def toggle_theme(self):
if session.get('theme', None) == 'dark':
session['theme'] = 'light'
else:
session['theme'] = 'dark'
session.save()
return session.get('theme', None)
def pwd_expired_change(self, **kw):
require_authenticated()
return_to = kw.get("return_to")
kw = F.password_change_form.to_python(kw, None)
ap = plugin.AuthenticationProvider.get(request)
try:
expired_username = session.get("expired-username")
expired_user = M.User.query.get(username=expired_username) if expired_username else None
ap.set_password(expired_user or c.user, kw["oldpw"], kw["pw"])
expired_user.set_tool_data("allura", pwd_reset_preserve_session=session.id)
expired_user.set_tool_data("AuthPasswordReset", hash="", hash_expiry="") # Clear password reset token
except wexc.HTTPUnauthorized:
flash("Incorrect password", "error")
redirect(tg.url("/auth/pwd_expired", dict(return_to=return_to)))
flash("Password changed")
session.pop("pwd-expired", None)
session["username"] = session.get("expired-username")
session.pop("expired-username", None)
session.save()
h.auditlog_user("Password reset (via expiration process)")
if return_to and return_to != request.url:
redirect(return_to)
else:
redirect("/")
def pwd_expired_change(self, **kw):
require_authenticated()
return_to = kw.get('return_to')
kw = F.password_change_form.to_python(kw, None)
ap = plugin.AuthenticationProvider.get(request)
try:
expired_username = session.get('expired-username')
expired_user = M.User.query.get(username=expired_username) if expired_username else None
ap.set_password(expired_user or c.user, kw['oldpw'], kw['pw'])
expired_user.set_tool_data('allura', pwd_reset_preserve_session=session.id)
expired_user.set_tool_data('AuthPasswordReset', hash='', hash_expiry='') # Clear password reset token
except wexc.HTTPUnauthorized:
flash('Incorrect password', 'error')
redirect(tg.url('/auth/pwd_expired', dict(return_to=return_to)))
flash('Password changed')
session.pop('pwd-expired', None)
session['username'] = session.get('expired-username')
session.pop('expired-username', None)
session.save()
h.auditlog_user('Password reset (via expiration process)')
if return_to and return_to != request.url:
redirect(return_to)
else:
redirect('/')
def pwd_expired_change(self, **kw):
require_authenticated()
return_to = kw.get('return_to')
kw = F.password_change_form.to_python(kw, None)
ap = plugin.AuthenticationProvider.get(request)
try:
expired_username = session.get('expired-username')
expired_user = M.User.query.get(
username=expired_username) if expired_username else None
ap.set_password(expired_user or c.user, kw['oldpw'], kw['pw'])
expired_user.set_tool_data('allura',
pwd_reset_preserve_session=session.id)
expired_user.set_tool_data(
'AuthPasswordReset', hash='',
hash_expiry='') # Clear password reset token
except wexc.HTTPUnauthorized:
flash('Incorrect password', 'error')
redirect(tg.url('/auth/pwd_expired', dict(return_to=return_to)))
flash('Password changed')
session.pop('pwd-expired', None)
session['username'] = session.get('expired-username')
session.pop('expired-username', None)
session.save()
h.auditlog_user('Password reset (via expiration process)')
if return_to and return_to != request.url:
redirect(return_to)
else:
redirect('/')
def check_phone_verification(self, pin, **kw):
p = plugin.ProjectRegistrationProvider.get()
request_id = session.get('phone_verification.request_id')
number_hash = session.get('phone_verification.number_hash')
res = p.check_phone_verification(c.user, request_id, pin, number_hash)
if 'error' in res:
res['error'] = jinja2.Markup.escape(res['error'])
res['error'] = h.really_unicode(res['error'])
return res
def clear(self):
try:
session.get('skip', set()).remove(self.name)
except KeyError:
pass
session['settings'].pop(self.name, None)
session.save()
flash(_('Settings cleared'))
redirect(self.url)
def check_phone_verification(self, pin, **kw):
p = plugin.ProjectRegistrationProvider.get()
request_id = session.get('phone_verification.request_id')
number_hash = session.get('phone_verification.number_hash')
res = p.check_phone_verification(c.user, request_id, pin, number_hash)
if 'error' in res:
res['error'] = jinja2.Markup.escape(res['error'])
res['error'] = h.really_unicode(res['error'])
return res
def session_update():
timeout = session.get('timeout', 0)
length = session.get('length', 0)
if timeout and length:
newexpire = datetime.utcnow() + timedelta(seconds=length)
log.debug("SESSION EXPIRE %s", session['expires'])
if newexpire >= session['expires'] + timedelta(seconds=timeout):
session['expires'] = newexpire
session.save()
def clear(self):
try:
session.get('skip', set()).remove(self.name)
except KeyError:
pass
session['settings'].pop(self.name, None)
session.save()
flash(_('Settings cleared'))
redirect(self.url)
def index(self):
result = None
if session.get('username') is not None:
user = DBSession.query(User).filter_by(user_name=session.get('username')).first()
if user is not None and user.is_cloud():
if session['cloud_only'] == True:
override_template(self.index, 'genshi:stackone.templates.clouddashboard')
result = self.controller_impl.index()
return dict(result)
def oauth_callback(self, **kw):
client_id = config.get("github_importer.client_id")
secret = config.get("github_importer.client_secret")
if not client_id or not secret:
return # GitHub app is not configured
oauth = OAuth2Session(client_id, state=session.get("github.oauth.state"))
token = oauth.fetch_token(
"https://github.com/login/oauth/access_token", client_secret=secret, authorization_response=request.url
)
c.user.set_tool_data("GitHubProjectImport", token=token["access_token"])
redirect(session.get("github.oauth.redirect", "/"))
def post_logout(self, came_from=url('/')):
try:
if session.get('username'):
