diff --git a/smash/db_scripts/create_dummy_data.py b/smash/db_scripts/create_dummy_data.py
index aef885576c0f122d9f64dab0fa4408b6c2b705ed..dfcb4ffff8a5da756d07e56e1e0eb635afb5b28d 100644
--- a/smash/db_scripts/create_dummy_data.py
+++ b/smash/db_scripts/create_dummy_data.py
@@ -431,15 +431,15 @@ class smashProvider(BaseProvider):
screening_number = self.createSmashScreeningNumber(
default_location.prefix)
- virus_test_1 = choice([None, True, False], 1, p=[0.2, 0.3, 0.5])[0]
+ virus_test_1_result = choice([None, "Positive", "Negative", "Inconclusive"], 1, p=[0.2, 0.2, 0.3, 0.3])[0]
virus_iga_1 = choice(["Borderline", "Positive", "Negative"], 1, p=[0.02, 0.03, 0.95])[0]
virus_igg_1 = choice(["Borderline", "Positive", "Negative"], 1, p=[0.02, 0.03, 0.95])[0]
- if virus_test_1 is None:
+ if virus_test_1_result is None:
+ virus_test_1_updated = fake.date_between(start_date='-30d', end_date='-4d')
+ elif virus_test_1_result == "Inconclusive":
virus_test_1_updated = fake.date_between(start_date='-30d', end_date='-4d')
- #inconclusive results have a date
- virus_test_1_updated = choice([None, virus_test_1_updated], 1, p=[0.7, 0.3])[0]
virus_test_1_collection_date = choice([None, virus_test_1_updated], 1, p=[0.7, 0.3])[0]
- elif virus_test_1 == True:
+ elif virus_test_1_result == "Positive":
virus_test_1_updated = fake.date_between(start_date='-30d', end_date='-4d')
virus_test_1_collection_date = fake.date_between(start_date='-30d', end_date='-4d')
else:
@@ -447,7 +447,8 @@ class smashProvider(BaseProvider):
virus_test_1_collection_date = fake.date_between(start_date='-30d', end_date='-4d')
study_subject, _ = StudySubject.objects.update_or_create(nd_number=nd_number, subject=subject,
- virus_test_1=virus_test_1, virus_test_1_updated=virus_test_1_updated,
+ virus_test_1_result=virus_test_1_result,
+ virus_test_1_updated=virus_test_1_updated,
virus_test_1_collection_date=virus_test_1_collection_date,
virus_test_1_iga_status=virus_iga_1,
virus_test_1_igg_status=virus_igg_1,
diff --git a/smash/web/api_views/subject.py b/smash/web/api_views/subject.py
index ca4f2ba097caae012c6ac47e0ad44cdeb71b63be..6796e46610f95e52857643fed375724fe3553097 100644
--- a/smash/web/api_views/subject.py
+++ b/smash/web/api_views/subject.py
@@ -8,7 +8,7 @@ from django.http import JsonResponse
from django.urls import reverse
from web.api_views.serialization_utils import str_to_yes_no_null, bool_to_yes_no, flying_team_to_str, location_to_str, \
- add_column, serialize_date, serialize_datetime, get_filters_for_data_table_request, virus_test_to_str
+ add_column, serialize_date, serialize_datetime, get_filters_for_data_table_request
from web.models import ConfigurationItem, StudySubject, Visit, Appointment, Subject, SubjectColumns, StudyColumns, \
Study, ContactAttempt
from web.models.constants import SUBJECT_TYPE_CHOICES, GLOBAL_STUDY_ID, VISIT_SHOW_VISIT_NUMBER_FROM_ZERO, \
@@ -97,7 +97,7 @@ def get_subject_columns(request, subject_list_type):
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
+ 'virus_test_{}_result'.format(one_based_idx), # always starts in 1
study_subject_columns,
'yes_no_null_inconclusive_filter', study.columns)
add_column(result,
@@ -280,7 +280,7 @@ def get_subjects_order(subjects_to_be_ordered: QuerySet, order_column, order_dir
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]$', order_column):
+ elif re.search(r'^virus_test_[1-5]_result$', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
elif re.search(r'^virus_test_[1-5]_updated$', order_column):
result = subjects_to_be_ordered.order_by(order_direction + order_column)
@@ -397,17 +397,14 @@ def get_subjects_filtered(subjects_to_be_filtered: QuerySet, filters) -> QuerySe
result = result.filter(resigned=(value == "true"))
elif column == "endpoint_reached":
result = result.filter(endpoint_reached=(value == "true"))
- elif re.search(r'^virus_test_[1-5]$', 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)
+ elif re.search(r'^virus_test_[1-5]_result$', column):
+ visit_number = column.replace("virus_test_", "").replace("_result","")
+ virus_test__isnull_param = "virus_test_{}_result__isnull".format(visit_number)
