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 new(self, *args, **kw):
#take the logged user
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()
projects = DBSession.query(Projects).filter(Projects.user_id == user.id).all()
for p in projects:
if p not in lab.projects:
projects.remove(p)
new_form = build_form("new", "sample", None)(action=url('/samples/post')).req()
#static fields
new_form.child.children[0].options = [(project.id, '%s' % project.project_name) for project in projects]
new_form.child.children[1].placeholder = "Your sample name..."
new_form.child.children[2].options = get_list_types(user_lab)
new_form.child.children[3].placeholder = "Your protocole here..."
return dict(page='samples', widget=new_form)
def get_sample_types():
user_lab = session.get("current_lab", None)
return [('%s' % type) for type in get_list_types(user_lab) if type != None]
def get_sample_types():
user_lab = session.get("current_lab", None)
return [('%s' % type) for type in get_list_types(user_lab) if type != None]
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 get_my_fields(self, mail, key):
'''
Get a JSON with all the Projects/Samples/Measurements fields by lab
input : mail and biorepo key
output : {"lab": {"Projects": [field1, field2], "Samples": [field1, field2, field3],
"Measurements": [field1, field2, field3, field4]}}
'''
dico_by_labs = {}
dico_fields = {}
user = DBSession.query(User).filter(User._email == mail).first()
if user is None:
return {'ERROR': "User " + mail + " not in BioRepo."}
else:
user_labs = user.labs
if len(user_labs) > 0:
for lab in user_labs:
lab_name = lab.name
fields_projects = {'id': 'auto assigned id', 'user_id': 'auto assigned id', 'project_name': 'free text', 'description': 'free text'}
fields_samples = {'id': 'auto assigned id', 'project_id': 'auto assigned id', 'name': 'free text', 'type': get_list_types(lab_name), 'protocole': 'free text'}
fields_meas = {'id': 'auto assigned id', 'user_id': 'auto assigned id', 'name': 'free text', 'description': 'free text', 'status_type': ['Public', 'Private'], 'type': ['Raw', 'Processed']}
lab_id = lab.id
sample_attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.owner == "sample", Attributs.deprecated == False)).all()
meas_attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.owner == "measurement", Attributs.deprecated == False)).all()
for s_att in sample_attributs:
if not s_att.deprecated and (s_att.widget == "textfield" or s_att.widget == "textarea" or s_att.widget == "hiding_textfield" or s_att.widget == "hiding_area"):
fields_samples[s_att.key] = "free text"
elif not s_att.deprecated and (s_att.widget == "singleselectfield" or s_att.widget == "multiselectfield" or s_att.widget == "hiding_singleselectfield" or s_att.widget == "hiding_multiselectfield"):
att_id = s_att.id
values = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == att_id, Attributs_values.deprecated == False)).all()
list_v = []
for v in values:
if v.value not in list_v:
list_v.append(v.value)
fields_samples[s_att.key] = list_v
elif not s_att.deprecated and (s_att.widget == "checkbox" or s_att.widget == "hiding_checkbox"):
fields_samples[s_att.key] = [s_att.key, "Not " + str(s_att.key)]
for m_att in meas_attributs:
if not m_att.deprecated and (m_att.widget == "textfield" or m_att.widget == "textarea" or m_att.widget == "hiding_textfield" or m_att.widget == "hiding_area"):
fields_meas[m_att.key] = "free text"
elif not m_att.deprecated and (m_att.widget == "singleselectfield" or m_att.widget == "multiselectfield" or m_att.widget == "hiding_singleselectfield" or m_att.widget == "hiding_multiselectfield"):
att_id = m_att.id
values = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == att_id, Attributs_values.deprecated == False)).all()
list_v = []
for v in values:
if v.value not in list_v:
list_v.append(v.value)
fields_meas[m_att.key] = list_v
elif not m_att.deprecated and (m_att.widget == "checkbox" or m_att.widget == "hiding_checkbox"):
fields_meas[s_att.key] = [m_att.key, "Not " + str(m_att.key)]
dico_fields["Projects"] = fields_projects
dico_fields["Samples"] = fields_samples
fields_samples = {}
dico_fields["Measurements"] = fields_meas
fields_meas = {}
dico_by_labs[str(lab.name) + '(' + str(lab.id) + ')'] = dico_fields
dico_fields = {}
return dico_by_labs
else:
return {'ERROR': "This user " + mail + " has no lab. Contact the administrator please."}
