Resolve "import of serology data"

Closes #335 (closed), #336 (closed)

smash/web/api_views/subject.py

 import logging
+import re
 
 from django.db.models import Count, Case, When, Min, Max
 from django.db.models import Q
@@ -81,33 +82,48 @@ def get_subject_columns(request, subject_list_type):
     add_column(result, "Info sent", "information_sent", study_subject_columns, "yes_no_filter", study.columns)
 
     visit_from_zero = ConfigurationItem.objects.get(type=VISIT_SHOW_VISIT_NUMBER_FROM_ZERO).value
-    #True values are y, yes, t, true, on and 1; false values are n, no, f, false, off and 0.
+    # True values are y, yes, t, true, on and 1; false values are n, no, f, false, off and 0.
     if strtobool(visit_from_zero):
         virus_visit_numbers = range(0, 5)
         visit_numbers = range(0, study.visits_to_show_in_subject_list + 0)
     else:
-        virus_visit_numbers = range(1, 5+1)
+        virus_visit_numbers = range(1, 5 + 1)
         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), 
-                  'virus_test_{}'.format(one_based_idx), #always starts in 1
-                  study_subject_columns,
-                  'yes_no_null_inconclusive_filter', study.columns)
-        add_column(result, 
-                   "Visit {} RT-PCR date".format(virus_visit_number), 
-                   "virus_test_{}_updated".format(one_based_idx), 
+        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)
+        add_column(result,
+                   "Visit {} RT-PCR update date".format(virus_visit_number),
+                   "virus_test_{}_updated".format(one_based_idx),
+                   study_subject_columns,
+                   "virus_test_date", study.columns)
+        add_column(result,
+                   "Visit {} RT-PCR collection date".format(virus_visit_number),
+                   "virus_test_{}_collection_date".format(one_based_idx),
                    study_subject_columns,
                    "virus_test_date", study.columns)
+        add_column(result,
+                   "Visit {} IgA Status".format(virus_visit_number),
+                   "virus_test_{}_iga_status".format(one_based_idx),
+                   study_subject_columns,
+                   'serology_filter', study.columns)
+        add_column(result,
+                   "Visit {} IgG Status".format(virus_visit_number),
+                   "virus_test_{}_igg_status".format(one_based_idx),
+                   study_subject_columns,
+                   'serology_filter', study.columns)
 
     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, 
-                    "visit_filter", visible_param=study_subject_list.visits)
+        visit_key = "visit_{}".format(one_based_idx)  # always starts in 1
+        add_column(result, "Visit {}".format(visit_number), visit_key, None,
+                   "visit_filter", visible_param=study_subject_list.visits)
 
     return JsonResponse({"columns": result})
 
