def test_messages(self):
add_system_message('SYS MESSAGE', datetime.now())
user = User('*****@*****.**')
obs = user.messages()
exp_msg = [
(4, 'SYS MESSAGE'),
(1, 'message 1'),
(2, 'Lorem ipsum dolor sit amet, consectetur adipiscing elit. '
'Pellentesque sed auctor ex, non placerat sapien. Vestibulum '
'vestibulum massa ut sapien condimentum, cursus consequat diam'
' sodales. Nulla aliquam arcu ut massa auctor, et vehicula '
'mauris tempor. In lacinia viverra ante quis pellentesque. '
'Nunc vel mi accumsan, porttitor eros ut, pharetra elit. Nulla'
' ac nisi quis dui egestas malesuada vitae ut mauris. Morbi '
'blandit non nisl a finibus. In erat velit, congue at ipsum '
'sit amet, venenatis bibendum sem. Curabitur vel odio sed est '
'rutrum rutrum. Quisque efficitur ut purus in ultrices. '
'Pellentesque eu auctor justo.'),
(3, 'message <a href="#">3</a>')]
self.assertEqual([(x[0], x[1]) for x in obs], exp_msg)
self.assertTrue(all(x[2] < datetime.now() for x in obs))
self.assertFalse(all(x[3] for x in obs))
self.assertEqual([x[4] for x in obs], [True, False, False, False])
obs = user.messages(1)
exp_msg = ['SYS MESSAGE']
self.assertEqual([x[1] for x in obs], exp_msg)
def post(self, code):
message = ""
level = ""
page = "change_lost_pass.html"
user = None
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
message = "Unable to reset password"
level = "danger"
else:
newpass = self.get_argument("newpass")
try:
changed = user.change_forgot_password(code, newpass)
except IncorrectPasswordError:
message = "The new password is not valid. Try again."
changed = False
except QiitaDBError:
message = "Invalid code. Request a new one."
changed = False
if changed:
message = ("Password reset successful. Please log in to "
"continue.")
level = "success"
page = "index.html"
else:
if message != "":
message = ("Unable to reset password. Most likely your "
"email is incorrect or your reset window has "
"timed out.")
level = "danger"
self.render(page, message=message, level=level, code=code)
def post(self):
message = ""
level = ""
page = "lost_pass.html"
user_id = None
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
message = "ERROR: Unknown user."
level = "danger"
else:
user_id = user.id
user.generate_reset_code()
info = user.info
try:
send_email(user.id, "Qiita: Password Reset", "Please go to "
"the following URL to reset your password: \n"
"%s/auth/reset/%s \nYou "
"have 30 minutes from the time you requested a "
"reset to change your password. After this period, "
"you will have to request another reset." %
(qiita_config.base_url, info["pass_reset_code"]))
message = ("Check your email for the reset code.")
level = "success"
page = "index.html"
except Exception as e:
message = ("Unable to send email. Error has been registered. "
"Your password has not been reset.")
level = "danger"
LogEntry.create('Runtime', "Unable to send forgot password "
"email: %s" % str(e), info={'User': user.id})
self.render(page, user=user_id, message=message, level=level)
def post(self, code):
message = ""
level = ""
page = "change_lost_pass.html"
user = None
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
message = "Unable to reset password"
level = "danger"
else:
newpass = self.get_argument("newpass")
changed = user.change_forgot_password(code, newpass)
if changed:
message = ("Password reset successful. Please log in to "
"continue.")
level = "success"
page = "index.html"
else:
message = ("Unable to reset password. Most likely your email "
"is incorrect or your reset window has timed out.")
level = "danger"
self.render(page, message=message, level=level, code=code)
def post(self):
message = ""
level = ""
page = "lost_pass.html"
user_id = None
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
message = "ERROR: Unknown user."
level = "danger"
else:
user_id = user.id
user.generate_reset_code()
info = user.info
try:
send_email(user.id, "Qiita: Password Reset", "Please go to "
"the following URL to reset your password: "******"http://qiita.colorado.edu/auth/reset/%s" %
info["pass_reset_code"])
message = ("Check your email for the reset code.")
level = "success"
page = "index.html"
except Exception as e:
message = ("Unable to send email. Error has been registered. "
"Your password has not been reset.")
level = "danger"
LogEntry.create('Runtime', "Unable to send forgot password "
"email: %s" % str(e), info={'User': user.id})
self.render(page, user=user_id, message=message, level=level)
def test_get(self):
response = self.get('/auth/verify/SOMETHINGHERE?email=test%40foo.bar')
self.assertEqual(response.code, 200)
User.create('*****@*****.**', 'Somesortofpass')
response = self.get('/auth/verify/SOMETHINGHERE?email=new%40test.bar')
self.assertEqual(response.code, 200)
def test_verify_code(self):
sql = ("insert into qiita.qiita_user values ('*****@*****.**', '1', "
"'testtest', 'testuser', '', '', '', 'verifycode', 'resetcode'"
",null)")
self.conn_handler.execute(sql)
self.assertFalse(User.verify_code('*****@*****.**', 'wrongcode',
'create'))
self.assertFalse(User.verify_code('*****@*****.**', 'wrongcode',
'reset'))
self.assertTrue(User.verify_code('*****@*****.**', 'verifycode',
'create'))
self.assertTrue(User.verify_code('*****@*****.**', 'resetcode',
'reset'))
# make sure errors raised if code already used or wrong type
with self.assertRaises(QiitaDBError):
User.verify_code('*****@*****.**', 'verifycode', 'create')
with self.assertRaises(QiitaDBError):
User.verify_code('*****@*****.**', 'resetcode', 'reset')
with self.assertRaises(IncompetentQiitaDeveloperError):
User.verify_code('*****@*****.**', 'fakecode', 'badtype')
# make sure default analyses created
sql = ("SELECT email, name, description, dflt FROM qiita.analysis "
"WHERE email = '*****@*****.**'")
obs = self.conn_handler.execute_fetchall(sql)
exp = [['*****@*****.**', '[email protected]', 'dflt', True],
