def to_json_test(self):
static_fields = {
'Description': self.meas.description,
'User': self.get_name(),
'Measurements': self.get_meas_name(),
'description': self.meas.description,
'Created': self.date.strftime(date_format),
'Samples': ' ; '.join(['%s' % (sample.name) for sample in self.samples]),
'Projects': self.get_projects(),
'Type': self.get_sample_type(),
'DataType': self.get_measurement_type(),
'scroll_info': genshi.Markup(self.get_img_scroll()),
'Attachment': self.get_extension,
'Actions': get_info_link(self.id) + get_dl_link(self.id) + get_public_link(self.id) + get_UCSC_link(self.id) + get_GViz_link(self.id) + get_SPAN_id(self.id)
}
#find None statics fields to change the display in datatables
for sf in static_fields.keys():
if static_fields[sf] is None or static_fields[sf] == "":
static_fields[sf] = None
dyn_in_searchgrid = session.get("search_grid_fields", [])
labo = session.get("current_lab")
for d in dyn_in_searchgrid:
new = d.replace("_", " ")
dyn_in_searchgrid.remove(d)
dyn_in_searchgrid.append(new)
meas_dynamic_fields = {}
samples_dynamic_fields = {}
attributs_meas = [a.to_json() for a in self.meas.attributs if not a.deprecated]
list_avalues_meas = self.meas.a_values
for avm in list_avalues_meas:
for am in attributs_meas:
key = am["key"].replace("_", " ")
if str(am["id"]) == str(avm.attribut_id):
if am["widget"] != "checkbox" and am["widget"] != "hiding_checkbox":
meas_dynamic_fields[key] = avm.value
else:
if check_boolean(avm.value):
meas_dynamic_fields[key] = key
else:
meas_dynamic_fields[key] = "NOT " + str(key)
attributs_samples = self.get_attributs_samples_json()
if len(self.samples) < 2:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s["widget"] != "hiding_checkbox":
samples_dynamic_fields[key] = avs.value
else:
if check_boolean(avs.value):
samples_dynamic_fields[key] = key
else:
samples_dynamic_fields[key] = "NOT " + str(key)
else:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s["widget"] != "hiding_checkbox":
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = [avs.value]
else:
if avs.value not in samples_dynamic_fields[key]:
samples_dynamic_fields[key].append(avs.value)
else:
if check_boolean(avs.value):
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = [key]
else:
samples_dynamic_fields[key].append(key)
else:
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = ["NOT " + str(key)]
else:
samples_dynamic_fields[key].append("NOT " + str(key))
for k in samples_dynamic_fields.keys():
samples_dynamic_fields[k] = " ; ".join(samples_dynamic_fields[k])
#Sorting dynamic fields with conf file to display in searchgrid
dyn_fields = {}
for k in samples_dynamic_fields:
if k in dyn_in_searchgrid:
dyn_fields[k.capitalize()] = samples_dynamic_fields[k]
for key in meas_dynamic_fields:
if key in dyn_in_searchgrid:
dyn_fields[key.capitalize()] = meas_dynamic_fields[key]
#for the empty fields
for k in dyn_in_searchgrid:
if k.capitalize() not in dyn_fields.keys():
k_db = k.replace(" ", "_")
lab = DBSession.query(Labs).filter(Labs.name == labo).first()
lab_id = lab.id
k_obj = DBSession.query(Attributs).filter(and_(Attributs.key == k_db, Attributs.lab_id == lab_id)).first()
if k_obj.widget != "checkbox" and k_obj.widget != "hiding_checkbox":
dyn_fields[k.capitalize()] = None
else:
dyn_fields[k.capitalize()] = ["NOT " + str(k)]
final = dict(static_fields.items() + dyn_fields.items())
return final
def build_search_grid(measurements):
search_grid = BootstrapGrid()
#static end
end_fields = [('Attachment', lambda obj: genshi.Markup(obj.get_extension)),
('Description', "description"), ("Date", "created"),
("Action", lambda obj: genshi.Markup(
get_info_link(obj.id) + get_dl_link(obj.id) +
get_public_link(obj.id) + get_UCSC_link(obj.id) +
get_GViz_link(obj.id) + get_SPAN_id(obj.id)))]
#static and dynamic fields
fields = []
fields_static = [("", "scroll_info"), ("User", "user"), ("Projects", lambda obj:genshi.Markup(obj.projects_display)), ("Samples", lambda obj:genshi.Markup(
obj.samples_display)), ("Type", lambda obj:genshi.Markup(obj.sample_type)),\
("Measurements", lambda obj:genshi.Markup(obj.name)), ("DataType", lambda obj:genshi.Markup(obj.measurement_type))]
fields_dyn = []
list_searchable = []
positions_not_searchable = []
hidden_list = []
lab_id = None
if not isinstance(measurements, list):
measurements = [measurements]
if len(measurements) > 0:
meas = measurements[0]
#dyn meas
for att in meas.attributs:
#get the lab_id
lab_id = att.lab_id
vals = lambda obj, a=att: obj.get_values_from_attributs_meas(a)
fields_dyn.append((att.key, vals))
if att.searchable == True:
list_searchable.append(att.key)
#dyn sample
if len(meas.samples) > 0:
sample = (meas.samples)[0]
for att in sample.attributs:
val = lambda obj, a=att: obj.get_values_from_attributs_sample(a
)
fields_dyn.append((att.key, val))
if att.searchable == True:
list_searchable.append(att.key)
############## CUSTOMIZE THE SEARCH GRID BY LAB #######################
#/!\ the grid begins at 0
#to customize hidden fields by lab
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
movable_fields = fields_static + fields_dyn
if lab:
if lab.name == "ptbb":
pass
elif lab.name == "updub":
pass
elif lab.name == "lvg":
#move some field in the grid
for f in movable_fields:
if f[0] == "flag_final":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
for f in movable_fields:
if f[0] == "quality":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
#hide Samples name
for f in movable_fields:
if f[0] == "Samples":
i = movable_fields.index(f)
hidden_list.append(i)
for f in movable_fields:
if f[0] == "ab_source":