UIUpdateManager().del_user_updated_entities(session['username'], session['group_names'])
UIUpdateManager().del_user_updated_tasks(session['username'])
TopCache().delete_usercache(session.get('auth'))
except Exception as e:
print_traceback()
LOGGER.error(to_str(e))
session.delete()
def index(self, *args, **kw):
'''
Find first not set up service
'''
for name, item in self.menu:
if name in session.get('skip', set()):
continue
if name not in session.get('settings', {}):
redirect(item.url)
# Redirect to the first item in list
# redirect(self.menu[0][1].url)
# Redirect to the last item in list
redirect(item.url)
def index(self, *args, **kw):
'''
Find first not set up service
'''
for name, item in self.menu:
if name in session.get('skip', set()):
continue
if name not in session.get('settings', {}):
redirect(item.url)
# Redirect to the first item in list
# redirect(self.menu[0][1].url)
# Redirect to the last item in list
redirect(item.url)
def oauth_callback(self, **kw):
client_id = config.get('github_importer.client_id')
secret = config.get('github_importer.client_secret')
if not client_id or not secret:
return # GitHub app is not configured
oauth = OAuth2Session(client_id,
state=session.get('github.oauth.state'))
token = oauth.fetch_token(
'https://github.com/login/oauth/access_token',
client_secret=secret,
authorization_response=request.url)
c.user.set_tool_data('GitHubProjectImport',
token=token['access_token'])
self.oauth_callback_complete()
redirect(session.get('github.oauth.redirect', '/'))
def oauth_callback(self, **kw):
client_id = config.get('github_importer.client_id')
secret = config.get('github_importer.client_secret')
if not client_id or not secret:
return # GitHub app is not configured
oauth = OAuth2Session(
client_id, state=session.get('github.oauth.state'))
token = oauth.fetch_token(
'https://github.com/login/oauth/access_token',
client_secret=secret,
authorization_response=request.url
)
c.user.set_tool_data('GitHubProjectImport',
token=token['access_token'])
redirect(session.get('github.oauth.redirect', '/'))
def fetch(self, page, rows, sidx, sord, **kw):
''' Function called on AJAX request made by FlexGrid
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * int(rows)
except:
offset = 0
page = 1
rows = 25
apps = DBSession.query(Campaign).filter(Campaign.deleted==None)
total = 1 + apps.count() / rows
column = getattr(Campaign, sidx)
apps = apps.order_by(getattr(column,sord)()).offset(offset).limit(rows)
rows = [ { 'id' : a.cmp_id, 'cell': row(a) } for a in apps ]
return dict(page=page, total=total, rows=rows)
def _clone_object(self):
params = session.get('entity')
entity = self._get_entity(params['entity'], params['_id'])
params['title'] += ' [NUOVO]'
new_obj = clone_obj(self.related_models[params['entity']], entity,
params)
return new_obj
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_TH_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
trackhubs = []
if os.path.exists(user_TH_path):
list_trackhubs = os.listdir(user_TH_path)
for t in list_trackhubs:
th_path = user_TH_path + "/" + t
#the only one directory into at this th level is named by the assembly used for it
for i in os.listdir(th_path):
path_to_test = th_path + "/" + i
if os.path.isdir(path_to_test):
assembly = i
if not assembly:
break
else:
#hub_url = th_path + "/hub.txt"
hostname = socket.gethostname().lower()
#because of aliasing
if hostname == "ptbbsrv2.epfl.ch":
hostname = "biorepo.epfl.ch"
hub_url = "http://" + hostname + url("/trackHubs/") + user_lab + "/" + mail_final + "/" + t + "/hub.txt"
th = Trackhub(t, 'http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=' + hub_url + "&db=" + assembly)
trackhubs.append(th)
all_trackhubs = [util.to_datagrid(TrackhubGrid(), trackhubs, " UCSC's Trackhub(s)", len(trackhubs) > 0)]
return dict(page='trackhubs', model=trackhubs, items=all_trackhubs, value=kw)
def ajaxAddtoCart( self, **kw ):
_id = kw.get( 'id', None ) or None
if not _id : return {'flag' : 1 , 'msg' : 'No ID provided!'}
try:
items = session.get( 'items', [] )
tmp = {
'_k' : "%s%s" % ( dt.now().strftime( "%Y%m%d%H%M%S" ), random.randint( 100, 10000 ) ) ,
'id' : _id,
}
qs = []
for qk, qv in self._filterAndSorted( "option_qty", kw ):
if not qv : continue
q, _ = qv.split( "|" )
if not q.isdigit() : continue
qs.append( int( q ) )
tmp['qty'] = sum( qs ) if qs else 0
p = qry( Product ).get( _id )
tmp['values'], tmp['optionstext'] = self._formatKW( kw, p )
items.append( tmp )
session['items'] = items
session.save()
return {'flag' : 0 , 'total' : len( session['items'] )}
except:
traceback.print_exc()
return {'flag' : 1, 'msg':'Error occur on the sever side!'}
def ajaxSavetoCart( self, **kw ):
_k = kw.get( "_k", None )
if not _k : return {'flag' : 1 , 'msg' : 'No ID provided!'}
try:
items = session.get( 'items', [] )
for index, item in enumerate( items ):
if item['_k'] != _k : continue
p = qry( Product ).get( item['id'] )
item['values'], item['optionstext'] = self._formatKW( kw , p )
qs = []
for qk, qv in self._filterAndSorted( "option_qty", kw ):
if not qv : continue
q, _ = qv.split( "|" )
if not q.isdigit() : continue
qs.append( int( q ) )
item['qty'] = sum( qs ) if qs else 0
items[index] = item
session['items'] = items
session.save()
return {'flag' : 0 , 'optionstext' : item['optionstext'], }
except:
traceback.print_exc()
return {'flag' : 1 , 'msg' : 'Error occur on the sever side!'}
return {'flag' : 1 , 'msg' : 'No such item!'}
def diff(self, commit, fmt=None, **kw):
try:
path, filename = os.path.split(self._blob.path())
a_ci = c.app.repo.commit(commit)
a = a_ci.get_path(self._blob.path())
apath = a.path()
except:
a = []
apath = ''
b = self._blob
if not self._blob.has_html_view:
diff = "Cannot display: file marked as a binary type."