['*****@*****.**', '[email protected]', 'dflt', True]]
self.assertEqual(obs, exp)
def test_verify_code(self):
add_system_message("TESTMESSAGE_OLD", datetime.now())
add_system_message("TESTMESSAGE",
datetime.now() + timedelta(seconds=59))
sql = ("insert into qiita.qiita_user values ('*****@*****.**', '1', "
"'testtest', 'testuser', '', '', '', 'verifycode', 'resetcode'"
",null)")
self.conn_handler.execute(sql)
self.assertFalse(User.verify_code('*****@*****.**', 'wrongcode',
'create'))
self.assertFalse(User.verify_code('*****@*****.**', 'wrongcode',
'reset'))
self.assertTrue(User.verify_code('*****@*****.**', 'verifycode',
'create'))
self.assertTrue(User.verify_code('*****@*****.**', 'resetcode',
'reset'))
# make sure errors raised if code already used or wrong type
with self.assertRaises(QiitaDBError):
User.verify_code('*****@*****.**', 'verifycode', 'create')
with self.assertRaises(QiitaDBError):
User.verify_code('*****@*****.**', 'resetcode', 'reset')
with self.assertRaises(IncompetentQiitaDeveloperError):
User.verify_code('*****@*****.**', 'fakecode', 'badtype')
# make sure default analyses created
sql = ("SELECT email, name, description, dflt FROM qiita.analysis "
"WHERE email = '*****@*****.**'")
obs = self.conn_handler.execute_fetchall(sql)
exp = [['*****@*****.**', '[email protected]', 'dflt', True],
['*****@*****.**', '[email protected]', 'dflt', True]]
self.assertEqual(obs, exp)
# Make sure default analyses are linked with the portal
sql = """SELECT COUNT(1)
FROM qiita.analysis
JOIN qiita.analysis_portal USING (analysis_id)
JOIN qiita.portal_type USING (portal_type_id)
WHERE email = '*****@*****.**' AND dflt = true"""
self.assertEqual(self.conn_handler.execute_fetchone(sql)[0], 2)
# Make sure new system messages are linked to user
sql = """SELECT message_id FROM qiita.message_user
WHERE email = '*****@*****.**'"""
m_id = get_count('qiita.message')
self.assertEqual(self.conn_handler.execute_fetchall(sql), [[m_id]])
def test_get_deselected(self):
s = Study(1)
u = User('*****@*****.**')
args = {'deselected': u.id, 'id': s.id}
self.assertEqual(s.shared_with, [u])
response = self.get('/study/sharing/', args)
self.assertEqual(response.code, 200)
exp = {'users': [], 'links': ''}
self.assertEqual(loads(response.body), exp)
self.assertEqual(s.shared_with, [])
# Make sure unshared message added to the system
self.assertEqual('Study \'Identification of the Microbiomes for '
'Cannabis Soils\' has been unshared from you.',
u.messages()[0][1])
def test_delete_messages(self):
# Make message 1 a system message
sql = """UPDATE qiita.message
SET expiration = '2015-08-05'
WHERE message_id = 1"""
self.conn_handler.execute(sql)
user = User('*****@*****.**')
user.delete_messages([1, 2])
obs = user.messages()
exp_msg = [(3, 'message <a href="#">3</a>')]
self.assertItemsEqual([(x[0], x[1]) for x in obs], exp_msg)
sql = "SELECT message_id FROM qiita.message"
obs = self.conn_handler.execute_fetchall(sql)
self.assertItemsEqual(obs, [[1], [3]])
def post(self):
username = self.get_argument("email", "").strip().lower()
password = self.get_argument("newpass", "")
info = {}
for info_column in ("name", "affiliation", "address", "phone"):
hold = self.get_argument(info_column, None)
if hold:
info[info_column] = hold
created = False
try:
created = User.create(username, password, info)
except QiitaDBDuplicateError:
msg = "Email already registered as a user"
if created:
info = created.info
try:
send_email(username, "QIITA: Verify Email Address", "Please "
"click the following link to verify email address: "
"%s/auth/verify/%s?email=%s"
% (qiita_config.base_url, info['user_verify_code'],
url_escape(username)))
except:
msg = ("Unable to send verification email. Please contact the "
"qiita developers at <a href='mailto:qiita-help"
"@gmail.com'>[email protected]</a>")
self.redirect(u"/?level=danger&message=" + url_escape(msg))
return
self.redirect(u"/")
else:
error_msg = u"?error=" + url_escape(msg)
self.redirect(u"/auth/create/" + error_msg)
def post(self):
username = self.get_argument("username", "").strip().lower()
passwd = self.get_argument("password", "")
nextpage = self.get_argument("next", "/")
msg = ""
# check the user level
try:
if User(username).level == "unverified":
# email not verified so dont log in
msg = "Email not verified"
except QiitaDBUnknownIDError:
msg = "Unknown user"
# Check the login information
login = None
try:
login = User.login(username, passwd)
except IncorrectEmailError:
msg = "Unknown user"
except IncorrectPasswordError:
msg = "Incorrect password"
if login:
# everything good so log in
self.set_current_user(username)
self.redirect(nextpage)
else:
self.render("index.html", user=None, loginerror=msg)
def test_get_deselected(self):
a = Analysis(1)
u = User('*****@*****.**')
args = {'deselected': u.id, 'id': a.id}
self.assertEqual(a.shared_with, [u])
response = self.get('/analysis/sharing/', args)
self.assertEqual(response.code, 200)
exp = {'users': [], 'links': ''}
self.assertEqual(loads(response.body), exp)
self.assertEqual(a.shared_with, [])
# Make sure unshared message added to the system
self.assertEqual('Analysis \'SomeAnalysis\' has been unshared from '
'you.', u.messages()[0][1])
# Share the analysis back with the user
a.share(u)
def post(self, code):
error = ""
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
error = "Unable to reset password"
else:
newpass = self.get_argument("newpass")
changed = user.change_forgot_password(code, newpass)
if changed:
error = "Password reset successful. Please log in to continue."
else:
error = "Unable to reset password"
self.render("change_lost_pass.html", user=None,
error=error, code=code)
def get(self, code):
email = self.get_argument("email").strip().lower()
if User.verify_code(email, code, "create"):
msg = "Successfully verified user! You are now free to log in."
else:
msg = "Code not valid!"