+ visit_test_param = "virus_test_{}_result".format(visit_number)
if value == "null":
- result = result.filter(**{virus_test__isnull_param: True, virus_test__updated__isnull_param: True})
- elif value == "inconclusive":
- result = result.filter(**{virus_test__isnull_param: True, virus_test__updated__isnull_param: False})
+ result = result.filter(**{virus_test__isnull_param: True})
else:
- result = result.filter(**{visit_test_param: (value == "true")})
+ result = result.filter(**{visit_test_param: value})
elif re.search(r'^virus_test_[1-5]_iga_status$', column):
visit_number = column.replace("virus_test_", "").replace("_iga_status", "")
virus_test_iga_status_param = "virus_test_{}_iga_status".format(visit_number)
@@ -530,7 +527,7 @@ def types(request):
})
-def serialize_subject(study_subject):
+def serialize_subject(study_subject:StudySubject):
location = location_to_str(study_subject.default_location)
flying_team = flying_team_to_str(study_subject.flying_team)
visits = Visit.objects.filter(subject=study_subject).order_by('visit_number')
@@ -620,8 +617,7 @@ def serialize_subject(study_subject):
"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_{}_result'.format(i)] = getattr(study_subject, "virus_test_{}_result".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))
diff --git a/smash/web/forms/study_subject_forms.py b/smash/web/forms/study_subject_forms.py
index 6211544bd6817c549a35561bb9ce1e60786a3b86..8b6d57082adc773c9af460cf7a1470bc6486f35b 100644
--- a/smash/web/forms/study_subject_forms.py
+++ b/smash/web/forms/study_subject_forms.py
@@ -124,7 +124,7 @@ class StudySubjectForm(ModelForm):
if strtobool(visit_from_zero):
virus_visit_numbers = list(range(0, 5))
for one_based_idx, virus_visit_number in enumerate(virus_visit_numbers, 1):
- field = 'virus_test_{}'.format(one_based_idx)
+ field = 'virus_test_{}_result'.format(one_based_idx)
self.fields[field].label = 'Visit {} RT-PCR'.format(virus_visit_number)
date_field = 'virus_test_{}_updated'.format(one_based_idx)
@@ -140,19 +140,6 @@ class StudySubjectForm(ModelForm):
for visit_number in range(1, 6):
disable_virus_test_field(self, visit_number)
- self.update_virus_inconclusive_data(visit_number)
-
- def update_virus_inconclusive_data(self, visit_number):
- test_result_column_name = 'virus_test_{}'.format(visit_number)
- test_date_column_name = 'virus_test_{}_updated'.format(visit_number)
-
- self.fields[test_result_column_name].widget.choices.append(("Inc", 'Inconclusive'))
- instance = getattr(self, 'instance', None)
- if instance and instance.id:
- test_result = getattr(instance, test_result_column_name)
- test_date = getattr(instance, test_date_column_name)
- if test_result is None and test_date is not None:
- self.initial[test_result_column_name] = "Inc"
def clean(self):
cleaned_data = super(StudySubjectForm, self).clean()
@@ -338,7 +325,7 @@ class StudySubjectEditForm(StudySubjectForm):
def disable_virus_test_field(self, visit_number):
- test_result_column_name = 'virus_test_{}'.format(visit_number)
+ test_result_column_name = 'virus_test_{}_result'.format(visit_number)
test_result_date_column_name = 'virus_test_{}_updated'.format(visit_number)
test_collection_date_column_name = 'virus_test_{}_collection_date'.format(visit_number)
test_iga_status_column_name = 'virus_test_{}_iga_status'.format(visit_number)
@@ -392,11 +379,11 @@ def prepare_study_subject_fields(fields, study):
prepare_field(fields, study.columns, 'previously_in_study')
prepare_field(fields, study.columns, 'voucher_types')
- prepare_field(fields, study.columns, 'virus_test_1')
- prepare_field(fields, study.columns, 'virus_test_2')
- prepare_field(fields, study.columns, 'virus_test_3')
- prepare_field(fields, study.columns, 'virus_test_4')
- prepare_field(fields, study.columns, 'virus_test_5')
+ prepare_field(fields, study.columns, 'virus_test_1_result')
+ prepare_field(fields, study.columns, 'virus_test_2_result')
+ prepare_field(fields, study.columns, 'virus_test_3_result')
+ prepare_field(fields, study.columns, 'virus_test_4_result')
+ prepare_field(fields, study.columns, 'virus_test_5_result')
prepare_field(fields, study.columns, 'virus_test_1_updated')
