def set_parameters(self, request):
self.user = request.user
self.registry_code = request.GET.get("registry_code")
self.registry_model = get_object_or_404(Registry,
code=self.registry_code)
self.clinicians_have_patients = self.registry_model.has_feature(
"clinicians_have_patients")
self.form_progress = FormProgress(self.registry_model)
self.supports_contexts = self.registry_model.has_feature("contexts")
self.rdrf_context_manager = RDRFContextManager(self.registry_model)
def getint(param):
try:
return int(request.POST.get(param) or 0)
except ValueError:
return 0
self.search_term = request.POST.get("search[value]") or ""
self.draw = getint("draw") # unknown
self.start = getint("start") # offset
self.length = getint("length") # page size
self.page_number = (
(self.start / self.length) if self.length else 0) + 1
self.sort_field, self.sort_direction = self.get_ordering(request)
self.columns = self.get_configure_columns()
def save_form_progress(self, registry_code, context_model=None):
from rdrf.forms.progress.form_progress import FormProgress
registry_model = Registry.objects.get(code=registry_code)
form_progress = FormProgress(registry_model)
dynamic_data = self.load_dynamic_data(registry_code,
"cdes",
flattened=False)
return form_progress.save_progress(self.obj, dynamic_data,
context_model)
def __init__(self,
registry_model,
patient_model,
form_model,
context_form_group,
context_model=None):
self.registry_model = registry_model
self.context_form_group = context_form_group
self.patient_model = patient_model
self.form_model = form_model
self.context_model = context_model
self.progress = FormProgress(self.registry_model)
# if no progress cdes defined on form, don't show any percentage
self.has_progress = form_model.has_progress_indicator
class FormWrapper(object):
def __init__(self,
registry_model,
patient_model,
form_model,
context_form_group,
context_model=None):
self.registry_model = registry_model
self.context_form_group = context_form_group
self.patient_model = patient_model
self.form_model = form_model
self.context_model = context_model
self.progress = FormProgress(self.registry_model)
# if no progress cdes defined on form, don't show any percentage
self.has_progress = form_model.has_progress_indicator
@property
def link(self):
return reverse('registry_form',
args=(self.registry_model.code, self.form_model.id,
self.patient_model.pk, self.context_model.id))
@property
def title(self):
if not self.context_form_group or self.context_form_group.context_type == "F":
return self.form_model.nice_name
else:
# multiple group
if self.context_form_group.supports_direct_linking:
value = self.context_form_group.get_name_from_cde(
self.patient_model, self.context_model)
if not value:
return "Not set"
else:
return value
else:
return self.context_form_group.name + " " + self.form_model.nice_name
@property
def progress_percentage(self):
return self.progress.get_form_progress(self.form_model,
self.patient_model,
self.context_model)
@property
def is_current(self):
return self.progress.get_form_currency(self.form_model,
self.patient_model,
self.context_model)
def _update_progress(self):
form_progress = FormProgress(self.registry_model)
for patient_model in Patient.objects.filter(
rdrf_registry__in=[self.registry_model]):
if not self.registry_model.has_feature("contexts"):
default_context = patient_model.default_context(
self.registry_model)
form_progress.save_for_patient(patient_model, default_context)
self.stdout.write("Recalculated progress for Patient %s" %
patient_model.pk)
else:
self.stderr.write(
"Script does not support registries with multiple contexts allowed, yet"
)
sys.exit(1)
def __init__(self,
registry_model,
column,
form_model=None,
section_model=None,
cde_model=None,
field=None):
self.registry_model = registry_model
self.column = column
self.form_model = form_model
self.section_model = section_model
self.form_progress = FormProgress(self.registry_model)
self.progress_percentage = None
