def insert_data(self):
""" Prepare tests by inserting some data into the DB.
Returns
-------
survey object, survey_id : str, notes_test : str and consent : dict
of the newly created survey.
"""
# Create random string to test update happens
# TODO: implement utf8 capability for notes! See issue #646
c = ascii_letters + '1234567890'
notes_test = ''.join([choice(c) for i in range(40)])
survey_id = '817ff95701f4dd10'
survey = Survey(2)
consent = {
'login_id': 'eba20873-b7db-33cc-e040-8a80115d392c',
'survey_id': survey_id,
'participant_name': 'some name that should be ignored',
'age_range': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'deceased_parent': False,
'participant_email': 'REMOVED',
'obtainer_name': 'ANIMAL_SURVEY',
'assent_obtainer': 'ANIMAL_SURVEY',
'is_juvenile': True}
with_fk = [(survey_id, 128, 'Other'),
(survey_id, 129, 'Wild'),
(survey_id, 131, 'Male'),
(survey_id, 132, 'Suburban'),
(survey_id, 133, 'Normal'),
(survey_id, 134, 'Omnivore'),
(survey_id, 135, 'Wild food'),
(survey_id, 136, 'Both'),
(survey_id, 137, 'Unspecified'),
(survey_id, 138, 'Lives alone with humans'),
(survey_id, 139, '8+'),
(survey_id, 140, 'Unspecified'),
(survey_id, 141, 'Never')]
without_fk = [(survey_id, 130, '["20"]'),
(survey_id, 142, '["Giant ratty pet!"]'),
(survey_id, 143, '["Capybara"]'),
(survey_id, 144, '["%s"]' % notes_test),
(survey_id, 145, '["29 - Male"]'),
(survey_id, 127, '["Fluffy"]')]
survey.store_survey(consent, with_fk, without_fk)
return survey, survey_id, notes_test, consent
def insert_data(self):
""" Prepare tests by inserting some data into the DB.
Returns
-------
survey object, survey_id : str, notes_test : str and consent : dict
of the newly created survey.
"""
# Create random string to test update happens
# TODO: implement utf8 capability for notes! See issue #646
c = ascii_letters + '1234567890'
notes_test = ''.join([choice(c) for i in range(40)])
survey_id = '817ff95701f4dd10'
survey = Survey(2)
consent = {
'login_id': 'eba20873-b7db-33cc-e040-8a80115d392c',
'survey_id': survey_id,
'participant_name': 'some name that should be ignored',
'age_range': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'deceased_parent': False,
'participant_email': 'REMOVED',
'obtainer_name': 'ANIMAL_SURVEY',
'assent_obtainer': 'ANIMAL_SURVEY',
'is_juvenile': True
}
with_fk = [(survey_id, 128, 'Other'), (survey_id, 129, 'Wild'),
(survey_id, 131, 'Male'), (survey_id, 132, 'Suburban'),
(survey_id, 133, 'Normal'), (survey_id, 134, 'Omnivore'),
(survey_id, 135, 'Wild food'), (survey_id, 136, 'Both'),
(survey_id, 137, 'Unspecified'),
(survey_id, 138, 'Lives alone with humans'),
(survey_id, 139, '8+'), (survey_id, 140, 'Unspecified'),
(survey_id, 141, 'Never')]
without_fk = [(survey_id, 130, '["20"]'),
(survey_id, 142, '["Giant ratty pet!"]'),
(survey_id, 143, '["Capybara"]'),
(survey_id, 144, '["%s"]' % notes_test),
(survey_id, 145, '["29 - Male"]'),
(survey_id, 127, '["Fluffy"]')]
survey.store_survey(consent, with_fk, without_fk)