prepare_field(fields, study.columns, 'virus_test_2_updated')
prepare_field(fields, study.columns, 'virus_test_3_updated')
diff --git a/smash/web/migrations/0188_studysubject_virus_test_1_result.py b/smash/web/migrations/0188_studysubject_virus_test_1_result.py
new file mode 100644
index 0000000000000000000000000000000000000000..5a7403bbaf2b91320cedfc11cf87dd4d662007db
--- /dev/null
+++ b/smash/web/migrations/0188_studysubject_virus_test_1_result.py
@@ -0,0 +1,98 @@
+# Generated by Django 3.1.3 on 2020-12-01 07:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0187_auto_20201130_1224'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1_result',
+ field=models.CharField(max_length=20, null=True),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2_result',
+ field=models.CharField(max_length=20, null=True),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3_result',
+ field=models.CharField(max_length=20, null=True),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4_result',
+ field=models.CharField(max_length=20, null=True),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5_result',
+ field=models.CharField(max_length=20, null=True),
+ ),
+ migrations.RunSQL("update web_studysubject set virus_test_1_result='Positive' "
+ "where virus_test_1 is not null and virus_test_1"),
+ migrations.RunSQL("update web_studysubject set virus_test_1_result='Negative' "
+ "where virus_test_1 is not null and not virus_test_1"),
+ migrations.RunSQL("update web_studysubject set virus_test_1_result='Inconclusive' "
+ "where virus_test_1 is null and virus_test_1_updated is not null"),
+
+ migrations.RunSQL("update web_studysubject set virus_test_2_result='Positive' "
+ "where virus_test_2 is not null and virus_test_2"),
+ migrations.RunSQL("update web_studysubject set virus_test_2_result='Negative' "
+ "where virus_test_2 is not null and not virus_test_2"),
+ migrations.RunSQL("update web_studysubject set virus_test_2_result='Inconclusive' "
+ "where virus_test_2 is null and virus_test_2_updated is not null"),
+
+ migrations.RunSQL("update web_studysubject set virus_test_3_result='Positive' "
+ "where virus_test_3 is not null and virus_test_3"),
+ migrations.RunSQL("update web_studysubject set virus_test_3_result='Negative' "
+ "where virus_test_3 is not null and not virus_test_3"),
+ migrations.RunSQL("update web_studysubject set virus_test_3_result='Inconclusive' "
+ "where virus_test_3 is null and virus_test_3_updated is not null"),
+
+ migrations.RunSQL("update web_studysubject set virus_test_4_result='Positive' "
+ "where virus_test_4 is not null and virus_test_4"),
+ migrations.RunSQL("update web_studysubject set virus_test_4_result='Negative' "
+ "where virus_test_4 is not null and not virus_test_4"),
+ migrations.RunSQL("update web_studysubject set virus_test_4_result='Inconclusive' "
+ "where virus_test_4 is null and virus_test_4_updated is not null"),
+
+ migrations.RunSQL("update web_studysubject set virus_test_5_result='Positive' "
+ "where virus_test_5 is not null and virus_test_5"),
+ migrations.RunSQL("update web_studysubject set virus_test_5_result='Negative' "
+ "where virus_test_5 is not null and not virus_test_5"),
+ migrations.RunSQL("update web_studysubject set virus_test_5_result='Inconclusive' "
+ "where virus_test_5 is null and virus_test_5_updated is not null"),
+ migrations.RenameField(
+ model_name='studycolumns',
+ old_name='virus_test_1',
+ new_name='virus_test_1_result',
+ ),
+ migrations.RenameField(
+ model_name='studycolumns',
+ old_name='virus_test_2',
+ new_name='virus_test_2_result',
+ ),
+ migrations.RenameField(
+ model_name='studycolumns',
+ old_name='virus_test_3',
+ new_name='virus_test_3_result',
+ ),
+ migrations.RenameField(
+ model_name='studycolumns',
+ old_name='virus_test_4',
+ new_name='virus_test_4_result',
+ ),
+ migrations.RenameField(
+ model_name='studycolumns',
+ old_name='virus_test_5',
+ new_name='virus_test_5_result',
+ ),
+
+ ]
diff --git a/smash/web/migrations/0189_remove_studysubject_virus_test_1.py b/smash/web/migrations/0189_remove_studysubject_virus_test_1.py
new file mode 100644
index 0000000000000000000000000000000000000000..e18f54cb8db7ba0a3d6dd133526dfac6e058e906