self.render("user_verified.html", msg=msg)
def test_create_user(self):
user = User.create('*****@*****.**', 'password')
self.assertEqual(user.id, '*****@*****.**')
sql = "SELECT * from qiita.qiita_user WHERE email = '*****@*****.**'"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'password': '',
'name': None,
'pass_reset_timestamp': None,
'affiliation': None,
'pass_reset_code': None,
'phone': None,
'user_verify_code': '',
'address': None,
'user_level_id': 5,
'email': '*****@*****.**'}
self._check_correct_info(obs, exp)
# make sure default analysis created
sql = ("SELECT email, name, description, dflt FROM qiita.analysis "
"WHERE email = '*****@*****.**'")
obs = self.conn_handler.execute_fetchall(sql)
exp = [['*****@*****.**', '[email protected]', 'dflt', True]]
self.assertEqual(obs, exp)
def post(self):
username = self.get_argument("username", "")
passwd = self.get_argument("password", "")
# check the user level
try:
if User(username).level == 4: # 4 is id for unverified
# email not verified so dont log in
msg = "Email not verified"
except QiitaDBUnknownIDError:
msg = "Unknown user"
# Check the login information
login = None
try:
login = User.login(username, passwd)
except IncorrectEmailError:
msg = "Unknown user"
except IncorrectPasswordError:
msg = "Incorrect password"
if login:
# everthing good so log in
self.set_current_user(username)
self.redirect("/")
return
self.render("index.html", user=None, loginerror=msg)
def test_get_selected(self):
s = Analysis(1)
u = User('*****@*****.**')
args = {'selected': u.id, 'id': s.id}
response = self.get('/analysis/sharing/', args)
self.assertEqual(response.code, 200)
exp = {
'users': ['*****@*****.**', u.id],
'links':
('<a target="_blank" href="mailto:[email protected]">Shared</a>, '
'<a target="_blank" href="mailto:[email protected]">Admin</a>')}
self.assertEqual(loads(response.body), exp)
self.assertEqual(s.shared_with, [User('*****@*****.**'), u])
# Make sure shared message added to the system
self.assertEqual('Analysis <a href="/analysis/results/1">'
'\'SomeAnalysis\'</a> has been shared with you.',
u.messages()[0][1])
def test_get_selected(self):
s = Study(1)
u = User('*****@*****.**')
args = {'selected': u.id, 'id': s.id}
response = self.get('/study/sharing/', args)
self.assertEqual(response.code, 200)
exp = {
'users': ['*****@*****.**', u.id],
'links':
('<a target="_blank" href="mailto:[email protected]">Shared</a>, '
'<a target="_blank" href="mailto:[email protected]">Admin</a>')}
self.assertEqual(loads(response.body), exp)
self.assertEqual(s.shared_with, [User('*****@*****.**'), u])
# Make sure shared message added to the system
self.assertEqual('Study <a href="/study/description/1">'
'\'Identification of the Microbiomes for Cannabis '
'Soils\'</a> has been shared with you.',
u.messages()[0][1])
def post(self):
passmsg = ""
msg = ""
user = User(self.current_user)
action = self.get_argument("action")
if action == "profile":
# tuple of colmns available for profile
# FORM INPUT NAMES MUST MATCH DB COLUMN NAMES
form_data = UserProfile()
form_data.process(data=self.request.arguments)
profile = {name: data[0] for name, data in
viewitems(form_data.data)}
# Turn default value as list into default strings
for field in form_data:
field.data = field.data[0]
try:
user.info = profile
msg = "Profile updated successfully"
except Exception as e:
msg = "ERROR: profile could not be updated"
LogEntry.create('Runtime', "Cound not update profile: %s" %
str(e), info={'User': user.id})
elif action == "password":
form_data = UserProfile()
form_data.process(data=user.info)
oldpass = self.get_argument("oldpass")
newpass = self.get_argument("newpass")
try:
changed = user.change_password(oldpass, newpass)
except Exception as e:
passmsg = "ERROR: could not change password"
LogEntry.create('Runtime', "Could not change password: %s" %
str(e), info={'User': user.id})
else:
if changed:
passmsg = "Password changed successfully"
else:
passmsg = "Incorrect old password"
self.render("user_profile.html", user=user.id, profile=form_data,
msg=msg, passmsg=passmsg)
def get(self, code):
email = self.get_argument("email").strip().lower()
if User.verify_code(email, code, "create"):
msg = "Successfully verified user! You are now free to log in."
color = "black"
r_client.zadd('qiita-usernames', email, 0)
else:
msg = "Code not valid!"
color = "red"
self.render("user_verified.html", msg=msg, color=color,
email=self.get_argument("email").strip())
def post(self):
error = ""
try:
user = User(self.get_argument("email"))
except QiitaDBUnknownIDError:
error = "ERROR: Unknown user."
else:
user.generate_reset_code()
info = user.info
try:
send_email(user, "QIITA: Password Reset", "Please go to the "
"following URL to reset your password: "******"http://qiita.colorado.edu/auth/reset/%s" %
info["pass_reset_code"])
error = "Password reset. Check your email for the reset code."
except Exception as e:
error = "Unable to send email."
LogEntry.create('Runtime', "Unable to send forgot password "
"email" % str(e), info={'User': user.id})
self.render("lost_pass.html", user=None, error=error)
def test_get(self):
a = Analysis(1)
u = User('*****@*****.**')
self.assertEqual(a.shared_with, [u])
# deselecting
args = {'deselected': u.id, 'id': a.id}
response = self.get('/analysis/sharing/', args)
self.assertEqual(response.code, 200)
exp = {'users': [], 'links': ''}
self.assertEqual(loads(response.body), exp)
self.assertEqual(a.shared_with, [])
# Make sure unshared message added to the system
self.assertEqual("Analysis 'SomeAnalysis' has been unshared with you.",
u.messages()[0][1])
# selecting
args = {'selected': u.id, 'id': a.id}
response = self.get('/analysis/sharing/', args)
self.assertEqual(response.code, 200)
exp = {
'users': ['*****@*****.**'],
'links':
('<a target="_blank" href="mailto:[email protected]">Shared</a>')}
self.assertEqual(loads(response.body), exp)