return survey, survey_id, notes_test, consent
def test_fetch_survey(self):
survey = Survey(2)
obs = survey.fetch_survey('cb367dcf9a9af7e9')
self.assertEqual(obs, {
'Pet_Information_127_0': 'REMOVED',
'Pet_Information_128_0': 1,
'Pet_Information_129_0': 2,
'Pet_Information_130_0': '6',
'Pet_Information_131_0': 1,
'Pet_Information_132_0': 1,
'Pet_Information_133_0': 3,
'Pet_Information_134_0': 2,
'Pet_Information_135_0': [1],
'Pet_Information_136_0': 3,
'Pet_Information_137_0': [0],
'Pet_Information_138_0': 1,
'Pet_Information_139_0': 3,
'Pet_Information_140_0': 3,
'Pet_Information_141_0': 4,
'Pet_Information_142_0': 'REMOVED',
'Pet_Information_143_0': 'REMOVED',
'Pet_Information_144_0': 'REMOVED',
'Pet_Information_145_0': 'Female: 50; Male: 59'})
from amgut.lib.data_access.survey import Survey primary_human_survey = Survey(1) primary_animal_survey = Survey(2) fermented_survey = Survey(3) surf_survey = Survey(4) personal_microbiome_survey = Survey(5)
def test_store_survey(self):
# Create new survey ID and make sure it is unused
survey = Survey(2)
c = ascii_letters + '1234567890'
survey_id = ''.join([choice(c) for i in range(16)])
name = ''.join([choice(ascii_letters) for i in range(20)])
with self.assertRaises(ValueError):
survey.fetch_survey(survey_id)
consent = {
'login_id': 'd8592c74-84b1-2135-e040-8a80115d6401',
'survey_id': survey_id,
'participant_name': name,
'age_range': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'deceased_parent': False,
'participant_email': 'REMOVED',
'obtainer_name': 'ANIMAL_SURVEY',
'assent_obtainer': 'ANIMAL_SURVEY',
'is_juvenile': True
}
with_fk = [(survey_id, 128, 'Other'), (survey_id, 129, 'Wild'),
(survey_id, 131, 'Male'), (survey_id, 132, 'Suburban'),
(survey_id, 133, 'Normal'), (survey_id, 134, 'Omnivore'),
(survey_id, 135, 'Wild food'), (survey_id, 136, 'Both'),
(survey_id, 137, 'Unspecified'),
(survey_id, 138, 'Lives alone with humans'),
(survey_id, 139, '8+'), (survey_id, 140, 'Unspecified'),
(survey_id, 141, 'Never')]
without_fk = [(survey_id, 130, '["20"]'),
(survey_id, 142, unicode('["Mötley Crüe!"]', 'utf-8')),
(survey_id, 143, '["Capybara"]'),
(survey_id, 144, '[""]'),
(survey_id, 145, '["29 - Male"]'),
(survey_id, 127, '["%s"]' % name)]
survey.store_survey(consent, with_fk, without_fk)
obs = survey.fetch_survey(survey_id)
exp = {
'Pet_Information_127_0': name,
'Pet_Information_137_0': [0],
'Pet_Information_143_0': 'Capybara',
'Pet_Information_132_0': 2,
'Pet_Information_138_0': 1,
'Pet_Information_144_0': '',
'Pet_Information_129_0': 4,
'Pet_Information_142_0': u'M\xf6tley Cr\xfce!'.encode('utf-8'),
'Pet_Information_133_0': 3,
'Pet_Information_139_0': 5,
'Pet_Information_130_0': '20',
'Pet_Information_128_0': 9,
'Pet_Information_134_0': 2,
'Pet_Information_140_0': 0,
'Pet_Information_131_0': 1,
'Pet_Information_145_0': '29 - Male',
'Pet_Information_136_0': 3,
'Pet_Information_135_0': [3],
'Pet_Information_141_0': 4
}
self.assertEqual(obs, exp)
