs)
sql = """SELECT * FROM qiita.analysis_filepath
WHERE analysis_id=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
def test_build_files(self):
self.analysis.build_files()
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)
def test_add_file(self):
new_id = get_count('qiita.filepath') + 1
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
with open(fp, 'w') as f:
f.write('testfile!')
self.analysis._add_file('testfile.txt', 'plain_text', '18S')
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.filepath WHERE filepath_id = %s',
(new_id,))
exp = [[new_id, 'testfile.txt', 9, '3675007573', 1, 1]]
self.assertEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.analysis_filepath WHERE filepath_id = %s',
(new_id,))
exp = [[1, new_id, 2]]
self.assertEqual(obs, exp)
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
_, self.fp = get_mountpoint("analysis")[0]
self.biom_fp = join(self.fp, "1_analysis_18S.biom")
self.map_fp = join(self.fp, "1_analysis_mapping.txt")
def tearDown(self):
with open(self.biom_fp, 'w') as f:
f.write("")
with open(self.map_fp, 'w') as f:
f.write("")
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
if exists(fp):
remove(fp)
mp = get_mountpoint("processed_data")[0][1]
study2fp = join(mp, "2_2_study_1001_closed_reference_otu_table.biom")
if exists(study2fp):
move(study2fp,
join(mp, "2_study_1001_closed_reference_otu_table.biom"))
def test_lock_check(self):
for status in ["queued", "running", "public", "completed", "error"]:
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.status = status
with self.assertRaises(QiitaDBStatusError):
new._lock_check(self.conn_handler)
def test_lock_check_ok(self):
self.analysis.status = "in_construction"
self.analysis._lock_check(self.conn_handler)
def test_status_setter_checks(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.status = "queued"
def test_get_by_status(self):
self.assertEqual(Analysis.get_by_status('public'), [])
self.analysis.status = "public"
self.assertEqual(Analysis.get_by_status('public'), [1])
def test_has_access_public(self):
self.conn_handler.execute("UPDATE qiita.analysis SET "
"analysis_status_id = 6")
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_shared(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_no_access(self):
self.assertFalse(self.analysis.has_access(User("*****@*****.**")))
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(
obs[0][:-1],
[3, '*****@*****.**', 'newAnalysis', 'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(
obs[0][:-1],
[3, '*****@*****.**', 'newAnalysis', 'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[1, 3]])
def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "*****@*****.**")
def test_retrieve_name(self):
self.assertEqual(self.analysis.name, "SomeAnalysis")
def test_retrieve_description(self):
self.assertEqual(self.analysis.description, "A test analysis")
def test_set_description(self):
self.analysis.description = "New description"
self.assertEqual(self.analysis.description, "New description")
def test_retrieve_samples(self):
exp = {
1: [
'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196',
'1.SKM9.640192', '1.SKM4.640180'
]
}
self.assertEqual(self.analysis.samples, exp)
def test_retrieve_dropped_samples(self):
# Create and populate second study to do test with
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"portal_type_id": 3,
"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)
}
metadata_dict = {
'SKB8.640193': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'str_column': 'Value for sample 1',
'latitude': 42.42,
'longitude': 41.41
},
'SKD8.640184': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 2',
'str_column': 'Value for sample 2',
'latitude': 4.2,
'longitude': 1.1
},
'SKB7.640196': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41
},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("*****@*****.**"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust",
1, [(study_fp, 6)],
study=Study(2),
data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {
1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']
}
self.analysis._build_biom_tables(samples,
10000,
conn_handler=self.conn_handler)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'}, 2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["*****@*****.**"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {12, 13, 14, 15}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, None)
def test_set_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, 2]])
def test_set_step_twice(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
new.step = 4
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, 4]])
def test_retrieve_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
self.assertEqual(new.step, 2)
def test_retrieve_step_new(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
with self.assertRaises(ValueError):
new.step
def test_retrieve_step_locked(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.step = 3
def test_retrieve_jobs(self):
self.assertEqual(self.analysis.jobs, [1, 2])
