def _build_study_info(studytype, user=None):
"""builds list of namedtuples for study listings"""
if studytype == "private":
studylist = user.user_studies
elif studytype == "shared":
studylist = user.shared_studies
elif studytype == "public":
studylist = Study.get_by_status('public')
else:
raise IncompetentQiitaDeveloperError("Must use private, shared, "
"or public!")
StudyTuple = namedtuple('StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
infolist = []
for s_id in studylist:
study = Study(s_id)
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
owner = study_person_linkifier((study.owner, study.owner))
info = study.info
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
pmids = ", ".join([pubmed_linkifier([pmid])
for pmid in study.pmids])
shared = _get_shared_links_for_study(study)
infolist.append(StudyTuple(study.id, study.title,
info["metadata_complete"],
info["number_samples_collected"],
shared, len(study.raw_data()),
PI, pmids, owner, status))
return infolist
def _build_study_info(studytype, user=None):
"""builds list of namedtuples for study listings"""
if studytype == "private":
studylist = user.user_studies
elif studytype == "shared":
studylist = user.shared_studies
elif studytype == "public":
studylist = Study.get_by_status('public')
else:
raise IncompetentQiitaDeveloperError("Must use private, shared, "
"or public!")
StudyTuple = namedtuple(
'StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
infolist = []
for s_id in studylist:
study = Study(s_id)
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
owner = study_person_linkifier((study.owner, study.owner))
info = study.info
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
pmids = ", ".join([pubmed_linkifier([pmid]) for pmid in study.pmids])
shared = _get_shared_links_for_study(study)
infolist.append(
StudyTuple(study.id, study.title, info["metadata_complete"],
info["number_samples_collected"], shared,
len(study.raw_data()), PI, pmids, owner, status))
return infolist
def _get_accessible_raw_data(user):
"""Retrieves a tuple of raw_data_id and one study title for that
raw_data
"""
d = {}
accessible_studies = user.user_studies.union(user.shared_studies)
for sid in accessible_studies:
study = Study(sid)
study_title = study.title
for rdid in study.raw_data():
d[int(rdid)] = study_title
return d
class TestStudy(TestCase):
def setUp(self):
self.study = Study(1)
self.portal = qiita_config.portal
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)
}
self.infoexp = {
"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": 2,
"principal_investigator_id": 3,
"lab_person_id": 1
}
self.existingexp = {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'number_samples_promised': 27,
'emp_person_id': StudyPerson(2),
'funding': None,
'vamps_id': None,
'first_contact': datetime(2014, 5, 19, 16, 10),
'principal_investigator_id': StudyPerson(3),
'timeseries_type_id': 1,
'study_abstract':
"This is a preliminary study to examine the "
"microbiota associated with the Cannabis plant. Soils samples "
"from the bulk soil, soil associated with the roots, and the "
"rhizosphere were extracted and the DNA sequenced. Roots "
"from three independent plants of different strains were "
"examined. These roots were obtained November 11, 2011 from "
"plants that had been harvested in the summer. Future "
"studies will attempt to analyze the soils and rhizospheres "
"from the same location at different time points in the plant "
"lifecycle.",
'spatial_series': False,
'study_description': 'Analysis of the Cannabis Plant Microbiome',
'study_alias': 'Cannabis Soils',
'most_recent_contact': '2014-05-19 16:11',
'most_recent_contact': datetime(2014, 5, 19, 16, 11),
'lab_person_id': StudyPerson(1),
'number_samples_collected': 27}
def tearDown(self):
qiita_config.portal = self.portal
def _change_processed_data_status(self, new_status):
# Change the status of the studies by changing the status of their
# processed data
id_status = convert_to_id(new_status, 'processed_data_status')
self.conn_handler.execute(
"UPDATE qiita.processed_data SET processed_data_status_id = %s",
(id_status,))
def test_get_info(self):
# Test get all info for single study
qiita_config.portal = 'QIITA'
obs = Study.get_info([1])
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'mixs_compliant': True, 'metadata_complete': True,
'reprocess': False, 'timeseries_type': 'None',
'number_samples_promised': 27, 'emp_person_id': 2,
'funding': None, 'vamps_id': None,
'first_contact': datetime(2014, 5, 19, 16, 10),
'principal_investigator_id': 3, 'timeseries_type_id': 1,
'pmid': ['123456', '7891011'], 'study_alias': 'Cannabis Soils',
'spatial_series': False,
'study_abstract': 'This is a preliminary study to examine the '
'microbiota associated with the Cannabis plant. Soils samples from'
' the bulk soil, soil associated with the roots, and the '
'rhizosphere were extracted and the DNA sequenced. Roots from '
'three independent plants of different strains were examined. '
'These roots were obtained November 11, 2011 from plants that had '
'been harvested in the summer. Future studies will attempt to '
'analyze the soils and rhizospheres from the same location at '
'different time points in the plant lifecycle.',
'study_description': 'Analysis of the Cannabis Plant Microbiome',
'intervention_type': 'None', 'email': '*****@*****.**',
'study_id': 1,
'most_recent_contact': datetime(2014, 5, 19, 16, 11),
'lab_person_id': 1,
'study_title': 'Identification of the Microbiomes for Cannabis '
'Soils', 'number_samples_collected': 27}
self.assertItemsEqual(obs, exp)
# Test get specific keys for single study
exp_keys = ['metadata_complete', 'reprocess', 'timeseries_type',
'pmid', 'study_title']
obs = Study.get_info([1], exp_keys)
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'metadata_complete': True, 'reprocess': False,
'timeseries_type': 'None',
'pmid': ['123456', '7891011'],
'study_title': 'Identification of the Microbiomes for Cannabis '
'Soils'}
self.assertItemsEqual(obs, exp)
# Test get specific keys for all studies
info = {
'timeseries_type_id': 1,
'lab_person_id': None,
'principal_investigator_id': 3,
'metadata_complete': False,
'mixs_compliant': True,
'study_description': 'desc',
'study_alias': 'alias',
'study_abstract': 'abstract'}
user = User('*****@*****.**')
Study.create(user, 'test_study_1', efo=[1], info=info)
obs = Study.get_info(info_cols=exp_keys)
exp = [[True, ['123456', '7891011'], False,
'Identification of the Microbiomes for Cannabis Soils',
'None'],
[False, None, False, 'test_study_1', 'None']]
self.assertEqual(obs, exp)
# test portal restriction working
qiita_config.portal = 'EMP'
with self.assertRaises(QiitaDBError):
Study.get_info([1])