obs = ag_data.getConsent(survey_id)
del obs['date_signed']
consent['ag_login_id'] = consent['login_id']
del consent['login_id']
del consent['obtainer_name']
consent['deceased_parent'] = 'false'
self.assertEqual(obs, consent)
# revert database
self.delete_survey(survey_id)
def test_fetch_survey_bad_id(self):
survey = Survey(1)
with self.assertRaises(ValueError):
survey.fetch_survey('BAD_ID_HERE')
def test_create(self):
survey = Survey(1)
self.assertEqual(survey.id, 1)
exp = ["<class 'amgut.lib.data_access.survey.Group'>"] * 7
self.assertEqual([str(type(x)) for x in survey.groups], exp)
exp = [-1, 0, 1, 2, 3, 4, 5]
self.assertEqual([x.id for x in survey.groups], exp)
exp = [
1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55,
56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72,
73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
90, 91, 92, 93, 94, 95, 96, 98, 99, 101, 103, 104, 105, 106, 107,
108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,
122, 124, 126, 146, 148, 149, 150, 153, 154, 155, 156, 157, 158,
159, 160, 162, 163, 164
]
self.assertEqual(survey.questions.keys(), exp)
exp = {
1: 'SINGLE',
2: 'SINGLE',
3: 'SINGLE',
4: 'SINGLE',
5: 'SINGLE',
6: 'SINGLE',
7: 'SINGLE',
8: 'SINGLE',
9: 'MULTIPLE',
11: 'SINGLE',
12: 'SINGLE',
13: 'SINGLE',
14: 'SINGLE',
15: 'SINGLE',
16: 'SINGLE',
17: 'SINGLE',
18: 'SINGLE',
19: 'SINGLE',
20: 'SINGLE',
21: 'SINGLE',
22: 'SINGLE',
23: 'SINGLE',
24: 'SINGLE',
25: 'SINGLE',
26: 'SINGLE',
27: 'SINGLE',
28: 'SINGLE',
29: 'SINGLE',
30: 'MULTIPLE',
31: 'SINGLE',
32: 'SINGLE',
33: 'SINGLE',
34: 'SINGLE',
35: 'SINGLE',
36: 'SINGLE',
37: 'SINGLE',
38: 'SINGLE',
39: 'SINGLE',
40: 'SINGLE',
41: 'SINGLE',
42: 'SINGLE',
43: 'SINGLE',
44: 'SINGLE',
45: 'SINGLE',
46: 'SINGLE',
47: 'SINGLE',
48: 'SINGLE',
49: 'SINGLE',
50: 'SINGLE',
51: 'SINGLE',
53: 'SINGLE',
54: 'MULTIPLE',
55: 'SINGLE',
56: 'SINGLE',
57: 'SINGLE',
58: 'SINGLE',
59: 'SINGLE',
60: 'SINGLE',
61: 'SINGLE',
62: 'SINGLE',
63: 'SINGLE',
64: 'SINGLE',
65: 'SINGLE',
66: 'SINGLE',
67: 'SINGLE',
68: 'SINGLE',
69: 'SINGLE',
70: 'SINGLE',
71: 'SINGLE',
72: 'SINGLE',
73: 'SINGLE',
74: 'SINGLE',
75: 'SINGLE',
76: 'SINGLE',
77: 'SINGLE',
78: 'SINGLE',
79: 'SINGLE',
80: 'SINGLE',
81: 'SINGLE',
82: 'SINGLE',
83: 'SINGLE',
84: 'SINGLE',
85: 'SINGLE',
86: 'SINGLE',
87: 'SINGLE',
88: 'SINGLE',
89: 'SINGLE',
90: 'SINGLE',
91: 'SINGLE',
92: 'SINGLE',
93: 'SINGLE',
94: 'SINGLE',
95: 'SINGLE',
96: 'SINGLE',
98: 'TEXT',
99: 'TEXT',
101: 'TEXT',
103: 'TEXT',
104: 'TEXT',
105: 'TEXT',
106: 'TEXT',
107: 'SINGLE',
108: 'STRING',
109: 'SINGLE',
110: 'SINGLE',
111: 'SINGLE',
112: 'SINGLE',
113: 'STRING',
114: 'SINGLE',
115: 'STRING',
116: 'TEXT',
117: 'TEXT',
118: 'TEXT',
119: 'TEXT',
120: 'TEXT',
122: 'TEXT',
124: 'TEXT',
126: 'TEXT',
146: 'SINGLE',
148: 'SINGLE',
149: 'SINGLE',
150: 'TEXT',
153: 'SINGLE',
154: 'MULTIPLE',
155: 'SINGLE',
156: 'SINGLE',
157: 'SINGLE',
158: 'SINGLE',
159: 'SINGLE',
160: 'SINGLE',
162: 'MULTIPLE',
163: 'SINGLE',
164: 'SINGLE'