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "upnae":
fields_to_hide = ["replica_id", "drug_dose", "lane_id", "paired_end_id", "strand",\
"source", "machine", "starting_material", "treatment", "paired_end", "polya", "strand_specific",\
"viewpoint", "protein_bait", "technical_replica_id", "feeding_type", "light_condition"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "stutz":
fields_to_hide = ["article_title", "strain", "time_point", "antibody", "treatment_time",\
"phase", "medium", "background"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "shore":
fields_to_hide = [
"article_title", "year", "time_point", "sequencing_method",
"treatment_time", "phase"
]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
#addition with the 3 common end-fields
fields = movable_fields + end_fields
#build the list (positions_not_searchable) to send to the js for the searchable buttons
for f in fields:
search_grid.fields.append(f)
for i, item in enumerate(search_grid.fields):
if item[0] not in list_searchable:
positions_not_searchable.append(i)
for f in fields_static:
for i, item in enumerate(movable_fields):
#and i not in list_tmp
if f[0] == item[0] and f[
0] != '' and f in fields_static and i in positions_not_searchable:
positions_not_searchable.remove(i)
#build the list (ignored_list) for the ignored fields
total = len(search_grid.fields) - 1
hidden_list.append(total - 2)
#positions_not_searchable = delete the search button of the field
#hidden_list = the field does not appear anymore into the searchgrid and its search button disappears BUT it is still searchable !
return search_grid, hidden_list, positions_not_searchable
def build_search_grid(measurements):
search_grid = BootstrapGrid()
#static end
end_fields = [('Attachment', lambda obj: genshi.Markup(obj.get_extension)), ('Description', "description"), ("Date", "created"), ("Action", lambda obj: genshi.Markup(
get_info_link(obj.id)
+ get_dl_link(obj.id)
+ get_public_link(obj.id)
+ get_UCSC_link(obj.id)
+ get_GViz_link(obj.id)
+ get_SPAN_id(obj.id)
))]
#static and dynamic fields
fields = []
fields_static = [("", "scroll_info"), ("User", "user"), ("Projects", lambda obj:genshi.Markup(obj.projects_display)), ("Samples", lambda obj:genshi.Markup(
obj.samples_display)), ("Type", lambda obj:genshi.Markup(obj.sample_type)),\
("Measurements", lambda obj:genshi.Markup(obj.name)), ("DataType", lambda obj:genshi.Markup(obj.measurement_type))]
fields_dyn = []
list_searchable = []
positions_not_searchable = []
hidden_list = []
lab_id = None
if not isinstance(measurements, list):
measurements = [measurements]
if len(measurements) > 0:
meas = measurements[0]
#dyn meas
for att in meas.attributs:
#get the lab_id
lab_id = att.lab_id
vals = lambda obj, a=att: obj.get_values_from_attributs_meas(a)
fields_dyn.append((att.key, vals))
if att.searchable == True:
list_searchable.append(att.key)
#dyn sample
if len(meas.samples) > 0:
sample = (meas.samples)[0]
for att in sample.attributs:
val = lambda obj, a=att: obj.get_values_from_attributs_sample(a)
fields_dyn.append((att.key, val))
if att.searchable == True:
list_searchable.append(att.key)
############## CUSTOMIZE THE SEARCH GRID BY LAB #######################
#/!\ the grid begins at 0
#to customize hidden fields by lab
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
movable_fields = fields_static + fields_dyn
if lab:
if lab.name == "ptbb":
pass
elif lab.name == "updub":
pass
elif lab.name == "lvg":
#move some field in the grid
for f in movable_fields:
if f[0] == "flag_final":
new_list = value_travel_into_da_list(movable_fields, movable_fields.index(f), len(movable_fields))
movable_fields = new_list
for f in movable_fields:
if f[0] == "quality":
new_list = value_travel_into_da_list(movable_fields, movable_fields.index(f), len(movable_fields))
movable_fields = new_list
#hide Samples name
for f in movable_fields:
if f[0] == "Samples":
i = movable_fields.index(f)
hidden_list.append(i)
for f in movable_fields:
if f[0] == "ab_source":
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "upnae":
fields_to_hide = ["replica_id", "drug_dose", "lane_id", "paired_end_id", "strand",\
"source", "machine", "starting_material", "treatment", "paired_end", "polya", "strand_specific",\
"viewpoint", "protein_bait", "technical_replica_id", "feeding_type", "light_condition"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "stutz":
fields_to_hide = ["article_title", "strain", "time_point", "antibody", "treatment_time",\
"phase", "medium", "background"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "shore":
fields_to_hide = ["article_title", "year", "time_point", "sequencing_method", "treatment_time", "phase"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
#addition with the 3 common end-fields
fields = movable_fields + end_fields
#build the list (positions_not_searchable) to send to the js for the searchable buttons
for f in fields:
search_grid.fields.append(f)
for i, item in enumerate(search_grid.fields):
if item[0] not in list_searchable:
positions_not_searchable.append(i)
for f in fields_static:
for i, item in enumerate(movable_fields):
#and i not in list_tmp
if f[0] == item[0] and f[0] != '' and f in fields_static and i in positions_not_searchable:
positions_not_searchable.remove(i)
#build the list (ignored_list) for the ignored fields
total = len(search_grid.fields) - 1
hidden_list.append(total - 2)
#positions_not_searchable = delete the search button of the field
#hidden_list = the field does not appear anymore into the searchgrid and its search button disappears BUT it is still searchable !
