def change_project_owner(self, p_id, new_owner_id, mail, key):
'''
Allow to change the owner of one given project (include its sample(s) and measurement(s))
'''
try:
p_target = DBSession.query(Projects).filter(Projects.id == p_id).first()
#just one lab by project, so the first is the good one
project_lab = p_target.labs[0]
new_owner = DBSession.query(User).filter(User.id == new_owner_id).first()
if project_lab in new_owner.labs:
list_samples = p_target.samples
for s in list_samples:
list_meas = s.measurements
for m in list_meas:
m.user_id = new_owner.id
DBSession.add(m)
DBSession.flush()
p_target.user_id = new_owner.id
DBSession.add(p_target)
DBSession.flush()
print "Update done."
else:
raise Exception("The new owner is not a member of this lab project. Impossible to continue the operation.")
except:
print_traceback()
def change_bis_sample(self, sending_s, reception_s):
'''
Allow to move all the measurements of one sample to an other one
and delete the sending sample after the operation.
Usefull for the "_bis" samples in spreadsheet.
@param principal : sending_s (sample id sending the measurements), reception_s (sample id receptioning the measurements)
'''
try:
# samples queries
from_sample = DBSession.query(Samples).filter(Samples.id == int(sending_s)).first()
to_sample = DBSession.query(Samples).filter(Samples.id == int(reception_s)).first()
# get the measurements lists
from_att = from_sample.attributs
to_att = to_sample.attributs
# lab checking
if from_att[0].lab_id != to_att[0].lab_id:
raise Exception("Samples from different labs. Impossible to move these measurements.")
# get list of measurements objects
meas_to_move = from_sample.measurements
meas_in_place = to_sample.measurements
# move the measurements
for m in meas_to_move:
if m not in meas_in_place:
(to_sample.measurements).append(m)
DBSession.delete(from_sample)
DBSession.add(to_sample)
DBSession.flush()
print "---> Sample " + sending_s + " was deleted and its measurements are now into the sample " + reception_s
except:
print_traceback()
def check_value_addition(self, list_type_att, dict_att_values_type,
dict_att_values_db, lab_id):
'''
Checking for value(s) addition
@param principal
@return an updated db
'''
for key_type in list_type_att:
for i in dict_att_values_type[key_type]:
#get the attribut and its value(s)
i_att = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id,
Attributs.key == key_type)).first()
#warning : i_att_value is a list !
i_att_value = DBSession.query(Attributs_values).filter(
and_(Attributs_values.attribut_id == i_att.id,
Attributs_values.value == i)).all()
try:
flag = False
if i not in dict_att_values_db[key_type] and i != "None":
for existant in i_att_value:
if existant.value == i and existant.deprecated == True:
existant.deprecated = False
DBSession.flush()
flag = True
if existant.value is None:
existant.deprecated = True
DBSession.flush()
if flag == False:
new_value = Attributs_values()
new_value.attribut_id = i_att.id
new_value.value = i
new_value.deprecated = False
DBSession.add(new_value)
DBSession.flush()
except Exception as e:
import sys, traceback
a, b, c = sys.exc_info()
traceback.print_exception(a, b, c)
print "--- error login.py check_value_addition() ---"
print "i --->", i
print "key_type --->", key_type
print "list_type_att --->", list_type_att
print "dict_att_values_type[key_type] -->", dict_att_values_type[
key_type]
print "i_att --> ", i_att
print "i_att_value", i_att_value
def post(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
p = Projects()
if kw['project_name'] == '':
flash("Bad Project : Your project must have a name", "error")
raise redirect("./new")
p.project_name = kw['project_name']
p.user_id = user.id
p.description = kw.get('description', None)
(p.labs).append(lab)
DBSession.add(p)
DBSession.flush()
flash("Project created !")
raise redirect('/projects')
def create_ext_lab(self, mail, key, lab_name):
#utilisation (only for admins) :
#wget --post-data "[email protected]&key=xxxxxxxxxxx&lab_name=bbcf" http://yourdomain.com/biorepo/create_ext_lab
lab_test = DBSession.query(Labs).filter(Labs.name == lab_name).first()
if lab_test is None:
try:
lab = Labs()
lab.name = lab_name
lab.path_raw = path_raw(lab_name)
lab.path_processed = path_processed(lab_name)
lab.path_tmp = path_tmp(lab_name)
DBSession.add(lab)
DBSession.flush()
print "Exterior lab created :", lab_name
except:
print_traceback()
print "Exterior lab NOT created --> ERROR"
else:
print "This lab : ", str(lab_name), " is in the db yet. --> ERROR"
def create_gone_user(self, mail, key, lab_id, firstname, name, user_mail):
#utilisation (only for admins) :
#wget --post-data "key=xxxxxxxxxxxxxxxxxxxxx&[email protected]&lab_id=lab_id&firstname=jean-michel&name=michel&[email protected]" \
# http://yourdomain.com/biorepo/create_gone_user
try:
user = User()
user.firstname = firstname.capitalize()
user.name = name.capitalize()
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
user.labs.append(lab)
user._email = user_mail
group = DBSession.query(Group).filter(Group.id == 1).first()
user.groups.append(group)
DBSession.add(user)
DBSession.flush()
print "Gone/Exterior user created :", user
except:
print_traceback()
print "Gone/Exterior user NOT created --> ERROR"
def check_value_addition(self, list_type_att, dict_att_values_type, dict_att_values_db, lab_id):
'''
Checking for value(s) addition
@param principal
@return an updated db
'''
for key_type in list_type_att:
for i in dict_att_values_type[key_type]:
#get the attribut and its value(s)
i_att = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == key_type)).first()
#warning : i_att_value is a list !
