def test_build_study_info_empty_study(self):
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'
}
Study.create(User('*****@*****.**'), "My study", efo=[1], info=info)
obs = _build_study_info(User('*****@*****.**'), 'user')
self.exp.append({
'metadata_complete': False,
'ebi_submission_status': 'not submitted',
'shared': [],
'pmid': [],
'pi': ('*****@*****.**', 'PIDude'),
'status': 'sandbox',
'proc_data_info': [],
'publication_doi': [],
'study_abstract': 'abstract',
'study_id': 2,
'ebi_study_accession': None,
'study_title': 'My study',
'number_samples_collected': 0
})
self.assertItemsEqual(obs, self.exp)
# Now testing that admin also sees this study
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
def test_build_study_info_empty_study(self):
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'}
Study.create(User('*****@*****.**'), "My study", efo=[1], info=info)
obs = _build_study_info(User('*****@*****.**'), 'user')
self.exp.append({
'metadata_complete': False,
'ebi_submission_status':
'not submitted',
'shared': [],
'publication_pid': [],
'pi': ('*****@*****.**', 'PIDude'),
'status': 'sandbox',
'proc_data_info': [],
'publication_doi': [],
'study_abstract': 'abstract',
'study_id': 2,
'ebi_study_accession': None,
'study_title': 'My study',
'number_samples_collected': 0})
self.assertItemsEqual(obs, self.exp)
# Now testing that admin also sees this study
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
def test_build_study_info(self):
obs = _build_study_info(User('*****@*****.**'))
self.assertEqual(obs, self.exp)
with self.assertRaises(IncompetentQiitaDeveloperError):
obs = _build_study_info(User('*****@*****.**'), study_proc={})
with self.assertRaises(IncompetentQiitaDeveloperError):
obs = _build_study_info(User('*****@*****.**'), proc_samples={})
def test_build_study_info(self):
obs = _build_study_info(User('*****@*****.**'))
self.assertEqual(obs, self.exp)
with self.assertRaises(IncompetentQiitaDeveloperError):
obs = _build_study_info(User('*****@*****.**'), study_proc={})
with self.assertRaises(IncompetentQiitaDeveloperError):
obs = _build_study_info(User('*****@*****.**'), proc_samples={})
def test_build_study_info_new_study(self):
ProcessedData(1).status = 'public'
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 = _build_study_info(user)
self.exp.append({
'status': 'sandbox',
'checkbox': "<input type='checkbox' value='2' />",
'abstract': 'abstract',
'meta_complete': "<span class='glyphicon glyphicon-remove'>"
"</span>",
'title': '<a href=\'#\' data-toggle=\'modal\' data-target=\'#study'
'-abstract-modal\' onclick=\'fillAbstract("studies-table"'
', 1)\'><span class=\'glyphicon glyphicon-file\' aria-hidden=\''
'true\'></span></a> | <a href=\'/study/description/2\' id=\''
'study1-title\'>test_study_1</a>',
'num_raw_data': 0, 'id': 2, 'num_samples': '0',
'shared': "<span id='shared_html_2'></span><br/><a class='btn "
"btn-primary btn-xs' data-toggle='modal' data-target='#share-study"
"-modal-view' onclick='modify_sharing(2);'>Modify</a>",
'pmid': '', 'pi':
'<a target="_blank" href="mailto:[email protected]">PIDude</a>'})
self.assertEqual(obs, self.exp)
def test_build_study_info_new_study(self):
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 = _build_study_info('private', user)
StudyTuple = namedtuple('StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
exp = [
StudyTuple(
id=2,
title='test_study_1',
meta_complete=False, num_samples_collected=None,
shared='',
num_raw_data=0,
pi='<a target="_blank" href="mailto:[email protected]">'
'PIDude</a>',
pmids='',
owner='<a target="_blank" href="mailto:[email protected]">'
'[email protected]</a>',
status='sandbox')]
self.assertEqual(obs, exp)
def test_build_study_info(self):
Study(1).status = 'public'
obs = _build_study_info('public', User('*****@*****.**'))
StudyTuple = namedtuple(
'StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
exp = [
StudyTuple(
id=1,
title='Identification of the Microbiomes for Cannabis Soils',
meta_complete=True,
num_samples_collected=27,
shared='<a target="_blank" href="mailto:[email protected]">'
'Shared</a>',
num_raw_data=4,
pi='<a target="_blank" href="mailto:[email protected]">'
'PIDude</a>',
pmids='<a target="_blank" href="http://www.ncbi.nlm.nih.gov/'
'pubmed/123456">123456</a>, '
'<a target="_blank" href="http://www.ncbi.nlm.nih.gov/'
'pubmed/7891011">7891011</a>',
owner='<a target="_blank" href="mailto:[email protected]">'
'[email protected]</a>',
status='public')
]
self.assertEqual(obs, exp)
def test_build_study_info_new_study(self):
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 = _build_study_info(user)