def test_retrieve_jobs_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.jobs, None)
def test_retrieve_pmid(self):
self.assertEqual(self.analysis.pmid, "121112")
def test_retrieve_pmid_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_add_samples(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.add_samples([(1, '1.SKB8.640193'), (1, '1.SKD5.640186')])
exp = {1: ['1.SKB8.640193', '1.SKD5.640186']}
self.assertEqual(new.samples, exp)
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {
1: [
'1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180'
]
}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {
1: [
'1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180'
]
}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with,
["*****@*****.**", "*****@*****.**"])
def test_unshare(self):
self.analysis.unshare(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {
1: [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'
]
}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
with open(self.map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', '1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = [
'BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT', 'CGGCCTAAGTTC'
]
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = [
'LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA'
]
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9', '1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]
exp = ['tot_org_carb', '5.0', '4.32', '5.0']
self.assertEqual(obs, exp)
obs = [line.split('\t')[-1] for line in mapdata]
exp = ['Description\n'] + ['Cannabis Soil Microbiome\n'] * 3
self.assertEqual(obs, exp)
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(ValueError):
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
def test_build_biom_tables(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples,
100,
conn_handler=self.conn_handler)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': self.biom_fp})
table = load_table(self.biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {
'Study': 'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1
}
self.assertEqual(obs, exp)
def test_build_files(self):
self.analysis.build_files()
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)
def test_add_file(self):
fp = join(get_mountpoint('analysis')[0][1], 'testfile.txt')
with open(fp, 'w') as f:
f.write('testfile!')
self.analysis._add_file('testfile.txt', 'plain_text', '18S')
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.filepath WHERE filepath_id = 19')
exp = [[19, 'testfile.txt', 9, '3675007573', 1, 1]]
self.assertEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
'SELECT * FROM qiita.analysis_filepath WHERE filepath_id = 19')
exp = [[1, 19, 2]]
self.assertEqual(obs, exp)
class TestAnalysis(TestCase):
def setUp(self):
self.analysis = Analysis(1)
_, self.fp = get_mountpoint("analysis")[0]
def test_lock_check(self):
for status in ["queued", "running", "public", "completed",
"error"]:
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.status = status
with self.assertRaises(QiitaDBStatusError):
new._lock_check(self.conn_handler)
def test_lock_check_ok(self):
self.analysis.status = "in_construction"
self.analysis._lock_check(self.conn_handler)
def test_status_setter_checks(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.status = "queued"
def test_get_by_status(self):
self.assertEqual(Analysis.get_by_status('public'), [])
self.analysis.status = "public"
self.assertEqual(Analysis.get_by_status('public'), [1])
def test_has_access_public(self):
self.conn_handler.execute("UPDATE qiita.analysis SET "
"analysis_status_id = 6")
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_shared(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_has_access_no_access(self):
self.assertFalse(self.analysis.has_access(User("*****@*****.**")))
def test_create(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [3, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
def test_create_parent(self):
sql = "SELECT EXTRACT(EPOCH FROM NOW())"
time1 = float(self.conn_handler.execute_fetchall(sql)[0][0])
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.id, 3)
sql = ("SELECT analysis_id, email, name, description, "
"analysis_status_id, pmid, EXTRACT(EPOCH FROM timestamp) "
"FROM qiita.analysis WHERE analysis_id = 3")
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs[0][:-1], [3, '*****@*****.**', 'newAnalysis',
'A New Analysis', 1, None])
self.assertTrue(time1 < float(obs[0][-1]))
sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[1, 3]])
def test_retrieve_owner(self):
self.assertEqual(self.analysis.owner, "*****@*****.**")
def test_retrieve_name(self):
self.assertEqual(self.analysis.name, "SomeAnalysis")
def test_retrieve_description(self):
self.assertEqual(self.analysis.description, "A test analysis")
def test_set_description(self):
self.analysis.description = "New description"
self.assertEqual(self.analysis.description, "New description")
def test_retrieve_samples(self):
exp = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196',