i_att_value = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == i_att.id,
Attributs_values.value == i)).all()
try:
flag = False
if i not in dict_att_values_db[key_type] and i != "None":
for existant in i_att_value:
if existant.value == i and existant.deprecated == True:
existant.deprecated = False
DBSession.flush()
flag = True
if existant.value is None:
existant.deprecated = True
DBSession.flush()
if flag == False:
new_value = Attributs_values()
new_value.attribut_id = i_att.id
new_value.value = i
new_value.deprecated = False
DBSession.add(new_value)
DBSession.flush()
except Exception as e:
import sys, traceback
a, b, c = sys.exc_info()
traceback.print_exception(a, b, c)
print "--- error login.py check_value_addition() ---"
print "i --->", i
print "key_type --->", key_type
print "list_type_att --->", list_type_att
print "dict_att_values_type[key_type] -->", dict_att_values_type[key_type]
print "i_att --> ", i_att
print "i_att_value", i_att_value
def create(self, *args, **kw):
user = handler.user.get_user_in_session(request)
project = Projects()
name = kw.get('project_name', None)
if name is None:
return {'ERROR': "You have to give a name to your project"}
project.project_name = name
lab_id = kw['lab']
if lab_id is None:
return {'ERROR': "We need to know the user's lab"}
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
(project.labs).append(lab)
#test if user is an admin
admin = isAdmin(user)
if admin:
project.user_id = kw.get('user_id', user.id)
else:
project.user_id = user.id
project.description = kw.get('description', None)
get_samples = kw.get('samples', None)
l = []
if get_samples is None:
project.samples = l
else:
for x in get_samples.split(','):
sam = DBSession.query(Samples).join(Projects).join(User).filter(Samples.id == x).first()
l.append(sam)
project.samples = l
#checking print
print project, " building project with wget"
DBSession.add(project)
DBSession.flush()
return {"user_id": user.id, "user_name": user.name, "project_id": project.id, "project_name": project.project_name,
"description": project.description}
def manage_fu_from_HTS(existing_fu, meas, filename, sha1, url_path, hts_path):
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE FROM HTS--------"
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
fu.path = hts_path
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
else:
fu.extension = "not specified"
fu.sha1 = sha1
fu.url_path = url_path
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
return fu
def manage_fu_from_HTS(existing_fu, meas, filename, sha1, url_path, hts_path):
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE FROM HTS--------"
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
fu.path = hts_path
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
else:
fu.extension = "not specified"
fu.sha1 = sha1
fu.url_path = url_path
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
return fu
def create(self, *args, **kw):
user = handler.user.get_user_in_session(request)
kw['user'] = user.id
lab = kw.get("lab", None)
if lab is None:
return {"ERROR": "We need to know the lab of the user..."}
sample = Samples()
if not kw.has_key('project_id'):
return {"ERROR": "project_id missing"}
type_ = kw.get('type', None)
sample.project_id = kw['project_id']
sample.name = kw.get('name', 'Give me a name please')
if type_ is not None:
try:
ret1 = list_lower(type_, get_list_types(lab))
sample.type = ret1
except:
return {"ERROR": "your " + type_ + " is not known in types list"}
elif type_ is None:
sample.type = type_
sample.protocole = kw.get('protocole', None)
get_meas = kw.get('measurements', None)
l = []
if get_meas is None:
sample.measurements = l
else:
for x in get_meas.split(','):
meas = DBSession.query(Measurements).filter(Measurements.id == x).first()
l.append(meas)
sample.measurements = l
#print server
print sample, "building sample with wget"
#dynamicity
list_static = ['project', 'name', 'type', 'protocole', 'measurements', 'lab', 'user', 'key', 'mail', 'project_id']
list_dynamic = []
labo = DBSession.query(Labs).filter(Labs.name == lab).first()
lab_id = labo.id
#save the attributs of the lab for final comparison
dynamic_keys = []
lab_attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.deprecated == False, Attributs.owner == "sample")).all()
for i in lab_attributs:
dynamic_keys.append(i.key)
for x in kw:
#exclude the static fields belonging to Samples()
if x not in list_static:
list_dynamic.append(x)
#get the attribut
a = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == x, Attributs.deprecated == False, Attributs.owner == "sample")).first()
if a is not None:
#get its value(s)
(sample.attributs).append(a)
#if values of the attribute are fixed
if a.fixed_value == True and kw[x] is not None and kw[x] != '' and a.widget != "checkbox" and a.widget != "hiding_checkbox":
value = kw[x]
list_value = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == a.id, Attributs_values.deprecated == False)).all()
for v in list_value:
#if the keyword value is in the value list, the attributs_values object is saved in the cross table
if (v.value).lower() == value.lower() and v not in sample.a_values:
(sample.a_values).append(v)
DBSession.flush()
#if values of the attribute are free
elif a.fixed_value == False and a.widget != "checkbox" and a.widget != "hiding_checkbox":
av = Attributs_values()
av.attribut_id = a.id
av.value = kw.get(x, None)
av.deprecated = False
DBSession.add(av)
DBSession.flush()
(sample.a_values).append(av)
DBSession.flush()
#special case for checkbox because of the "on" and None value of TW2 for True and False...(here it's True)
elif a.widget == "checkbox" or a.widget == "hiding_checkbox":
#Why 3 ? Because 3 cases max registred : True, False and None ---> so <3
if len(a.values) < 3:
av = Attributs_values()
av.attribut_id = a.id
#for True value, Attribut key and value have to be similar into the excel sheet...