--- /dev/null
+++ b/smash/web/migrations/0189_remove_studysubject_virus_test_1.py
@@ -0,0 +1,33 @@
+# Generated by Django 3.1.3 on 2020-12-01 08:03
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0188_studysubject_virus_test_1_result'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='studysubject',
+ name='virus_test_1',
+ ),
+ migrations.RemoveField(
+ model_name='studysubject',
+ name='virus_test_2',
+ ),
+ migrations.RemoveField(
+ model_name='studysubject',
+ name='virus_test_3',
+ ),
+ migrations.RemoveField(
+ model_name='studysubject',
+ name='virus_test_4',
+ ),
+ migrations.RemoveField(
+ model_name='studysubject',
+ name='virus_test_5',
+ ),
+ ]
diff --git a/smash/web/models/mail_template.py b/smash/web/models/mail_template.py
index bf101409a62f905e7c1c9f658bc262460517e4a9..4879740c5566148c0573732fa27d53a42d6aaa7b 100644
--- a/smash/web/models/mail_template.py
+++ b/smash/web/models/mail_template.py
@@ -277,11 +277,11 @@ class MailTemplate(models.Model):
if appointment.datetime_when is not None:
# TODO: 2to3
# Was:
- #appointment_date_full = appointment.datetime_when.strftime(DATETIME_FORMAT).decode(
+ # appointment_date_full = appointment.datetime_when.strftime(DATETIME_FORMAT).decode(
# date_format_encoding())
- #appointment_date_short = appointment.datetime_when.strftime(DATE_FORMAT_SHORT).decode(
+ # appointment_date_short = appointment.datetime_when.strftime(DATE_FORMAT_SHORT).decode(
# date_format_encoding())
- #appointment_date_time = appointment.datetime_when.strftime(DATE_FORMAT_TIME).decode(
+ # appointment_date_time = appointment.datetime_when.strftime(DATE_FORMAT_TIME).decode(
# date_format_encoding())
# Is:
appointment_date_full = appointment.datetime_when.strftime(DATETIME_FORMAT)
@@ -315,8 +315,8 @@ class MailTemplate(models.Model):
# "##V_DATE_START_FULL##": visit.datetime_begin.strftime(DATETIME_FORMAT).decode(date_format_encoding()),
# "##V_DATE_START_SHORT##": visit.datetime_begin.strftime(DATE_FORMAT_SHORT).decode(
# date_format_encoding()),
- #"##V_DATE_ENDS_FULL##": visit.datetime_end.strftime(DATETIME_FORMAT).decode(date_format_encoding()),
- #"##V_DATE_ENDS_SHORT##": visit.datetime_end.strftime(DATE_FORMAT_SHORT).decode(date_format_encoding()),
+ # "##V_DATE_ENDS_FULL##": visit.datetime_end.strftime(DATETIME_FORMAT).decode(date_format_encoding()),
+ # "##V_DATE_ENDS_SHORT##": visit.datetime_end.strftime(DATE_FORMAT_SHORT).decode(date_format_encoding()),
# Is:
"##V_DATE_START_FULL##": visit.datetime_begin.strftime(DATETIME_FORMAT),
"##V_DATE_START_SHORT##": visit.datetime_begin.strftime(DATE_FORMAT_SHORT),
@@ -368,8 +368,9 @@ class MailTemplate(models.Model):
for i in range(1, 6):
virus_test_field = "##S_VIRUS_{}_RESULT##".format(i)
- virus_test_value = virus_test_to_str(getattr(study_subject, "virus_test_{}".format(i)),
- getattr(study_subject, "virus_test_{}_updated".format(i)))
+ virus_test_value = getattr(study_subject, "virus_test_{}_result".format(i))
+ if virus_test_value == "" or virus_test_value is None:
+ virus_test_value = "N/A"
virus_test_date_field = "##S_VIRUS_{}_SAMPLE_COLLECTION_DATE##".format(i)
virus_test_date_value = date_to_str(getattr(study_subject, "virus_test_{}_collection_date".format(i)),
@@ -386,8 +387,6 @@ class MailTemplate(models.Model):
virus_igg_status_value = ""
if virus_test_date_value != "":
- if virus_test_value == "":
- virus_test_value = "N/A"
if virus_iga_status_value == "":
virus_iga_status_value = "N/A"
if virus_igg_status_value == "":
@@ -428,14 +427,3 @@ class MailTemplate(models.Model):
"##C_HOURS##": str(voucher.hours),
}
return {}
-
-
-def virus_test_to_str(test, date):
- if test is None and date is not None:
- return "Inconclusive"
- if test is None:
- return ""
- if test:
- return "Positive"
- else:
- return "Negative"
diff --git a/smash/web/models/study_columns.py b/smash/web/models/study_columns.py
index 03f8d30a1b0ea34662af991c58b27359a5c47fdd..1f89f2bd2452848125b68fc087b09b4a418bfde2 100644
--- a/smash/web/models/study_columns.py
+++ b/smash/web/models/study_columns.py
@@ -124,23 +124,23 @@ class StudyColumns(models.Model):