}
self.assertItemsEqual(survey.question_types, exp)
self.assertEqual(survey.unspecified, 'Unspecified')
def test_edit_survey(self):
# creating a new participant for existing ag_login_id
main_survey_id = '38792874'
sec_survey_id_fermented = '3879287455'
sec_survey_id_surfer = '3879287456'
ag_login_id = 'd8592c74-9694-2135-e040-8a80115d6401'
participant_name = 'test_dude_stefan'
email = '*****@*****.**'
with_fk_inserts =\
[(main_survey_id, _id, 'Unspecified') for _id in
[1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 107, 109, 110, 111, 112, 114, 146, 148, 149, 153, 154,
155, 156, 157, 158, 159, 160, 162, 163, 164]]
without_fk_inserts =\
[(main_survey_id, _id, '[""]') for _id in
[98, 99, 150, 103, 104, 105, 106, 108, 113, 115, 116, 117, 118,
119, 120, 122, 124, 126, 101]]
self.mock_login(ag_data.ut_get_supplied_kit_id(ag_login_id))
s = Survey(main_survey_id)
s.store_survey(
{u'login_id': ag_login_id,
u'age_range': u'18-plus',
u'parent_1_name': None,
u'participant_email': email,
u'obtainer_name': None,
u'parent_2_name': None,
u'deceased_parent': u'No',
u'participant_name': participant_name,
u'survey_id': main_survey_id,
u'is_juvenile': False},
with_fk_inserts, without_fk_inserts)
# confirm that no secondary surveys are present
response = self.post('/participants/%s' % participant_name,
{'participant_type': 'human'})
self.assertEqual(response.code, 200)
self.assertNotIn('fermented', response.body)
self.assertNotIn('surf', response.body)
# add a new fermented food survey
data = {'questions': {'Fermented_Foods_170_0': [''],
'Fermented_Foods_173_0': [''],
'Fermented_Foods_169_0': None,
'Fermented_Foods_171_0': ['13'],
'Fermented_Foods_168_0': [''],
'Fermented_Foods_167_0': ['1'],
'Fermented_Foods_166_0': ['0'],
'Fermented_Foods_165_0': ['0'],
'Fermented_Foods_172_0': ['']}}
consent = {
'login_id': ag_login_id,
'participant_name': participant_name,
'survey_id': sec_survey_id_fermented,
'secondary': True
}
redis.hset(sec_survey_id_fermented, 'consent', dumps(consent))
redis.hset(sec_survey_id_fermented, 0, dumps(data))
redis.expire(sec_survey_id_fermented, 86400)
store_survey(fermented_survey, sec_survey_id_fermented)
# confirm that now a fermented food survey is present
response = self.post('/participants/%s' % participant_name,
{'participant_type': 'human'})
self.assertEqual(response.code, 200)
self.assertIn('fermented', response.body)
self.assertNotIn('surf', response.body)
self.assertIn('secondary_survey/?type=%s&participant_name=%s&survey=%s'
% ('fermented',
participant_name,
sec_survey_id_fermented), response.body)
# check human_survey_completed links:
# TODO: I don't know how to set a secured cookie for
# completed_survey_id and could need some help to actually test values
# for the rendered page /authed/human_survey_completed/
# response = self.get('/authed/human_survey_completed/')
# add a new surfers survey
data = {'questions': {'Surfers_182_0': ['0'],
'Surfers_176_0': ['0'],
'Surfers_175_0': ['0'],