self.exp.append({
'study_id': 2,
'status': 'sandbox',
'study_abstract': 'abstract',
'metadata_complete': False,
'study_title': 'test_study_1',
'num_raw_data': 0,
'number_samples_collected': 0,
'shared': '',
'pmid': '',
'publication_doi': '',
'pi':
'<a target="_blank" href="mailto:[email protected]">PIDude</a>',
'proc_data_info': []})
self.assertEqual(obs, self.exp)
def test_build_study_info_new_study(self):
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 = _build_study_info(user)
self.exp.append({
'study_id': 2,
'status': 'sandbox',
'study_abstract': 'abstract',
'metadata_complete': False,
'study_title': 'test_study_1',
'num_raw_data': 0,
'number_samples_collected': 0,
'shared': '',
'pmid': '',
'publication_doi': '',
'pi':
'<a target="_blank" href="mailto:[email protected]">PIDude</a>',
'proc_data_info': []
})
self.assertEqual(obs, self.exp)
def test_build_study_info(self):
for a in Study(1).artifacts():
a.visibility = 'private'
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
# make all the artifacts public - (1) the only study in the tests,
for a in Study(1).artifacts():
a.visibility = 'public'
self.exp[0]['status'] = 'public'
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, self.exp)
# return to it's private status
for a in Study(1).artifacts():
a.visibility = 'private'
def test_build_study_info_erros(self):
with self.assertRaises(IncompetentQiitaDeveloperError):
_build_study_info(User('*****@*****.**'), 'user', study_proc={})
with self.assertRaises(IncompetentQiitaDeveloperError):
_build_study_info(User('*****@*****.**'), 'user', proc_samples={})
with self.assertRaises(ValueError):
_build_study_info(User('*****@*****.**'), 'wrong')
def test_build_study_info_erros(self):
with self.assertRaises(IncompetentQiitaDeveloperError):
_build_study_info(User('*****@*****.**'), 'user', study_proc={})
with self.assertRaises(IncompetentQiitaDeveloperError):
_build_study_info(User('*****@*****.**'), 'user', proc_samples={})
with self.assertRaises(ValueError):
_build_study_info(User('*****@*****.**'), 'wrong')
def test_build_study_info_new_study(self):
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 = _build_study_info('private', user)
StudyTuple = namedtuple(
'StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
exp = [
StudyTuple(id=2,
title='test_study_1',
meta_complete=False,
num_samples_collected=None,
shared='',
num_raw_data=0,
pi='<a target="_blank" href="mailto:[email protected]">'
'PIDude</a>',
pmids='',
owner='<a target="_blank" href="mailto:[email protected]">'
'[email protected]</a>',
status='sandbox')
]
self.assertEqual(obs, exp)
def test_build_study_info(self):
Study(1).status = 'public'
obs = _build_study_info('public', User('*****@*****.**'))
StudyTuple = namedtuple('StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
exp = [
StudyTuple(
id=1,
title='Identification of the Microbiomes for Cannabis Soils',
meta_complete=True, num_samples_collected=27,
shared='<a target="_blank" href="mailto:[email protected]">'
'Shared</a>',
num_raw_data=2,
pi='<a target="_blank" href="mailto:[email protected]">'
'PIDude</a>',
pmids='<a target="_blank" href="http://www.ncbi.nlm.nih.gov/'
'pubmed/123456">123456</a>, '
'<a target="_blank" href="http://www.ncbi.nlm.nih.gov/'
'pubmed/7891011">7891011</a>',
owner='<a target="_blank" href="mailto:[email protected]">'
'[email protected]</a>',
status='public')]
self.assertEqual(obs, exp)
def test_build_study_info(self):
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
def test_build_study_info(self):
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
def test_build_study_info(self):
for a in Study(1).artifacts():
a.visibility = 'private'
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
# make all the artifacts public - (1) the only study in the tests,
for a in Study(1).artifacts():
a.visibility = 'public'
self.exp[0]['status'] = 'public'
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, [])
# make all the artifacts awaiting_approval - (1) the only study
# in the tests,
for a in Study(1).artifacts():
a.visibility = 'awaiting_approval'
self.exp[0]['status'] = 'awaiting_approval'
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'public')
self.assertEqual(obs, [])
obs = _build_study_info(User('*****@*****.**'), 'user')
self.assertEqual(obs, self.exp)
# awaiting_approval
# return to it's private status
for a in Study(1).artifacts():
a.visibility = 'private'
def test_build_study_info(self):
ProcessedData(1).status = 'public'
obs = _build_study_info(User('*****@*****.**'))
self.assertEqual(obs, self.exp)