def test_has_access_public(self):
self._change_processed_data_status('public')
qiita_config.portal = 'QIITA'
self.assertTrue(self.study.has_access(User("*****@*****.**")))
qiita_config.portal = 'EMP'
with self.assertRaises(QiitaDBError):
Study(1).has_access(User("*****@*****.**"))
def test_has_access_no_public(self):
self._change_processed_data_status('public')
self.assertFalse(self.study.has_access(User("*****@*****.**"), True))
def test_owner(self):
self.assertEqual(self.study.owner, "*****@*****.**")
def test_share(self):
# Clear all sharing associations
self._change_processed_data_status('sandbox')
self.conn_handler.execute("delete from qiita.study_users")
self.assertEqual(self.study.shared_with, [])
# Try to share with the owner, which should not work
self.study.share(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, [])
# Then share the study with [email protected]
self.study.share(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, ["*****@*****.**"])
def test_unshare(self):
self._change_processed_data_status('sandbox')
self.study.unshare(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, [])
def test_has_access_shared(self):
self._change_processed_data_status('sandbox')
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self._change_processed_data_status('sandbox')
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
self._change_processed_data_status('sandbox')
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_no_access(self):
self._change_processed_data_status('sandbox')
self.assertFalse(self.study.has_access(User("*****@*****.**")))
def test_get_by_status(self):
obs = Study.get_by_status('sandbox')
self.assertEqual(obs, set())
Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_by_status('private')
self.assertEqual(obs, {1})
obs = Study.get_by_status('sandbox')
self.assertEqual(obs, {2})
obs = Study.get_by_status('public')
self.assertEqual(obs, set())
obs = Study.get_by_status('awaiting_approval')
self.assertEqual(obs, set())
def test_exists(self):
self.assertTrue(Study.exists('Identification of the Microbiomes for '
'Cannabis Soils'))
self.assertFalse(Study.exists('Not Cannabis Soils'))
def test_create_duplicate(self):
with self.assertRaises(QiitaDBDuplicateError):
Study.create(
User('*****@*****.**'),
'Identification of the Microbiomes for Cannabis Soils',
[1], self.info)
def test_create_study_min_data(self):
"""Insert a study into the database"""
before = datetime.now()
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
after = datetime.now()
self.assertEqual(obs.id, 2)
exp = {'mixs_compliant': True, 'metadata_complete': True,
'reprocess': False,
'number_samples_promised': 28, 'emp_person_id': 2,
'funding': None, 'vamps_id': None,
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**', 'spatial_series': None,
'study_description': 'Microbiome of people who eat nothing but'
' fried chicken',
'study_alias': 'FCM', 'study_id': 2,
'most_recent_contact': None, 'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 2")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
# Check the timestamp separately, since it is set by the database
# to the microsecond, and we can't predict it a priori
ins_timestamp = obsins.pop('first_contact')
self.assertTrue(before < ins_timestamp < after)
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
efo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 2")
self.assertEqual(efo, [[1]])
def test_create_nonqiita_portal(self):
qiita_config.portal = "EMP"
Study.create(User('*****@*****.**'), "NEW!",
[1], self.info, Investigation(1))
# make sure portal is associated
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.study_portal WHERE study_id = 2")
self.assertEqual(obs, [[2, 2], [2, 1]])
def test_create_study_with_investigation(self):
"""Insert a study into the database with an investigation"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info, Investigation(1))
self.assertEqual(obs.id, 2)
# check the investigation was assigned
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.investigation_study WHERE study_id = 2")
self.assertEqual(obs, [[1, 2]])
def test_create_study_all_data(self):
"""Insert a study into the database with every info field"""
self.info.update({
'vamps_id': 'MBE_1111111',
'funding': 'FundAgency',
'spatial_series': True,
'metadata_complete': False,
'reprocess': True,
'first_contact': "10/24/2014 12:47PM",
'study_id': 3827
})
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 3827)
exp = {'mixs_compliant': True, 'metadata_complete': False,
'reprocess': True,
'number_samples_promised': 28, 'emp_person_id': 2,
'funding': 'FundAgency', 'vamps_id': 'MBE_1111111',
'first_contact': datetime(2014, 10, 24, 12, 47),
'principal_investigator_id': 3, 'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**', 'spatial_series': True,
'study_description': 'Microbiome of people who eat nothing '
'but fried chicken',
'study_alias': 'FCM', 'study_id': 3827,
'most_recent_contact': None, 'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 3827")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
obsefo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 3827")
self.assertEqual(obsefo, [[1]])
def test_create_missing_required(self):
""" Insert a study that is missing a required info key"""
self.info.pop("study_alias")
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_create_empty_efo(self):
""" Insert a study that is missing a required info key"""
with self.assertRaises(IncompetentQiitaDeveloperError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[], self.info)
def test_create_study_with_not_allowed_key(self):
"""Insert a study with key from _non_info present"""
self.info.update({"email": "*****@*****.**"})
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_create_unknown_db_col(self):
""" Insert a study with an info key not in the database"""
self.info["SHOULDNOTBEHERE"] = "BWAHAHAHAHAHA"
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_delete(self):
title = "Fried chicken microbiome"
# the study is assigned to investigation 1
study = Study.create(User('*****@*****.**'), title, [1], self.info,
Investigation(1))
# sharing with other user
study.share(User("*****@*****.**"))
study.delete(study.id)
self.assertFalse(study.exists(title))
with self.assertRaises(QiitaDBError):
Study.delete(1)
with self.assertRaises(QiitaDBUnknownIDError):
Study.delete(41)
def test_retrieve_title(self):
self.assertEqual(self.study.title, 'Identification of the Microbiomes'
' for Cannabis Soils')
def test_set_title(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.title = "Cannabis soils"
self.assertEqual(new.title, "Cannabis soils")
def test_get_efo(self):
self.assertEqual(self.study.efo, [1])