if self.section_model:
self.is_multiple = section_model.allow_multiple
else:
self.is_multiple = False
self.cde_model = cde_model
self.field = field
class PatientsListingView(View):
def __init__(self, *args, **kwargs):
super(PatientsListingView, self).__init__(*args, **kwargs)
self.registry_model = None
self.user = None
self.registries = []
self.patient_id = None
# grid params
self.custom_ordering = None
self.start = None
self.length = None
self.page_number = None
self.sort_field = None
self.sort_direction = None
self.columns = None
self.queryset = None
self.records_total = None
self.filtered_total = None
self.context = {}
def get(self, request):
# get just displays the empty table and writes the page
# which initiates an ajax/post request on registry select
# the protocol is the jquery DataTable
# see http://datatables.net/manual/server-side
self.user = request.user
if self.user and self.user.is_anonymous:
login_url = "%s?next=%s" % (reverse("two_factor:login"),
reverse("login_router"))
return redirect(login_url)
self.do_security_checks()
self.set_csrf(request)
self.set_registry(request)
self.set_registries() # for drop down
self.patient_id = request.GET.get("patient_id", None)
template_context = self.build_context()
template = self.get_template()
return render(request, template, template_context)
def get_template(self):
template = 'rdrf_cdes/patients_listing_no_registries.html' if len(
self.registries) == 0 else 'rdrf_cdes/patients_listing.html'
return template
def build_context(self):
return {
"registries":
self.registries,
"location":
_("Patient Listing"),
"patient_id":
self.patient_id,
"registry_code":
self.registry_model.code if self.registry_model else None,
"columns": [
col.to_dict(i)
for (i, col) in enumerate(self.get_configure_columns())
],
}
def get_columns(self):
return [
ColumnFullName(_("Patient"), "patients.can_see_full_name"),
ColumnDateOfBirth(_("Date of Birth"), "patients.can_see_dob"),
ColumnCodeField(_("Code"), "patients.can_see_code_field"),
ColumnWorkingGroups(_("Working Groups"),
"patients.can_see_working_groups"),
ColumnDiagnosisProgress(_("Diagnosis Entry Progress"),
"patients.can_see_diagnosis_progress"),
ColumnDiagnosisCurrency(_("Updated < 365 days"),
"patients.can_see_diagnosis_currency"),
ColumnGeneticDataMap(_("Genetic Data"),
"patients.can_see_genetic_data_map"),
ColumnContextMenu(_("Modules"), "patients.can_see_data_modules"),
]
def get_configure_columns(self):
columns = self.get_columns()
for i, col in enumerate(columns):
col.configure(self.registry_model, self.user, i)
return [col for col in columns if col.user_can_see]
def do_security_checks(self):
if self.user.is_patient:
raise PermissionDenied()
def set_csrf(self, request):
self.context.update(csrf(request))
def set_registry(self, request):
registry_code = request.GET.get("registry_code", None)
if registry_code is not None:
try:
self.registry_model = Registry.objects.get(code=registry_code)
except Registry.DoesNotExist:
return HttpResponseRedirect("/")
def set_registries(self):
if self.registry_model is None:
if self.user.is_superuser:
self.registries = [
registry_model
for registry_model in Registry.objects.all()
]
else:
self.registries = [
registry_model
for registry_model in self.user.registry.all()
]
else:
self.registries = [self.registry_model]
def json(self, data):
json_data = json.dumps(data)
return HttpResponse(json_data, content_type="application/json")
def post(self, request):
# see http://datatables.net/manual/server-side
self.user = request.user
if self.user and self.user.is_anonymous:
login_url = "%s?next=%s" % (reverse("two_factor:login"),
reverse("login_router"))
return redirect(login_url)
self.set_parameters(request)
self.set_csrf(request)
rows = self.get_results(request)
results_dict = self.get_results_dict(self.draw, self.page_number,
self.record_total,
self.filtered_total, rows)
return self.json(results_dict)
def set_parameters(self, request):
