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 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 build_user(self, principal):
'''
Build an User and his/her Lab(s) from a principal hash from Tequila
@param principal: the hash from Tequila
@return: an User, his/her Lab(s)
'''
hash = dict(item.split('=') for item in principal.split('\n') if len(item.split('=')) > 1)
user = User()
lab = Labs()
#initialize the configparser
configp = ConfigParser.RawConfigParser()
print "################# NEW CONNEXION ###############"
print hash, "--- connexion"
now2 = datetime.datetime.now()
print "############## TIME #############"
print now2.ctime()
if(hash.has_key('firstname')):
user.firstname = hash.get('firstname').decode("utf-8")
if(hash.has_key('name')):
user.name = hash.get('name').decode("utf-8")
if(hash.has_key('email')):
user.email = hash.get('email')
#testing unit
tmp_u = hash['allunits'].lower()
list_units = tmp_u.split(',')
print list_units, "list_units"
#possibility to add one or several external lab(s) to a collaborator without Shibboleth agreement
test_user = DBSession.query(User).filter(User._email == user.email).first()
#if it is not the first connexion for the user
if test_user is not None:
#get his/her lab(s) registered
test_labs = test_user.labs
#check if we get a Shibboleth bypass for this one
if len(test_labs) > 0:
for l in test_labs:
if str(l.name) not in list_units:
print "Shibboleth bypass for : " + str(l.name)
list_units.append(str(l.name))
#parsing conf file labs.ini
configp.read(path_conf_labs())
list_labs = (configp.get('LABS:main', 'keys')).split(',')
print list_labs, "list_labs in labs.ini"
valid = False
# try:
# test = session['current_lab']
# exist = True
# except:
# exist = False
if len(list_units) > 1 and session['first_passage'] == True:
cpt_labs = len(list_units)
cpt = 0
for u in list_units:
if u in list_labs:
raise redirect('choose_lab', {'list_units': list_units})
else:
cpt += 1
pass
if cpt == cpt_labs:
flash("Sorry, your lab is not registered in BioRepo, please contact the administrator", 'error')
raise redirect('/')
elif len(list_units) > 1 and session['first_passage'] == False:
valid = True
u = session["current_lab"]
lab.name = u
lab.path_raw = path_raw(u)
lab.path_processed = path_processed(u)
lab.path_tmp = path_tmp(u)
session["tmp_user"] = user
session["tmp_lab"] = lab
session.save()
#the user is affiliated to one lab
elif len(list_units) < 2 and list_units != ['unsupported']:
for u in list_units:
if u in list_labs:
#creating the Labs keys
valid = True
lab.name = u
lab.path_raw = path_raw(u)
lab.path_processed = path_processed(u)
lab.path_tmp = path_tmp(u)
session['current_lab'] = u
session.save()
else:
flash("Sorry, your lab is not registered in BioRepo, please contact the administrator to do it", 'error')
raise redirect('/')
#the user is an external collaborator, not from EPFL
elif len(list_units) == 1 and list_units == ['unsupported']:
print "---- OUTSIDE USER DETECTED ----"
valid = True
mail = user.email
user_tocheck = DBSession.query(User).filter(User._email == mail).first()
if user_tocheck is None or len(user_tocheck.labs) == 0 or len(user_tocheck.labs) > 2:
valid = False
#ext_users have only one lab
else:
for l in user_tocheck.labs:
lab_name = str(l.name)
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)
session['current_lab'] = lab_name
session.save()
#IMPORTANT : where you have to put your name if you are a super admin
if valid == True or hash['user'] == 'mouscaz' or hash['user'] == 'fdavid':
return user, lab
else:
flash("Sorry, your lab is not registered in BioRepo", 'error')
raise redirect('/')
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 build_user(self, principal):
'''
Build an User and his/her Lab(s) from a principal hash from Tequila
@param principal: the hash from Tequila
@return: an User, his/her Lab(s)
'''
hash = dict(
item.split('=') for item in principal.split('\n')
if len(item.split('=')) > 1)
user = User()
lab = Labs()
#initialize the configparser
configp = ConfigParser.RawConfigParser()
print "################# NEW CONNEXION ###############"
print hash, "--- connexion"
now2 = datetime.datetime.now()
print "############## TIME #############"
print now2.ctime()
if (hash.has_key('firstname')):
user.firstname = hash.get('firstname').decode("utf-8")
if (hash.has_key('name')):
user.name = hash.get('name').decode("utf-8")
if (hash.has_key('email')):
user.email = hash.get('email')
#testing unit
tmp_u = hash['allunits'].lower()
list_units = tmp_u.split(',')
print list_units, "list_units"
#possibility to add one or several external lab(s) to a collaborator without Shibboleth agreement
test_user = DBSession.query(User).filter(
User._email == user.email).first()
#if it is not the first connexion for the user
if test_user is not None:
#get his/her lab(s) registered
test_labs = test_user.labs
#check if we get a Shibboleth bypass for this one
if len(test_labs) > 0:
for l in test_labs:
if str(l.name) not in list_units:
print "Shibboleth bypass for : " + str(l.name)
list_units.append(str(l.name))
#parsing conf file labs.ini
configp.read(path_conf_labs())
list_labs = (configp.get('LABS:main', 'keys')).split(',')
print list_labs, "list_labs in labs.ini"
valid = False
# try:
# test = session['current_lab']
# exist = True
# except:
# exist = False
if len(list_units) > 1 and session['first_passage'] == True:
cpt_labs = len(list_units)
cpt = 0
for u in list_units:
if u in list_labs:
raise redirect('choose_lab', {'list_units': list_units})
else:
cpt += 1
pass
if cpt == cpt_labs:
flash(
"Sorry, your lab is not registered in BioRepo, please contact the administrator",
'error')
raise redirect('/')
elif len(list_units) > 1 and session['first_passage'] == False:
valid = True
u = session["current_lab"]
lab.name = u
lab.path_raw = path_raw(u)
lab.path_processed = path_processed(u)
lab.path_tmp = path_tmp(u)
session["tmp_user"] = user
session["tmp_lab"] = lab
session.save()
#the user is affiliated to one lab
elif len(list_units) < 2 and list_units != ['unsupported']:
for u in list_units:
if u in list_labs:
#creating the Labs keys
valid = True
lab.name = u
lab.path_raw = path_raw(u)
lab.path_processed = path_processed(u)
lab.path_tmp = path_tmp(u)
session['current_lab'] = u
session.save()
else:
flash(
"Sorry, your lab is not registered in BioRepo, please contact the administrator to do it",
'error')
raise redirect('/')
#the user is an external collaborator, not from EPFL
elif len(list_units) == 1 and list_units == ['unsupported']:
print "---- OUTSIDE USER DETECTED ----"
valid = True
mail = user.email
user_tocheck = DBSession.query(User).filter(
User._email == mail).first()
if user_tocheck is None or len(
user_tocheck.labs) == 0 or len(user_tocheck.labs) > 2:
valid = False
#ext_users have only one lab
else:
for l in user_tocheck.labs:
lab_name = str(l.name)
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)
session['current_lab'] = lab_name
session.save()
#IMPORTANT : where you have to put your name if you are a super admin
if valid == True or hash['user'] == 'mouscaz' or hash[
'user'] == 'fdavid':
return user, lab
else:
flash("Sorry, your lab is not registered in BioRepo", 'error')
raise redirect('/')