def test_set_efo(self):
"""Set efo with list efo_id"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.efo = [3, 4]
self.assertEqual(new.efo, [3, 4])
def test_set_efo_empty(self):
"""Set efo with list efo_id"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.efo = []
def test_set_efo_public(self):
"""Set efo on a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.efo = 6
def test_portals(self):
self.assertEqual(self.study._portals, ['QIITA'])
def test_retrieve_info(self):
for key, val in viewitems(self.existingexp):
if isinstance(val, QiitaObject):
self.existingexp[key] = val.id
self.assertEqual(self.study.info, self.existingexp)
def test_set_info(self):
"""Set info in a study"""
newinfo = {
"timeseries_type_id": 2,
"metadata_complete": False,
"number_samples_collected": 28,
"lab_person_id": StudyPerson(2),
"vamps_id": 'MBE_111222',
}
self.info['first_contact'] = "6/11/2014"
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.infoexp.update(newinfo)
new.info = newinfo
# add missing table cols
self.infoexp["funding"] = None
self.infoexp["spatial_series"] = None
self.infoexp["most_recent_contact"] = None
self.infoexp["reprocess"] = False
self.infoexp["lab_person_id"] = 2
self.infoexp["first_contact"] = datetime(2014, 6, 11)
self.assertEqual(new.info, self.infoexp)
def test_set_info_public(self):
"""Tests for fail if editing info of a public study"""
self.study.info = {"vamps_id": "12321312"}
def test_set_info_public_error(self):
"""Tests for fail if trying to modify timeseries of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.info = {"timeseries_type_id": 2}
def test_set_info_disallowed_keys(self):
"""Tests for fail if sending non-info keys in info dict"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(QiitaDBColumnError):
new.info = {"email": "*****@*****.**"}
def test_info_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.info = {}
def test_retrieve_status(self):
self.assertEqual(self.study.status, "private")
def test_retrieve_shared_with(self):
self.assertEqual(self.study.shared_with, ['*****@*****.**'])
def test_retrieve_pmids(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
def test_retrieve_pmids_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.pmids, [])
def test_pmids_setter(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
new_values = ['654321', '1101987']
self.study.pmids = new_values
self.assertEqual(self.study.pmids, new_values)
def test_pmids_setter_typeerror(self):
with self.assertRaises(TypeError):
self.study.pmids = '123456'
def test_retrieve_investigation(self):
self.assertEqual(self.study.investigation, 1)
def test_retrieve_investigation_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.investigation, None)
def test_retrieve_sample_template(self):
self.assertEqual(self.study.sample_template, 1)
def test_retrieve_data_types(self):
self.assertEqual(self.study.data_types, ['18S'])
def test_retrieve_data_types_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.data_types, [])
def test_retrieve_raw_data(self):
self.assertEqual(self.study.raw_data(), [1])
def test_retrieve_raw_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.raw_data(), [])
def test_retrieve_prep_templates(self):
self.assertEqual(self.study.prep_templates(), [1])
def test_retrieve_prep_templates_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.prep_templates(), [])
def test_retrieve_preprocessed_data(self):
self.assertEqual(self.study.preprocessed_data(), [1, 2])
def test_retrieve_preprocessed_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.preprocessed_data(), [])
def test_retrieve_processed_data(self):
self.assertEqual(self.study.processed_data(), [1])
def test_retrieve_processed_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.processed_data(), [])
def test_add_pmid(self):
self._change_processed_data_status('sandbox')
self.study.add_pmid('4544444')
exp = ['123456', '7891011', '4544444']
self.assertEqual(self.study.pmids, exp)
def test_environmental_packages(self):
obs = self.study.environmental_packages
exp = ['soil', 'plant-associated']
self.assertEqual(sorted(obs), sorted(exp))
def test_environmental_packages_setter(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = new.environmental_packages
exp = []
self.assertEqual(obs, exp)
new_values = ['air', 'human-oral']
new.environmental_packages = new_values
obs = new.environmental_packages
self.assertEqual(sorted(obs), sorted(new_values))
def test_environmental_packages_setter_typeerror(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(TypeError):
new.environmental_packages = 'air'
def test_environmental_packages_setter_valueerror(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(ValueError):
new.environmental_packages = ['air', 'not a package']
def test_environmental_packages_sandboxed(self):
with self.assertRaises(QiitaDBStatusError):
self.study.environmental_packages = ['air']
class TestStudy(TestCase):
def setUp(self):
self.study = Study(1)
self.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)
}
self.infoexp = {
"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": 2,
"principal_investigator_id": 3,
"lab_person_id": 1
}
self.existingexp = {
'mixs_compliant':
True,
'metadata_complete':
True,
'reprocess':
False,
'number_samples_promised':
27,
'emp_person_id':
StudyPerson(2),
'funding':
None,
'vamps_id':
None,
'first_contact':
datetime(2014, 5, 19, 16, 10),
'principal_investigator_id':
StudyPerson(3),
'timeseries_type_id':
1,
'study_abstract':
"This is a preliminary study to examine the "
"microbiota associated with the Cannabis plant. Soils samples "
"from the bulk soil, soil associated with the roots, and the "
"rhizosphere were extracted and the DNA sequenced. Roots "
"from three independent plants of different strains were "
"examined. These roots were obtained November 11, 2011 from "
"plants that had been harvested in the summer. Future "
"studies will attempt to analyze the soils and rhizospheres "
"from the same location at different time points in the plant "
"lifecycle.",
'spatial_series':
False,
'study_description':
'Analysis of the Cannabis Plant Microbiome',
'portal_type_id':
2,
'study_alias':
'Cannabis Soils',
'most_recent_contact':
'2014-05-19 16:11',
'most_recent_contact':
datetime(2014, 5, 19, 16, 11),
'lab_person_id':
StudyPerson(1),
'number_samples_collected':
27
}
def _make_private(self):
# make studies private
self.conn_handler.execute("UPDATE qiita.study SET study_status_id = 4")
def _make_sandbox(self):
# make studies private
self.conn_handler.execute("UPDATE qiita.study SET study_status_id = 1")
def test_has_access_public(self):
self.study.status = 'public'
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_no_public(self):