verbose_name='Brain donation agreement',
)
- virus_test_1 = models.BooleanField(
+ virus_test_1_result = models.BooleanField(
default=False,
verbose_name='Visit 1 virus results',
)
- virus_test_2 = models.BooleanField(
+ virus_test_2_result = models.BooleanField(
default=False,
verbose_name='Visit 2 virus results',
)
- virus_test_3 = models.BooleanField(
+ virus_test_3_result = models.BooleanField(
default=False,
verbose_name='Visit 3 virus results',
)
- virus_test_4 = models.BooleanField(
+ virus_test_4_result = models.BooleanField(
default=False,
verbose_name='Visit 4 virus results',
)
- virus_test_5 = models.BooleanField(
+ virus_test_5_result = models.BooleanField(
default=False,
verbose_name='Visit 5 virus results',
)
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index 39c77a02dac4b98add0562649b69cb6f6f44c07e..57b25a0f86e4758e3cff929b5e460c3e5b25b4fa 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -8,9 +8,11 @@ from django.db.models.signals import post_save
from django.dispatch import receiver
from web.models import VoucherType, Appointment, Location, Visit, Provenance
-from web.models.constants import BOOL_CHOICES, SUBJECT_TYPE_CHOICES, FILE_STORAGE, BOOL_CHOICES_WITH_NONE
+from web.models.constants import BOOL_CHOICES, SUBJECT_TYPE_CHOICES, FILE_STORAGE
from web.models.custom_data import CustomStudySubjectValue, CustomStudySubjectField
+VIRUS_CHOICES = ((None, 'N/A'), ('Inconclusive', 'Inconclusive'), ('Positive', 'Positive'), ('Negative', 'Negative'))
+
logger = logging.getLogger(__name__)
@@ -205,31 +207,12 @@ class StudySubject(models.Model):
verbose_name='Endpoint reached comments'
)
- virus_test_1 = models.BooleanField(choices=BOOL_CHOICES_WITH_NONE,
- verbose_name='Visit 1 virus result',
- default=None,
- null=True
- )
- virus_test_2 = models.BooleanField(choices=BOOL_CHOICES_WITH_NONE,
- verbose_name='Visit 2 virus result',
- default=None,
- null=True
- )
- virus_test_3 = models.BooleanField(choices=BOOL_CHOICES_WITH_NONE,
- verbose_name='Visit 3 virus result',
- default=None,
- null=True
- )
- virus_test_4 = models.BooleanField(choices=BOOL_CHOICES_WITH_NONE,
- verbose_name='Visit 4 virus result',
- default=None,
- null=True
- )
- virus_test_5 = models.BooleanField(choices=BOOL_CHOICES_WITH_NONE,
- verbose_name='Visit 5 virus result',
- default=None,
- null=True
- )
+ virus_test_1_result = models.CharField(max_length=20, null=True, choices=VIRUS_CHOICES)
+ virus_test_2_result = models.CharField(max_length=20, null=True, choices=VIRUS_CHOICES)
+ virus_test_3_result = models.CharField(max_length=20, null=True, choices=VIRUS_CHOICES)
+ virus_test_4_result = models.CharField(max_length=20, null=True, choices=VIRUS_CHOICES)
+ virus_test_5_result = models.CharField(max_length=20, null=True, choices=VIRUS_CHOICES)
+
virus_test_1_updated = models.DateField(verbose_name='Visit 1 virus result date',
blank=True,
null=True,
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index 70ae1d34e475aca3d2ab02faa0a0383fa9c5e8b3..57c63767745448f654fb525bce5829967ca54c4e 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -245,20 +245,20 @@ class RedcapConnector(object):
smasch_appointment.visit.save()
if visit.virus is not None or visit.virus_inconclusive:
changes = []
- if visit.visit_number == 1 and subject.virus_test_1 != visit.virus:
- changes.extend([('virus_test_1', visit.virus),
+ if visit.visit_number == 1 and subject.virus_test_1_result != visit.virus:
+ changes.extend([('virus_test_1_result', visit.virus),
('virus_test_1_updated', datetime.datetime.now())])
- if visit.visit_number == 2 and subject.virus_test_2 != visit.virus:
- changes.extend([('virus_test_2', visit.virus),
+ if visit.visit_number == 2 and subject.virus_test_2_result != visit.virus:
+ changes.extend([('virus_test_2_result', visit.virus),
('virus_test_2_updated', datetime.datetime.now())])
- if visit.visit_number == 3 and subject.virus_test_3 != visit.virus:
- changes.extend([('virus_test_3', visit.virus),
+ if visit.visit_number == 3 and subject.virus_test_3_result != visit.virus:
+ changes.extend([('virus_test_3_result', visit.virus),
('virus_test_3_updated', datetime.datetime.now())])