'Surfers_185_0': ['0'],
'Surfers_179_0': ['0'],
'Surfers_183_0': ['0'],
'Surfers_180_0': ['0'],
'Surfers_174_0': ['0'],
'Surfers_178_0': ['0'],
'Surfers_181_0': ['0'],
'Surfers_177_0': ['0'],
'Surfers_184_0': ['0']}}
consent = {
'login_id': ag_login_id,
'participant_name': participant_name,
'survey_id': sec_survey_id_surfer,
'secondary': True
}
redis.hset(sec_survey_id_surfer, 'consent', dumps(consent))
redis.hset(sec_survey_id_surfer, 0, dumps(data))
redis.expire(sec_survey_id_surfer, 86400)
store_survey(surf_survey, sec_survey_id_surfer)
# confirm that now a surfers and fermented food survey is present
response = self.post('/participants/%s' % participant_name,
{'participant_type': 'human'})
self.assertEqual(response.code, 200)
self.assertIn('fermented', response.body)
self.assertIn('surf', response.body)
self.assertIn('secondary_survey/?type=%s&participant_name=%s&survey=%s'
% ('fermented',
participant_name,
sec_survey_id_fermented),
response.body)
self.assertIn('secondary_survey/?type=%s&participant_name=%s&survey=%s'
% ('surf',
participant_name,
sec_survey_id_surfer),
response.body)
import re from collections import defaultdict from future.utils import viewitems from amgut import text_locale from amgut.lib.data_access.survey import Survey primary_human_survey = Survey(1)
def test_store_survey_edit(self):
# Create random string to test update happens
c = ascii_letters + '1234567890'
notes_test = ''.join([choice(c) for i in range(40)])
# Set up survey
survey_id = '817ff95701f4dd10'
survey = Survey(2)
consent = {
'login_id': 'eba20873-b7db-33cc-e040-8a80115d392c',
'survey_id': survey_id,
'participant_name': 'some name that should be ignored',
'age_range': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'deceased_parent': False,
'participant_email': 'REMOVED',
'obtainer_name': 'ANIMAL_SURVEY',
'assent_obtainer': 'ANIMAL_SURVEY',
'is_juvenile': True}
with_fk = [(survey_id, 128, 'Other'),
(survey_id, 129, 'Wild'),
(survey_id, 131, 'Male'),
(survey_id, 132, 'Suburban'),
(survey_id, 133, 'Normal'),
(survey_id, 134, 'Omnivore'),
(survey_id, 135, 'Wild food'),
(survey_id, 136, 'Both'),
(survey_id, 137, 'Unspecified'),
(survey_id, 138, 'Lives alone with humans'),
(survey_id, 139, '8+'),
(survey_id, 140, 'Unspecified'),
(survey_id, 141, 'Never')]
without_fk = [(survey_id, 130, '["20"]'),
(survey_id, 142, '["Giant ratty pet!"]'),
(survey_id, 143, '["Capybara"]'),
(survey_id, 144, '["%s"]' % notes_test),
(survey_id, 145, '["29 - Male"]'),
(survey_id, 127, '["Fluffy"]')]
survey.store_survey(consent, with_fk, without_fk)
obs = survey.fetch_survey(survey_id)
exp = {'Pet_Information_127_0': 'Fluffy',
'Pet_Information_137_0': [0],
'Pet_Information_143_0': 'Capybara',
'Pet_Information_132_0': 2,
'Pet_Information_138_0': 1,
'Pet_Information_144_0': notes_test,
'Pet_Information_129_0': 4,
'Pet_Information_142_0': 'Giant ratty pet!',
'Pet_Information_133_0': 3,
'Pet_Information_139_0': 5,
'Pet_Information_130_0': '20',
'Pet_Information_128_0': 9,