self.study.status = 'public'
self.assertFalse(self.study.has_access(User("*****@*****.**"), True))
def test_owner(self):
self.assertEqual(self.study.owner, "*****@*****.**")
def test_share(self):
# Clear all sharing associations
self._make_private()
self.conn_handler.execute("delete from qiita.study_users")
self.assertEqual(self.study.shared_with, [])
# Try to share with the owner, which should not work
self.study.share(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, [])
# Then share the study with [email protected]
self.study.share(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, ["*****@*****.**"])
def test_unshare(self):
self._make_private()
self.study.unshare(User("*****@*****.**"))
self.assertEqual(self.study.shared_with, [])
def test_has_access_shared(self):
self._make_private()
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_private(self):
self._make_private()
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_admin(self):
self._make_private()
self.assertTrue(self.study.has_access(User("*****@*****.**")))
def test_has_access_no_access(self):
self._make_private()
self.assertFalse(self.study.has_access(User("*****@*****.**")))
def test_get_by_status(self):
Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_by_status('private')
self.assertEqual(obs, [1])
def test_exists(self):
self.assertTrue(
Study.exists('Identification of the Microbiomes for '
'Cannabis Soils'))
self.assertFalse(Study.exists('Not Cannabis Soils'))
def test_create_study_min_data(self):
"""Insert a study into the database"""
before = datetime.now()
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
after = datetime.now()
self.assertEqual(obs.id, 2)
exp = {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'study_status_id': 4,
'number_samples_promised': 28,
'emp_person_id': 2,
'funding': None,
'vamps_id': None,
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**',
'spatial_series': None,
'study_description': 'Microbiome of people who eat nothing but'
' fried chicken',
'portal_type_id': 3,
'study_alias': 'FCM',
'study_id': 2,
'most_recent_contact': None,
'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25
}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 2")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
# Check the timestamp separately, since it is set by the database
# to the microsecond, and we can't predict it a priori
ins_timestamp = obsins.pop('first_contact')
self.assertTrue(before < ins_timestamp < after)
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
efo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 2")
self.assertEqual(efo, [[1]])
def test_create_study_with_investigation(self):
"""Insert a study into the database with an investigation"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info, Investigation(1))
self.assertEqual(obs.id, 2)
# check the investigation was assigned
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.investigation_study WHERE study_id = 2")
self.assertEqual(obs, [[1, 2]])
def test_create_study_all_data(self):
"""Insert a study into the database with every info field"""
self.info.update({
'vamps_id': 'MBE_1111111',
'funding': 'FundAgency',
'spatial_series': True,
'metadata_complete': False,
'reprocess': True,
'first_contact': "10/24/2014 12:47PM",
'study_id': 3827
})
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 3827)
exp = {
'mixs_compliant': True,
'metadata_complete': False,
'reprocess': True,
'study_status_id': 4,
'number_samples_promised': 28,
'emp_person_id': 2,
'funding': 'FundAgency',
'vamps_id': 'MBE_1111111',
'first_contact': datetime(2014, 10, 24, 12, 47),
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**',
'spatial_series': True,
'study_description': 'Microbiome of people who eat nothing '
'but fried chicken',
'portal_type_id': 3,
'study_alias': 'FCM',
'study_id': 3827,
'most_recent_contact': None,
'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25
}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 3827")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
obsefo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 3827")
self.assertEqual(obsefo, [[1]])
def test_create_missing_required(self):
""" Insert a study that is missing a required info key"""
self.info.pop("study_alias")
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_create_empty_efo(self):
""" Insert a study that is missing a required info key"""
with self.assertRaises(IncompetentQiitaDeveloperError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [],
self.info)
def test_create_study_with_not_allowed_key(self):
"""Insert a study with key from _non_info present"""
self.info.update({"email": "*****@*****.**"})
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_create_unknown_db_col(self):
""" Insert a study with an info key not in the database"""
self.info["SHOULDNOTBEHERE"] = "BWAHAHAHAHAHA"
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_retrieve_title(self):
self.assertEqual(
self.study.title, 'Identification of the Microbiomes'
' for Cannabis Soils')
def test_set_title(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.title = "Cannabis soils"
self.assertEqual(new.title, "Cannabis soils")
def test_get_efo(self):
self.assertEqual(self.study.efo, [1])
def test_set_efo(self):
"""Set efo with list efo_id"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.efo = [3, 4]
self.assertEqual(new.efo, [3, 4])
def test_set_efo_empty(self):
"""Set efo with list efo_id"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.efo = []
def test_set_efo_public(self):
"""Set efo on a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.efo = 6
def test_retrieve_info(self):
for key, val in viewitems(self.existingexp):
if isinstance(val, QiitaObject):
self.existingexp[key] = val.id
self.assertEqual(self.study.info, self.existingexp)
def test_set_info(self):
"""Set info in a study"""
newinfo = {
"timeseries_type_id": 2,
"metadata_complete": False,
"number_samples_collected": 28,
"lab_person_id": StudyPerson(2),
"vamps_id": 'MBE_111222',
}
self.info['first_contact'] = "6/11/2014"
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.infoexp.update(newinfo)
new.info = newinfo
# add missing table cols
self.infoexp["funding"] = None
self.infoexp["spatial_series"] = None
self.infoexp["most_recent_contact"] = None
self.infoexp["reprocess"] = False
self.infoexp["lab_person_id"] = 2
self.infoexp["first_contact"] = datetime(2014, 6, 11)
self.assertEqual(new.info, self.infoexp)
def test_set_info_public(self):
"""Tests for fail if editing info of a public study"""
self.study.info = {"vamps_id": "12321312"}
def test_set_info_public_error(self):