'1.SKM9.640192', '1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_retrieve_dropped_samples(self):
biom_fp = join(self.fp, "1_analysis_18S.biom")
try:
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100,
conn_handler=self.conn_handler)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'}}
self.assertEqual(self.analysis.dropped_samples, exp)
finally:
with open(biom_fp, 'w') as f:
f.write("")
def test_retrieve_data_types(self):
exp = ['18S']
self.assertEqual(self.analysis.data_types, exp)
def test_retrieve_shared_with(self):
self.assertEqual(self.analysis.shared_with, ["*****@*****.**"])
def test_retrieve_biom_tables(self):
exp = {"18S": join(self.fp, "1_analysis_18S.biom")}
self.assertEqual(self.analysis.biom_tables, exp)
def test_all_associated_filepaths(self):
exp = {14, 15}
self.assertEqual(self.analysis.all_associated_filepath_ids, exp)
def test_retrieve_biom_tables_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, None)
def test_set_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, 2]])
def test_set_step_twice(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
new.step = 4
sql = "SELECT * FROM qiita.analysis_workflow WHERE analysis_id = 3"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(obs, [[3, 4]])
def test_retrive_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
self.assertEqual(new.step, 2)
def test_retrieve_step_new(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
with self.assertRaises(ValueError):
new.step
def test_retrieve_step_locked(self):
self.analysis.status = "public"
with self.assertRaises(QiitaDBStatusError):
self.analysis.step = 3
def test_retrieve_jobs(self):
self.assertEqual(self.analysis.jobs, [1, 2])
def test_retrieve_jobs_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.jobs, None)
def test_retrieve_pmid(self):
self.assertEqual(self.analysis.pmid, "121112")
def test_retrieve_pmid_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_set_pmid(self):
self.analysis.pmid = "11211221212213"
self.assertEqual(self.analysis.pmid, "11211221212213")
def test_retrieve_mapping_file(self):
exp = join(self.fp, "1_analysis_mapping.txt")
obs = self.analysis.mapping_file
self.assertEqual(obs, exp)
self.assertTrue(exists(exp))
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
# def test_get_parent(self):
# raise NotImplementedError()
# def test_get_children(self):
# raise NotImplementedError()
def test_add_samples(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.add_samples([(1, '1.SKB8.640193'), (1, '1.SKD5.640186')])
exp = {1: ['1.SKB8.640193', '1.SKD5.640186']}
self.assertEqual(new.samples, exp)
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, ["*****@*****.**",
"*****@*****.**"])
def test_unshare(self):
self.analysis.unshare(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
map_fp = join(self.fp, "1_analysis_mapping.txt")
try:
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, map_fp)
with open(map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', '1.SKB8.640193', '1.SKD8.640184',
'1.SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = ['BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT',
'CGGCCTAAGTTC']
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = ['LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA']
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9',
'1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]
exp = ['tot_org_carb', '5.0', '4.32', '5.0']
self.assertEqual(obs, exp)
obs = [line.split('\t')[-1] for line in mapdata]
exp = ['Description\n'] + ['Cannabis Soil Microbiome\n'] * 3
self.assertEqual(obs, exp)
finally:
with open(map_fp, 'w') as f:
f.write("")
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(ValueError):
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
def test_build_biom_tables(self):
biom_fp = join(self.fp, "1_analysis_18S.biom")
try:
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_biom_tables(samples, 100,
conn_handler=self.conn_handler)
obs = self.analysis.biom_tables
self.assertEqual(obs, {'18S': biom_fp})
table = load_table(biom_fp)
obs = set(table.ids(axis='sample'))
exp = {'1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'}
self.assertEqual(obs, exp)
obs = table.metadata('1.SKB8.640193')
exp = {'Study':
'Identification of the Microbiomes for Cannabis Soils',
'Processed_id': 1}
self.assertEqual(obs, exp)
finally:
with open(biom_fp, 'w') as f:
f.write("")
def test_build_files(self):
biom_fp = join(self.fp, "1_analysis_18S.biom")
map_fp = join(self.fp, "1_analysis_mapping.txt")
try:
self.analysis.build_files()
finally:
with open(biom_fp, 'w') as f:
f.write("")
with open(map_fp, 'w') as f:
f.write("")
def test_build_files_raises_type_error(self):
with self.assertRaises(TypeError):
self.analysis.build_files('string')
with self.assertRaises(TypeError):
self.analysis.build_files(100.5)
def test_build_files_raises_value_error(self):
with self.assertRaises(ValueError):
self.analysis.build_files(0)
with self.assertRaises(ValueError):
self.analysis.build_files(-10)