'Pet_Information_134_0': 2,
'Pet_Information_140_0': 0,
'Pet_Information_131_0': 1,
'Pet_Information_145_0': '29 - Male',
'Pet_Information_136_0': 3,
'Pet_Information_135_0': [3],
'Pet_Information_141_0': 4}
self.assertEqual(obs, exp)
obs = ag_data.getConsent(survey_id)
consent['ag_login_id'] = consent['login_id']
del consent['login_id']
del consent['obtainer_name']
consent['deceased_parent'] = 'false'
consent['date_signed'] = date(2015, 9, 27)
consent['parent_1_name'] = 'REMOVED'
consent['parent_2_name'] = 'REMOVED'
consent['participant_name'] = 'REMOVED-0'
consent['parent_1_name'] = 'REMOVED'
self.assertEqual(obs, consent)
def test_store_survey(self):
# Create new survey ID and make sure it is unused
survey = Survey(2)
c = ascii_letters + '1234567890'
survey_id = ''.join([choice(c) for i in range(16)])
name = ''.join([choice(ascii_letters) for i in range(20)])
with self.assertRaises(ValueError):
survey.fetch_survey(survey_id)
consent = {
'login_id': 'd8592c74-84b1-2135-e040-8a80115d6401',
'survey_id': survey_id,
'participant_name': name,
'age_range': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'deceased_parent': False,
'participant_email': 'REMOVED',
'obtainer_name': 'ANIMAL_SURVEY',
'assent_obtainer': 'ANIMAL_SURVEY',
'is_juvenile': True}
with_fk = [(survey_id, 128, 'Other'),
(survey_id, 129, 'Wild'),
(survey_id, 131, 'Male'),
(survey_id, 132, 'Suburban'),
(survey_id, 133, 'Normal'),
(survey_id, 134, 'Omnivore'),
(survey_id, 135, 'Wild food'),
(survey_id, 136, 'Both'),
(survey_id, 137, 'Unspecified'),
(survey_id, 138, 'Lives alone with humans'),
(survey_id, 139, '8+'),
(survey_id, 140, 'Unspecified'),
(survey_id, 141, 'Never')]
without_fk = [(survey_id, 130, '["20"]'),
(survey_id, 142, unicode('["Mötley Crüe!"]', 'utf-8')),
(survey_id, 143, '["Capybara"]'),
(survey_id, 144, '[""]'),
(survey_id, 145, '["29 - Male"]'),
(survey_id, 127, '["%s"]' % name)]
survey.store_survey(consent, with_fk, without_fk)
obs = survey.fetch_survey(survey_id)
exp = {'Pet_Information_127_0': name,
'Pet_Information_137_0': [0],
'Pet_Information_143_0': 'Capybara',
'Pet_Information_132_0': 2,
'Pet_Information_138_0': 1,
'Pet_Information_144_0': '',
'Pet_Information_129_0': 4,
'Pet_Information_142_0': u'M\xf6tley Cr\xfce!'.encode('utf-8'),
'Pet_Information_133_0': 3,
'Pet_Information_139_0': 5,
'Pet_Information_130_0': '20',
'Pet_Information_128_0': 9,
'Pet_Information_134_0': 2,
'Pet_Information_140_0': 0,
'Pet_Information_131_0': 1,
'Pet_Information_145_0': '29 - Male',
'Pet_Information_136_0': 3,
'Pet_Information_135_0': [3],
'Pet_Information_141_0': 4}
self.assertEqual(obs, exp)
obs = ag_data.getConsent(survey_id)
del obs['date_signed']
consent['ag_login_id'] = consent['login_id']
del consent['login_id']
del consent['obtainer_name']
consent['deceased_parent'] = 'false'
self.assertEqual(obs, consent)
def test_fetch_survey_bad_id(self):
survey = Survey(1)
with self.assertRaises(ValueError):
survey.fetch_survey('BAD_ID_HERE')