"""Tests for fail if trying to modify timeseries of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.info = {"timeseries_type_id": 2}
def test_set_info_disallowed_keys(self):
"""Tests for fail if sending non-info keys in info dict"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(QiitaDBColumnError):
new.info = {"email": "*****@*****.**"}
def test_info_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.info = {}
def test_retrieve_status(self):
self.assertEqual(self.study.status, "private")
def test_set_status(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.status = "private"
self.assertEqual(new.status, "private")
def test_retrieve_shared_with(self):
self.assertEqual(self.study.shared_with, ['*****@*****.**'])
def test_retrieve_pmids(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
def test_retrieve_pmids_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.pmids, [])
def test_pmids_setter(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
new_values = ['654321', '1101987']
self.study.pmids = new_values
self.assertEqual(self.study.pmids, new_values)
def test_pmids_setter_typeerror(self):
with self.assertRaises(TypeError):
self.study.pmids = '123456'
def test_retrieve_investigation(self):
self.assertEqual(self.study.investigation, 1)
def test_retrieve_investigation_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.investigation, None)
def test_retrieve_sample_template(self):
self.assertEqual(self.study.sample_template, 1)
def test_retrieve_data_types(self):
self.assertEqual(self.study.data_types, ['18S'])
def test_retrieve_data_types_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.data_types, [])
def test_retrieve_raw_data(self):
self.assertEqual(self.study.raw_data(), [1, 2, 3, 4])
def test_retrieve_raw_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.raw_data(), [])
def test_add_raw_data(self):
self._make_sandbox()
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.add_raw_data([RawData(1), RawData(2)])
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study_raw_data WHERE study_id=%s", (new.id, ))
self.assertEqual(obs, [[new.id, 1], [new.id, 2]])
def test_add_raw_data_private(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.status = 'private'
with self.assertRaises(QiitaDBStatusError):
new.add_raw_data([RawData(2)])
def test_retrieve_preprocessed_data(self):
self.assertEqual(self.study.preprocessed_data(), [1, 2])
def test_retrieve_preprocessed_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.preprocessed_data(), [])
def test_retrieve_processed_data(self):
self.assertEqual(self.study.processed_data(), [1])
def test_retrieve_processed_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.processed_data(), [])
def test_add_pmid(self):
self._make_private()
self.study.add_pmid('4544444')
exp = ['123456', '7891011', '4544444']
self.assertEqual(self.study.pmids, exp)
def test_environmental_packages(self):
obs = self.study.environmental_packages
exp = ['soil', 'plant-associated']
self.assertEqual(sorted(obs), sorted(exp))
def test_environmental_packages_setter(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = new.environmental_packages
exp = []
self.assertEqual(obs, exp)
new_values = ['air', 'human-oral']
new.environmental_packages = new_values
obs = new.environmental_packages
self.assertEqual(sorted(obs), sorted(new_values))
def test_environmental_packages_setter_typeerror(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(TypeError):
new.environmental_packages = 'air'
def test_environmental_packages_setter_valueerror(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(ValueError):
new.environmental_packages = ['air', 'not a package']
def test_environmental_packages_sandboxed(self):
with self.assertRaises(QiitaDBStatusError):
self.study.environmental_packages = ['air']
class TestStudy(TestCase):
def setUp(self):
self.study = Study(1)
self.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)
}
self.infoexp = {
"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": 2,
"principal_investigator_id": 3,
"lab_person_id": 1
}
self.existingexp = {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'number_samples_promised': 27,
'emp_person_id': StudyPerson(2),
'funding': None,
'vamps_id': None,
'first_contact': '2014-05-19 16:10',
'principal_investigator_id': StudyPerson(3),
'timeseries_type_id': 1,
'study_abstract':
"This is a preliminary study to examine the "
"microbiota associated with the Cannabis plant. Soils samples "
"from the bulk soil, soil associated with the roots, and the "
"rhizosphere were extracted and the DNA sequenced. Roots "
"from three independent plants of different strains were "
"examined. These roots were obtained November 11, 2011 from "
"plants that had been harvested in the summer. Future "
"studies will attempt to analyze the soils and rhizospheres "
"from the same location at different time points in the plant "
"lifecycle.",
'spatial_series': False,
'study_description': 'Analysis of the Cannabis Plant Microbiome',
'portal_type_id': 2,
'study_alias': 'Cannabis Soils',
'most_recent_contact': '2014-05-19 16:11',
'lab_person_id': StudyPerson(1),
'number_samples_collected': 27}
def test_get_public(self):
Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_public()
self.assertEqual(obs, [1])
def test_exists(self):
self.assertTrue(Study.exists('Identification of the Microbiomes for '
'Cannabis Soils'))
self.assertFalse(Study.exists('Not Cannabis Soils'))
def test_create_study_min_data(self):
"""Insert a study into the database"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 2)
exp = {'mixs_compliant': True, 'metadata_complete': True,
'reprocess': False, 'study_status_id': 1,
'number_samples_promised': 28, 'emp_person_id': 2,
'funding': None, 'vamps_id': None,
'first_contact': date.today().isoformat(),
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**', 'spatial_series': None,
'study_description': 'Microbiome of people who eat nothing but'
' fried chicken',
'portal_type_id': 3, 'study_alias': 'FCM', 'study_id': 2,
'most_recent_contact': None, 'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 2")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
efo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 2")
self.assertEqual(efo, [[1]])
def test_create_study_with_investigation(self):
"""Insert a study into the database with an investigation"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info, Investigation(1))
self.assertEqual(obs.id, 2)
# check the investigation was assigned
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.investigation_study WHERE study_id = 2")
self.assertEqual(obs, [[1, 2]])
def test_create_study_all_data(self):
"""Insert a study into the database with every info field"""
self.info.update({