- if visit.visit_number == 4 and subject.virus_test_4 != visit.virus:
- changes.extend([('virus_test_4', visit.virus),
+ if visit.visit_number == 4 and subject.virus_test_4_result != visit.virus:
+ changes.extend([('virus_test_4_result', visit.virus),
('virus_test_4_updated', datetime.datetime.now())])
- if visit.visit_number == 5 and subject.virus_test_5 != visit.virus:
- changes.extend([('virus_test_5', visit.virus),
+ if visit.visit_number == 5 and subject.virus_test_5_result != visit.virus:
+ changes.extend([('virus_test_5_result', visit.virus),
('virus_test_5_updated', datetime.datetime.now())])
if visit.visit_number == 1 and subject.virus_test_1_updated is None and visit.virus_inconclusive:
changes.extend([('virus_test_1_updated', datetime.datetime.now())])
@@ -435,11 +435,11 @@ class RedcapConnector(object):
visit.visit_number = 1
if self.virus_field != "":
if row.get(self.virus_field) == "Negative":
- visit.virus = False
+ visit.virus = "Negative"
elif row.get(self.virus_field) == "Positive":
- visit.virus = True
+ visit.virus = "Positive"
elif row.get(self.virus_field) == "Inconclusive":
- visit.virus_inconclusive = True
+ visit.virus_inconclusive = "Inconclusive"
if self.sample_date_field != "":
date_str = row.get(self.sample_date_field)
if date_str is not None and date_str != "" and date_str != "Not done" and date_str != "Not known":
@@ -474,11 +474,11 @@ class RedcapConnector(object):
visit.visit_number = i + self.study.redcap_first_visit_number + 1
if self.virus_field != "":
if row.get(self.virus_field) == "Negative":
- visit.virus = False
+ visit.virus = "Negative"
elif row.get(self.virus_field) == "Positive":
- visit.virus = True
+ visit.virus = "Positive"
elif row.get(self.virus_field) == "Inconclusive":
- visit.virus_inconclusive = True
+ visit.virus_inconclusive = "Inconclusive"
if self.sample_date_field != "":
date_str = row.get(self.sample_date_field)
if date_str is not None and date_str != "" and date_str != "Not done" and date_str != "Not known":
diff --git a/smash/web/static/js/smash.js b/smash/web/static/js/smash.js
index a7a3dcba9c3c820b7337fd3d5ec3451fdf77d8a7..408d2335df9751b63a12085aedc5e8e70d810ad4 100644
--- a/smash/web/static/js/smash.js
+++ b/smash/web/static/js/smash.js
@@ -314,7 +314,7 @@ function createTable(params) {
$(this).html('<select style="width:60px" ><option value selected="selected">---</option><option value="true">YES</option><option value="false">NO</option><option value="null">N/A</option></select>');
});
$(tableElement).find('tfoot div[name="yes_no_null_inconclusive_filter"]').each(function () {
- $(this).html('<select style="width:100px" ><option value selected="selected">---</option><option value="true">Positive</option><option value="false">Negative</option><option value="null">N/A</option><option value="inconclusive">Inconclusive</option></select>');
+ $(this).html('<select style="width:100px" ><option value selected="selected">---</option><option value="Positive">Positive</option><option value="Negative">Negative</option><option value="null">N/A</option><option value="Inconclusive">Inconclusive</option></select>');
});
$(tableElement).find('tfoot div[name="serology_filter"]').each(function () {
$(this).html('<select style="width:100px" ><option value selected="selected">---</option><option value="Positive">Positive</option><option value="Negative">Negative</option><option value="Borderline">Borderline</option></select>');
diff --git a/smash/web/tests/api_views/test_subject.py b/smash/web/tests/api_views/test_subject.py
index 9ecdc98169c49f37ccd62eb893bdd55c3bc1a57c..47caeef1f6356594efa88948aee41a3d11ae24f4 100644
--- a/smash/web/tests/api_views/test_subject.py
+++ b/smash/web/tests/api_views/test_subject.py
@@ -29,7 +29,7 @@ logger = logging.getLogger(__name__)
class TestSubjectApi(LoggedInWithWorkerTestCase):
def setUp(self):
- super(TestSubjectApi, self).setUp()
+ super().setUp()
self.study_subject = create_study_subject()
self.warning_counter = MsgCounterHandler()
logging.getLogger('').addHandler(self.warning_counter)
@@ -701,22 +701,22 @@ class TestSubjectApi(LoggedInWithWorkerTestCase):
self.assertEqual(self.get_warning_count(), 0, msg="Sorting by \"" + order + "\" does not work")