if (kw[x]).lower() == x.lower():
av.value = True
#...and different for the False :)
else:
av.value = False
av.deprecated = False
DBSession.add(av)
DBSession.flush()
(sample.a_values).append(av)
DBSession.flush()
else:
if (kw[x]).lower() == x.lower():
for v in a.values:
if check_boolean(v.value) and v.value is not None:
(sample.a_values).append(v)
else:
for v in a.values:
if check_boolean(v.value) == False and v.value is not None:
(sample.a_values).append(v)
DBSession.flush()
#to take in account the empty dynamic fields in the excel sheet
for k in dynamic_keys:
if k not in list_dynamic:
print k, " -------------------- NOT FOUND IN SAMPLE DESCRIPTION EXCEL SHEET"
a = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == k, Attributs.deprecated == False, Attributs.owner == "sample")).first()
(sample.attributs).append(a)
DBSession.flush()
DBSession.add(sample)
DBSession.flush()
return {"sample": sample, "measurements": l}
def manage_fu(existing_fu, meas, public_dirname, filename, sha1, up_data, url_path, url_up, dest_raw, dest_processed, tmp_path, lab):
tmpdir_to_delete = os.path.abspath(os.path.join(tmp_path, os.path.pardir))
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE --------"
#create symbolic link
source = existing_fu.path + "/" + sha1
if meas.type:
dest = dest_raw + sha1
#test symlin existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
#test symlink existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
flash(symlink_e + ", measurement created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
#raise redirect("./")
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
#raw test for path orientation
if meas.type:
fu.path = path_raw(lab)
data_dirname = os.path.join(public_dirname, fu.path)
else:
fu.path = path_processed(lab)
data_dirname = os.path.join(public_dirname, fu.path)
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
# root, ext = os.path.splitext(filename)
# DOUBLE_EXTENSIONS = ['tar.gz','tar.bz2','bedGraph.gz','bed.gz']
# if any([filename.endswith(x) for x in DOUBLE_EXTENSIONS]):
# root, first_ext = os.path.splitext(root)
# ext = first_ext + ext
# fu.extension = ext
# else:
# fu.extension = ext
else:
fu.extension = "not specified"
data_path = os.path.join(data_dirname, str(sha1))
fu.sha1 = sha1
fu.url_path = url_path
#writing the file into the server HD
#version browser
try:
with open(data_path, "w") as d:
if up_data is not None:
d.write(up_data.value)
elif url_path is not None and url_up:
u = urllib2.urlopen(url_path)
while True:
buffer = u.read(8192)
if not buffer:
break
d.write(buffer)
else:
print "ERROR"
#version commandline
except:
shutil.move(tmp_path, data_path)
#symlink
source = data_path
if meas.type:
dest = dest_raw + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
if meas.type:
flash(symlink_e + ", raw data was successfully created")
else:
flash(symlink_e + ", processed data was successfully created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
return fu
def manage_fu(existing_fu, meas, public_dirname, filename, sha1, up_data,
url_path, url_up, dest_raw, dest_processed, tmp_path, lab):
tmpdir_to_delete = os.path.abspath(os.path.join(tmp_path, os.path.pardir))
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE --------"
#create symbolic link
source = existing_fu.path + "/" + sha1
if meas.type:
dest = dest_raw + sha1
#test symlin existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
#test symlink existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
flash(symlink_e + ", measurement created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
#raise redirect("./")
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
#raw test for path orientation
if meas.type:
fu.path = path_raw(lab)
data_dirname = os.path.join(public_dirname, fu.path)
else:
fu.path = path_processed(lab)
data_dirname = os.path.join(public_dirname, fu.path)
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
# root, ext = os.path.splitext(filename)
# DOUBLE_EXTENSIONS = ['tar.gz','tar.bz2','bedGraph.gz','bed.gz']
# if any([filename.endswith(x) for x in DOUBLE_EXTENSIONS]):
# root, first_ext = os.path.splitext(root)
# ext = first_ext + ext
# fu.extension = ext
# else:
# fu.extension = ext
else:
fu.extension = "not specified"
data_path = os.path.join(data_dirname, str(sha1))
fu.sha1 = sha1
fu.url_path = url_path
#writing the file into the server HD
#version browser
try:
with open(data_path, "w") as d:
if up_data is not None:
d.write(up_data.value)
elif url_path is not None and url_up:
u = urllib2.urlopen(url_path)
while True:
buffer = u.read(8192)
if not buffer:
break
d.write(buffer)
else:
print "ERROR"
#version commandline
except:
shutil.move(tmp_path, data_path)
#symlink
source = data_path
if meas.type:
dest = dest_raw + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
if meas.type:
flash(symlink_e + ", raw data was successfully created")
else:
flash(symlink_e + ", processed data was successfully created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
return fu
def auth(self, came_from='/', **kw):
'''
Fetch user back from tequila.
Validate the key from tequila.
Log user.
'''
if not kw.has_key('key'):
raise redirect(came_from)
# take parameters
key = kw.get('key')
environ = request.environ
authentication_plugins = environ['repoze.who.plugins']
identifier = authentication_plugins['ticket']
secret = identifier.secret
cookiename = identifier.cookie_name
remote_addr = environ['REMOTE_ADDR']
# get user
principal = tequila.validate_key(key, 'tequila.epfl.ch')
if principal is None:
raise redirect('./login')
#in case of user gets several labs
try:
if session["first_passage"] == False:
#second passage
tmp_user = session["tmp_user"]
tmp_lab = session['tmp_lab']
except:
#first passage
session["first_passage"] = True
session["principal_tequila"] = principal
session.save()
tmp_user, tmp_lab = self.build_user(principal)
try:
mail = tmp_user.email
except:
flash("Sorry, you've been disconnected. You can try to relog yourself now", 'error')
raise redirect('/login/out')
# log or create him
user = DBSession.query(User).filter(User.email == tmp_user.email).first()
if user is None:
user_group = DBSession.query(Group).filter(Group.name == gl.group_users).first()
user_group.users.append(tmp_user)
DBSession.add(tmp_user)
DBSession.flush()
user = DBSession.query(User).filter(User.email == mail).first()
flash(u'Your account has been created %s' % (user.firstname + ' ' + user.name, ))
DBSession.flush()
print "######################"
print "key user :"******"######################"
print "key user :"******"######################"
print "key user :"******"lab created : ", lab
else:
if lab not in user.labs:
lab.users.append(user)
DBSession.flush()
print "lab existing : ", lab
#create attributs / check existing attributs
attributs = DBSession.query(Attributs).filter(Attributs.lab_id == lab.id).all()
if len(attributs) == 0:
attributs = None
lab_id = lab.id
#parsing "unit".ini
config = ConfigParser.RawConfigParser()
config.read(path_conf_unit(lab.name))
list_sample_att = (config.get('samples_attributs:main', 'keys')).split(',')
list_sample_hiding = (config.get('samples_hiding:main', 'keys')).split(',')
if len(list_sample_hiding) == 1 and list_sample_hiding[0] == '':
list_sample_hiding = ''
list_measurement_att = (config.get('meas_attributs:main', 'keys')).split(',')
list_meas_hiding = (config.get('meas_hiding:main', 'keys')).split(',')
if len(list_meas_hiding) == 1 and list_meas_hiding[0] == '':
list_meas_hiding = ''
list_searchable = (config.get('searchable_attributs:main', 'keys')).split(',')
list_deprecated = (config.get('deprecated_attributs:main', 'keys')).split(',')
dict_att_values_sample = {}
dict_att_values_meas = {}
dict_widgets_sample_att = {}
dict_widgets_meas_att = {}
dict_hiding_s_att = {}
dict_hiding_m_att = {}