'vamps_id': 'MBE_1111111',
'funding': 'FundAgency',
'spatial_series': True,
'metadata_complete': False,
'reprocess': True,
'first_contact': "Today",
'study_id': 3827
})
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 3827)
exp = {'mixs_compliant': True, 'metadata_complete': False,
'reprocess': True, 'study_status_id': 1,
'number_samples_promised': 28, 'emp_person_id': 2,
'funding': 'FundAgency', 'vamps_id': 'MBE_1111111',
'first_contact': "Today",
'principal_investigator_id': 3, 'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**', 'spatial_series': True,
'study_description': 'Microbiome of people who eat nothing '
'but fried chicken',
'portal_type_id': 3, 'study_alias': 'FCM', 'study_id': 3827,
'most_recent_contact': None, 'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 3827")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
obsefo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 3827")
self.assertEqual(obsefo, [[1]])
def test_create_missing_required(self):
""" Insert a study that is missing a required info key"""
self.info.pop("study_alias")
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_create_empty_efo(self):
""" Insert a study that is missing a required info key"""
with self.assertRaises(IncompetentQiitaDeveloperError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[], self.info)
def test_create_study_with_not_allowed_key(self):
"""Insert a study with key from _non_info present"""
self.info.update({"email": "*****@*****.**"})
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_create_unknown_db_col(self):
""" Insert a study with an info key not in the database"""
self.info["SHOULDNOTBEHERE"] = "BWAHAHAHAHAHA"
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome",
[1], self.info)
def test_retrieve_title(self):
self.assertEqual(self.study.title, 'Identification of the Microbiomes'
' for Cannabis Soils')
def test_set_title(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.title = "Cannabis soils"
self.assertEqual(new.title, "Cannabis soils")
def test_set_title_public(self):
"""Tests for fail if editing title of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.title = "FAILBOAT"
def test_get_efo(self):
self.assertEqual(self.study.efo, [1])
def test_set_efo(self):
"""Set efo with list efo_id"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.efo = [3, 4]
self.assertEqual(new.efo, [3, 4])
def test_set_efo_empty(self):
"""Set efo with list efo_id"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.efo = []
def test_set_efo_public(self):
"""Set efo on a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.efo = 6
def test_retrieve_info(self):
for key, val in viewitems(self.existingexp):
if isinstance(val, QiitaObject):
self.existingexp[key] = val.id
self.assertEqual(self.study.info, self.existingexp)
def test_set_info(self):
"""Set info in a study"""
newinfo = {
"timeseries_type_id": 2,
"metadata_complete": False,
"number_samples_collected": 28,
"lab_person_id": StudyPerson(2),
"vamps_id": 'MBE_111222',
"first_contact": "June 11, 2014"
}
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.infoexp.update(newinfo)
new.info = newinfo
# add missing table cols
self.infoexp["funding"] = None
self.infoexp["spatial_series"] = None
self.infoexp["most_recent_contact"] = None
self.infoexp["reprocess"] = False
self.infoexp["lab_person_id"] = 2
self.assertEqual(new.info, self.infoexp)
def test_set_info_public(self):
"""Tests for fail if editing info of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.info = {"vamps_id": "12321312"}
def test_set_info_disallowed_keys(self):
"""Tests for fail if sending non-info keys in info dict"""
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(QiitaDBColumnError):
new.info = {"email": "*****@*****.**"}
def test_info_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.info = {}
def test_retrieve_status(self):
self.assertEqual(self.study.status, "public")
def test_set_status(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.status = "private"
self.assertEqual(new.status, "private")
def test_retrieve_shared_with(self):
self.assertEqual(self.study.shared_with, ['*****@*****.**',
'*****@*****.**'])
def test_retrieve_pmids(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
def test_retrieve_pmids_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.pmids, [])
def test_retrieve_investigation(self):
self.assertEqual(self.study.investigation, 1)
def test_retrieve_investigation_empty(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.investigation, None)
def test_retrieve_sample_template(self):
self.assertEqual(self.study.sample_template, 1)
def test_retrieve_data_types(self):
self.assertEqual(self.study.data_types, ['18S'])
def test_retrieve_data_types_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.data_types, [])
def test_retrieve_raw_data(self):
self.assertEqual(self.study.raw_data(), [1, 2])
def test_retrieve_raw_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.raw_data(), [])
def test_retrieve_preprocessed_data(self):
self.assertEqual(self.study.preprocessed_data(), [1, 2])
def test_retrieve_preprocessed_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.preprocessed_data(), [])
def test_retrieve_processed_data(self):
self.assertEqual(self.study.processed_data(), [1])
def test_retrieve_processed_data_none(self):
new = Study.create(User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.processed_data(), [])
def test_add_pmid(self):
self.study.add_pmid('4544444')
exp = ['123456', '7891011', '4544444']
self.assertEqual(self.study.pmids, exp)
def _build_study_info(user, results=None):
"""builds list of dicts for studies table, with all html formatted"""
# get list of studies for table
study_list = user.user_studies.union(
Study.get_by_status('public')).union(user.shared_studies)
if results is not None:
study_list = study_list.intersection(results)
if not study_list:
# No studies left so no need to continue
return []
# get info for the studies
cols = ['study_id', 'email', 'principal_investigator_id',
'pmid', 'study_title', 'metadata_complete',
'number_samples_collected', 'study_abstract']
study_info = Study.get_info(study_list, cols)
infolist = []
for row, info in enumerate(study_info):
study = Study(info['study_id'])
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
if info['pmid'] is not None:
pmids = ", ".join([pubmed_linkifier([p])
for p in info['pmid']])
else:
pmids = ""
if info["number_samples_collected"] is None:
info["number_samples_collected"] = "0"
shared = _get_shared_links_for_study(study)
meta_complete_glyph = "ok" if info["metadata_complete"] else "remove"
# build the HTML elements needed for table cell
title = ("<a href='#' data-toggle='modal' "