self.assertEqual(a.shared_with, [u])
# Make sure shared message added to the system
self.assertEqual(
'Analysis <a href="/analysis/description/1/">\'SomeAnalysis\'</a> '
'has been shared with you.', u.messages()[0][1])
# admins can share
BaseHandler.get_current_user = Mock(return_value=User("*****@*****.**"))
args = {'deselected': u.id, 'id': a.id}
response = self.get('/analysis/sharing/', args)
self.assertEqual(response.code, 200)
exp = {'users': [], 'links': ''}
self.assertEqual(loads(response.body), exp)
self.assertEqual(a.shared_with, [])
def test_generate_reset_code(self):
user = User.create('*****@*****.**', 'password')
sql = "SELECT LOCALTIMESTAMP"
before = self.conn_handler.execute_fetchone(sql)[0]
user.generate_reset_code()
after = self.conn_handler.execute_fetchone(sql)[0]
sql = ("SELECT pass_reset_code, pass_reset_timestamp FROM "
"qiita.qiita_user WHERE email = %s")
obscode, obstime = self.conn_handler.execute_fetchone(
sql, ('*****@*****.**',))
self.assertEqual(len(obscode), 20)
self.assertTrue(before < obstime < after)
def setUp(self):
self.user = User('*****@*****.**')
self.userinfo = {
'name': 'Dude',
'affiliation': 'Nowhere University',
'address': '123 fake st, Apt 0, Faketown, CO 80302',
'phone': '111-222-3344',
'pass_reset_code': None,
'pass_reset_timestamp': None,
'user_verify_code': None
}
def post(self):
username = self.get_argument("email", "").strip().lower()
password = self.get_argument("newpass", "")
info = {}
for info_column in ("name", "affiliation", "address", "phone"):
hold = self.get_argument(info_column, None)
if hold:
info[info_column] = hold
created = False
try:
created = User.create(username, password, info)
except QiitaDBDuplicateError:
msg = "Email already registered as a user"
if created:
info = created.info
try:
# qiita_config.base_url doesn't have a / at the end, but the
# qiita_config.portal_dir has it at the beginning but not at
# the end. This constructs the correct URL
url = qiita_config.base_url + qiita_config.portal_dir
send_email(username, "QIITA: Verify Email Address", "Please "
"click the following link to verify email address: "
"%s/auth/verify/%s?email=%s\n\nBy clicking you are "
"accepting our term and conditions: "
"%s/iframe/?iframe=qiita-terms"
% (url, info['user_verify_code'],
url_escape(username), url))
except Exception:
msg = ("Unable to send verification email. Please contact the "
"qiita developers at <a href='mailto:qiita-help"
"@gmail.com'>[email protected]</a>")
self.redirect(u"%s/?level=danger&message=%s"
% (qiita_config.portal_dir, url_escape(msg)))
return
msg = ("<h3>User Successfully Created</h3><p>Your Qiita account "
"has been successfully created. An email has been sent to "
"the email address you provided. This email contains "
"instructions on how to activate your account.</p>"
"<p>If you don't receive your activation email within a "
"couple of minutes, check your spam folder. If you still "
"don't see it, send us an email at <a "
"href=\"mailto:[email protected]\">[email protected]"
"</a>.</p>")
self.redirect(u"%s/?level=success&message=%s" %
(qiita_config.portal_dir, url_escape(msg)))
else:
error_msg = u"?error=" + url_escape(msg)
self.redirect(u"%s/auth/create/%s"
% (qiita_config.portal_dir, error_msg))
def test_mark_messages(self):
user = User('*****@*****.**')
user.mark_messages([1, 2])
obs = user.messages()
exp = [True, True, False]
self.assertEqual([x[3] for x in obs], exp)
user.mark_messages([1], read=False)
obs = user.messages()
exp = [False, True, False]
self.assertEqual([x[3] for x in obs], exp)
def post(self):
if r_client.get('maintenance') is not None:
raise HTTPError(503, "Site is down for maintenance")
username = self.get_argument("username", "").strip().lower()
passwd = self.get_argument("password", "")
nextpage = self.get_argument("next", None)
if nextpage is None:
if "auth/" not in self.request.headers['Referer']:
nextpage = self.request.headers['Referer']
else:
nextpage = "%s/" % qiita_config.portal_dir
msg = ""
# check the user level
try:
if User(username).level == "unverified":
# email not verified so dont log in
msg = ("Email not verified. Please check your email and click "
"the verify link. You may need to check your spam "
"folder to find the email.<br/>If a verification email"
" has not arrived in 15 minutes, please email <a href='"
"mailto:[email protected]'>[email protected]</a>")
except QiitaDBUnknownIDError:
msg = "Unknown user"
except RuntimeError:
# means DB not available, so set maintenance mode and failover
r_client.set("maintenance", "Database connection unavailable, "
"please try again later.")
self.redirect("%s/" % qiita_config.portal_dir)
return
# Check the login information
login = None
try:
login = User.login(username, passwd)
except IncorrectEmailError:
msg = "Unknown user"
except IncorrectPasswordError:
msg = "Incorrect password"
except UnverifiedEmailError:
msg = "You have not verified your email address"
if login:
# everything good so log in
self.set_current_user(username)
self.redirect(nextpage)
else:
self.render("index.html", message=msg, level='danger')
def post(self):
if r_client.get('maintenance') is not None:
raise HTTPError(503, "Site is down for maintenance")
username = self.get_argument("username", "").strip().lower()
passwd = self.get_argument("password", "")
nextpage = self.get_argument("next", None)
if nextpage is None:
if "auth/" not in self.request.headers['Referer']:
nextpage = self.request.headers['Referer']
else:
nextpage = "/"
msg = ""
# check the user level
try:
if User(username).level == "unverified":
# email not verified so dont log in
msg = "Email not verified"
except QiitaDBUnknownIDError:
msg = "Unknown user"
except RuntimeError:
# means DB not available, so set maintenance mode and failover
r_client.set("maintenance", "Database connection unavailable, "
"please try again later.")
