def sample_template_checks(study_id, user, check_exists=False):
"""Performs different checks and raises errors if any of the checks fail
Parameters
----------
study_id : int
The study id
user : qiita_db.user.User
The user trying to access the study
check_exists : bool, optional
If true, check if the sample template exists
Raises
------
HTTPError
404 if the study does not exist
403 if the user does not have access to the study
404 if check_exists == True and the sample template doesn't exist
"""
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(404, reason='Study does not exist')
if not study.has_access(user):
raise HTTPError(403, reason='User does not have access to study')
# Check if the sample template exists
if check_exists and not SampleTemplate.exists(study_id):
raise HTTPError(404, reason="Study %s doesn't have sample information"
% study_id)
def sample_template_checks(study_id, user, check_exists=False):
"""Performs different checks and raises errors if any of the checks fail
Parameters
----------
study_id : int
The study id
user : qiita_db.user.User
The user trying to access the study
check_exists : bool, optional
If true, check if the sample template exists
Raises
------
HTTPError
404 if the study does not exist
403 if the user does not have access to the study
404 if check_exists == True and the sample template doesn't exist
"""
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(404, reason='Study does not exist')
if not study.has_access(user):
raise HTTPError(403, reason='User does not have access to study')
# Check if the sample template exists
if check_exists and not SampleTemplate.exists(study_id):
raise HTTPError(404,
reason="Study %s doesn't have sample information" %
study_id)
def check_access(study_id, user_id):
"""Checks if user given has access to the study given
Parameters
----------
study_id : int
ID of the study to check access to
user_id : str
ID of the user to check access for
Returns
-------
dict
Empty dict if access allowed, else a dict in the form
{'status': 'error',
'message': reason for error}
"""
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
return {'status': 'error',
'message': 'Study does not exist'}
if not study.has_access(User(user_id)):
return {'status': 'error',
'message': 'User does not have access to study'}
return {}
def check_access(study_id, user_id):
"""Checks if user given has access to the study given
Parameters
----------
study_id : int
ID of the study to check access to
user_id : str
ID of the user to check access for
Returns
-------
dict
Empty dict if access allowed, else a dict in the form
{'status': 'error',
'message': reason for error}
"""
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
return {'status': 'error', 'message': 'Study does not exist'}
if not study.has_access(User(user_id)):
return {
'status': 'error',
'message': 'User does not have access to study'
}
return {}
def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# this block is tricky because you can either pass the sample or the
# prep template and if none is passed then we will let an exception
# be raised because template will not be declared for the logic below
if self.get_argument('prep_template', None):
template = PrepTemplate(int(self.get_argument('prep_template')))
if self.get_argument('sample_template', None):
template = None
tid = int(self.get_argument('sample_template'))
try:
template = SampleTemplate(tid)
except QiitaDBUnknownIDError:
raise HTTPError(404, "SampleTemplate %d does not exist" % tid)
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(User(self.current_user)):
raise HTTPError(403, "You do not have access to access this "
"information.")
df = dataframe_from_template(template)
stats = stats_from_df(df)
self.render('metadata_summary.html', user=self.current_user,
study_title=study.title, stats=stats,
study_id=study_id)
def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# Get the arguments
prep_template = self.get_argument('prep_template', None)
sample_template = self.get_argument('sample_template', None)
if prep_template and sample_template:
raise HTTPError(
500, "You should provide either a sample template "
"or a prep template, but not both")
elif prep_template:
# The prep template has been provided
template = self._get_template(PrepTemplate, prep_template)
back_button_path = (
"/study/description/%s?top_tab=raw_data_tab&sub_tab=%s"
"&prep_tab=%s" % (study_id, template.raw_data, template.id))
elif sample_template:
# The sample template has been provided
template = self._get_template(SampleTemplate, sample_template)
back_button_path = ("/study/description/%s" % study_id)
else:
# Neither a sample template or a prep template has been provided
# Fail nicely
raise HTTPError(
500, "You should provide either a sample template "
"or a prep template")
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(self.current_user):
raise HTTPError(
403, "You do not have access to access this "
"information.")
df = dataframe_from_template(template)
num_samples = df.shape[0]
stats = stats_from_df(df)
self.render('metadata_summary.html',
study_title=study.title,
stats=stats,
num_samples=num_samples,
back_button_path=back_button_path)
def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# Get the arguments
prep_template = self.get_argument('prep_template', None)
sample_template = self.get_argument('sample_template', None)
if prep_template and sample_template:
raise HTTPError(500, "You should provide either a sample template "
"or a prep template, but not both")
elif prep_template:
# The prep template has been provided
template = self._get_template(PrepTemplate, prep_template)
back_button_path = (
"/study/description/%s?top_tab=prep_template_tab&sub_tab=%s"
% (study_id, template.id))
elif sample_template:
# The sample template has been provided
template = self._get_template(SampleTemplate, sample_template)
back_button_path = (
"/study/description/%s"
% study_id)
else:
# Neither a sample template or a prep template has been provided
# Fail nicely
raise HTTPError(500, "You should provide either a sample template "
"or a prep template")
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(self.current_user):
raise HTTPError(403, "You do not have access to access this "
"information.")