"data-target='#study-abstract-modal' "
"onclick='fillAbstract(\"studies-table\", {0})'>"
"<span class='glyphicon glyphicon-file' "
"aria-hidden='true'></span></a> | "
"<a href='/study/description/{1}' "
"id='study{0}-title'>{2}</a>").format(
str(row), str(study.id), info["study_title"])
meta_complete = "<span class='glyphicon glyphicon-%s'></span>" % \
meta_complete_glyph
if status == 'public':
shared = "Not Available"
else:
shared = ("<span id='shared_html_{0}'>{1}</span><br/>"
"<a class='btn btn-primary btn-xs' data-toggle='modal' "
"data-target='#share-study-modal-view' "
"onclick='modify_sharing({0});'>Modify</a>".format(
study.id, shared))
infolist.append({
"checkbox": "<input type='checkbox' value='%d' />" % study.id,
"id": study.id,
"title": title,
"meta_complete": meta_complete,
"num_samples": info["number_samples_collected"],
"shared": shared,
"num_raw_data": len(study.raw_data()),
"pi": PI,
"pmid": pmids,
"status": status,
"abstract": info["study_abstract"]
})
return infolist
class TestStudy(TestCase):
def setUp(self):
self.study = Study(1)
self.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)
}
self.infoexp = {
"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": 2,
"principal_investigator_id": 3,
"lab_person_id": 1
}
self.existingexp = {
'mixs_compliant':
True,
'metadata_complete':
True,
'reprocess':
False,
'number_samples_promised':
27,
'emp_person_id':
StudyPerson(2),
'funding':
None,
'vamps_id':
None,
'first_contact':
'2014-05-19 16:10',
'principal_investigator_id':
StudyPerson(3),
'timeseries_type_id':
1,
'study_abstract':
"This is a preliminary study to examine the "
"microbiota associated with the Cannabis plant. Soils samples "
"from the bulk soil, soil associated with the roots, and the "
"rhizosphere were extracted and the DNA sequenced. Roots "
"from three independent plants of different strains were "
"examined. These roots were obtained November 11, 2011 from "
"plants that had been harvested in the summer. Future "
"studies will attempt to analyze the soils and rhizospheres "
"from the same location at different time points in the plant "
"lifecycle.",
'spatial_series':
False,
'study_description':
'Analysis of the Cannabis Plant Microbiome',
'portal_type_id':
2,
'study_alias':
'Cannabis Soils',
'most_recent_contact':
'2014-05-19 16:11',
'lab_person_id':
StudyPerson(1),
'number_samples_collected':
27
}
def test_get_public(self):
Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
obs = Study.get_public()
self.assertEqual(obs, [1])
def test_exists(self):
self.assertTrue(
Study.exists('Identification of the Microbiomes for '
'Cannabis Soils'))
self.assertFalse(Study.exists('Not Cannabis Soils'))
def test_create_study_min_data(self):
"""Insert a study into the database"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 2)
exp = {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'study_status_id': 1,
'number_samples_promised': 28,
'emp_person_id': 2,
'funding': None,
'vamps_id': None,
'first_contact': date.today().isoformat(),
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**',
'spatial_series': None,
'study_description': 'Microbiome of people who eat nothing but'
' fried chicken',
'portal_type_id': 3,
'study_alias': 'FCM',
'study_id': 2,
'most_recent_contact': None,
'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25
}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 2")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
efo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 2")
self.assertEqual(efo, [[1]])
def test_create_study_with_investigation(self):
"""Insert a study into the database with an investigation"""
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info, Investigation(1))
self.assertEqual(obs.id, 2)
# check the investigation was assigned
obs = self.conn_handler.execute_fetchall(
"SELECT * from qiita.investigation_study WHERE study_id = 2")
self.assertEqual(obs, [[1, 2]])
def test_create_study_all_data(self):
"""Insert a study into the database with every info field"""
self.info.update({
'vamps_id': 'MBE_1111111',
'funding': 'FundAgency',
'spatial_series': True,
'metadata_complete': False,
'reprocess': True,
'first_contact': "Today",
'study_id': 3827
})
obs = Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], self.info)
self.assertEqual(obs.id, 3827)
exp = {
'mixs_compliant': True,
'metadata_complete': False,
'reprocess': True,
'study_status_id': 1,
'number_samples_promised': 28,
'emp_person_id': 2,
'funding': 'FundAgency',
'vamps_id': 'MBE_1111111',
'first_contact': "Today",
'principal_investigator_id': 3,
'timeseries_type_id': 1,
'study_abstract': 'Exploring how a high fat diet changes the '
'gut microbiome',
'email': '*****@*****.**',
'spatial_series': True,
'study_description': 'Microbiome of people who eat nothing '
'but fried chicken',
'portal_type_id': 3,
'study_alias': 'FCM',
'study_id': 3827,
'most_recent_contact': None,
'lab_person_id': 1,
'study_title': 'Fried chicken microbiome',
'number_samples_collected': 25
}
obsins = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study WHERE study_id = 3827")
self.assertEqual(len(obsins), 1)
obsins = dict(obsins[0])
self.assertEqual(obsins, exp)
# make sure EFO went in to table correctly
obsefo = self.conn_handler.execute_fetchall(
"SELECT efo_id FROM qiita.study_experimental_factor "
"WHERE study_id = 3827")
self.assertEqual(obsefo, [[1]])
def test_create_missing_required(self):
""" Insert a study that is missing a required info key"""
self.info.pop("study_alias")
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_create_empty_efo(self):
""" Insert a study that is missing a required info key"""
with self.assertRaises(IncompetentQiitaDeveloperError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [],
self.info)
def test_create_study_with_not_allowed_key(self):
"""Insert a study with key from _non_info present"""
self.info.update({"email": "*****@*****.**"})
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_create_unknown_db_col(self):
""" Insert a study with an info key not in the database"""
self.info["SHOULDNOTBEHERE"] = "BWAHAHAHAHAHA"
with self.assertRaises(QiitaDBColumnError):
Study.create(User('*****@*****.**'), "Fried Chicken Microbiome", [1],
self.info)
def test_retrieve_title(self):
self.assertEqual(
self.study.title, 'Identification of the Microbiomes'
' for Cannabis Soils')
def test_set_title(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.title = "Cannabis soils"
self.assertEqual(new.title, "Cannabis soils")
def test_set_title_public(self):
"""Tests for fail if editing title of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.title = "FAILBOAT"
def test_get_efo(self):
self.assertEqual(self.study.efo, [1])