return search_grid, hidden_list, positions_not_searchable
def to_json_test(self):
static_fields = {
'Description':
self.meas.description,
'User':
self.get_name(),
'Measurements':
self.get_meas_name(),
'description':
self.meas.description,
'Created':
self.date.strftime(date_format),
'Samples':
' ; '.join(['%s' % (sample.name) for sample in self.samples]),
'Projects':
self.get_projects(),
'Type':
self.get_sample_type(),
'DataType':
self.get_measurement_type(),
'scroll_info':
genshi.Markup(self.get_img_scroll()),
'Attachment':
self.get_extension,
'Actions':
get_info_link(self.id) + get_dl_link(self.id) +
get_public_link(self.id) + get_UCSC_link(self.id) +
get_GViz_link(self.id) + get_SPAN_id(self.id)
}
#find None statics fields to change the display in datatables
for sf in static_fields.keys():
if static_fields[sf] is None or static_fields[sf] == "":
static_fields[sf] = None
dyn_in_searchgrid = session.get("search_grid_fields", [])
labo = session.get("current_lab")
for d in dyn_in_searchgrid:
new = d.replace("_", " ")
dyn_in_searchgrid.remove(d)
dyn_in_searchgrid.append(new)
meas_dynamic_fields = {}
samples_dynamic_fields = {}
attributs_meas = [
a.to_json() for a in self.meas.attributs if not a.deprecated
]
list_avalues_meas = self.meas.a_values
for avm in list_avalues_meas:
for am in attributs_meas:
key = am["key"].replace("_", " ")
if str(am["id"]) == str(avm.attribut_id):
if am["widget"] != "checkbox" and am[
"widget"] != "hiding_checkbox":
meas_dynamic_fields[key] = avm.value
else:
if check_boolean(avm.value):
meas_dynamic_fields[key] = key
else:
meas_dynamic_fields[key] = "NOT " + str(key)
attributs_samples = self.get_attributs_samples_json()
if len(self.samples) < 2:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
samples_dynamic_fields[key] = avs.value
else:
if check_boolean(avs.value):
samples_dynamic_fields[key] = key
else:
samples_dynamic_fields[key] = "NOT " + str(
key)
else:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = [avs.value]
else:
if avs.value not in samples_dynamic_fields[
key]:
samples_dynamic_fields[key].append(
avs.value)
else:
if check_boolean(avs.value):
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [key]
else:
samples_dynamic_fields[key].append(key)
else:
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [
"NOT " + str(key)
]
else:
samples_dynamic_fields[key].append(
"NOT " + str(key))
for k in samples_dynamic_fields.keys():
samples_dynamic_fields[k] = " ; ".join(
samples_dynamic_fields[k])
#Sorting dynamic fields with conf file to display in searchgrid
dyn_fields = {}
for k in samples_dynamic_fields:
if k in dyn_in_searchgrid:
dyn_fields[k.capitalize()] = samples_dynamic_fields[k]
for key in meas_dynamic_fields:
if key in dyn_in_searchgrid:
dyn_fields[key.capitalize()] = meas_dynamic_fields[key]
#for the empty fields
for k in dyn_in_searchgrid:
if k.capitalize() not in dyn_fields.keys():
k_db = k.replace(" ", "_")
lab = DBSession.query(Labs).filter(Labs.name == labo).first()
lab_id = lab.id
k_obj = DBSession.query(Attributs).filter(
and_(Attributs.key == k_db,
Attributs.lab_id == lab_id)).first()
if k_obj.widget != "checkbox" and k_obj.widget != "hiding_checkbox":
dyn_fields[k.capitalize()] = None
else:
dyn_fields[k.capitalize()] = ["NOT " + str(k)]
final = dict(static_fields.items() + dyn_fields.items())
return final