return dict(a=a, b=b, diff=diff)
la = list(a)
lb = list(b)
adesc = (u'a' + h.really_unicode(apath)).encode('utf-8')
bdesc = (u'b' + h.really_unicode(b.path())).encode('utf-8')
if not fmt:
fmt = web_session.get('diformat', '')
else:
web_session['diformat'] = fmt
web_session.save()
if fmt == 'sidebyside':
hd = HtmlSideBySideDiff()
diff = hd.make_table(la, lb, adesc, bdesc)
else:
diff = ''.join(difflib.unified_diff(la, lb, adesc, bdesc))
return dict(a=a, b=b, diff=diff)
def diff(self, commit, fmt=None):
try:
path, filename = os.path.split(self._blob.path())
a_ci = c.app.repo.commit(commit)
a = a_ci.get_path(self._blob.path())
apath = a.path()
except:
a = []
apath = ''
b = self._blob
if not self._blob.has_html_view:
diff = "Cannot display: file marked as a binary type."
return dict(a=a, b=b, diff=diff)
la = list(a)
lb = list(b)
adesc = (u'a' + h.really_unicode(apath)).encode('utf-8')
bdesc = (u'b' + h.really_unicode(b.path())).encode('utf-8')
if not fmt:
fmt = web_session.get('diformat', '')
else:
web_session['diformat'] = fmt
web_session.save()
if fmt == 'sidebyside':
hd = HtmlSideBySideDiff()
diff = hd.make_table(la, lb, adesc, bdesc)
else:
diff = ''.join(difflib.unified_diff(la, lb, adesc, bdesc))
return dict(a=a, b=b, diff=diff)
def send_email_to_user(self, msg):
self.msg = msg
curr_user_id = session.get('userid')
userRecord = DBSession.query(User.email_address).filter(User.user_name == curr_user_id).first()
if userRecord:
self.receivers = userRecord.email_address
emailservers = self.get_mailservers()
for eachmailserver in emailservers:
if eachmailserver:
self.mail_server = eachmailserver['MailSetup'].mail_server
self.port = int(eachmailserver['MailSetup'].port)
self.secure_type = int(eachmailserver['MailSetup'].use_secure)
self.cred_details = eachmailserver['Creds'].cred_details
self.password = self.cred_details['password']
self.sender = self.cred_details['user_email']
result = False
if self.secure_type == NONSECURE:
result = EmailManager().send_nonsecure(self.mail_server, self.port, self.sender, self.receivers, msg)
else:
if self.secure_type == TLS:
result = EmailManager().send_tls(self.mail_server, self.port, self.sender, self.password, self.receivers, msg)
else:
result = EmailManager().send_ssl(self.mail_server, self.port, self.sender, self.password, self.receivers, msg)
if result == True:
return 'Test mail sent from ' + eachmailserver['MailSetup'].mail_server
def build_columns():
list_columns = [
{"title": "", "data": "scroll_info"},
{"title": "Description", "data": "Description", "defaultContent": ""},
{"title": "User", "data": "User", "defaultContent": ""},
{"title": "Projects", "data": "Projects", "defaultContent": ""},
{"title": "Samples", "data": "Samples", "defaultContent": ""},
{"title": "Type", "data": "Type", "defaultContent": ""},
{"title": "Measurements", "data": "Measurements", "defaultContent": ""},
#6
{"title": "DataType", "data": "DataType", "defaultContent": ""},
{"title": "Attachment", "data": "Attachment", "defaultContent": ""},
{"title": "Created", "data": "Created", "defaultContent": ""},
{"title": "Actions", "data": "Actions", "defaultContent": ""}]
dyn_fields = sorted(session.get("search_grid_fields", []))
for d in dyn_fields:
dic_column = {}
d = d.replace("_", " ")
d = d.capitalize()
dic_column["title"] = d
dic_column["data"] = d
dic_column["defaultContent"] = ""
#insert dynamic fields after "DataType" and before "Attachment"
list_columns[6:6] = [dic_column]
return list_columns
def fetch(self, page, rows, sidx, sord, **kw):
""" Function called on AJAX request made by FlexGrid
Fetch data from DB, return the list of rows + total + current page
"""
# Try and use grid preference
grid_rows = session.get("grid_rows", None)
if rows == "-1": # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session["grid_rows"] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page - 1) * int(rp)
except:
offset = 0
page = 1
rows = 25
apps = DBSession.query(Application)
total = apps.count()
column = getattr(Application, sidx)
apps = apps.order_by(getattr(column, sord)()).offset(offset).limit(rows)
rows = [{"id": a.app_id, "cell": row(a)} for a in apps]
return dict(page=page, total=total, rows=rows)
def search_to_json(self, *args, **kw):
#TODO : sort by column on user's click
user_lab = session.get("current_lab", None)
#get parameters from ajax request
search_value = kw.get("search[value]", None)
if search_value == '':
search_value = None
#word lenght > 2 to avoid DDoS in your server....