for x in list_sample_att:
dict_att_values_sample[x] = (config.get('samples_attributs:' + x, x)).split(',')
dict_widgets_sample_att[x] = (config.get('samples_attributs:' + x, 'widget')).split(',')
for x in list_measurement_att:
dict_att_values_meas[x] = (config.get('meas_attributs:' + x, x)).split(',')
dict_widgets_meas_att[x] = (config.get('meas_attributs:' + x, 'widget')).split(',')
#to build the search page
search_fields_to_display = (config.get('search_grid_fields:main', 'keys')).split(',')
session["search_grid_fields"] = search_fields_to_display
#hidingradiobutton lists
#samples
if isinstance(list_sample_hiding, list):
for x in list_sample_hiding:
dic_mapping = {}
list_possibilities = (config.get('samples_attributs:' + x, x)).split(',')
for p in list_possibilities:
attribs_by_poss = (config.get('samples_attributs:' + x, p + "_mapping")).split(',')
dic_mapping[p] = attribs_by_poss
dict_hiding_s_att[x] = dic_mapping
if len(dict_hiding_s_att.keys()) > 0:
session["hiding_sample"] = dict_hiding_s_att
else:
session["hiding_sample"] = {}
#measurements
if isinstance(list_meas_hiding, list):
for x in list_meas_hiding:
dic_mapping = {}
list_possibilities = (config.get('meas_attributs:' + x, x)).split(',')
for p in list_possibilities:
attribs_by_poss = (config.get('meas_attributs:' + x, p + "_mapping")).split(',')
dic_mapping[p] = attribs_by_poss
dict_hiding_m_att[x] = dic_mapping
if len(dict_hiding_m_att.keys()) > 0:
session["hiding_meas"] = dict_hiding_m_att
else:
session["hiding_meas"] = {}
session.save()
#creating fixed values list
list_fixed_values_samples = []
list_fixed_values_meas = []
fixed_value_case = ['singleselectfield', 'multiselectfield', 'hiding_singleselectfield', 'hiding_multiselectfield']
for fix_s in list_sample_att:
for i in dict_att_values_sample[fix_s]:
if i != "None":
if fix_s not in list_fixed_values_samples:
list_fixed_values_samples.append(fix_s)
for fix_m in list_measurement_att:
for i in dict_att_values_meas[fix_m]:
if i != "None":
if fix_m not in list_fixed_values_meas:
list_fixed_values_meas.append(fix_m)
print list_fixed_values_samples, "<--- fixed sample"
print list_fixed_values_meas, "<---- fixed meas"
if attributs is None:
#########################################
###### creating samples attributs #######
#########################################
for s in list_sample_att:
#TODO virer cast str
widget = str(dict_widgets_sample_att[s])
owner_widget = "sample"
attribut = self.build_attribut(s, lab_id, list_fixed_values_samples, list_searchable, list_deprecated, widget, owner_widget)
DBSession.add(attribut)
DBSession.flush()
if attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
#### creating measurements attributs ####
#########################################
for m in list_measurement_att:
widget = str(dict_widgets_meas_att[m])
owner_widget = "measurement"
attribut = self.build_attribut(m, lab_id, list_fixed_values_meas, list_searchable, list_deprecated, widget, owner_widget)
DBSession.add(attribut)
DBSession.flush()
if attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
####### for samples #######
#########################################
dict_fixed_values_samples = {}
list_attributs_samples_values = self.build_attribut_value('samples_attributs:', lab_id, dict_fixed_values_samples, list_fixed_values_samples, config)
for att_v in list_attributs_samples_values:
DBSession.add(att_v)
DBSession.flush()
#########################################
###### for measurements #######
#########################################
dict_fixed_values_meas = {}
list_attributs_meas_values = self.build_attribut_value('meas_attributs:', lab_id, dict_fixed_values_meas, list_fixed_values_meas, config)
for att_v in list_attributs_meas_values:
DBSession.add(att_v)
DBSession.flush()
#check if there is a new key (or several...) in the config file of the lab
else:
list_existant_keys = []
print list_searchable, "-------------searchable"
for k in attributs:
list_existant_keys.append(str(k.key))
for att_s in list_sample_att:
att_s = unicode(att_s)
if att_s not in list_existant_keys:
#########################################
###### creating samples attributs #######
#########################################
widget = str(dict_widgets_sample_att[att_s])
owner_widget = "sample"
new_sample_attribut = self.build_attribut(att_s, lab_id, list_fixed_values_samples, list_searchable, list_deprecated, widget, owner_widget)
print new_sample_attribut
DBSession.add(new_sample_attribut)
DBSession.flush()
if new_sample_attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(new_sample_attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
####### for samples #######
#########################################
dict_fixed_values_samples = {}
list_attributs_samples_values = self.build_attribut_value('samples_attributs:', lab_id, dict_fixed_values_samples, list_fixed_values_samples, config)
for att_v in list_attributs_samples_values:
DBSession.add(att_v)
DBSession.flush()
#check widgets type
att_2_check = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == att_s, Attributs.owner == "sample")).first()
wid_sample_tmp = dict_widgets_sample_att[att_s]
for w_s in wid_sample_tmp:
if w_s != att_2_check.widget:
in_db_before = att_2_check.widget
in_db_now = w_s
att_2_check.widget = w_s
if in_db_before in fixed_value_case and in_db_now not in fixed_value_case:
att_2_check.fixed_value = False
elif in_db_before not in fixed_value_case and in_db_now in fixed_value_case:
att_2_check.fixed_value = True
DBSession.flush()
#check and update search buttons
if att_2_check is None:
print att_s, "not in db"
if att_2_check is not None and not att_2_check.searchable and att_2_check.key in list_searchable:
att_2_check.searchable = True
DBSession.flush()
elif att_2_check is not None and att_2_check.searchable and att_2_check.key not in list_searchable:
att_2_check.searchable = False
DBSession.flush()
for att_m in list_measurement_att:
att_m = unicode(att_m)
if att_m not in list_existant_keys:
#########################################
#### creating measurements attributs ####
#########################################
#TODO virer cast str
widget = str(dict_widgets_meas_att[att_m])
owner_widget = "measurement"
new_meas_attribut = self.build_attribut(att_m, lab_id, list_fixed_values_meas, list_searchable, list_deprecated, widget, owner_widget)
DBSession.add(new_meas_attribut)
DBSession.flush()
if new_meas_attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(new_meas_attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
###### for measurements #######
#########################################
dict_fixed_values_meas = {}
list_attributs_meas_values = self.build_attribut_value('meas_attributs:', lab_id, dict_fixed_values_meas, list_fixed_values_meas, config)
for att_v in list_attributs_meas_values:
DBSession.add(att_v)
DBSession.flush()
#check the widgets
att_2_check = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == att_m, Attributs.owner == "measurement")).first()
wid_meas_tmp = dict_widgets_meas_att[att_m]
for w_m in wid_meas_tmp:
if w_m != att_2_check.widget:
in_db_before = att_2_check.widget
in_db_now = w_m
att_2_check.widget = w_m
if in_db_before in fixed_value_case and in_db_now not in fixed_value_case:
att_2_check.fixed_value = False
elif in_db_before not in fixed_value_case and in_db_now in fixed_value_case:
att_2_check.fixed_value = True
DBSession.flush()
#check and update search buttons
if att_2_check is None:
print att_m, "not in db"
if att_2_check is not None and not att_2_check.searchable and att_2_check.key in list_searchable:
att_2_check.searchable = True
DBSession.flush()
elif att_2_check is not None and att_2_check.searchable and att_2_check.key not in list_searchable:
att_2_check.searchable = False
DBSession.flush()
#if lab choose to delete an attributs (or undelete a key...)