self.redirect("/")
return
# Check the login information
login = None
try:
login = User.login(username, passwd)
except IncorrectEmailError:
msg = "Unknown user"
except IncorrectPasswordError:
msg = "Incorrect password"
except UnverifiedEmailError:
msg = "You have not verified your email address"
if login:
# everything good so log in
self.set_current_user(username)
self.redirect(nextpage)
else:
self.render("index.html", message=msg, level='danger')
def test_create_user_info(self):
user = User.create('*****@*****.**', 'password', self.userinfo)
self.assertEqual(user.id, '*****@*****.**')
sql = "SELECT * from qiita.qiita_user WHERE email = '*****@*****.**'"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'password': '',
'name': 'Dude',
'affiliation': 'Nowhere University',
'address': '123 fake st, Apt 0, Faketown, CO 80302',
'phone': '111-222-3344',
'pass_reset_timestamp': None,
'pass_reset_code': None,
'user_verify_code': '',
'user_level_id': 5,
'email': '*****@*****.**'}
self._check_correct_info(obs, exp)
def _unshare(self, study, user, callback):
user = User(user)
add_message('Study \'%s\' has been unshared from you.' %
study.title, [user])
callback(study.unshare(user))
def test_get_shared_studies(self):
user = User('*****@*****.**')
self.assertEqual(user.shared_studies, [1])
class UserTest(TestCase):
"""Tests the User object and all properties/methods"""
def setUp(self):
self.user = User('*****@*****.**')
self.userinfo = {
'name': 'Dude',
'affiliation': 'Nowhere University',
'address': '123 fake st, Apt 0, Faketown, CO 80302',
'phone': '111-222-3344',
'pass_reset_code': None,
'pass_reset_timestamp': None,
'user_verify_code': None
}
def test_instantiate_user(self):
User('*****@*****.**')
def test_instantiate_unknown_user(self):
with self.assertRaises(QiitaDBUnknownIDError):
User('*****@*****.**')
def _check_correct_info(self, obs, exp):
self.assertEqual(set(exp.keys()), set(obs.keys()))
for key in exp:
# user_verify_code and password seed randomly generated so just
# making sure they exist and is correct length
if key == 'user_verify_code':
self.assertEqual(len(obs[key]), 20)
elif key == "password":
self.assertEqual(len(obs[key]), 60)
else:
self.assertEqual(obs[key], exp[key])
def test_create_user(self):
user = User.create('*****@*****.**', 'password')
self.assertEqual(user.id, '*****@*****.**')
sql = "SELECT * from qiita.qiita_user WHERE email = '*****@*****.**'"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'password': '',
'name': None,
'pass_reset_timestamp': None,
'affiliation': None,
'pass_reset_code': None,
'phone': None,
'user_verify_code': '',
'address': None,
'user_level_id': 5,
'email': '*****@*****.**'
}
self._check_correct_info(obs, exp)
def test_create_user_info(self):
user = User.create('*****@*****.**', 'password', self.userinfo)
self.assertEqual(user.id, '*****@*****.**')
sql = "SELECT * from qiita.qiita_user WHERE email = '*****@*****.**'"
obs = self.conn_handler.execute_fetchall(sql)
self.assertEqual(len(obs), 1)
obs = dict(obs[0])
exp = {
'password': '',
'name': 'Dude',
'affiliation': 'Nowhere University',
'address': '123 fake st, Apt 0, Faketown, CO 80302',
'phone': '111-222-3344',
'pass_reset_timestamp': None,
'pass_reset_code': None,
'user_verify_code': '',
'user_level_id': 5,
'email': '*****@*****.**'
}
self._check_correct_info(obs, exp)
def test_create_user_column_not_allowed(self):
self.userinfo["email"] = "FAIL"
with self.assertRaises(QiitaDBColumnError):
User.create('*****@*****.**', 'password', self.userinfo)
def test_create_user_non_existent_column(self):
self.userinfo["BADTHING"] = "FAIL"
with self.assertRaises(QiitaDBColumnError):
User.create('*****@*****.**', 'password', self.userinfo)
def test_create_user_duplicate(self):
with self.assertRaises(QiitaDBDuplicateError):
User.create('*****@*****.**', 'password')
def test_create_user_bad_email(self):
with self.assertRaises(IncorrectEmailError):
User.create('notanemail', 'password')
def test_create_user_bad_password(self):
with self.assertRaises(IncorrectPasswordError):
User.create('*****@*****.**', '')
def test_login(self):
self.assertEqual(User.login("*****@*****.**", "password"),
User("*****@*****.**"))
def test_login_incorrect_user(self):
with self.assertRaises(IncorrectEmailError):
User.login("*****@*****.**", "password")
def test_login_incorrect_password(self):
with self.assertRaises(IncorrectPasswordError):
User.login("*****@*****.**", "WRONGPASSWORD")
def test_login_invalid_password(self):
with self.assertRaises(IncorrectPasswordError):
User.login("*****@*****.**", "SHORT")
def test_exists(self):
self.assertTrue(User.exists("*****@*****.**"))
def test_exists_notindb(self):
self.assertFalse(User.exists("*****@*****.**"))
def test_exists_invaid_email(self):
with self.assertRaises(IncorrectEmailError):
User.exists("notanemail@badformat")
def test_get_email(self):
self.assertEqual(self.user.email, '*****@*****.**')
def test_get_level(self):
self.assertEqual(self.user.level, "admin")
def test_get_info(self):
expinfo = {
'name': 'Admin',
'affiliation': 'Owner University',
'address': '312 noname st, Apt K, Nonexistantown, CO 80302',
'phone': '222-444-6789',
'pass_reset_code': None,
'pass_reset_timestamp': None,
'user_verify_code': None,
'phone': '222-444-6789'
}
self.assertEqual(self.user.info, expinfo)
def test_set_info(self):
self.user.info = self.userinfo
self.assertEqual(self.user.info, self.userinfo)
def test_set_info_not_info(self):
"""Tests setting info with a non-allowed column"""
self.userinfo["email"] = "FAIL"
with self.assertRaises(QiitaDBColumnError):
self.user.info = self.userinfo
def test_set_info_bad_info(self):
"""Test setting info with a key not in the table"""
self.userinfo["BADTHING"] = "FAIL"
with self.assertRaises(QiitaDBColumnError):
self.user.info = self.userinfo
def test_get_user_studies(self):
user = User('*****@*****.**')
self.assertEqual(user.user_studies, [1])
def test_get_shared_studies(self):
user = User('*****@*****.**')
self.assertEqual(user.shared_studies, [1])
def test_get_private_analyses(self):
self.assertEqual(self.user.private_analyses, [])
def test_get_shared_analyses(self):
self.assertEqual(self.user.shared_analyses, [])
def test_verify_code(self):
sql = ("insert into qiita.qiita_user values ('*****@*****.**', '1', "
"'testtest', 'testuser', '', '', '', 'verifycode', 'resetcode'"
",null)")
self.conn_handler.execute(sql)
self.assertTrue(
User.verify_code('*****@*****.**', 'verifycode', 'create'))
self.assertTrue(User.verify_code('*****@*****.**', 'resetcode',
'reset'))
self.assertFalse(
User.verify_code('*****@*****.**', 'wrongcode', 'create'))
self.assertFalse(
User.verify_code('*****@*****.**', 'wrongcode', 'reset'))
with self.assertRaises(IncompetentQiitaDeveloperError):
User.verify_code('*****@*****.**', 'fakecode', 'badtype')
def _check_pass(self, passwd):
obspass = self.conn_handler.execute_fetchone(
"SELECT password FROM qiita.qiita_user WHERE email = %s",
(self.user.id, ))[0]
self.assertEqual(hash_password(passwd, obspass), obspass)
def test_change_pass(self):
self.user._change_pass("newpassword")
self._check_pass("newpassword")
self.assertIsNone(self.user.info["pass_reset_code"])
def test_change_pass_short(self):
with self.assertRaises(IncorrectPasswordError):
self.user._change_pass("newpass")
self._check_pass("password")
def test_change_password(self):
self.user.change_password("password", "newpassword")
self._check_pass("newpassword")
def test_change_password_wrong_oldpass(self):
self.user.change_password("WRONG", "newpass")
self._check_pass("password")
def test_generate_reset_code(self):
user = User.create('*****@*****.**', 'password')
sql = "SELECT LOCALTIMESTAMP"
before = self.conn_handler.execute_fetchone(sql)[0]
user.generate_reset_code()
after = self.conn_handler.execute_fetchone(sql)[0]
sql = ("SELECT pass_reset_code, pass_reset_timestamp FROM "
"qiita.qiita_user WHERE email = %s")
obscode, obstime = self.conn_handler.execute_fetchone(
sql, ('*****@*****.**', ))
self.assertEqual(len(obscode), 20)
self.assertTrue(before < obstime < after)
def test_change_forgot_password(self):
self.user.generate_reset_code()
code = self.user.info["pass_reset_code"]
