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Resolve "import of serology data"

Merged Resolve "import of serology data"
335-import-of-serology-data into master
Merged Piotr Gawron requested to merge 335-import-of-serology-data into master
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smash/web/api_views/subject.py
+ 28
− 44
import logging
import re
from django.db.models import Count, Case, When, Min, Max
from django.db.models import Q
from django.http import JsonResponse
@@ -90,8 +91,8 @@ def get_subject_columns(request, subject_list_type):
visit_numbers = range(1, study.visits_to_show_in_subject_list + 1)
for one_based_idx, virus_visit_number in enumerate(virus_visit_numbers, 1):
add_column(result,
'Virus {} RT-PCR'.format(virus_visit_number),
add_column(result,
'Virus {} RT-PCR'.format(virus_visit_number),
'virus_test_{}'.format(one_based_idx), #always starts in 1
study_subject_columns,
'yes_no_null_inconclusive_filter', study.columns)
@@ -118,10 +119,10 @@ def get_subject_columns(request, subject_list_type):
add_column(result, "Type", "type", study_subject_columns, "type_filter", study.columns)
add_column(result, "Edit", "edit", None, None, sortable=False)
for one_based_idx, visit_number in enumerate(visit_numbers, 1):
visit_key = "visit_{}".format(one_based_idx) #always starts in 1
add_column(result, "Visit {}".format(visit_number), visit_key, None,
add_column(result, "Visit {}".format(visit_number), visit_key, None,
"visit_filter", visible_param=study_subject_list.visits)
return JsonResponse({"columns": result})
@@ -215,15 +216,15 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
elif str(order_column).startswith("visit_"):
visit_number = get_visit_number_from_visit_x_string(order_column)
result = order_by_visit(subjects_to_be_ordered, order_direction, visit_number)
elif re.search(r'^virus_test_[1-5]$',order_column):
elif re.search(r'^virus_test_[1-5]$', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
elif re.search(r'^virus_test_[1-5]_updated$',order_column):
elif re.search(r'^virus_test_[1-5]_updated$', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
elif re.search(r'^virus_test_[1-5]_collection_date',order_column):
elif re.search(r'^virus_test_[1-5]_collection_date', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
elif re.search(r'^virus_test_[1-5]_iga_status',order_column):
elif re.search(r'^virus_test_[1-5]_iga_status', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
elif re.search(r'^virus_test_[1-5]_igg_status',order_column):
elif re.search(r'^virus_test_[1-5]_igg_status', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
else:
logger.warn("Unknown sort column: " + str(order_column))
@@ -360,25 +361,25 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
else:
result = result.filter(virus_test_5=(value == "true"))
elif column == "virus_test_1_iga_status":
result = result.filter( virus_test_1_iga_status=value)
result = result.filter(virus_test_1_iga_status=value)
elif column == "virus_test_1_igg_status":
result = result.filter( virus_test_1_igg_status=value)
result = result.filter(virus_test_1_igg_status=value)
elif column == "virus_test_2_iga_status":
result = result.filter( virus_test_2_iga_status=value)
result = result.filter(virus_test_2_iga_status=value)
elif column == "virus_test_2_igg_status":
result = result.filter( virus_test_2_igg_status=value)
result = result.filter(virus_test_2_igg_status=value)
elif column == "virus_test_3_iga_status":
result = result.filter( virus_test_3_iga_status=value)
result = result.filter(virus_test_3_iga_status=value)
elif column == "virus_test_3_igg_status":
result = result.filter( virus_test_3_igg_status=value)
result = result.filter(virus_test_3_igg_status=value)
