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 _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
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',
'portal_description': 'EMP portal',
'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',
'portal': 'EMP',
'portal_type_id': 2,
'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',
'portal_description', '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',
'portal_description': 'EMP portal',
'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,
'portal_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'], 'EMP portal', False,
'Identification of the Microbiomes for Cannabis Soils',
'None'],
[False, None, 'QIIME portal', False, 'test_study_1', 'None']]
self.assertEqual(obs, exp)
def test_has_access_public(self):
self._change_processed_data_status('public')
self.assertTrue(self.study.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_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',
'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,
'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_delete(self):
title = "Fried chicken microbiome"
study = Study.create(User('*****@*****.**'), title, [1], self.info)
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_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, 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._change_processed_data_status('awaiting_approval')
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):
with self.assertRaises(QiitaDBStatusError):
self.study.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._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']
def post(self, study_id):
study_id = int(study_id)
user = User(self.current_user)
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(User(self.current_user), study,
raise_error=True)
# vars to add sample template
msg = ''
msg_level = ''
tab_to_display = ''
sample_template = self.get_argument('sample_template', None)
# vars to add raw data
filetype = self.get_argument('filetype', None)
previous_raw_data = self.get_argument('previous_raw_data', None)
# vars to add prep template
add_prep_template = self.get_argument('add_prep_template', None)
raw_data_id = self.get_argument('raw_data_id', None)
data_type_id = self.get_argument('data_type_id', None)
make_public = self.get_argument('make_public', False)
make_sandbox = self.get_argument('make_sandbox', False)
approve_study = self.get_argument('approve_study', False)
request_approval = self.get_argument('request_approval', False)
investigation_type = self.get_argument('investigation-type', None)
user_defined_investigation_type = self.get_argument(
'user-defined-investigation-type', None)
new_investigation_type = self.get_argument('new-investigation-type',
None)
# None Selected is the equivalent to the user not specifying the info
# thus we should make the investigation_type None
if investigation_type == "" or investigation_type == "None Selected":
investigation_type = None
# to update investigation type
update_investigation_type = self.get_argument(
'update_investigation_type', None)
edit_investigation_type = self.get_argument('edit-investigation-type',
None)
edit_user_defined_investigation_type = self.get_argument(
'edit-user-defined-investigation-type', None)
edit_new_investigation_type = self.get_argument(
'edit-new-investigation-type', None)
# None Selected is the equivalent to the user not specifying the info
# thus we should make the investigation_type None
if edit_investigation_type == "" or \
edit_investigation_type == "None Selected":
edit_investigation_type = None
msg_level = 'success'
if sample_template:
# processing sample templates
_, base_fp = get_mountpoint("uploads")[0]
fp_rsp = join(base_fp, str(study_id), sample_template)
if not exists(fp_rsp):
raise HTTPError(400, "This file doesn't exist: %s" % fp_rsp)
try:
# deleting previous uploads and inserting new one
yield Task(self.remove_add_study_template,
study.raw_data,
study_id, fp_rsp)
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError, KeyError,
CParserError, QiitaDBDuplicateHeaderError) as e:
msg = html_error_message % ('parsing the sample template:',
basename(fp_rsp), str(e))
self.display_template(study, msg, "danger")
return
msg = ("The sample template '%s' has been added" %
sample_template)
tab_to_display = ""
elif request_approval:
study.status = 'awaiting_approval'
msg = "Study sent to admin for approval"
tab_to_display = ""
elif make_public:
msg = ''
study.status = 'public'
msg = "Study set to public"
tab_to_display = ""
elif make_sandbox:
msg = ''
study.status = 'sandbox'
msg = "Study reverted to sandbox"
tab_to_display = ""
elif approve_study:
# make sure user is admin, then make full private study
if user.level == 'admin' or not \
qiita_config.require_approval:
study.status = 'private'
msg = "Study approved"
tab_to_display = ""
elif filetype or previous_raw_data:
# adding blank raw data
if filetype and previous_raw_data:
msg = ("You can not specify both a new raw data and a "
"previouly used one")
elif filetype:
try:
RawData.create(filetype, [study])
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError, KeyError,
CParserError) as e:
msg = html_error_message % ("creating a new raw data "
"object for study:",
str(study.id), str(e))
self.display_template(study, msg, "danger")
return
msg = ""
else:
raw_data = [RawData(rd) for rd in previous_raw_data]
study.add_raw_data(raw_data)
msg = ""
tab_to_display = ""
elif add_prep_template and raw_data_id and data_type_id:
# adding prep templates
if investigation_type == 'Other' and \
user_defined_investigation_type == 'New Type':
investigation_type = new_investigation_type
# this is a new user defined investigation type so store it
ontology = Ontology(convert_to_id('ENA', 'ontology'))
ontology.add_user_defined_term(investigation_type)
elif investigation_type == 'Other' and \
user_defined_investigation_type != 'New Type':
investigation_type = user_defined_investigation_type
raw_data_id = int(raw_data_id)
_, base_path = get_mountpoint("uploads")[0]
fp_rpt = join(base_path, str(study_id), add_prep_template)
if not exists(fp_rpt):
raise HTTPError(400, "This file doesn't exist: %s" % fp_rpt)
try:
# inserting prep templates
yield Task(self.remove_add_prep_template, fp_rpt, raw_data_id,
study, data_type_id, investigation_type)
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError,
CParserError) as e:
msg = html_error_message % ("parsing the prep template: ",
basename(fp_rpt), str(e))
self.display_template(study, msg, "danger",
str(raw_data_id))
return
msg = "Your prep template was added"
tab_to_display = str(raw_data_id)
elif update_investigation_type:
# updating the prep template investigation type
pt = PrepTemplate(update_investigation_type)
investigation_type = edit_investigation_type
# figure out whether to add it as a user defined term or not
if edit_investigation_type == 'Other' and \
edit_user_defined_investigation_type == 'New Type':
investigation_type = edit_new_investigation_type
# this is a new user defined investigation type so store it
ontology = Ontology(convert_to_id('ENA', 'ontology'))
ontology.add_user_defined_term(investigation_type)
elif investigation_type == 'Other' and \
user_defined_investigation_type != 'New Type':
investigation_type = edit_user_defined_investigation_type
try:
pt.investigation_type = investigation_type
except QiitaDBColumnError as e:
msg = html_error_message % (", invalid investigation type: ",
investigation_type, str(e))
self.display_template(study, msg, "danger",
str(pt.raw_data))
return
msg = "The prep template has been updated!"
tab_to_display = str(pt.raw_data)
else:
msg = ("Error, did you select a valid uploaded file or are "
"passing the correct parameters?")
msg_level = 'danger'
tab_to_display = ""
self.display_template(study, msg, msg_level, tab_to_display)