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 delete(self, *args, **kw):
user = handler.user.get_user_in_session(request)
project = DBSession.query(Projects).filter(Projects.id == args[0]).first()
admin = isAdmin(user)
if project.user_id == user.id or admin:
try:
flash("Your project " + str(project.project_name) + " has been deleted with success")
except:
flash("Your project " + (project.project_name) + " has been deleted with success")
DBSession.delete(project)
DBSession.flush()
raise redirect('/projects')
else:
flash("It is not your project -> you are not allowed to delete it", 'error')
raise redirect('/projects')
def delete(self, *args, **kw):
user = handler.user.get_user_in_session(request)
sample = DBSession.query(Samples).filter(Samples.id == args[0]).first()
admin = isAdmin(user)
if sample.get_userid == user.id or admin:
try:
flash("Your sample " + str(sample.name) + " has been deleted with success")
except:
flash("Your sample " + (sample.name) + " has been deleted with success")
DBSession.delete(sample)
DBSession.flush()
raise redirect("/samples")
#TO CHECK : check if sample get already an user as owner
elif sample.get_userid == None or admin:
DBSession.delete(sample)
DBSession.flush()
flash("Your sample has been deleted")
raise redirect("/samples")
else:
flash("It is not your sample -> you are not allowed to delete it", 'error')
raise redirect('/samples')
def multi_meas_delete(self, p_id, s_id, mail, key):
'''
deleted ALL the measurements for a given sample
/!\ IRREVERSIBLE /!\
'''
try:
project = DBSession.query(Projects).filter(Projects.id == p_id).first()
sample = DBSession.query(Samples).filter(Samples.id == s_id).first()
user = DBSession.query(User).filter(User._email == mail).first()
#checking
print "--- Check your inputs... ---"
if project is None:
print "Project " + str(p_id) + " not found."
if sample is None:
print "Sample " + str(s_id) + " not found."
if user is None:
print "Your mail " + mail + " is not recorded in BioRepo."
if project.id == sample.project_id and user.id == project.user_id:
print "--- Begin the purge... ---"
list_meas = sample.measurements
print "Today, " + str(len(list_meas)) + " will die..."
print "--------------------------"
for m in list_meas:
list_fus = m.fus
for f in list_fus:
#delete the file on the server only if it is not used by anyone else anymore
if len(f.measurements) == 1 and not (f.path).startswith(HTS_path_data()) and not (f.path).startswith(HTS_path_archive()):
path_fu = f.path + "/" + f.sha1
mail = user._email
mail_tmp = mail.split('@')
path_mail = "AT".join(mail_tmp)
path_symlink = f.path + "/" + path_mail + "/" + f.sha1
DBSession.delete(f)
path_symlink = f.path + "/" + path_mail + "/" + f.sha1
try:
os.remove(path_symlink)
except:
print "---- path_symlink deleted yet ----"
pass
os.remove(path_fu)
elif (f.path).startswith(HTS_path_data()) or (f.path).startswith(HTS_path_archive()):
DBSession.delete(f)
#TODO send back something to hts to notify that it's not into biorepo anymore
print str(m.name) + "(" + str(m.id) + ") ... Sorry ... PAN."
DBSession.delete(m)
DBSession.flush()
print "--- They are all died T_T ---"
else:
print "It's not your project/sample. The FBI was notified. Run."
except:
print_traceback()
print "Something went wrong...Please, don't cry."