self.user = request.user
self.registry_code = request.GET.get("registry_code")
self.registry_model = get_object_or_404(Registry,
code=self.registry_code)
self.clinicians_have_patients = self.registry_model.has_feature(
"clinicians_have_patients")
self.form_progress = FormProgress(self.registry_model)
self.supports_contexts = self.registry_model.has_feature("contexts")
self.rdrf_context_manager = RDRFContextManager(self.registry_model)
def getint(param):
try:
return int(request.POST.get(param) or 0)
except ValueError:
return 0
self.search_term = request.POST.get("search[value]") or ""
self.draw = getint("draw") # unknown
self.start = getint("start") # offset
self.length = getint("length") # page size
self.page_number = (
(self.start / self.length) if self.length else 0) + 1
self.sort_field, self.sort_direction = self.get_ordering(request)
self.columns = self.get_configure_columns()
def get_results(self, request):
if self.registry_model is None:
return []
if not self.check_security():
return []
patients = self.run_query()
return patients
def check_security(self):
self.do_security_checks()
if not self.user.is_superuser:
if self.registry_model.code not in [
r.code for r in self.user.registry.all()
]:
logger.warning(
"User id %s tried to browse patients in registry %s of which they are not a member"
% (self.user.id, self.registry_model.code))
return False
return True
def get_ordering(self, request):
# columns[0][data]:full_name
# order[0][column]:1
# order[0][dir]:asc
sort_column_index = None
sort_direction = None
for key in request.POST:
if key.startswith("order"):
if "[column]" in key:
sort_column_index = request.POST[key]
elif "[dir]" in key:
sort_direction = request.POST[key]
column_name = "columns[%s][data]" % sort_column_index
sort_field = request.POST.get(column_name, None)
return sort_field, sort_direction
def run_query(self):
self.get_initial_queryset()
self.filter_by_user_group()
self.apply_ordering()
self.record_total = self.patients.count()
self.apply_search_filter()
self.filtered_total = self.patients.count()
return self.get_rows_in_page()
def _get_main_or_default_context(self, patient_model):
# for registries which do not have multiple contexts this will be the single context model
# assigned to the patient
# for registries which allow multiple form groups, it will be the
# (only) context with cfg marked as default
context_model = patient_model.default_context(self.registry_model)
assert context_model is not None, "Expected context model to exist always"
if context_model.context_form_group:
assert context_model.context_form_group.is_default, "Expected to always get a context of the default form group"
return context_model
def apply_custom_ordering(self, qs):
key_func = [
col.sort_key(self.supports_contexts, self.form_progress,
self.rdrf_context_manager) for col in self.columns
if col.field == self.sort_field and col.sort_key
and not col.sort_fields
]
if key_func:
# we have to retrieve all rows - otherwise , queryset has already been
# ordered on base model
k = key_func[0]
def key_func_wrapper(thing):
value = k(thing)
if value is None:
return self.bottom
else:
return value
return sorted(qs,
key=key_func_wrapper,
reverse=(self.sort_direction == "desc"))
else:
return qs
def get_rows_in_page(self):
results = self.apply_custom_ordering(self.patients)
rows = []
paginator = Paginator(results, self.length)
try:
page = paginator.page(self.page_number)
except InvalidPage:
logger.error("invalid page number: %s" % self.page_number)
return []
self.append_rows(page, rows)
return rows
def append_rows(self, page_object, row_list_to_update):
if self.registry_model.has_feature("consent_checks"):
row_list_to_update.extend([
self._get_row_dict(obj)
for obj in page_object.object_list if consent_check(
self.registry_model, self.user, obj, "see_patient")
])
else:
row_list_to_update.extend(
[self._get_row_dict(obj) for obj in page_object.object_list])
def _get_row_dict(self, instance):