elif column == "virus_test_4_iga_status":
result = result.filter( virus_test_4_iga_status=value)
result = result.filter(virus_test_4_iga_status=value)
elif column == "virus_test_4_igg_status":
result = result.filter( virus_test_4_igg_status=value)
result = result.filter(virus_test_4_igg_status=value)
elif column == "virus_test_5_iga_status":
result = result.filter( virus_test_5_iga_status=value)
result = result.filter(virus_test_5_iga_status=value)
elif column == "virus_test_5_igg_status":
result = result.filter( virus_test_5_igg_status=value)
result = result.filter(virus_test_5_igg_status=value)
elif column == "brain_donation_agreement":
result = result.filter(brain_donation_agreement=(value == "true"))
elif column == "postponed":
@@ -544,31 +545,6 @@ def serialize_subject(study_subject):
"dead": bool_to_yes_no(study_subject.subject.dead),
"resigned": bool_to_yes_no(study_subject.resigned),
"endpoint_reached": bool_to_yes_no(study_subject.endpoint_reached),
"virus_test_1": virus_test_to_str(study_subject.virus_test_1, study_subject.virus_test_1_updated),
"virus_test_2": virus_test_to_str(study_subject.virus_test_2, study_subject.virus_test_2_updated),
"virus_test_3": virus_test_to_str(study_subject.virus_test_3, study_subject.virus_test_3_updated),
"virus_test_4": virus_test_to_str(study_subject.virus_test_4, study_subject.virus_test_4_updated),
"virus_test_5": virus_test_to_str(study_subject.virus_test_5, study_subject.virus_test_5_updated),
"virus_test_1_updated": study_subject.virus_test_1_updated,
"virus_test_2_updated": study_subject.virus_test_2_updated,
"virus_test_3_updated": study_subject.virus_test_3_updated,
"virus_test_4_updated": study_subject.virus_test_4_updated,
"virus_test_5_updated": study_subject.virus_test_5_updated,
"virus_test_1_collection_date": study_subject.virus_test_1_collection_date,
"virus_test_2_collection_date": study_subject.virus_test_2_collection_date,
"virus_test_3_collection_date": study_subject.virus_test_3_collection_date,
"virus_test_4_collection_date": study_subject.virus_test_4_collection_date,
"virus_test_5_collection_date": study_subject.virus_test_5_collection_date,
"virus_test_1_iga_status": study_subject.virus_test_1_iga_status,
"virus_test_1_igg_status": study_subject.virus_test_1_igg_status,
"virus_test_2_iga_status": study_subject.virus_test_2_iga_status,
"virus_test_2_igg_status": study_subject.virus_test_2_igg_status,
"virus_test_3_iga_status": study_subject.virus_test_3_iga_status,
"virus_test_3_igg_status": study_subject.virus_test_3_igg_status,
"virus_test_4_iga_status": study_subject.virus_test_4_iga_status,
"virus_test_4_igg_status": study_subject.virus_test_4_igg_status,
"virus_test_5_iga_status": study_subject.virus_test_5_iga_status,
"virus_test_5_igg_status": study_subject.virus_test_5_igg_status,
"postponed": bool_to_yes_no(study_subject.postponed),
"brain_donation_agreement": bool_to_yes_no(study_subject.brain_donation_agreement),
"excluded": bool_to_yes_no(study_subject.excluded),
@@ -580,4 +556,12 @@ def serialize_subject(study_subject):
"id": study_subject.id,
"visits": serialized_visits,
}
for i in range(1, 6):
result['virus_test_{}'.format(i)] = virus_test_to_str(getattr(study_subject, "virus_test_{}".format(i)),
getattr(study_subject, "virus_test_{}_updated".format(i)))
result["virus_test_{}_updated".format(i)] = getattr(study_subject, "virus_test_{}_updated".format(i))
result["virus_test_{}_collection_date".format(i)] = getattr(study_subject,
"virus_test_{}_collection_date".format(i))
result["virus_test_{}_iga_status".format(i)] = getattr(study_subject, "virus_test_{}_iga_status".format(i))
result["virus_test_{}_igg_status".format(i)] = getattr(study_subject, "virus_test_{}_igg_status".format(i))
return result