elif search_value is not None:
list_search_words = [x for x in search_value.split(" ") if len(x) > 2]
draw = int(kw.get("draw", 1))
start_point = int(kw.get("start", 0))
data_by_page = int(kw.get("length", 50))
stop_point = start_point + data_by_page
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
measurements_total = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
measurements = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).distinct()[start_point:stop_point]
if search_value is not None:
final_request = self.search_engine(list_search_words, lab)
#query mixed with results from all the table of interest
paginated_request = final_request[start_point:stop_point]
searching_tosort = [SW(meas).to_json_test() for meas in paginated_request]
searching = sorted(searching_tosort, key=lambda k: (k['User'], k['Type']))
return json.dumps({"draw": draw, "recordsTotal": len(measurements_total), "recordsFiltered": len(final_request), "data": searching})
searching_tosort = [SW(meas).to_json_test() for meas in measurements]
searching = sorted(searching_tosort, key=lambda k: (k['User'], k['Type']))
return json.dumps({"draw": draw, "recordsTotal": len(measurements_total), "recordsFiltered": len(measurements_total), "data": searching})
def fetch(self, page, rows, sidx='name', sord='desc', _search='false',
searchOper=None, searchField=None, searchString=None, **kw):
''' Function called on AJAX request made by Grid JS component
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * rows
except:
offset = 0
page = 1
rows = 25
queue = DBSession.query(Queue)
total = queue.count()/rows + 1
column = getattr(Queue, sidx)
queue = queue.order_by(getattr(column,sord)()).offset(offset).limit(rows)
data = [ { 'id' : q.queue_id, 'cell': row(q) } for q in queue ]
return dict(page=page, total=total, rows=data)
def outcall_fetch(self, page, rows, sidx, sord, cust_id, **kw):
''' Function called on AJAX request made by FlexGrid
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * int(rp)
except:
offset = 0
page = 1
rows = 25
data = DBSession.query(Outcall, CDR) \
.outerjoin(CDR, Outcall.uniqueid==CDR.uniqueid) \
.filter(Outcall.cust_id==cust_id)
total = 1 + data.count() / rows
column = getattr(Outcall, sidx)
data = data.order_by(getattr(column,sord)()).offset(offset).limit(rows)
rows = [
{ 'id' : a.Outcall.out_id, 'cell': outcall_row(a) } for a in data ]
return dict(page=page, total=total, rows=rows)
def __call__(self, environ, context):
try:
request.ip_addr = _get_ip_addr(environ)
# make sure that we update permissions each time we call controller
self._basic_security_checks()
#set globals for auth user
bearer_token = None
try:
# Request.authorization may raise ValueError on invalid input
type, params = request.authorization
except (ValueError, TypeError):
pass
else:
if type.lower() == 'bearer':
bearer_token = params
request.authuser = request.user = self._determine_auth_user(
request.GET.get('api_key'),
bearer_token,
session.get('authuser'),
)
log.info('IP: %s User: %s accessed %s',
request.ip_addr, request.authuser,
safe_unicode(_get_access_path(environ)),
)
return super(BaseController, self).__call__(environ, context)
except webob.exc.HTTPException as e:
return e
def fetch(self, page, rows, sidx='lastname', sord='asc', _search='false',
searchOper=None, searchField=None, searchString=None, **kw):
''' Function called on AJAX request made by Grid JS component
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * rows
except:
offset = 0
page = 1
rows = 25
pb = sorted(phonebook_list(request.identity['user'].user_id,
searchOper,
searchField,
searchString),
key = itemgetter(sidx),
reverse = True if sord=='desc' else False)
total = len(pb)/rows+1
data = [ { 'id' : b['pb_id'], 'cell': row(b) } for b in pb[offset:offset+rows] ]
return dict(page=page, total=total, rows=data)
def customer_fetch(self, page, rows, sidx, sord, cmp_id, **kw):
''' Function called on AJAX request made by FlexGrid
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * int(rows)
except:
offset = 0
page = 1
rows = 25
data = DBSession.query(Customer). \
filter(Customer.cmp_id==cmp_id). \
filter(Customer.active==True)
total = 1 + data.count() / rows
column = getattr(Customer, sidx if sidx!='name' else 'lastname')
data = data.order_by(getattr(column,sord)()).offset(offset).limit(rows)
rows = [ { 'id' : a.cust_id, 'cell': customer_row(a) } for a in data ]
return dict(page=page, total=total, rows=rows)
def send_email_to_user(self, msg):
# Query sender and password from email credential table
# Query mail_server,port,use_secure from the email setup table for curenly logged in user
# receiver: to be queried from users table
self.msg = msg
curr_user_id = session.get("userid")
# query users table to retrieve email address of currenlt logged in user
userRecord = DBSession.query(User.email_address).filter(User.user_name == curr_user_id).first()
if userRecord:
self.receivers = userRecord.email_address
emailservers = self.get_mailservers()
for eachmailserver in emailservers:
if eachmailserver:
self.mail_server = eachmailserver["MailSetup"].mail_server
self.port = int(eachmailserver["MailSetup"].port)
self.secure_type = int(eachmailserver["MailSetup"].use_secure)
self.cred_details = eachmailserver["Creds"].cred_details
self.password = self.cred_details["password"]