# we need to do this so that the progress data for this instance
# loaded!
self.form_progress.reset()
self.form_progress._set_current(instance)
return {
col.field: col.fmt(
col.cell(instance, self.supports_contexts, self.form_progress,
self.rdrf_context_manager))
for col in self.columns
}
def get_initial_queryset(self):
self.registry_queryset = Registry.objects.filter(
code=self.registry_model.code)
self.patients = Patient.objects.all().prefetch_related(
"working_groups").prefetch_related("rdrf_registry").filter(
rdrf_registry__code=self.registry_model.code)
def apply_search_filter(self):
if self.search_term:
self.patients = self.patients.filter(
Q(given_names__icontains=self.search_term)
| Q(family_name__icontains=self.search_term))
def filter_by_user_group(self):
if not self.user.is_superuser:
if self.user.is_curator:
query_patients = Q(
rdrf_registry__in=self.registry_queryset) & Q(
working_groups__in=self.user.working_groups.all())
self.patients = self.patients.filter(query_patients)
elif self.user.is_genetic_staff:
self.patients = self.patients.filter(
working_groups__in=self.user.working_groups.all())
elif self.user.is_genetic_curator:
self.patients = self.patients.filter(
working_groups__in=self.user.working_groups.all())
elif self.user.is_working_group_staff:
self.patients = self.patients.filter(
working_groups__in=self.user.working_groups.all())
elif self.user.is_clinician and self.clinicians_have_patients:
self.patients = self.patients.filter(clinician=self.user)
elif self.user.is_clinician and not self.clinicians_have_patients:
query_patients = Q(
rdrf_registry__in=self.registry_queryset) & Q(
working_groups__in=self.user.working_groups.all())
self.patients = self.patients.filter(query_patients)
elif self.user.is_patient:
self.patients = self.patients.filter(user=self.user)
else:
self.patients = self.patients.none()
else:
self.patients = self.patients.filter(
rdrf_registry__in=self.registry_queryset)
def apply_ordering(self):
if self.sort_field and self.sort_direction:
def sdir(field):
return "-" + field if self.sort_direction == "desc" else field
sort_fields = chain(*[
map(sdir, col.sort_fields) for col in self.columns
if col.field == self.sort_field
])
self.patients = self.patients.order_by(*sort_fields)
def get_results_dict(self, draw, page, total_records,
total_filtered_records, rows):
return {
"draw": draw,
"recordsTotal": total_records,
"recordsFiltered": total_filtered_records,
"rows": rows
}
class DataSource:
def __init__(self,
registry_model,
column,
form_model=None,
section_model=None,
cde_model=None,
field=None):
self.registry_model = registry_model
self.column = column
self.form_model = form_model
self.section_model = section_model
self.form_progress = FormProgress(self.registry_model)
self.progress_percentage = None
if self.section_model:
self.is_multiple = section_model.allow_multiple
else:
self.is_multiple = False
self.cde_model = cde_model
self.field = field
@property
def datatype(self):
return lower_strip(self.cde_model.datatype)
@property
def column_name(self):
return self.column.name
def get_value(self, patient_model, context_model):
if self.field:
return self._get_field_value(patient_model, context_model)
else:
return self._get_cde_value(patient_model, context_model)
def _get_field_value(self, patient_model, context_model):
if self.field == "patient_id":
return patient_model.pk
elif self.field == "form":
return self.form_model.name
elif self.field == "context_id":
return context_model.pk
elif self.field == "section":
return self.section_model.display_name
elif self.field == "form_group":
return get_form_group(context_model)
elif self.field == "username":
return self._get_last_user(patient_model, context_model)
elif self.field == "timestamp":
return patient_model.get_form_timestamp(self.form_model,
context_model)
elif self.field == "progress":
return self._get_form_progress(patient_model, context_model)
else:
raise Exception("Unknown field: %s" % self.field)
def _get_form_progress(self, patient_model, context_model):
if self.progress_percentage is None:
self.progress_percentage = self.form_progress.get_form_progress(
self.form_model, patient_model, context_model)
return self.progress_percentage
def _get_last_user(self, patient_model, context_model):
# last user to edit the _form_ in this context
history = ClinicalData.objects.collection(self.registry_model.code,
"history")
snapshots = history.find(patient_model, record_type="snapshot")
snapshots = sorted([s for s in snapshots],
key=attrgetter("pk"),
reverse=True)
for snapshot in snapshots:
if snapshot.data and "record" in snapshot.data:
record = snapshot.data["record"]
if "context_id" in record:
if context_model.pk == record["context_id"]:
if "form_name" in snapshot.data:
form_name = snapshot.data["form_name"]
if form_name == self.form_model.name:
if "form_user" in snapshot.data:
return snapshot.data["form_user"]
def _get_cde_value(self, patient_model, context_model):
try:
data = get_clinical_data(self.registry_model.code,
patient_model.pk, context_model.pk)
raw_value = patient_model.get_form_value(
self.registry_model.code,
self.form_model.name,
self.section_model.code,
self.cde_model.code,
False,
context_id=context_model.pk,
clinical_data=data)
except KeyError:
# the dynamic data record is empty
return None
value = self.cde_model.get_display_value(raw_value)
return fix_display_value(self.cde_model.datatype, value)