def test_subjects_filter_virus_test(self):
- study_subject_positive = create_study_subject(2)
- study_subject_positive.virus_test_1 = True
+ study_subject_positive = create_study_subject()
+ study_subject_positive.virus_test_1_result = "Positive"
study_subject_positive.save()
- study_subject_negative = create_study_subject(2)
- study_subject_negative.virus_test_1 = False
+ study_subject_negative = create_study_subject()
+ study_subject_negative.virus_test_1_result = "Negative"
study_subject_negative.save()
- study_subject_inconclusive = create_study_subject(2)
- study_subject_inconclusive.virus_test_1 = None
+ study_subject_inconclusive = create_study_subject()
+ study_subject_inconclusive.virus_test_1_result = "Inconclusive"
study_subject_inconclusive.virus_test_1_updated = timezone.now()
study_subject_inconclusive.save()
- self.check_subject_filtered([["virus_test_1", "true"]], [study_subject_positive])
- self.check_subject_filtered([["virus_test_1", "false"]], [study_subject_negative])
- self.check_subject_filtered([["virus_test_1", "inconclusive"]], [study_subject_inconclusive])
+ self.check_subject_filtered([["virus_test_1_result", "Positive"]], [study_subject_positive])
+ self.check_subject_filtered([["virus_test_1_result", "Negative"]], [study_subject_negative])
+ self.check_subject_filtered([["virus_test_1_result", "Inconclusive"]], [study_subject_inconclusive])
@parameterized.expand([
('text', CUSTOM_FIELD_TYPE_TEXT, 'bla'),
diff --git a/smash/web/tests/view/test_mail.py b/smash/web/tests/view/test_mail.py
index 1f11340a796aedc4e9c0eebf7662ddd50d3cce33..36fbf90a0d6fca6ca9b0d5d03da612f167d645e2 100644
--- a/smash/web/tests/view/test_mail.py
+++ b/smash/web/tests/view/test_mail.py
@@ -1,31 +1,13 @@
import logging
-from django.urls import reverse
-
-from web.models import MailTemplate
-from web.models.constants import MAIL_TEMPLATE_CONTEXT_VOUCHER
from web.tests import LoggedInTestCase
-from web.tests.functions import create_voucher, get_resource_path
+from web.views.virus_mail import KitRequestEmailSendJob
logger = logging.getLogger(__name__)
-class MailTests(LoggedInTestCase):
- def test_generate_vouchers(self):
- voucher = create_voucher()
- MailTemplate(name="name", language=None,
- context=MAIL_TEMPLATE_CONTEXT_VOUCHER,
- template_file=get_resource_path('upcoming_appointment_FR.docx')).save()
-
- page = reverse('web.views.mail_template_generate_for_vouchers') + "?voucher_id=" + str(voucher.id)
- response = self.client.get(page)
- self.assertEqual(response.status_code, 200)
-
- def test_list_mail_templates(self):
- self.login_as_admin()
- response = self.client.get(reverse("web.views.mail_templates"))
- self.assertEqual(response.status_code, 200)
-
- def test_list_mail_templates_without_permission(self):
- response = self.client.get(reverse("web.views.mail_templates"))
- self.assertEqual(response.status_code, 302)
+class VirusMailTests(LoggedInTestCase):
+ def test_send_email(self):
+ job = KitRequestEmailSendJob()
+ result = job.do()
+ self.assertEqual("mail sent", result)
diff --git a/smash/web/tests/view/test_subjects.py b/smash/web/tests/view/test_subjects.py
index 9551f3e7ed64921324fd712cca08a5634e9b06b1..c7cf50653eb0743465fdb64b200cb2737594a94f 100644
--- a/smash/web/tests/view/test_subjects.py
+++ b/smash/web/tests/view/test_subjects.py
@@ -21,7 +21,7 @@ logger = logging.getLogger(__name__)
class SubjectsViewTests(LoggedInWithWorkerTestCase):
def setUp(self):
- super(SubjectsViewTests, self).setUp()
+ super().setUp()
self.study_subject = create_study_subject()
self.study = get_test_study()
diff --git a/smash/web/tests/view/test_virus_mail.py b/smash/web/tests/view/test_virus_mail.py
new file mode 100644
index 0000000000000000000000000000000000000000..1f11340a796aedc4e9c0eebf7662ddd50d3cce33
--- /dev/null
+++ b/smash/web/tests/view/test_virus_mail.py
@@ -0,0 +1,31 @@
+import logging
+
+from django.urls import reverse
+
+from web.models import MailTemplate
+from web.models.constants import MAIL_TEMPLATE_CONTEXT_VOUCHER
+from web.tests import LoggedInTestCase
+from web.tests.functions import create_voucher, get_resource_path