#Attributs obj have to stay into the db but user can not add others Attributs() with this key --> deprecated == True
not_deprecated_in_db = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.deprecated == False)).all()
for k in not_deprecated_in_db:
if k.key in list_deprecated:
k.deprecated = True
DBSession.add(k)
DBSession.flush()
deprecated_in_db = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.deprecated == True)).all()
for k in deprecated_in_db:
if k.key not in list_deprecated:
k.deprecated = False
DBSession.add(k)
DBSession.flush()
#test if deleted attributs_values
#build a dictionnary to fast check what is into db
dict_att_values_db = {}
for a in attributs:
#dict_att_values_db[a.key] = empty_list
list_tmp = []
for v in a.values:
if v.deprecated == False:
try:
list_tmp.append(str(v.value))
except:
list_tmp.append(v.value)
if len(list_tmp) == 0:
list_tmp = [None]
dict_att_values_db[str(a.key)] = list_tmp
#You have to check deletion BEFORE addition
#checking attribut value(s) deletion(s) in samples attributs
self.check_value_deletion(list_sample_att, dict_att_values_sample, dict_att_values_db, lab_id)
#checking attribut value(s) deletion(s) in measurements attributs
self.check_value_deletion(list_measurement_att, dict_att_values_meas, dict_att_values_db, lab_id)
#checking attribut value(s) addition in sample attributs
self.check_value_addition(list_sample_att, dict_att_values_sample, dict_att_values_db, lab_id)
#checking attribut value(s) addition in measurements attributs
self.check_value_addition(list_measurement_att, dict_att_values_meas, dict_att_values_db, lab_id)
# look if an user is admin or not
admins = tg.config.get('admin.mails')
group_admins = DBSession.query(Group).filter(Group.name == gl.group_admins).first()
if user.email in admins:
user not in group_admins.users and group_admins.users.append(user)
else:
user in group_admins.users and group_admins.users.remove(user)
DBSession.flush()
# create the authentication ticket
user = DBSession.query(User).filter(User.email == mail).first()
userdata = str(user.id)
ticket = auth_tkt.AuthTicket(
secret, user.email, remote_addr, tokens=token,
user_data=userdata, time=None, cookie_name=cookiename,
secure=True)
val = ticket.cookie_value()
# set it in the cookies
response.set_cookie(
cookiename,
value=val,
max_age=None,
path='/',
domain=None,
secure=False,
httponly=False,
comment=None,
expires=None,
overwrite=False)
#transaction.commit()
extern_meas = session.get("extern_meas", False)
check_tequila = session.get("check_tequila", False)
if extern_meas is False and check_tequila is False:
raise redirect(came_from)
elif extern_meas is False and check_tequila:
raise redirect("/search")
else:
del session["extern_meas"]
raise redirect(url('/measurements/external_add'))
def post(self, *args, **kw):
user_lab = session.get("current_lab", None)
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
lab_id = lab.id
s = Samples()
list_static = ['project', 'name', 'type', 'protocole']
list_dynamic = []
#new sample object
if 'project' not in kw:
flash("You have to choose a project to attach to your new sample, retry please", "error")
raise redirect('./')
s.project_id = kw['project']
#TODO : make a correct validator for NewSample
if kw['name'] == '':
flash("Bad Sample : you have to give a name to your sample", "error")
raise redirect('./new')
s.name = kw['name']
s.type = kw.get('type', None)
s.protocole = kw.get('protocole', None)
DBSession.add(s)
DBSession.flush()
#link the new sample to the attributs object
for x in kw:
#exclude the static fields belonging to Samples()
if x not in list_static:
list_dynamic.append(x)
#get the attribut
a = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == x, Attributs.deprecated == False, Attributs.owner == "sample")).first()
if a is not None:
#get its value(s)
(s.attributs).append(a)
#if values of the attribute are fixed
if a.fixed_value == True and kw[x] is not None and kw[x] != '' and a.widget != "checkbox" and a.widget != "hiding_checkbox":
value = kw[x]
list_value = DBSession.query(Attributs_values).filter(Attributs_values.attribut_id == a.id).all()
for v in list_value:
#if the keyword value is in the value list, the attributs_values object is saved in the cross table
if v.value == value and v not in s.a_values:
(s.a_values).append(v)
DBSession.flush()
#if values of the attribute are free
elif a.fixed_value == False and a.widget != "checkbox" and a.widget != "hiding_checkbox":
av = Attributs_values()
av.attribut_id = a.id
av.value = kw.get(x, None)
av.deprecated = False
DBSession.add(av)
DBSession.flush()
(s.a_values).append(av)
DBSession.flush()
#special case for checkbox because of the "on" and None value of TW2 for True and False...(here it's True)
elif a.widget == "checkbox" or a.widget == "hiding_checkbox":
found = False
for v in a.values:
if check_boolean(v.value) and v.value is not None:
(s.a_values).append(v)
found = True
if not found:
av = Attributs_values()
av.attribut_id = a.id
av.value = True
av.deprecated = False
DBSession.add(av)
DBSession.flush()
(s.a_values).append(av)
DBSession.flush()
#special case for checkbox because of the "on" and None value of TW2 for True and False...(here it's False)
dynamic_booleans = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.deprecated == False, Attributs.owner == "sample", or_(Attributs.widget == "checkbox", Attributs.widget == "hiding_checkbox"))).all()
if len(dynamic_booleans) > 0:
for d in dynamic_booleans:
if d.key not in list_dynamic:
if d.widget == "checkbox" or d.widget == "hiding_checkbox":
found = False
for v in d.values:
if not check_boolean(v.value) and v.value is not None:
(s.attributs).append(d)
(s.a_values).append(v)
found = True
#to avoid IntegrityError in the db
break
if not found:
av = Attributs_values()
av.attribut_id = d.id
av.value = False
av.deprecated = False
DBSession.add(av)
DBSession.flush()
(s.attributs).append(d)
(s.a_values).append(av)
DBSession.flush()
flash("Sample created !")