self.sender = self.cred_details["user_email"]
result = False
if self.secure_type == NONSECURE:
result = EmailManager().send_nonsecure(
self.mail_server, self.port, self.sender, self.receivers, msg
)
elif self.secure_type == TLS:
result = EmailManager().send_tls(
self.mail_server, self.port, self.sender, self.password, self.receivers, msg
)
else:
result = EmailManager().send_ssl(
self.mail_server, self.port, self.sender, self.password, self.receivers, msg
)
if result == True:
return "Test mail sent from " + eachmailserver["MailSetup"].mail_server
def fetch(self, page, rows, sidx='user_name', sord='asc', _search='false',
searchOper=None, searchField=None, searchString=None, **kw):
''' Function called on AJAX request made by FlexGrid
Fetch data from DB, return the list of rows + total + current page
'''
# Try and use grid preference
grid_rows = session.get('grid_rows', None)
if rows=='-1': # Default value
rows = grid_rows if grid_rows is not None else 25
# Save grid preference
session['grid_rows'] = rows
session.save()
rows = int(rows)
try:
page = int(page)
rows = int(rows)
offset = (page-1) * rows
except:
offset = 0
page = 1
rows = 25
sounds = DBSession.query(Sound)
total = sounds.count()/rows + 1
column = getattr(Sound, sidx)
sounds = sounds.order_by(getattr(column,sord)()).offset(offset).limit(rows)
rows = [ { 'id' : s.sound_id, 'cell': row(s) } for s in sounds ]
return dict(page=page, total=total, rows=rows)
def get_all_instance_categories(self):
try:
return self.csep_service.get_all_instance_categories_db(session.get('servicepoint_id'))
except Exception as ex:
print_traceback()
LOGGER.error(to_str(ex))
raise ex
def index(self, *args):
"""
Display a list of all plugins in BioScript
"""
# get BioScript Server url (usually from config file)
bs_server_url = tg.config.get('main.proxy') + '/'
# build request to send to BioScript server
bs_url = bs_server_url + 'plugins?ordered=true'
# get the operation list back
operation_list = urllib2.urlopen(bs_url).read()
# fields can be pre-filled
meth = 'get'
if len(args) > 0 and args[0] == 'prefill':
meth = 'get_prefill'
# get previous launched jobs taht are in the session
task_ids = session.get('task_ids', [])
jobs = []
if task_ids:
jobs = DBSession.query(Job).join(PluginRequest).filter(
Job.task_id.in_(task_ids)).order_by(
desc(PluginRequest.date_done)).all()
# serve result on visual_index.mak template file
return {
'oplist': operation_list,
'serv': bs_server_url,
'method': meth,
'jobs': jobs
}
def send_email_to_user(self, msg):
# Query sender and password from email credential table
# Query mail_server,port,use_secure from the email setup table for curenly logged in user
# receiver: to be queried from users table
self.msg = msg
curr_user_id = session.get('userid')
#query users table to retrieve email address of currenlt logged in user
userRecord = DBSession.query(User.email_address).filter(User.user_name == curr_user_id).first()
if userRecord:
self.receivers = userRecord.email_address
emailservers = self.get_mailservers()
for eachmailserver in emailservers:
if eachmailserver:
self.mail_server = eachmailserver['MailSetup'].mail_server
self.port = int(eachmailserver['MailSetup'].port)
self.secure_type = int(eachmailserver['MailSetup'].use_secure)
self.cred_details = eachmailserver['Creds'].cred_details
self.password = self.cred_details['password']
self.sender = self.cred_details['user_email']
result = False
if (self.secure_type== NONSECURE):
result = EmailManager().send_nonsecure(self.mail_server,self.port,self.sender,self.receivers,msg)
elif (self.secure_type== TLS):
result = EmailManager().send_tls(self.mail_server,self.port,self.sender,self.password,self.receivers,msg)
else:
result = EmailManager().send_ssl(self.mail_server,self.port,self.sender,self.password,self.receivers,msg)
if (result == True):
return "Test mail sent from " + eachmailserver['MailSetup'].mail_server
def edit(self, *args, **kw):
th_name = str(args[0])
session["th_name"] = th_name
session.save()
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@', 'AT')
if user_lab is None:
flash(
"Problem detected with your lab in session. Contact your administrator please",
'error')
raise redirect('/trackhubs')
complementary_path = str(
user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open(genome_path, 'r') as gen:
l = gen.readline()
while l != '':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
final_path = th_path + trackdb_path + "trackDb.txt"
with open(final_path, 'r') as final:
l = final.readline()
dic_colors = {}
cpt = 0
while l != '':
if l.startswith("\ttrack"):
track = l.split("\ttrack")[1].strip()
dic_colors[cpt] = track
cpt += 1
elif l.startswith("\tcolor"):
color = l.split("\tcolor")[1].strip()
dic_colors[cpt] = color
cpt += 1
l = final.readline()
t_length = len(dic_colors.keys())
edit_form = build_form_edit_th(t_length)(
action=url('/trackhubs/post_edit')).req()
for k, v in dic_colors.items():
#even --> track
if (k % 2 == 0):
edit_form.child.children[k].value = v
#odd --> color
else:
edit_form.child.children[k].value = v
return dict(page='trackhubs', widget=edit_form, value=kw)
else:
flash(
"Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.",
'error')
raise redirect('/trackhubs')
def login(self, came_from=url('/')):
"""Start the user login."""