@@ -137,7 +153,9 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
         order_direction = ""
     else:
         order_direction = "-"
-    if order_column == "first_name":
+    if order_column is None:
+        logger.warn("Column cannot be null")
+    elif order_column == "first_name":
         result = subjects_to_be_ordered.order_by(order_direction + 'subject__first_name')
     elif order_column == "last_name":
         result = subjects_to_be_ordered.order_by(order_direction + 'subject__last_name')
@@ -200,26 +218,16 @@ 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 order_column == "virus_test_1":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1')
-    elif order_column == "virus_test_2":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2')
-    elif order_column == "virus_test_3":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3')
-    elif order_column == "virus_test_4":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4')
-    elif order_column == "virus_test_5":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5')
-    elif order_column == "virus_test_1_updated":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1_updated')
-    elif order_column == "virus_test_2_updated":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2_updated')
-    elif order_column == "virus_test_3_updated":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3_updated')
-    elif order_column == "virus_test_4_updated":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4_updated')
-    elif order_column == "virus_test_5_updated":
-        result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_updated')
+    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):
+        result = subjects_to_be_ordered.order_by(order_direction + 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):
+        result = subjects_to_be_ordered.order_by(order_direction + 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))
     return result
@@ -295,7 +303,9 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
     for row in filters:
         column = row[0]
         value = row[1]
-        if column == "first_name":
+        if column is None:
+            logger.warn("Filter column cannot be null")
+        elif column == "first_name":
             result = result.filter(subject__first_name__icontains=value)
         elif column == "last_name":
             result = result.filter(subject__last_name__icontains=value)
@@ -319,41 +329,25 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
             result = result.filter(resigned=(value == "true"))
         elif column == "endpoint_reached":
             result = result.filter(endpoint_reached=(value == "true"))
-        elif column == "virus_test_1":
-            if value == "null":
-                result = result.filter(virus_test_1__isnull=True, virus_test_1_updated__isnull=True)
-            elif value == "inconclusive":
-                result = result.filter(virus_test_1__isnull=True, virus_test_1_updated__isnull=False)
-            else:
-                result = result.filter(virus_test_1=(value == "true"))
-        elif column == "virus_test_2":
-            if value == "null":
-                result = result.filter(virus_test_2__isnull=True, virus_test_2_updated__isnull=True)
-            elif value == "inconclusive":
-                result = result.filter(virus_test_2__isnull=True, virus_test_2_updated__isnull=False)
-            else:
-                result = result.filter(virus_test_2=(value == "true"))
-        elif column == "virus_test_3":
-            if value == "null":
-                result = result.filter(virus_test_3__isnull=True, virus_test_3_updated__isnull=True)
-            elif value == "inconclusive":
-                result = result.filter(virus_test_3__isnull=True, virus_test_3_updated__isnull=False)
-            else:
-                result = result.filter(virus_test_3=(value == "true"))
-        elif column == "virus_test_4":
-            if value == "null":
-                result = result.filter(virus_test_4__isnull=True, virus_test_4_updated__isnull=True)
-            elif value == "inconclusive":
-                result = result.filter(virus_test_4__isnull=True, virus_test_4_updated__isnull=False)
-            else:
-                result = result.filter(virus_test_4=(value == "true"))
-        elif column == "virus_test_5":
+        elif re.search(r'^virus_test_[1-5]$', column):
+            visit_number = column.replace("virus_test_", "")
+            virus_test__isnull_param = "virus_test_{}__isnull".format(visit_number)
+            virus_test__updated__isnull_param = "virus_test_{}_updated__isnull".format(visit_number)
+            visit_test_param = "virus_test_{}".format(visit_number)
             if value == "null":
-                result = result.filter(virus_test_5__isnull=True, virus_test_5_updated__isnull=True)
+                result = result.filter(**{virus_test__isnull_param: True, virus_test__updated__isnull_param: True})
             elif value == "inconclusive":
-                result = result.filter(virus_test_5__isnull=True, virus_test_5_updated__isnull=False)
+                result = result.filter(**{virus_test__isnull_param: True, virus_test__updated__isnull_param: False})
             else:
-                result = result.filter(virus_test_5=(value == "true"))
+                result = result.filter(**{visit_test_param: (value == "true")})
+        elif re.search(r'^virus_test_[1-5]_iga_status$', column):
+            visit_number = column.replace("virus_test_", "").replace("_iga_status", "")
+            virus_test_iga_status_param = "virus_test_{}_iga_status".format(visit_number)
+            result = result.filter(**{virus_test_iga_status_param: value})
+        elif re.search(r'^virus_test_[1-5]_igg_status$', column):
+            visit_number = column.replace("virus_test_", "").replace("_igg_status", "")
+            virus_test_igg_status_param = "virus_test_{}_igg_status".format(visit_number)
+            result = result.filter(**{virus_test_igg_status_param: value})
         elif column == "brain_donation_agreement":
             result = result.filter(brain_donation_agreement=(value == "true"))
         elif column == "postponed":
@@ -519,16 +513,6 @@ 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,
         "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),
@@ -540,4 +524,12 @@ 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