def test_study_get_req_no_access(self):
obs = study_get_req(1, '*****@*****.**')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
def test_study_get_req(self):
obs = study_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'study_info': {
'mixs_compliant':
True,
'metadata_complete':
True,
'level':
'',
'reprocess':
False,
'owner':
'*****@*****.**',
'message':
'',
'emp_person_id':
2,
'number_samples_promised':
27,
'funding':
None,
'show_biom_download_button':
True,
'publication_pid': ['123456', '7891011'],
'vamps_id':
None,
'first_contact':
datetime(2014, 5, 19, 16, 10),
'ebi_submission_status':
'submitted',
'show_raw_download_button':
True,
'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.'),
'status':
'private',
'spatial_series':
False,
'specimen_id_column':
None,
'study_description':
('Analysis of the Cannabis Plant Microbiome'),
'shared_with': ['*****@*****.**'],
'publication_doi': ['10.100/123456', '10.100/7891011'],
'has_access_to_raw_data':
True,
'lab_person': {
'affiliation': 'knight lab',
'name': 'LabDude',
'email': '*****@*****.**'
},
'principal_investigator': {
'affiliation': 'Wash U',
'name': 'PIDude',
'email': '*****@*****.**'
},
'study_alias':
'Cannabis Soils',
'study_id':
1,
'most_recent_contact':
datetime(2014, 5, 19, 16, 11),
'ebi_study_accession':
'EBI123456-BB',
'num_samples':
27,
'study_title':
('Identification of the Microbiomes for Cannabis Soils'),
'number_samples_collected':
27
},
'message': '',
'editable': True
}
self.assertEqual(obs, exp)
# Test with no lab person
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "DESC",
"study_abstract": "ABS",
"principal_investigator_id": qdb.study.StudyPerson(3),
'first_contact': datetime(2015, 5, 19, 16, 10),
'most_recent_contact': datetime(2015, 5, 19, 16, 11),
}
new_study = qdb.study.Study.create(qdb.user.User('*****@*****.**'),
"Some New Study for test", info)
obs = study_get_req(new_study.id, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'study_info': {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'emp_person_id': None,
'number_samples_promised': 28,
'funding': None,
'vamps_id': None,
'first_contact': datetime(2015, 5, 19, 16, 10),
'timeseries_type_id': 1,
'study_abstract': 'ABS',
'status': 'private',
'spatial_series': False,
'study_description': 'DESC',
'shared_with': [],
'lab_person': None,
'study_alias': "FCM",
'owner': 'Dude',
'principal_investigator': {
'affiliation': 'Wash U',
'name': 'PIDude',
'email': '*****@*****.**'
},
'study_alias': 'FCM',
'study_id': new_study.id,
'most_recent_contact': datetime(2015, 5, 19, 16, 11),
'publication_doi': [],
'publication_pid': [],
'num_samples': 25,
'study_title': 'Some New Study',
'number_samples_collected': 27
},
'editable': True
}
self.assertItemsEqual(obs, exp)
def test_study_get_req_no_exists(self):
obs = study_get_req(4000, '*****@*****.**')
exp = {'status': 'error', 'message': 'Study does not exist'}
self.assertEqual(obs, exp)
def test_study_get_req(self):
obs = study_get_req(1, '*****@*****.**')
exp = {
'status': 'success',
'study_info': {
'mixs_compliant': True, 'metadata_complete': True, 'level': '',
'reprocess': False, 'owner': '*****@*****.**', 'message': '',
'emp_person_id': 2, 'number_samples_promised': 27,
'funding': None, 'show_biom_download_button': True,
'publication_pid': ['123456', '7891011'], 'vamps_id': None,
'first_contact': datetime(2014, 5, 19, 16, 10),
'ebi_submission_status': 'submitted',
'show_raw_download_button': True, '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.'),
'status': 'private', 'spatial_series': False,
'study_description': (
'Analysis of the Cannabis Plant Microbiome'),
'shared_with': ['*****@*****.**'], 'publication_doi': [
'10.100/123456', '10.100/7891011'],
'has_access_to_raw_data': True, 'lab_person': {
'affiliation': 'knight lab', 'name': 'LabDude',
'email': '*****@*****.**'},
'principal_investigator': {
'affiliation': 'Wash U', 'name': 'PIDude',
'email': '*****@*****.**'},
'study_alias': 'Cannabis Soils', 'study_id': 1,
'most_recent_contact': datetime(2014, 5, 19, 16, 11),
'ebi_study_accession': 'EBI123456-BB', 'num_samples': 27,
'study_title': (
'Identification of the Microbiomes for Cannabis Soils'),
'number_samples_collected': 27},
'message': '',
'editable': True}
self.assertEqual(obs, exp)
# Test with no lab person
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "DESC",
"study_abstract": "ABS",
"principal_investigator_id": qdb.study.StudyPerson(3),
'first_contact': datetime(2015, 5, 19, 16, 10),
'most_recent_contact': datetime(2015, 5, 19, 16, 11),
}
new_study = qdb.study.Study.create(
qdb.user.User('*****@*****.**'), "Some New Study for test", info)
obs = study_get_req(new_study.id, '*****@*****.**')
exp = {
'status': 'success',
'message': '',
'study_info': {
'mixs_compliant': True,
'metadata_complete': True,
'reprocess': False,
'emp_person_id': None,
'number_samples_promised': 28,
'funding': None,
'vamps_id': None,
'first_contact': datetime(2015, 5, 19, 16, 10),
'timeseries_type_id': 1,
'study_abstract': 'ABS',
'status': 'private',
'spatial_series': False,
'study_description': 'DESC',
'shared_with': [],
'lab_person': None,
'study_alias': "FCM",
'owner': 'Dude',
'principal_investigator': {'affiliation': 'Wash U',
'name': 'PIDude',
'email': '*****@*****.**'},
'study_alias': 'FCM',
'study_id': new_study.id,
'most_recent_contact': datetime(2015, 5, 19, 16, 11),
'publication_doi': [],
'publication_pid': [],
'num_samples': 25,
'study_title': 'Some New Study',
'number_samples_collected': 27},
'editable': True}
self.assertItemsEqual(obs, exp)
def test_study_get_req_no_exists(self):
obs = study_get_req(4000, '*****@*****.**')
exp = {'status': 'error',
'message': 'Study does not exist'}
self.assertEqual(obs, exp)
def test_study_get_req_no_access(self):
obs = study_get_req(1, '*****@*****.**')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)