obsbool = self.user.change_forgot_password(code, "newpassword")
self.assertEqual(obsbool, True)
self._check_pass("newpassword")
def test_change_forgot_password_bad_code(self):
self.user.generate_reset_code()
code = "AAAAAAA"
obsbool = self.user.change_forgot_password(code, "newpassword")
self.assertEqual(obsbool, False)
self._check_pass("password")
def _unshare(self, analysis, user, callback):
user = User(user)
add_message(
'Analysis \'%s\' has been unshared with you.' % analysis.name,
[user])
callback(analysis.unshare(user))
def test_has_access_public(self):
self.conn_handler.execute("UPDATE qiita.analysis SET "
"analysis_status_id = 6")
self.assertTrue(self.analysis.has_access(User("*****@*****.**")))
def test_retrieve_biom_tables_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.biom_tables, None)
def test_retrieve_dropped_samples(self):
# Create and populate second study to do test with
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)
}
metadata_dict = {
'SKB8.640193': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 1',
'str_column': 'Value for sample 1',
'latitude': 42.42,
'longitude': 41.41
},
'SKD8.640184': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 2',
'str_column': 'Value for sample 2',
'latitude': 4.2,
'longitude': 1.1
},
'SKB7.640196': {
'physical_location': 'location1',
'has_physical_specimen': True,
'has_extracted_data': True,
'sample_type': 'type1',
'required_sample_info_status': 'received',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 3',
'str_column': 'Value for sample 3',
'latitude': 4.8,
'longitude': 4.41
},
}
metadata = pd.DataFrame.from_dict(metadata_dict, orient='index')
Study.create(User("*****@*****.**"), "Test study 2", [1], info)
SampleTemplate.create(metadata, Study(2))
mp = get_mountpoint("processed_data")[0][1]
study_fp = join(mp, "2_study_1001_closed_reference_otu_table.biom")
ProcessedData.create("processed_params_uclust",
1, [(study_fp, 6)],
study=Study(2),
data_type="16S")
self.conn_handler.execute(
"INSERT INTO qiita.analysis_sample (analysis_id, "
"processed_data_id, sample_id) VALUES "
"(1,2,'2.SKB8.640193'), (1,2,'2.SKD8.640184'), "
"(1,2,'2.SKB7.640196')")
samples = {
1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196'],
2: ['2.SKB8.640193', '2.SKD8.640184']
}
self.analysis._build_biom_tables(samples,
10000,
conn_handler=self.conn_handler)
exp = {1: {'1.SKM4.640180', '1.SKM9.640192'}, 2: {'2.SKB7.640196'}}
self.assertEqual(self.analysis.dropped_samples, exp)
def post(self):
try:
payload = json_decode(self.request.body)
except ValueError:
self.fail('Could not parse body', 400)
return
required = {
'title', 'study_abstract', 'study_description', 'study_alias',
'owner', 'contacts'
}
if not required.issubset(payload):
self.fail('Not all required arguments provided', 400)
return
title = payload['title']
study_abstract = payload['study_abstract']
study_desc = payload['study_description']
study_alias = payload['study_alias']
notes = payload['notes']
owner = payload['owner']
if not User.exists(owner):
self.fail('Unknown user', 403)
return
else:
owner = User(owner)
contacts = payload['contacts']
if Study.exists(title):
self.fail('Study title already exists', 409)
return
pi_name = contacts['principal_investigator'][0]
pi_aff = contacts['principal_investigator'][1]
if not StudyPerson.exists(pi_name, pi_aff):
self.fail('Unknown principal investigator', 403)
return
else:
pi = StudyPerson.from_name_and_affiliation(pi_name, pi_aff)
lp_name = contacts['lab_person'][0]
lp_aff = contacts['lab_person'][1]
if not StudyPerson.exists(lp_name, lp_aff):
self.fail('Unknown lab person', 403)
return
else:
lp = StudyPerson.from_name_and_affiliation(lp_name, lp_aff)
info = {
'lab_person_id': lp,
'principal_investigator_id': pi,
'study_abstract': study_abstract,
'study_description': study_desc,
'study_alias': study_alias,
'notes': notes,
# TODO: we believe it is accurate that mixs is false and
# metadata completion is false as these cannot be known
# at study creation here no matter what.
# we do not know what should be done with the timeseries.
'mixs_compliant': False,
'metadata_complete': False,
'timeseries_type_id': 1
}
study = Study.create(owner, title, info)
self.set_status(201)
self.write({'id': study.id})
self.finish()
def test_get(self):
BaseHandler.get_current_user = Mock(return_value=User("*****@*****.**"))
Artifact(4).visibility = "awaiting_approval"
response = self.get('/admin/approval/')
self.assertEqual(response.code, 200)
self.assertIn("*****@*****.**", response.body)
def test_artifact_patch_request(self):
a = Artifact(1)
test_user = User('*****@*****.**')
self.assertEqual(a.name, 'Raw data 1')
artifact_patch_request(test_user,
1,
'replace',
'/name/',
req_value='NEW_NAME')
self.assertEqual(a.name, 'NEW_NAME')
# Reset the name
a.name = 'Raw data 1'
# No access
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(User('*****@*****.**'),
1,
'replace',
'/name/',
req_value='NEW_NAME')
# Incorrect path parameter
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/name/wrong/',
req_value='NEW_NAME')
# Missing value
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user, 1, 'replace', '/name/')
# Wrong attribute
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/wrong/',
req_value='NEW_NAME')
# Wrong operation
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'add',
'/name/',
req_value='NEW_NAME')
# Changing visibility
self.assertEqual(a.visibility, 'private')
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='sandbox')
self.assertEqual(a.visibility, 'sandbox')
# Admin can change to private
artifact_patch_request(User('*****@*****.**'),
1,
'replace',
'/visibility/',
req_value='private')
self.assertEqual(a.visibility, 'private')
# Test user can't change to private
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='private')
# Unkown req value
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='wrong')
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_p_jobs = [[
'063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None
],
[
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'Split libraries', 'running', 'demultiplexing', None
]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')
]
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job': [job.id, 'queued', None],
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
exp_summary_path = relpath(a.html_summary_fp[1],
qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
exp_summary_path,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_parameters': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_p_jobs = [[
'd19f76ee-274e-4c1b-b3a2-a12d73507c55',
'Pick closed-reference OTUs', 'error', 'generating demux file',
'Error message'
]]
exp_files = [(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {
'name':
'Demultiplexed 1',
'artifact_id':
2,
'artifact_type':
'Demultiplexed',
'artifact_timestamp':
'2012-10-01 10:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_parameters': {
'max_barcode_errors': 1.5,
'sequence_max_n': 0,
'max_bad_run_length': 3,
'phred_offset': u'auto',
'rev_comp': False,
'phred_quality_threshold': 3,
'input_data': 1,
'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
'barcode_type': u'golay_12'
},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {
'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': '',
'processing_parameters': {},
'files': [(27, 'biom_table.biom (biom)')],
'is_from_analysis': True,
'summary': None,
'job': None,
'processing_jobs': [],
'errored_jobs': []
}
self.assertEqual(obs, exp)
def sample_template_summary_get_req(samp_id, user_id):
"""Returns a summary of the sample template metadata columns
Parameters
----------
samp_id : int
SampleTemplate id to get info for
user_id : str
User requesting the sample template info
Returns
-------
dict
Returns summary information in the form
{'status': str,
'message': str,
'info': dict of {str: object}
status can be success, warning, or error depending on result
message has the warnings or errors
info dictionary contains the keys as the metadata categories
and the values are list of tuples. Each tuple is an observed value in
the category and the number of times its seen.