raise redirect('/samples')
def post_edit(self, *args, **kw):
id_sample = kw['IDselected']
sample = DBSession.query(Samples).filter(Samples.id == id_sample).first()
try:
project_id = kw.get("project")
if project_id is None or project_id == "":
flash("Edition rejected : Your sample must be in a project", 'error')
raise redirect("./")
sample.project_id = project_id
except:
flash("Your sample must be in a project", 'error')
raise redirect("./")
if kw['name'] == '' or kw['name'] is None:
flash("Bad Sample : you have to give a name to your sample", "error")
raise redirect("./edit/" + id_sample)
sample.name = kw.get("name", None)
sample.protocole = kw.get("protocole", None)
sample.type = kw.get("type", None)
meas_ids = kw.get("measurements", None)
if meas_ids is not None:
if not isinstance(meas_ids, (list, tuple)):
meas_ids = [int(meas_ids)]
else:
#from unicode to integer for comparison
list_tmp = []
for i in meas_ids:
i = int(i)
list_tmp.append(i)
meas_ids = list_tmp
else:
meas_ids = []
list_meas = []
for m in meas_ids:
measurement = DBSession.query(Measurements).filter(Measurements.id == m).first()
list_meas.append(measurement)
sample.measurements = list_meas
#DYNAMICITY
list_static = ['project', 'name', 'type', 'protocole', 'IDselected', 'measurements']
list_attributs = []
list_a_values = sample.a_values
for a in sample.attributs:
if a.deprecated == False:
list_attributs.append(a)
for x in kw:
if x not in list_static:
for a in list_attributs:
if x == a.key:
val_kw = kw[x]
object_2_delete = None
#search if the field was edited
for v in list_a_values:
v_value = v.value
if a.widget == "checkbox" or a.widget == "hiding_checkbox":
val_kw = check_boolean(kw[x])
v_value = check_boolean(v.value)
if v.attribut_id == a.id and v_value != val_kw and a.widget != "multipleselectfield" and a.widget != "hiding_multipleselectfield":
object_2_delete = v
if a.widget == "textfield" or a.widget == "hiding_textfield" or a.widget == "textarea" or a.widget == "hiding_textarea":
if object_2_delete:
object_2_delete.value = kw[x]
elif a.widget == "checkbox" or a.widget == "hiding_checkbox":
if len(a.values) < 3:
for old_v in a.values:
if old_v.value is not None and old_v.value != '':
list_a_values.remove(old_v)
av = Attributs_values()
av.attribut_id = a.id
av.value = True
av.deprecated = False
DBSession.add(av)
list_a_values.append(av)
DBSession.flush()
elif len(a.values) == 3:
if object_2_delete:
list_a_values.remove(object_2_delete)
v = object_2_delete.value
for val in a.values:
val_to_avoid = [None, ""]
if v not in val_to_avoid:
val_to_avoid.append(v)
if val.value not in val_to_avoid:
list_a_values.append(val)
DBSession.flush()
else:
print "----- BOOLEAN ERROR -----"
print str(a.id), " attributs id"
print "boolean with more than 2 values"
raise
elif a.widget == "singleselectfield" or a.widget == "hiding_singleselectfield":
#edition : delete the connexion to the older a_value, make the connexion between the new a_value and the sample
if object_2_delete:
list_a_values.remove(object_2_delete)
list_possible = a.values
for p in list_possible:
if p.value == kw[x]:
list_a_values.append(p)
#if the value was "None", just add the new value edited
elif object_2_delete is None:
list_possible = a.values
for p in list_possible:
if p.value == kw[x]:
list_a_values.append(p)
elif a.widget == "multipleselectfield" or a.widget == "hiding_multipleselectfield":
#!!! NOT TESTED !!!
list_objects_2_delete = []
for v in list_a_values:
#warning : types of i and v.value have to be similar...
for i in kw[x]:
if v.attribut_id == a.id and v.value != i:
list_objects_2_delete.append(v)
if len(list_objects_2_delete) > 0:
for v in list_objects_2_delete:
list_a_values.remove(v)
if a.fixed_value == True:
to_add = DBSession.query(Attributs_values).filter(and_(Attributs_values.value == i, Attributs_values.attribut_id == a.id)).first()
list_a_values.append(to_add)
else:
#mutliple selected field can't be not a fixed value.
print "something wrong happenned - illogical - controller sample post_edit()"
raise
#special case for checkbox because of the "on" and None value of TW2 for True and False... (Here it's False)
lab = session.get('current_lab', None)
labo = DBSession.query(Labs).filter(Labs.name == lab).first()
lab_id = labo.id
dynamic_booleans = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.deprecated == False, Attributs.owner == "sample", or_(Attributs.widget == "checkbox", Attributs.widget == "hiding_checkbox"))).all()
if len(dynamic_booleans) > 0:
for b in dynamic_booleans:
if b.key not in kw:
list_value = b.values
#2 cases possibles
#1 : values are None and (True or False)
if len(list_value) == 2:
for v in list_value:
#1.1 : None and True
if v.value is not None:
val = check_boolean(v.value)
else:
val = None
if val == True:
list_a_values.remove(v)
av = Attributs_values()
av.attribut_id = b.id
av.value = False
av.deprecated = False
DBSession.add(av)
list_a_values.append(av)
DBSession.flush()
break
#1.2 : None and False
elif val == False:
#because nothing was edited for the field
pass
#2 : values are None, True and False
elif len(list_value) == 3:
for v in list_value:
if v.value is not None:
val = check_boolean(v.value)
else:
val = None
if val == True:
try:
list_a_values.remove(v)
except:
pass
elif val == False:
list_a_values.append(v)
elif len(list_value) > 3:
print "----- ERROR -----"
print str(b.key), " gets more than 3 values."
print "-----------------"
flash("Sample edited !")
raise redirect("./")
def auth(self, came_from='/', **kw):
'''
Fetch user back from tequila.
Validate the key from tequila.
Log user.
