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 edit(self, *args, **kw):
user = handler.user.get_user_in_session(request)
sample = DBSession.query(Samples).filter(Samples.id == args[0]).first()
admin = isAdmin(user)
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
if admin:
projects = DBSession.query(Projects).all()
measurements = DBSession.query(Measurements).all()
else:
projects = DBSession.query(Projects).filter(Projects.user_id == user.id).all()
for p in projects:
if p not in lab.projects:
projects.remove(p)
attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
measurements = []
for a in attributs:
for m in a.measurements:
if m not in measurements and m.user_id == user.id:
measurements.append(m)
if sample.get_userid == user.id or admin:
edit_form = build_form("edit", "sample", sample.id)(action=url('/samples/post_edit'))
edit_form.child.children[0].value = sample.id
projects_list = [(p.id, '%s' % p.project_name) for p in projects]
edit_form.child.children[1].options = projects_list
id_project = DBSession.query(Projects.id).filter(Projects.id == sample.project_id).first()
#measurement(s) attached to the sample
list_unselected = [m for m in measurements if m not in sample.measurements]
meas_selected = [(meas.id, '%s' % (meas.name)) for meas in list_unselected] + [(meas.id, '%s' % (meas.name), {'selected': True}) for meas in sample.measurements]
edit_form.child.children[1].value = id_project[0]
edit_form.child.children[2].value = sample.name
edit_form.child.children[3].options = get_list_types(user_lab)
edit_form.child.children[3].value = sample.type
edit_form.child.children[4].value = sample.protocole
edit_form.child.children[5].options = meas_selected
return dict(page='samples', widget=edit_form.req(), value=kw)
else:
flash("It is not your sample -> you are not allowed to edit this sample", 'error')
raise redirect('/samples')
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 edit(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
if user_lab is not None:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
admin = isAdmin(user)
project = DBSession.query(Projects).filter(Projects.id == args[0]).first()
samples = []
if admin:
samples = DBSession.query(Samples).all()
else:
attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
projects = [p.id for p in user.projects if p in lab.projects]
for a in attributs:
for s in a.samples:
if s not in samples and s.project_id in projects:
samples.append(s)
if project.user_id == user.id or admin:
edit_form = EditProject(action=url('/projects/post_edit'))
edit_form.child.children[0].value = project.id
edit_form.child.children[1].value = project.project_name
edit_form.child.children[2].value = project.description
list_unselected = [s for s in samples if s not in project.samples]
samples_selected = [(sample.id, '%s' % (sample.name)) for sample in list_unselected] + [(sample.id, '%s' % (sample.name), {'selected': True}) for sample in project.samples]
edit_form.child.children[3].options = samples_selected
list_selected = []
for x in samples_selected:
#take only those with "selected : True"
if len(x) > 2:
list_selected.append(x[0])
edit_form.child.children[4].value = list_selected
return dict(page='projects', widget=edit_form, value=kw)
else:
flash("It is not your project -> you are not allowed to edit it", 'error')
raise redirect('/projects')
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 profile(self, *args, **kw):
'''
Get information about logged user
'''
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
u_id = kw.get("u_id", None)
u_lab = kw.get("lab", None)
#admin choice
if isAdmin(user):
if u_id is None or u_lab is None:
pass
else:
user = DBSession.query(User).filter(User.id == u_id).first()
if user is None:
flash("Wrong user id : " + u_id , "error")
raise redirect(url('./'))
user_lab = u_lab
elif not isAdmin(user) and u_id is not None or u_lab is not None:
flash("I'm watching you... Do not try to use admin's method if you're not one of them." , "error")
#normal user
user_id = user.id
name = user.name
firstname = user.firstname
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
if lab is None:
flash("Lab unknown : " + user_lab , "error")
raise redirect(url('./'))
elif lab not in user.labs:
flash("User " + name + " do not belong to this lab : " + user_lab , "error")
raise redirect(url('./'))
key = user.key
#save general information
profile_info = {"Name": name, "Firstname": firstname, "Your key": key, "Lab": user_lab}
#requests to get more information
meas = DBSession.query(Measurements).join(Measurements.attributs)\
.filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False))\
.filter(Measurements.user_id == user_id).all()
meas_lab = DBSession.query(Measurements).join(Measurements.attributs)\
.filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
if meas is None:
len_meas = 0
else:
len_meas = len(meas)
profile_info["Number of my measurements created"] = len_meas
#get each files
total_size_perso = 0
total_size_lab = 0
for m in meas:
if len(m.fus) > 0:
for fu in m.fus:
sha1 = fu.sha1
semi_path = fu.path
path_fu = semi_path + "/" + sha1
if path_fu.startswith(HTS_path_archive()):
path_fu = path_fu + ".tar.gz"
try:
file_size = os.path.getsize(path_fu)
except:
print ">>>>> PATH ERROR DETECTED : " + path_fu
file_size = 0
total_size_perso = total_size_perso + file_size
for measu in meas_lab:
if len(measu.fus) > 0:
for fu in measu.fus:
sha1 = fu.sha1
semi_path = fu.path
path_fu = semi_path + "/" + sha1
if path_fu.startswith(HTS_path_archive()):
path_fu = path_fu + ".tar.gz"
try:
file_size = os.path.getsize(path_fu)
except:
print ">>>>> PATH ERROR DETECTED : " + path_fu
file_size = 0
total_size_lab = total_size_lab + file_size
if total_size_lab != 0:
percentage_util = float("{0:.2f}".format((float(total_size_perso) / float(total_size_lab)) * 100))
else:
percentage_util = 0
profile_info["My lab in BioRepo"] = display_file_size(total_size_lab)
profile_info["My data in BioRepo"] = display_file_size(total_size_perso) + " (" + str(percentage_util) + " % of my lab's data)"
return dict(
page='profile',
dico=profile_info,
value=kw
)