Format {num_samples: value,
category: [(val1, count1), (val2, count2), ...], ...}
"""
access_error = check_access(samp_id, user_id)
if access_error:
return access_error
processing, alert_type, alert_msg = get_sample_template_processing_status(
samp_id)
exists = _check_sample_template_exists(int(samp_id))
if exists['status'] != 'success':
return {
'status': 'success',
'message': '',
'num_samples': 0,
'num_columns': 0,
'editable': not processing,
'alert_type': alert_type,
'alert_message': alert_msg,
'stats': {}
}
template = SampleTemplate(int(samp_id))
df = template.to_dataframe()
editable = (Study(template.study_id).can_edit(User(user_id))
and not processing)
out = {
'status': 'success',
'message': '',
'num_samples': df.shape[0],
'num_columns': df.shape[1],
'editable': editable,
'alert_type': alert_type,
'alert_message': alert_msg,
'stats': {}
}
# drop the samp_id column if it exists
if 'study_id' in df.columns:
df.drop('study_id', axis=1, inplace=True)
for column in df.columns:
counts = df[column].value_counts()
out['stats'][str(column)] = [(str(key), counts[key])
for key in natsorted(counts.index)]
return out
def test_unshare(self):
self.collection.unshare(User("*****@*****.**"))
obs = self.collection.shared_with
exp = []
self.assertEqual(obs, exp)
def test_retrieve_step(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
new.step = 2
self.assertEqual(new.step, 2)
def test_complete_job(self):
# Complete success
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
exp_artifact_count = get_count('qiita.artifact') + 1
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'success')
self.assertEqual(get_count('qiita.artifact'), exp_artifact_count)
# Complete job error
payload = dumps({'success': False, 'error': 'Job failure'})
job = self._create_job('complete_job', {
'job_id': 'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
c_job = ProcessingJob('bcc7ebcd-39c1-43e4-af2d-822e3589f14d')
self.assertEqual(c_job.status, 'error')
self.assertEqual(c_job.log, LogEntry.newest_records(numrecords=1)[0])
self.assertEqual(c_job.log.msg, 'Job failure')
# Complete internal error
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fp = '/surprised/if/this/path/exists.biom'
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'error')
self.assertIn('No such file or directory', c_job.log.msg)
def test_retrieve_step_new(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
with self.assertRaises(ValueError):
new.step
def test_instantiate_unknown_user(self):
with self.assertRaises(QiitaDBUnknownIDError):
User('*****@*****.**')
def test_retrieve_pmid_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
self.assertEqual(new.pmid, None)
def test_instantiate_user(self):
User('*****@*****.**')
def test_retrieve_mapping_file_none(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis", Analysis(1))
obs = new.mapping_file
self.assertEqual(obs, None)
def prep_template_ajax_get_req(user_id, prep_id):
"""Returns the prep tempalte information needed for the AJAX handler
Parameters
----------
user_id : str
The user id
prep_id : int
The prep template id
Returns
-------
dict of {str: object}
A dictionary with the following keys:
- status: str, whether the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
- name: str, the name of the prep template
- files: list of str, the files available to update the prep template
- download_prep: int, the filepath_id of the prep file
- download_qiime, int, the filepath_id of the qiime mapping file
- num_samples: int, the number of samples present in the template
- num_columns: int, the number of columns present in the template
- investigation_type: str, the investigation type of the template
- ontology: str, dict of {str, list of str} containing the information
of the ENA ontology
- artifact_attached: bool, whether the template has an artifact
attached
- study_id: int, the study id of the template
"""
pt = PrepTemplate(prep_id)
name = pt.name
# Initialize variables here
processing = False
alert_type = ''
alert_msg = ''
job_info = r_client.get(PREP_TEMPLATE_KEY_FORMAT % prep_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:
alert_type = 'info'
alert_msg = 'This prep template is currently being updated'
elif job_status == 'error':
alert_type = 'danger'
alert_msg = job.log.msg.replace('\n', '</br>')
else:
alert_type = job_info['alert_type']
alert_msg = job_info['alert_msg'].replace('\n', '</br>')
artifact_attached = pt.artifact is not None
study_id = pt.study_id
files = [
f for _, f, _ in get_files_from_uploads_folders(study_id)
if f.endswith(('.txt', '.tsv', '.xlsx'))
]
# The call to list is needed because keys is an iterator
num_samples = len(list(pt.keys()))
num_columns = len(pt.categories())
investigation_type = pt.investigation_type
download_prep_id = None
download_qiime_id = None
other_filepaths = []
for fp_id, fp in pt.get_filepaths():
fp = basename(fp)
if 'qiime' in fp:
if download_qiime_id is None:
download_qiime_id = fp_id
else:
if download_prep_id is None:
download_prep_id = fp_id
else:
other_filepaths.append(fp)
ontology = _get_ENA_ontology()
editable = Study(study_id).can_edit(User(user_id)) and not processing
success, restrictions = pt.validate_restrictions()
return {
'status': 'success',
'message': '',
'name': name,
'files': files,
'download_prep_id': download_prep_id,
'download_qiime_id': download_qiime_id,
'other_filepaths': other_filepaths,
'num_samples': num_samples,
'num_columns': num_columns,
'investigation_type': investigation_type,
'ontology': ontology,
'artifact_attached': artifact_attached,
'study_id': study_id,
'editable': editable,
'data_type': pt.data_type(),
'alert_type': alert_type,
'is_submitted_to_ebi': pt.is_submitted_to_ebi,
'prep_restrictions': restrictions,
'samples': sorted(list(pt.keys())),
'alert_message': alert_msg
}
def _get_all_emails(self, callback):
callback(list(User.iter()))
def test_get_user_studies(self):
user = User('*****@*****.**')
self.assertEqual(user.user_studies, [1])
def test_unshare(self):
self.analysis.unshare(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with, [])
def _share(self, study, user, callback):
user = User(user)
add_message('Study <a href="%s/study/description/%d">\'%s\'</a> '
'has been shared with you.' %