if session.get('userid') is None and request.identity is not None:
self.redirect_to(url('/user_logout'))
# login_counter = request.environ['repoze.who.logins']
# if login_counter > 0:
# flash(_('Wrong credentials'), 'warning')
return dict(page='login',came_from=came_from)
def manually_resolve(self, workspace, **kw):
entity = session.get('entity')
return dict(
entity=entity['entity'],
values=entity,
workspace=workspace
)
def create_volume(self, name, size, zone, snapshot, vdc_name):
try:
csep_id = session.get('servicepoint_id')
return self.csep_service.create_volume(name, size, zone, snapshot, csep_id, vdc_name)
except Exception as ex:
print_traceback()
LOGGER.error(to_str(ex))
raise ex
def login(self, came_from=url('/')):
"""Start the user login."""
if session.get('userid') is None and request.identity is not None:
self.redirect_to(url('/user_logout'))
# login_counter = request.environ['repoze.who.logins']
# if login_counter > 0:
# flash(_('Wrong credentials'), 'warning')
return dict(page='login',came_from=came_from)
def searchlists_to_json(self, *args, **kw):
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
one_meas = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).first()
search_grid, hidden_positions, positions_not_searchable = build_search_grid(one_meas)
searchlists = json.dumps([hidden_positions, positions_not_searchable])
return searchlists
def mensajes(self, id):
""" imprime un mensaje flash"""
mensaje = session.get(id, "")
if (mensaje == ""):
flash(u"Relacionado exitósamente")
else:
flash(mensaje, "warning")
redirect("../../")
def _end_mex_session(self):
"""Close a mex associated with the visit to record changes"""
try:
mexuri = session.get('mex_uri')
if mexuri:
module_service.end_internal_mex(mexuri)
except AttributeError:
pass
return ""
def set_prefs(self, menu=None):
log.debug('menu -> %s' % menu)
if menu is not None:
grid_rows = session.get('grid_rows', None)
session['menu'] = menu
session.save()
return dict(status='ok')
def event(self, idevent, page):
"""
Affichage de l'historique d'un événement brut.
Pour accéder à cette page, l'utilisateur doit être authentifié.
@param idevent: identifiant de l'événement brut souhaité.
@type idevent: C{int}
@param page: numéro de la page à afficher.
@type page: C{int}
Cette méthode permet de satisfaire l'exigence
VIGILO_EXIG_VIGILO_BAC_0080.
"""
# Auto-supervision
self.get_failures()
user = get_current_user()
events = VigiboardRequest(user, False)
events.add_table(
Event,
events.items.c.hostname.label('hostname'),
events.items.c.servicename.label('servicename'),
)
events.add_join((EVENTSAGGREGATE_TABLE, \
EVENTSAGGREGATE_TABLE.c.idevent == Event.idevent))
events.add_join((CorrEvent, CorrEvent.idcorrevent == \
EVENTSAGGREGATE_TABLE.c.idcorrevent))
events.add_join((events.items,
Event.idsupitem == events.items.c.idsupitem))
events.add_filter(Event.idevent == idevent)
if events.num_rows() != 1:
flash(_('No such event or access denied'), 'error')
redirect('/')
events.format_events(0, 1)
events.generate_tmpl_context()
history = events.format_history()
# Pagination des résultats
items_per_page = int(session.get('items_per_page', config['vigiboard_items_per_page']))
page = paginate.Page(history, page=page, items_per_page=items_per_page)
event = events.req[0]
return dict(
idevent = idevent,
hostname = event.hostname,
servicename = event.servicename,
plugins_data = {},
page = page,
search_form = create_search_form,
search = {},
fixed_search = {},
)
def session(self):
sess = etree.Element('session',
uri=posixpath.join(self.uri, "session"))
if identity.not_anonymous():
#vk = tgidentity.current.visit_link.visit_key
#log.debug ("session_timout for visit %s" % str(vk))
#visit = Visit.lookup_visit (vk)
#expire = (visit.expiry - datetime.now()).seconds
#KGKif 'mex_auth' not in session:
#KGKlog.warn ("INVALID Session or session deleted: forcing logout on client")
#KGK return etree.tostring (sess)
#KGK #redirect ('/auth_service/logout_handler')
timeout = int(session.get('timeout', 0))
length = int(session.get('length', 0))
expires = session.get('expires', datetime(2100, 1, 1))
current_user = identity.get_user()
if current_user:
# Pylint misses type of current_user
# pylint: disable=no-member
etree.SubElement(sess,
'tag',
name='user',
value=data_service.uri() + current_user.uri)
etree.SubElement(sess,
'tag',
name='group',
value=",".join([
g.group_name
for g in current_user.get_groups()
]))
# https://stackoverflow.com/questions/19654578/python-utc-datetime-objects-iso-format-doesnt-include-z-zulu-or-zero-offset
etree.SubElement(sess,
'tag',
name='expires',
value=expires.isoformat() + 'Z')
etree.SubElement(sess, 'tag', name='timeout', value=str(timeout))
etree.SubElement(sess, 'tag', name='length', value=str(length))