'''
if not kw.has_key('key'):
raise redirect(came_from)
# take parameters
key = kw.get('key')
environ = request.environ
authentication_plugins = environ['repoze.who.plugins']
identifier = authentication_plugins['ticket']
secret = identifier.secret
cookiename = identifier.cookie_name
remote_addr = environ['REMOTE_ADDR']
# get user
principal = tequila.validate_key(key, 'tequila.epfl.ch')
if principal is None:
raise redirect('./login')
#in case of user gets several labs
try:
if session["first_passage"] == False:
#second passage
tmp_user = session["tmp_user"]
tmp_lab = session['tmp_lab']
except:
#first passage
session["first_passage"] = True
session["principal_tequila"] = principal
session.save()
tmp_user, tmp_lab = self.build_user(principal)
try:
mail = tmp_user.email
except:
flash(
"Sorry, you've been disconnected. You can try to relog yourself now",
'error')
raise redirect('/login/out')
# log or create him
user = DBSession.query(User).filter(
User.email == tmp_user.email).first()
if user is None:
user_group = DBSession.query(Group).filter(
Group.name == gl.group_users).first()
user_group.users.append(tmp_user)
DBSession.add(tmp_user)
DBSession.flush()
user = DBSession.query(User).filter(User.email == mail).first()
flash(u'Your account has been created %s' %
(user.firstname + ' ' + user.name, ))
DBSession.flush()
print "######################"
print "key user :"******"######################"
print "key user :"******"######################"
print "key user :"******"lab created : ", lab
else:
if lab not in user.labs:
lab.users.append(user)
DBSession.flush()
print "lab existing : ", lab
#create attributs / check existing attributs
attributs = DBSession.query(Attributs).filter(
Attributs.lab_id == lab.id).all()
if len(attributs) == 0:
attributs = None
lab_id = lab.id
#parsing "unit".ini
config = ConfigParser.RawConfigParser()
config.read(path_conf_unit(lab.name))
list_sample_att = (config.get('samples_attributs:main',
'keys')).split(',')
list_sample_hiding = (config.get('samples_hiding:main',
'keys')).split(',')
if len(list_sample_hiding) == 1 and list_sample_hiding[0] == '':
list_sample_hiding = ''
list_measurement_att = (config.get('meas_attributs:main',
'keys')).split(',')
list_meas_hiding = (config.get('meas_hiding:main', 'keys')).split(',')
if len(list_meas_hiding) == 1 and list_meas_hiding[0] == '':
list_meas_hiding = ''
list_searchable = (config.get('searchable_attributs:main',
'keys')).split(',')
list_deprecated = (config.get('deprecated_attributs:main',
'keys')).split(',')
dict_att_values_sample = {}
dict_att_values_meas = {}
dict_widgets_sample_att = {}
dict_widgets_meas_att = {}
dict_hiding_s_att = {}
dict_hiding_m_att = {}
for x in list_sample_att:
dict_att_values_sample[x] = (config.get('samples_attributs:' + x,
x)).split(',')
dict_widgets_sample_att[x] = (config.get('samples_attributs:' + x,
'widget')).split(',')
for x in list_measurement_att:
dict_att_values_meas[x] = (config.get('meas_attributs:' + x,
x)).split(',')
dict_widgets_meas_att[x] = (config.get('meas_attributs:' + x,
'widget')).split(',')
#to build the search page
search_fields_to_display = (config.get('search_grid_fields:main',
'keys')).split(',')
session["search_grid_fields"] = search_fields_to_display
#hidingradiobutton lists
#samples
if isinstance(list_sample_hiding, list):
for x in list_sample_hiding:
dic_mapping = {}
list_possibilities = (config.get('samples_attributs:' + x,
x)).split(',')
for p in list_possibilities:
attribs_by_poss = (config.get('samples_attributs:' + x,
p + "_mapping")).split(',')
dic_mapping[p] = attribs_by_poss
dict_hiding_s_att[x] = dic_mapping
if len(dict_hiding_s_att.keys()) > 0:
session["hiding_sample"] = dict_hiding_s_att
else:
session["hiding_sample"] = {}
#measurements
if isinstance(list_meas_hiding, list):
for x in list_meas_hiding:
dic_mapping = {}
list_possibilities = (config.get('meas_attributs:' + x,
x)).split(',')
for p in list_possibilities:
attribs_by_poss = (config.get('meas_attributs:' + x,
p + "_mapping")).split(',')
dic_mapping[p] = attribs_by_poss
dict_hiding_m_att[x] = dic_mapping
if len(dict_hiding_m_att.keys()) > 0:
session["hiding_meas"] = dict_hiding_m_att
else:
session["hiding_meas"] = {}
session.save()
#creating fixed values list
list_fixed_values_samples = []
list_fixed_values_meas = []
fixed_value_case = [
'singleselectfield', 'multiselectfield',
'hiding_singleselectfield', 'hiding_multiselectfield'
]
for fix_s in list_sample_att:
for i in dict_att_values_sample[fix_s]:
if i != "None":
if fix_s not in list_fixed_values_samples:
list_fixed_values_samples.append(fix_s)
for fix_m in list_measurement_att:
for i in dict_att_values_meas[fix_m]:
if i != "None":
if fix_m not in list_fixed_values_meas:
list_fixed_values_meas.append(fix_m)
print list_fixed_values_samples, "<--- fixed sample"
print list_fixed_values_meas, "<---- fixed meas"
if attributs is None:
#########################################
###### creating samples attributs #######
#########################################
for s in list_sample_att:
#TODO virer cast str
widget = str(dict_widgets_sample_att[s])
owner_widget = "sample"
attribut = self.build_attribut(s, lab_id,
list_fixed_values_samples,
list_searchable,
list_deprecated, widget,
owner_widget)
DBSession.add(attribut)
DBSession.flush()
if attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
#### creating measurements attributs ####
#########################################
for m in list_measurement_att:
widget = str(dict_widgets_meas_att[m])
owner_widget = "measurement"
attribut = self.build_attribut(m, lab_id,
list_fixed_values_meas,
list_searchable,
list_deprecated, widget,
owner_widget)
DBSession.add(attribut)
DBSession.flush()
if attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
####### for samples #######
#########################################
dict_fixed_values_samples = {}
list_attributs_samples_values = self.build_attribut_value(
'samples_attributs:', lab_id, dict_fixed_values_samples,
list_fixed_values_samples, config)
for att_v in list_attributs_samples_values:
DBSession.add(att_v)
DBSession.flush()
#########################################
###### for measurements #######
#########################################
dict_fixed_values_meas = {}
list_attributs_meas_values = self.build_attribut_value(
'meas_attributs:', lab_id, dict_fixed_values_meas,
list_fixed_values_meas, config)
for att_v in list_attributs_meas_values:
DBSession.add(att_v)
DBSession.flush()
#check if there is a new key (or several...) in the config file of the lab
else:
list_existant_keys = []
print list_searchable, "-------------searchable"
for k in attributs:
list_existant_keys.append(str(k.key))
for att_s in list_sample_att:
att_s = unicode(att_s)
if att_s not in list_existant_keys:
#########################################
###### creating samples attributs #######
#########################################
widget = str(dict_widgets_sample_att[att_s])
owner_widget = "sample"
new_sample_attribut = self.build_attribut(
att_s, lab_id, list_fixed_values_samples,
list_searchable, list_deprecated, widget, owner_widget)
print new_sample_attribut
DBSession.add(new_sample_attribut)
DBSession.flush()
if new_sample_attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(
new_sample_attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
####### for samples #######
#########################################
dict_fixed_values_samples = {}
list_attributs_samples_values = self.build_attribut_value(
'samples_attributs:', lab_id,
dict_fixed_values_samples, list_fixed_values_samples,
config)
for att_v in list_attributs_samples_values:
DBSession.add(att_v)
DBSession.flush()
#check widgets type
att_2_check = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id, Attributs.key == att_s,
Attributs.owner == "sample")).first()
wid_sample_tmp = dict_widgets_sample_att[att_s]
for w_s in wid_sample_tmp:
if w_s != att_2_check.widget:
in_db_before = att_2_check.widget
in_db_now = w_s
att_2_check.widget = w_s
if in_db_before in fixed_value_case and in_db_now not in fixed_value_case:
att_2_check.fixed_value = False
elif in_db_before not in fixed_value_case and in_db_now in fixed_value_case:
att_2_check.fixed_value = True
DBSession.flush()
#check and update search buttons
if att_2_check is None:
print att_s, "not in db"
if att_2_check is not None and not att_2_check.searchable and att_2_check.key in list_searchable:
att_2_check.searchable = True
DBSession.flush()
elif att_2_check is not None and att_2_check.searchable and att_2_check.key not in list_searchable:
att_2_check.searchable = False
DBSession.flush()
for att_m in list_measurement_att:
att_m = unicode(att_m)
if att_m not in list_existant_keys:
#########################################
#### creating measurements attributs ####
#########################################
#TODO virer cast str
widget = str(dict_widgets_meas_att[att_m])
owner_widget = "measurement"
new_meas_attribut = self.build_attribut(
att_m, lab_id, list_fixed_values_meas, list_searchable,
list_deprecated, widget, owner_widget)
DBSession.add(new_meas_attribut)
DBSession.flush()
if new_meas_attribut.fixed_value == False:
#if Attribut do not get fixed values
att_value = self.build_None_attribut_value(
new_meas_attribut.id)
DBSession.add(att_value)
DBSession.flush()
#########################################
####### creating attributs values #######
#########################################
###### for measurements #######
#########################################
dict_fixed_values_meas = {}
list_attributs_meas_values = self.build_attribut_value(
'meas_attributs:', lab_id, dict_fixed_values_meas,
list_fixed_values_meas, config)
for att_v in list_attributs_meas_values:
DBSession.add(att_v)
DBSession.flush()
#check the widgets
att_2_check = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id, Attributs.key == att_m,
Attributs.owner == "measurement")).first()
wid_meas_tmp = dict_widgets_meas_att[att_m]
for w_m in wid_meas_tmp:
if w_m != att_2_check.widget:
in_db_before = att_2_check.widget
in_db_now = w_m
att_2_check.widget = w_m
if in_db_before in fixed_value_case and in_db_now not in fixed_value_case:
att_2_check.fixed_value = False
elif in_db_before not in fixed_value_case and in_db_now in fixed_value_case:
att_2_check.fixed_value = True
DBSession.flush()
#check and update search buttons
if att_2_check is None:
print att_m, "not in db"
if att_2_check is not None and not att_2_check.searchable and att_2_check.key in list_searchable:
att_2_check.searchable = True
DBSession.flush()
elif att_2_check is not None and att_2_check.searchable and att_2_check.key not in list_searchable:
att_2_check.searchable = False
DBSession.flush()
#if lab choose to delete an attributs (or undelete a key...)
#Attributs obj have to stay into the db but user can not add others Attributs() with this key --> deprecated == True
not_deprecated_in_db = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id,
Attributs.deprecated == False)).all()
for k in not_deprecated_in_db:
if k.key in list_deprecated:
k.deprecated = True
DBSession.add(k)
DBSession.flush()
deprecated_in_db = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id,
Attributs.deprecated == True)).all()
for k in deprecated_in_db:
if k.key not in list_deprecated:
k.deprecated = False
DBSession.add(k)
DBSession.flush()
#test if deleted attributs_values
#build a dictionnary to fast check what is into db
dict_att_values_db = {}
for a in attributs:
#dict_att_values_db[a.key] = empty_list
list_tmp = []
for v in a.values:
if v.deprecated == False:
try:
list_tmp.append(str(v.value))
except:
list_tmp.append(v.value)
if len(list_tmp) == 0:
list_tmp = [None]
dict_att_values_db[str(a.key)] = list_tmp
#You have to check deletion BEFORE addition
#checking attribut value(s) deletion(s) in samples attributs
self.check_value_deletion(list_sample_att, dict_att_values_sample,
dict_att_values_db, lab_id)
#checking attribut value(s) deletion(s) in measurements attributs
self.check_value_deletion(list_measurement_att,
dict_att_values_meas, dict_att_values_db,
lab_id)
#checking attribut value(s) addition in sample attributs
self.check_value_addition(list_sample_att, dict_att_values_sample,
dict_att_values_db, lab_id)
#checking attribut value(s) addition in measurements attributs
self.check_value_addition(list_measurement_att,
dict_att_values_meas, dict_att_values_db,
lab_id)
# look if an user is admin or not
admins = tg.config.get('admin.mails')
group_admins = DBSession.query(Group).filter(
Group.name == gl.group_admins).first()
if user.email in admins:
user not in group_admins.users and group_admins.users.append(user)
else:
user in group_admins.users and group_admins.users.remove(user)
DBSession.flush()
# create the authentication ticket
user = DBSession.query(User).filter(User.email == mail).first()
userdata = str(user.id)
ticket = auth_tkt.AuthTicket(secret,
user.email,
remote_addr,
tokens=token,
user_data=userdata,
time=None,
cookie_name=cookiename,
secure=True)
val = ticket.cookie_value()
# set it in the cookies
response.set_cookie(cookiename,
value=val,
max_age=None,
path='/',
domain=None,
secure=False,
httponly=False,
comment=None,
expires=None,
overwrite=False)
#transaction.commit()
extern_meas = session.get("extern_meas", False)
check_tequila = session.get("check_tequila", False)
if extern_meas is False and check_tequila is False:
raise redirect(came_from)
elif extern_meas is False and check_tequila:
raise redirect("/search")
else:
del session["extern_meas"]
raise redirect(url('/measurements/external_add'))