(qiita_config.portal_dir, study.id, study.title), [user])
callback(study.share(user))
def test_share(self):
self.collection.share(User("*****@*****.**"))
obs = self.collection.shared_with
exp = ["*****@*****.**", "*****@*****.**"]
self.assertEqual(obs, exp)
def test_add_samples(self):
new = Analysis.create(User("*****@*****.**"), "newAnalysis",
"A New Analysis")
new.add_samples([(1, '1.SKB8.640193'), (1, '1.SKD5.640186')])
exp = {1: ['1.SKB8.640193', '1.SKD5.640186']}
self.assertEqual(new.samples, exp)
def prep_template_patch_req(user_id,
req_op,
req_path,
req_value=None,
req_from=None):
"""Modifies an attribute of the prep template
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the prep information
req_path : str
The prep information and attribute to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str, str, str}
A dictionary with the following keys:
- status: str, whether if the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
- row_id: str, the row_id that we tried to delete
"""
req_path = [v for v in req_path.split('/') if v]
if req_op == 'replace':
# The structure of the path should be /prep_id/attribute_to_modify/
# so if we don't have those 2 elements, we should return an error
if len(req_path) != 2:
return {'status': 'error', 'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
attribute = req_path[1]
# Check if the user actually has access to the prep template
prep = PrepTemplate(prep_id)
access_error = check_access(prep.study_id, user_id)
if access_error:
return access_error
status = 'success'
msg = ''
if attribute == 'investigation_type':
prep.investigation_type = req_value
elif attribute == 'data':
fp = check_fp(prep.study_id, req_value)
if fp['status'] != 'success':
return fp
fp = fp['file']
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('update_prep_template')
params = Parameters.load(cmd,
values_dict={
'prep_template': prep_id,
'template_fp': fp
})
job = ProcessingJob.create(User(user_id), params, True)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job.id}))
job.submit()
elif attribute == 'name':
prep.name = req_value.strip()
else:
# We don't understand the attribute so return an error
return {
'status':
'error',
'message':
'Attribute "%s" not found. '
'Please, check the path parameter' % attribute
}
return {'status': status, 'message': msg}
elif req_op == 'remove':
# The structure of the path should be:
# /prep_id/row_id/{columns|samples}/name
if len(req_path) != 4:
return {'status': 'error', 'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
row_id = req_path[1]
attribute = req_path[2]
attr_id = req_path[3]
# Check if the user actually has access to the study
pt = PrepTemplate(prep_id)
access_error = check_access(pt.study_id, user_id)
if access_error:
return access_error
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('delete_sample_or_column')
params = Parameters.load(cmd,
values_dict={
'obj_class': 'PrepTemplate',
'obj_id': prep_id,
'sample_or_col': attribute,
'name': attr_id
})
job = ProcessingJob.create(User(user_id), params, True)
# Store the job id attaching it to the sample template id
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job.id}))
job.submit()
return {'status': 'success', 'message': '', 'row_id': row_id}
else:
return {
'status':
'error',
'message':
'Operation "%s" not supported. '
'Current supported operations: replace, remove' % req_op,
'row_id':
'0'
}
def test_share(self):
self.analysis.share(User("*****@*****.**"))
self.assertEqual(self.analysis.shared_with,
["*****@*****.**", "*****@*****.**"])
def artifact_post_req(user_id,
filepaths,
artifact_type,
name,
prep_template_id,
artifact_id=None):
"""Creates the initial artifact for the prep template
Parameters
----------
user_id : str
User adding the atrifact
filepaths : dict of str
Comma-separated list of files to attach to the artifact,
keyed by file type
artifact_type : str
The type of the artifact
name : str
Name to give the artifact
prep_template_id : int or str castable to int
Prep template to attach the artifact to
artifact_id : int or str castable to int, optional
The id of the imported artifact
Returns
-------
dict of objects
A dictionary containing the new artifact ID
{'status': status,
'message': message,
'artifact': id}
"""
prep_template_id = int(prep_template_id)
prep = PrepTemplate(prep_template_id)
study_id = prep.study_id
# First check if the user has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
user = User(user_id)
if artifact_id:
# if the artifact id has been provided, import the artifact
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('copy_artifact')
params = Parameters.load(cmd,
values_dict={
'artifact': artifact_id,
'prep_template': prep.id
})
job = ProcessingJob.create(user, params, True)
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = {}
for ftype, file_list in viewitems(filepaths):
# JavaScript sends us this list as a comma-separated list
for fp in file_list.split(','):
# JavaScript will send this value as an empty string if the
# list of files was empty. In such case, the split will
# generate a single element containing the empty string. Check
# for that case here and, if fp is not the empty string,
# proceed to check if the file exists
if fp:
# Check if filepath being passed exists for study
full_fp = path_builder(fp)
exists = check_fp(study_id, full_fp)
if exists['status'] != 'success':
return {
'status': 'error',
'message': 'File does not exist: %s' % fp
}
if ftype not in cleaned_filepaths:
cleaned_filepaths[ftype] = []
cleaned_filepaths[ftype].append(full_fp)
# This should never happen, but it doesn't hurt to actually have
# a explicit check, in case there is something odd with the JS
if not cleaned_filepaths:
return {
'status': 'error',
'message': "Can't create artifact, no files provided."
}
command = Command.get_validator(artifact_type)
job = ProcessingJob.create(
user,
Parameters.load(command,
values_dict={
'template': prep_template_id,
'files': dumps(cleaned_filepaths),
'artifact_type': artifact_type,
'name': name,
'analysis': None,
}), True)
# Submit the job
job.submit()
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
dumps({
'job_id': job.id,
'is_qiita_job': True
}))
return {'status': 'success', 'message': ''}