return etree.tostring(sess)
def update(self, *args, **kw):
# Make sure passwords won't leak from session
session.setdefault('settings', password_dict({}))
# This is the first time this service is set up
first_time = self.name not in session['settings']
session['settings'].setdefault(self.name, {})
if 'password' in kw.get(self.name, {}):
if not kw[self.name]['password']:
logging.debug('Not updating %r password. No value given.',
self.name)
old_password = session['settings'][self.name].get('password')
kw[self.name]['password'] = old_password
# Check if actually changed settings
old_settings = copy.deepcopy(session['settings'][self.name])
new_settings = copy.deepcopy(kw.get(self.name))
# Don't include 'enable' in comparison
old_settings.pop('enable', None)
new_settings.pop('enable', None)
settings_changed = old_settings != new_settings
session['settings'].update(kw)
logging.debug('update: session: %r', session)
try:
session.get('skip', set()).remove(self.name)
except KeyError:
pass
session.save()
if settings_changed:
flash(_('Changes saved'))
if first_time:
# Pick the next uncofigured service
redirect(self.menu.base)
else:
redirect(self.url)
def updateIndicator(self, **kw):
#print kw;
df = loads(request.body, encoding=request.charset)
data = df['root']
years_id = session.get('years_id')
months_id = session.get('months_id')
for value in data:
print value['indicator_value']
#years_id = value['years_id'];
#months_id = value['months_id'];
indicators_service = str(
self.util.valueNull(value['indicators_service_id']))
indicators_detail_id = value['indicators_detail_id']
risk_section_id = value['risk_section_id']
indicator_value = value['indicator_value']
years_id = value['years_id']
if (len(indicators_service) == 0):
indicatorsService = app_model.IndicatorsService()
indicatorsService.indicators_detail_id = indicators_detail_id
indicatorsService.years_id = years_id
indicatorsService.months_id = months_id
indicatorsService.risk_section_id = risk_section_id
indicatorsService.indicator_value = indicator_value
log.info("save service indicators:")
indicatorsService.save()
else:
indicatorsService = app_model.IndicatorsService.getById(
indicators_service)
indicatorsService.indicator_value = indicator_value
log.info("update service indicators:")
#print request.POST['root'].getall();
#print request.GET.get['indicator_value'];
return dict(success=True, message="update success")
def post_logout(self, came_from=url('/')):
"""Redirect the user to the initially requested page on logout and say
goodbye as well."""
#flash(_('We hope to see you soon!'))
# sessionInfo = getSession()
# sessionInfo.logout()
try:
if session.get('username'):
UIUpdateManager().del_user_updated_entities(session['username'])
UIUpdateManager().del_user_updated_tasks(session['username'])
except Exception, e:
print_traceback()
LOGGER.error(to_str(e))
def __call__(self, environ, context):
try:
ip_addr = _get_ip_addr(environ)
self._basic_security_checks()
api_key = request.GET.get('api_key')
try:
# Request.authorization may raise ValueError on invalid input
type, params = request.authorization
except (ValueError, TypeError):
pass
else:
if type.lower() == 'bearer':
api_key = params # bearer token is an api key too
if api_key is None:
authuser = self._determine_auth_user(
session.get('authuser'),
ip_addr=ip_addr,
)
needs_csrf_check = request.method not in ['GET', 'HEAD']
else:
dbuser = User.get_by_api_key(api_key)
if dbuser is None:
log.info(
'No db user found for authentication with API key ****%s from %s',
api_key[-4:], ip_addr)
authuser = AuthUser.make(dbuser=dbuser,
is_external_auth=True,
ip_addr=ip_addr)
needs_csrf_check = False # API key provides CSRF protection
if authuser is None:
log.info('No valid user found')
raise webob.exc.HTTPForbidden()
# set globals for auth user
request.authuser = authuser
request.ip_addr = ip_addr
request.needs_csrf_check = needs_csrf_check
log.info(
'IP: %s User: %s Request: %s',
request.ip_addr,
request.authuser,
get_path_info(environ),
)
return super(BaseController, self).__call__(environ, context)
except webob.exc.HTTPException as e:
return e
def diff(self, prev_commit, fmt=None, prev_file=None, **kw):
'''
:param prev_commit: previous commit to compare against
:param fmt: "sidebyside", or anything else for "unified"
:param prev_file: previous filename, if different
:return:
'''
try:
path, filename = os.path.split(self._blob.path())
a_ci = c.app.repo.commit(prev_commit)
a = a_ci.get_path(prev_file or self._blob.path())
apath = a.path()
except Exception:
# prev commit doesn't have the file
a = M.repository.EmptyBlob()
apath = ''
b = self._blob
if not self._blob.has_html_view:
diff = "Cannot display: file marked as a binary type."
return dict(a=a, b=b, diff=diff)