df = template.to_dataframe()
num_samples = df.shape[0]
stats = stats_from_df(df)
self.render('metadata_summary.html',
study_title=study.title, stats=stats,
num_samples=num_samples, back_button_path=back_button_path)
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
study_info['public_raw_download'] = study.public_raw_download
study_info['notes'] = study.notes
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation
}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation
}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id; this
# with study.public_raw_download will define has_access_to_raw_data
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True) or study.public_raw_download
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()
]
study_info['show_raw_download_button'] = any(
[True for pt in study.prep_templates() if pt.artifact is not None])
# getting study processing status from redis
processing = False
study_info['level'] = ''
study_info['message'] = ''
job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
if job_info:
job_info = defaultdict(lambda: '', loads(job_info))
job_id = job_info['job_id']
job = ProcessingJob(job_id)
job_status = job.status
processing = job_status not in ('success', 'error')
if processing:
study_info['level'] = 'info'
study_info['message'] = 'This study is currently being processed'
elif job_status == 'error':
study_info['level'] = 'danger'
study_info['message'] = job.log.msg.replace('\n', '</br>')
else:
study_info['level'] = job_info['alert_type']
study_info['message'] = job_info['alert_msg'].replace(
'\n', '</br>')
return {
'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))
}
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']
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True)
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()]
study_info['show_raw_download_button'] = any([
True for pt in study.prep_templates() if pt.artifact is not None])
# getting study processing status from redis
processing = False
study_info['level'] = ''
study_info['message'] = ''
job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
if job_info:
job_info = defaultdict(lambda: '', loads(job_info))
job_id = job_info['job_id']
job = ProcessingJob(job_id)
job_status = job.status
processing = job_status not in ('success', 'error')
if processing:
study_info['level'] = 'info'
study_info['message'] = 'This study is currently being processed'
elif job_status == 'error':
study_info['level'] = 'danger'
study_info['message'] = job.log.msg.replace('\n', '</br>')
else:
study_info['level'] = job_info['alert_type']
study_info['message'] = job_info['alert_msg'].replace(
'\n', '</br>')
return {'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))}
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']
def study_get_req(study_id, user_id):
"""Returns information available for the given study
Parameters
----------
study_id : int
Study id to get prep template info for
user_id : str
User requesting the info
Returns
-------
dict
Data types information in the form
{'status': status,
'message': message,
'info': dict of objects
status can be success, warning, or error depending on result
message has the warnings or errors
info contains study information seperated by data type, in the form
{col_name: value, ...} with value being a string, int, or list of
strings or ints
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
# Can only pass ids over API, so need to instantiate object
study = Study(study_id)
study_info = study.info
# Add needed info that is not part of the initial info pull
study_info['publication_doi'] = []
study_info['publication_pid'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publication_doi'].append(pub)
else:
study_info['publication_pid'].append(pub)
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
study_info['principal_investigator'] = {
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation}
lab_person = study_info['lab_person']
if lab_person:
study_info['lab_person'] = {
'name': lab_person.name,
'email': lab_person.email,
'affiliation': lab_person.affiliation}
samples = study.sample_template
study_info['num_samples'] = 0 if samples is None else len(list(samples))
study_info['owner'] = study.owner.id
# Study.has_access no_public=True, will return True only if the user_id is
# the owner of the study or if the study is shared with the user_id
study_info['has_access_to_raw_data'] = study.has_access(
User(user_id), True)
study_info['show_biom_download_button'] = 'BIOM' in [
a.artifact_type for a in study.artifacts()]
study_info['show_raw_download_button'] = any([
True for pt in study.prep_templates() if pt.artifact is not None])
return {'status': 'success',
'message': '',
'study_info': study_info,
'editable': study.can_edit(User(user_id))}
def get(self, study_id):
study_id = int(study_id)
# Check general access to study
study_info = study_get_req(study_id, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(
405,
"%s: %s, %s" % (study_info['message'], self.current_user.email,
str(study_id)))
study = Study(study_id)
user = self.current_user
# Check "owner" access to the study
if not study.has_access(user, True):
raise HTTPError(
405, "%s: %s, %s" %
('No raw data access', self.current_user.email, str(study_id)))
basedir = get_db_files_base_dir()
basedir_len = len(basedir) + 1
# loop over artifacts and retrieve raw data (no parents)
to_download = []
for a in study.artifacts():
if not a.parents:
for i, (fid, path, data_type) in enumerate(a.filepaths):
if data_type == 'directory':
# If we have a directory, we actually need to list
# all the files from the directory so NGINX can
# actually download all of them
for dp, _, fps in walk(path):
for fname in fps:
fullpath = join(dp, fname)
spath = fullpath
if fullpath.startswith(basedir):
spath = fullpath[basedir_len:]
to_download.append((fullpath, spath, spath))
elif path.startswith(basedir):
spath = path[basedir_len:]
to_download.append((path, spath, spath))
else:
# We are not aware of any case that can trigger this
# situation, but we wanted to be overly cautious
# There is no test for this line cause we don't know
# how to trigger it
to_download.append((path, path, path))
for pt in a.prep_templates:
qmf = pt.qiime_map_fp
if qmf is not None:
sqmf = qmf
if qmf.startswith(basedir):
sqmf = qmf[basedir_len:]
to_download.append(
(qmf, sqmf,
'mapping_files/%s_mapping_file.txt' % a.id))
# If we don't have nginx, write a file that indicates this
# Note that this configuration will automatically create and download
# ("on the fly") the zip file via the contents in all_files
all_files = '\n'.join([
"- %s /protected/%s %s" % (getsize(fp), sfp, n)
for fp, sfp, n in to_download
])
self.write("%s\n" % all_files)
zip_fn = 'study_raw_data_%d_%s.zip' % (
study_id, datetime.now().strftime('%m%d%y-%H%M%S'))
self.set_header('Content-Description', 'File Transfer')
self.set_header('Expires', '0')
self.set_header('Cache-Control', 'no-cache')
self.set_header('X-Archive-Files', 'zip')
self.set_header('Content-Disposition',
'attachment; filename=%s' % zip_fn)
self.finish()