def test_set_efo(self):
"""Set efo with list efo_id"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.efo = [3, 4]
self.assertEqual(new.efo, [3, 4])
def test_set_efo_empty(self):
"""Set efo with list efo_id"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.efo = []
def test_set_efo_public(self):
"""Set efo on a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.efo = 6
def test_retrieve_info(self):
for key, val in viewitems(self.existingexp):
if isinstance(val, QiitaObject):
self.existingexp[key] = val.id
self.assertEqual(self.study.info, self.existingexp)
def test_set_info(self):
"""Set info in a study"""
newinfo = {
"timeseries_type_id": 2,
"metadata_complete": False,
"number_samples_collected": 28,
"lab_person_id": StudyPerson(2),
"vamps_id": 'MBE_111222',
"first_contact": "June 11, 2014"
}
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.infoexp.update(newinfo)
new.info = newinfo
# add missing table cols
self.infoexp["funding"] = None
self.infoexp["spatial_series"] = None
self.infoexp["most_recent_contact"] = None
self.infoexp["reprocess"] = False
self.infoexp["lab_person_id"] = 2
self.assertEqual(new.info, self.infoexp)
def test_set_info_public(self):
"""Tests for fail if editing info of a public study"""
with self.assertRaises(QiitaDBStatusError):
self.study.info = {"vamps_id": "12321312"}
def test_set_info_disallowed_keys(self):
"""Tests for fail if sending non-info keys in info dict"""
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(QiitaDBColumnError):
new.info = {"email": "*****@*****.**"}
def test_info_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
with self.assertRaises(IncompetentQiitaDeveloperError):
new.info = {}
def test_retrieve_status(self):
self.assertEqual(self.study.status, "public")
def test_set_status(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
new.status = "private"
self.assertEqual(new.status, "private")
def test_retrieve_shared_with(self):
self.assertEqual(self.study.shared_with,
['*****@*****.**', '*****@*****.**'])
def test_retrieve_pmids(self):
exp = ['123456', '7891011']
self.assertEqual(self.study.pmids, exp)
def test_retrieve_pmids_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.pmids, [])
def test_retrieve_investigation(self):
self.assertEqual(self.study.investigation, 1)
def test_retrieve_investigation_empty(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.investigation, None)
def test_retrieve_sample_template(self):
self.assertEqual(self.study.sample_template, 1)
def test_retrieve_data_types(self):
self.assertEqual(self.study.data_types, ['18S'])
def test_retrieve_data_types_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.data_types, [])
def test_retrieve_raw_data(self):
self.assertEqual(self.study.raw_data(), [1, 2])
def test_retrieve_raw_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.raw_data(), [])
def test_retrieve_preprocessed_data(self):
self.assertEqual(self.study.preprocessed_data(), [1, 2])
def test_retrieve_preprocessed_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.preprocessed_data(), [])
def test_retrieve_processed_data(self):
self.assertEqual(self.study.processed_data(), [1])
def test_retrieve_processed_data_none(self):
new = Study.create(
User('*****@*****.**'), 'NOT Identification of the '
'Microbiomes for Cannabis Soils', [1], self.info)
self.assertEqual(new.processed_data(), [])
def test_add_pmid(self):
self.study.add_pmid('4544444')
exp = ['123456', '7891011', '4544444']
self.assertEqual(self.study.pmids, exp)
class TestUpdateRawDataFromCmd(TestCase):
def setUp(self):
fd, seqs_fp = mkstemp(suffix='_seqs.fastq')
close(fd)
fd, barcodes_fp = mkstemp(suffix='_barcodes.fastq')
close(fd)
self.filepaths = [seqs_fp, barcodes_fp]
self.checksums = []
for fp in sorted(self.filepaths):
with open(fp, 'w') as f:
f.write("%s\n" % fp)
self.checksums.append(compute_checksum(fp))
self.filepaths_types = ["raw_forward_seqs", "raw_barcodes"]
self._clean_up_files = [seqs_fp, barcodes_fp]
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)
}
self.new_study = Study.create(User("*****@*****.**"),
"Update raw data test",
efo=[1], info=info)
self.study = Study(1)
# The files for the RawData object attached to study 1 does not exist.
# Create them so we can actually perform the tests
for _, fp, _ in RawData(1).get_filepaths():
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
self.uploaded_files = get_files_from_uploads_folders(
str(self.study.id))
def tearDown(self):
new_uploaded_files = get_files_from_uploads_folders(str(self.study.id))
new_files = set(new_uploaded_files).difference(self.uploaded_files)
path_builder = partial(join, get_mountpoint("uploads")[0][1], '1')
for _, fp in new_files:
self._clean_up_files.append(path_builder(fp))
for f in self._clean_up_files:
if exists(f):
remove(f)
def test_update_raw_data_from_cmd_diff_length(self):
with self.assertRaises(ValueError):
update_raw_data_from_cmd(self.filepaths[1:], self.filepaths_types,
self.study.id)
with self.assertRaises(ValueError):
update_raw_data_from_cmd(self.filepaths, self.filepaths_types[1:],
self.study.id)
def test_update_raw_data_from_cmd_no_raw_data(self):
with self.assertRaises(ValueError):
update_raw_data_from_cmd(self.filepaths, self.filepaths_types,
self.new_study.id)
def test_update_raw_data_from_cmd_wrong_raw_data_id(self):
# Using max(raw_data_ids) + 1 to make sure that the raw data id
# passed does not belong to the study
with self.assertRaises(ValueError):
update_raw_data_from_cmd(self.filepaths, self.filepaths_types,
self.study.id,
max(self.study.raw_data()) + 1)
def test_update_raw_data_from_cmd(self):
rd = update_raw_data_from_cmd(self.filepaths, self.filepaths_types,
self.study.id)
# Make sure that we are cleaning the environment
for _, fp, _ in rd.get_filepaths():
self._clean_up_files.append(fp)
# The checkums are in filepath order. If we sort the rd.get_filepath()
# result by the filepath (itemgetter(1)) we will get them in the same
# order, so the checksums will not fail
for obs, exp in zip(sorted(rd.get_filepaths(), key=itemgetter(1)),
self.checksums):
self.assertEqual(compute_checksum(obs[1]), exp)
def test_update_raw_data_from_cmd_rd_id(self):
rd = update_raw_data_from_cmd(self.filepaths, self.filepaths_types,
self.study.id, self.study.raw_data()[0])
# Make sure that we are cleaning the environment
for _, fp, _ in rd.get_filepaths():
self._clean_up_files.append(fp)
# The checkums are in filepath order. If we sort the rd.get_filepath()
# result by the filepath (itemgetter(1)) we will get them in the same
# order, so the checksums will not fail
for obs, exp in zip(sorted(rd.get_filepaths(), key=itemgetter(1)),
self.checksums):
self.assertEqual(compute_checksum(obs[1]), exp)
