def case(institute_id, case_id):
"""View a specific case."""
institute = validate_user(current_user, institute_id)
# fetch a single, specific case from the data store
case_model = store.case(institute_id, case_id)
case_comments = store.events(institute, case=case_model, comments=True)
case_events = store.events(institute, case=case_model)
# map internal + external sample ids
sample_map = {"alt_{}".format(sample.individual_id): sample.display_name for sample in case_model.individuals}
group_id = "alt_{}".format(case_model.owner_case_id)
sample_map[group_id] = case_model.display_name
# default coverage report
default_panel_names = [panel.name_and_version for panel in case_model.default_panel_objs()]
return dict(
institute=institute,
case=case_model,
statuses=Case.status.choices,
case_comments=case_comments,
case_events=case_events,
institute_id=institute_id,
case_id=case_id,
panel_names=default_panel_names,
sample_map=sample_map,
)
def variant(institute_id, case_id, variant_id):
"""View a single variant in a single case."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
comments = store.events(institute, case=case_model, variant_id=variant_model.variant_id, comments=True)
events = store.events(institute, case=case_model, variant_id=variant_model.variant_id)
individuals = {individual.individual_id: individual for individual in case_model.individuals}
prev_variant = store.previous_variant(document_id=variant_id)
next_variant = store.next_variant(document_id=variant_id)
return dict(
institute=institute,
institute_id=institute_id,
case=case_model,
case_id=case_id,
variant=variant_model,
variant_id=variant_id,
comments=comments,
events=events,
prev_variant=prev_variant,
next_variant=next_variant,
manual_rank_options=Variant.manual_rank.choices,
individuals=individuals,
)
def case(institute_id, case_id):
"""View a specific case."""
institute = validate_user(current_user, institute_id)
# fetch a single, specific case from the data store
case_model = store.case(institute_id, case_id)
case_comments = store.events(institute, case=case_model, comments=True)
case_events = store.events(institute, case=case_model)
return dict(institute=institute, case=case_model, statuses=Case.status.choices,
case_comments=case_comments, case_events=case_events,
institute_id=institute_id, case_id=case_id)
