def cases(institute_id):
"""Display a list of cases for an institute."""
institute_obj = institute_and_case(store, institute_id)
query = request.args.get("query")
limit = 100
if request.args.get("limit"):
limit = int(request.args.get("limit"))
skip_assigned = request.args.get("skip_assigned")
is_research = request.args.get("is_research")
all_cases = store.cases(
collaborator=institute_id,
name_query=query,
skip_assigned=skip_assigned,
is_research=is_research,
)
sort_by = request.args.get("sort")
sort_order = request.args.get("order") or "asc"
if sort_by:
pymongo_sort = pymongo.ASCENDING
if sort_order == "desc":
pymongo_sort = pymongo.DESCENDING
if sort_by == "analysis_date":
all_cases.sort("analysis_date", pymongo_sort)
elif sort_by == "track":
all_cases.sort("track", pymongo_sort)
elif sort_by == "status":
all_cases.sort("status", pymongo_sort)
LOG.debug("Prepare all cases")
prioritized_cases = store.prioritized_cases(institute_id=institute_id)
data = controllers.cases(store, all_cases, prioritized_cases, limit)
data["sort_order"] = sort_order
data["sort_by"] = sort_by
data["nr_cases"] = store.nr_cases(institute_id=institute_id)
sanger_unevaluated = controllers.get_sanger_unevaluated(
store, institute_id, current_user.email)
if len(sanger_unevaluated) > 0:
data["sanger_unevaluated"] = sanger_unevaluated
return dict(
institute=institute_obj,
skip_assigned=skip_assigned,
is_research=is_research,
query=query,
**data,
)
def cases(store, request, institute_id):
"""Preprocess case objects.
Add all the necessary information to display the 'cases' view
Args:
store(adapter.MongoAdapter)
request(flask.request) request sent by browser to the api_institutes endpoint
institute_id(str): An _id of an institute
Returns:
data(dict): includes the cases, how many there are and the limit.
"""
data = {"search_terms": CASE_SEARCH_TERMS}
institute_obj = institute_and_case(store, institute_id)
data["institute"] = institute_obj
name_query = None
if request.args.get("search_term"):
name_query = "".join([
request.args.get("search_type"),
re.escape(request.args["search_term"].strip())
])
data["name_query"] = name_query
limit = int(request.args.get("search_limit")) if request.args.get(
"search_limit") else 100
skip_assigned = request.args.get("skip_assigned")
data["form"] = populate_case_filter_form(request.args)
data["skip_assigned"] = skip_assigned
is_research = request.args.get("is_research")
data["is_research"] = is_research
prioritized_cases = store.prioritized_cases(institute_id=institute_id)
all_cases = store.cases(
collaborator=institute_id,
name_query=name_query,
skip_assigned=skip_assigned,
is_research=is_research,
)
all_cases = _sort_cases(data, request, all_cases)
data["nr_cases"] = store.nr_cases(institute_id=institute_id)
sanger_unevaluated = get_sanger_unevaluated(store, institute_id,
current_user.email)
if len(sanger_unevaluated) > 0:
data["sanger_unevaluated"] = sanger_unevaluated
case_groups = {status: [] for status in CASE_STATUSES}
nr_cases = 0
# local function to add info to case obj
def populate_case_obj(case_obj):
analysis_types = set(ind["analysis_type"]
for ind in case_obj["individuals"])
LOG.debug("Analysis types found in %s: %s", case_obj["_id"],
",".join(analysis_types))
if len(analysis_types) > 1:
LOG.debug("Set analysis types to {'mixed'}")
analysis_types = set(["mixed"])
case_obj["analysis_types"] = list(analysis_types)
case_obj["assignees"] = [
store.user(user_email)
for user_email in case_obj.get("assignees", [])
]
# Check if case was re-runned
analyses = case_obj.get("analyses", [])
now = datetime.datetime.now()
case_obj["is_rerun"] = (len(analyses) > 1
or analyses and analyses[0].get("date", now) <
case_obj.get("analysis_date", now))
case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
case_obj["display_track"] = TRACKS[case_obj.get("track", "rare")]
return case_obj
for nr_cases, case_obj in enumerate(all_cases.limit(limit), 1):
case_obj = populate_case_obj(case_obj)
case_groups[case_obj["status"]].append(case_obj)
if prioritized_cases:
extra_prioritized = 0
for case_obj in prioritized_cases:
if any(
group_obj.get("display_name") == case_obj.get(
"display_name")
for group_obj in case_groups[case_obj["status"]]):
continue
else:
extra_prioritized += 1
case_obj = populate_case_obj(case_obj)
case_groups[case_obj["status"]].append(case_obj)
# extra prioritized cases are potentially shown in addition to the case query limit
nr_cases += extra_prioritized
data["cases"] = [(status, case_groups[status]) for status in CASE_STATUSES]
data["found_cases"] = nr_cases
data["limit"] = limit
return data