# could consider making Blob.__iter__ do unicode conversion?
# py2 unified_diff can handle some unicode but not consistently, so best to do ensure_str (can drop it on py3)
la = [six.ensure_str(h.really_unicode(line)) for line in a]
lb = [six.ensure_str(h.really_unicode(line)) for line in b]
adesc = 'a' + h.really_unicode(apath)
bdesc = 'b' + h.really_unicode(b.path())
if not fmt:
fmt = web_session.get('diformat', '')
else:
web_session['diformat'] = fmt
web_session.save()
if fmt == 'sidebyside':
if max(a.size, b.size) > asint(
tg.config.get('scm.view.max_syntax_highlight_bytes',
500000)):
# have to check the original file size, not diff size, because difflib._mdiff inside HtmlSideBySideDiff
# can take an extremely long time on large files (and its even a generator)
diff = '<em>File too large for side-by-side view</em>'
else:
hd = HtmlSideBySideDiff()
diff = hd.make_table(la, lb, adesc, bdesc)
else:
# py2 unified_diff can handle some unicode but not consistently, so best to do str() and ensure_str()
# (can drop it on py3)
diff = str('').join(
difflib.unified_diff(la, lb, six.ensure_str(adesc),
six.ensure_str(bdesc)))
return dict(a=a, b=b, diff=diff)
def relacionar_ph(self, *args, **kw):
#recibe los elementos seleccionados en relacionar_item
#relaciona, y retorna. Ajax
id_item = UrlParser.parse_id(request.url, "items")
item = Item.por_id(id_item)
p_item = PropiedadItem.por_id(item.id_propiedad_item)
ids = []
id = None
if kw:
for k, pk in kw.items():
if not k.isalnum():
continue
ids.append(int(pk))
else:
try:
id = int(args[0])
if (id > 0):
ids.append(id)
except:
id = 0
flash(u"Argumento inválido", "warning")
retorno, creado = p_item.agregar_relaciones(ids, 'p-h')
if (creado
): #si por lo menos se pudo crear una relacion se guarda en el
#historial
usuario = Usuario.by_user_name(
request.identity['repoze.who.userid'])
item.guardar_historial(u"relacionar-PH", usuario)
mensaje = ""
if (retorno == u"" and not creado):
mensaje = u"No se crearon relaciones"
elif (retorno != u""):
mensaje = u"No se pudo crear la relación con %s" % retorno
#no sé como pasar strings como parámetro, fea solución
indice = session.get('indice_mensaje', 0)
session['indice_mensaje'] = indice + 1
session[str(indice)] = mensaje
if (id):
redirect('../mensajes/%d' % indice)
else:
transaction.commit()
#return "/items/%d/edit" % id_item
return './mensajes/%d' % indice
def post_edit(self, *args, **kw):
dic_colors = {}
th_name = session["th_name"]
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@', 'AT')
for key in kw.keys():
if key.startswith('Color_Track_'):
key_id = key.replace('Color_Track_', '')
dic_colors[int(key_id)] = kw[key] + "\n\n"
#paths...
complementary_path = str(
user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open(genome_path, 'r') as gen:
l = gen.readline()
while l != '':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
source_path = th_path + trackdb_path + "trackDb.txt"
final_path_tmp = th_path + trackdb_path + "trackDb_tmp.txt"
with open(source_path, 'r') as source:
with open(final_path_tmp, 'a') as destination:
l = source.readline()
color_cpt = 0
while l != '':
if l.startswith("\tcolor "):
color_cpt += 1
destination.write("\tcolor " +
dic_colors[color_cpt])
else:
destination.write(l)
l = source.readline()
# remove old file
os.remove(source_path)
# rename new one
os.rename(final_path_tmp, source_path)
flash("Trackhub edited !")
raise redirect("/trackhubs")
else:
flash(
"Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.",
'error')
raise redirect('/trackhubs')
def mark_resolved(self, list_to_new=None, list_to_old=None, **kw):
entity = session.get('entity')
if len(list_to_new) >= 1:
if len(list_to_old) >= 1:
# worst case, we have some objects that refer to new and other that refer ro old, need a clone
self._clone_and_modify_(entity, list_to_new)
else:
# we can just edit old object because no one refer more to old object
self._original_edit()
else:
# all objects refer to old, we can just edit old object
self._original_edit()
session.delete()
flash(_(u'All the conflicts are successfully resolved'))
return dict(errors=None)
def delete(self, *args, **kw):
th_name = str(args[0])
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
th_path = user_path + "/" + th_name
try:
shutil.rmtree(th_path)
flash("Your trackhub " + th_name + " was deleted.")
except:
flash(
"Error : your trackhub was not deleted. Contact the administrator please.",
'error')
raise redirect(url('/trackhubs'))
def add_storage_def_task(self, auth, site_id, group_id, node_id, type,
opts, op_level, sp_ids):
from tg import session
task_service = self.svc_central.get_service(self.task_service_id)
user_name = self._get_username(auth)
#get scan result
scan_result = session.get(constants.SCAN_RESULT)
t= AddStorageDefTask(u'Add Storage Definition', {}, [], dict(site_id=site_id, group_id=group_id,\
node_id=node_id, type=type, opts=opts, op_level=op_level, sp_ids=sp_ids,\
scan_result=scan_result), None, user_name)
t.set_entity_details(site_id)
task_service.submit_sync(t)
logger.debug("Add Storage Definition task submitted")
#remove scan result from session
session[constants.SCAN_RESULT] = None
session.save()
return t.task_id
def _original_edit(self):
params = session.get('entity')
params['_workspace'] = to_object_id(params.get('_workspace'))
params['_precondition'] = to_object_id(params.get('_precondition'))
entity = entity_from_id(params['_id'])
if (type(entity) is model.Precondition):
if entity.is_advanced:
params['condition'] = [to_object_id(__) if __ not in model.Precondition.PRECONDITION_OPERATOR else __ for __ in params['condition'] ]
else:
params['condition'][0] = ObjectId(params['condition'][0])
old_hash = entity['hash']
params.pop('entity', None)
for k, v in params.items():
setattr(entity, k, v)
DBSession.flush(entity)
entity.update_dependencies(old_hash)
return entity
def do_login(self, return_to=None, **kw):
location = '/'
if session.get('expired-username'):
if return_to and return_to not in plugin.AuthenticationProvider.pwd_expired_allowed_urls:
location = tg.url(
plugin.AuthenticationProvider.pwd_expired_allowed_urls[0],
dict(return_to=return_to))
else:
location = tg.url(
plugin.AuthenticationProvider.pwd_expired_allowed_urls[0])
elif return_to and return_to != request.url:
rt_host = urlparse(urljoin(config['base_url'], return_to)).netloc
base_host = urlparse(config['base_url']).netloc
if rt_host == base_host:
location = return_to
redirect(location)