+
+logger = logging.getLogger(__name__)
+
+
+class MailTests(LoggedInTestCase):
+ def test_generate_vouchers(self):
+ voucher = create_voucher()
+ MailTemplate(name="name", language=None,
+ context=MAIL_TEMPLATE_CONTEXT_VOUCHER,
+ template_file=get_resource_path('upcoming_appointment_FR.docx')).save()
+
+ page = reverse('web.views.mail_template_generate_for_vouchers') + "?voucher_id=" + str(voucher.id)
+ response = self.client.get(page)
+ self.assertEqual(response.status_code, 200)
+
+ def test_list_mail_templates(self):
+ self.login_as_admin()
+ response = self.client.get(reverse("web.views.mail_templates"))
+ self.assertEqual(response.status_code, 200)
+
+ def test_list_mail_templates_without_permission(self):
+ response = self.client.get(reverse("web.views.mail_templates"))
+ self.assertEqual(response.status_code, 302)
diff --git a/smash/web/views/virus_mail.py b/smash/web/views/virus_mail.py
index 9b6099cc04263b73261772d4e28f37317ad8f232..cd03ad1dde02831db43340784c1c556154ac8cee 100644
--- a/smash/web/views/virus_mail.py
+++ b/smash/web/views/virus_mail.py
@@ -14,40 +14,20 @@ from ..smash_email import EmailSender
logger = logging.getLogger(__name__)
+def count_subjects(date_from: datetime, status: str) -> int:
+ return StudySubject.objects.filter(virus_test_1_updated__gt=date_from, virus_test_1_result=str).count() + \
+ StudySubject.objects.filter(virus_test_2_updated__gt=date_from, virus_test_2_result=str).count() + \
+ StudySubject.objects.filter(virus_test_3_updated__gt=date_from, virus_test_3_result=str).count() + \
+ StudySubject.objects.filter(virus_test_4_updated__gt=date_from, virus_test_4_result=str).count() + \
+ StudySubject.objects.filter(virus_test_5_updated__gt=date_from, virus_test_5_result=str).count()
+
+
def get_subject_statistics():
date_from = datetime.datetime.now() - datetime.timedelta(days=1)
- subjects_positive_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from, virus_test_1=True).count()
- subjects_positive_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
- virus_test_2=True).count()
- subjects_positive_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
- virus_test_3=True).count()
- subjects_positive_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
- virus_test_4=True).count()
- subjects_positive_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
- virus_test_5=True).count()
-
- subjects_negative_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from,
- virus_test_1=False).count()
- subjects_negative_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
- virus_test_2=False).count()
- subjects_negative_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
- virus_test_3=False).count()
- subjects_negative_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
- virus_test_4=False).count()
- subjects_negative_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
- virus_test_5=False).count()
-
- subjects_inconclusive_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from,
- virus_test_1__isnull=True).count()
- subjects_inconclusive_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
- virus_test_2__isnull=True).count()
- subjects_inconclusive_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
- virus_test_3__isnull=True).count()
- subjects_inconclusive_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
- virus_test_4__isnull=True).count()
- subjects_inconclusive_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
- virus_test_5__isnull=True).count()
+ subjects_positive_count = count_subjects(date_from, "Positive")
+ subjects_negative_count = count_subjects(date_from, "Negative")
+ subjects_inconclusive_count = count_subjects(date_from, "Inconclusive")
return {"Positive": subjects_positive_count, "Negative": subjects_negative_count,
"Inconclusive": subjects_inconclusive_count,
@@ -87,11 +67,11 @@ def create_statistic_email_content(data, title):
email_body += "</table>"
- #SARS-COV2 Virus  | Number of Donors
- #Inconclusive  | 5
- #Positive  | 15
- #Negative  | 45
- #Total  | 65
+ # SARS-COV2 Virus  | Number of Donors
+ # Inconclusive  | 5
+ # Positive  | 15
+ # Negative  | 45
+ # Total  | 65
return email_body