From b4330dabd89f4184ea041c43c9b8ff45be104cc3 Mon Sep 17 00:00:00 2001
From: Carlos Vega <carlos.vega@uni.lu>
Date: Wed, 31 Oct 2018 11:40:11 +0100
Subject: [PATCH] added excluded and excluded reason fields to studysubject
---
smash/web/api_views/subject.py | 130 ++++++++++++------
smash/web/models/study_columns.py | 135 ++++++++++---------
smash/web/models/study_subject.py | 14 ++
smash/web/tests/models/test_study_subject.py | 15 +++
4 files changed, 187 insertions(+), 107 deletions(-)
diff --git a/smash/web/api_views/subject.py b/smash/web/api_views/subject.py
index 65039448..881fb347 100644
--- a/smash/web/api_views/subject.py
+++ b/smash/web/api_views/subject.py
@@ -19,7 +19,8 @@ logger = logging.getLogger(__name__)
# noinspection PyUnusedLocal
def cities(request):
- result_subjects = Subject.objects.filter(city__isnull=False).values_list('city').distinct()
+ result_subjects = Subject.objects.filter(
+ city__isnull=False).values_list('city').distinct()
return JsonResponse({
"cities": [x[0] for x in result_subjects]
})
@@ -27,7 +28,8 @@ def cities(request):
# noinspection PyUnusedLocal
def referrals(request):
- result_subjects = StudySubject.objects.filter(referral__isnull=False).values_list('referral').distinct()
+ result_subjects = StudySubject.objects.filter(
+ referral__isnull=False).values_list('referral').distinct()
return JsonResponse({
"referrals": [x[0] for x in result_subjects]
})
@@ -35,7 +37,8 @@ def referrals(request):
def get_subject_columns(request, subject_list_type):
study = Study.objects.filter(id=GLOBAL_STUDY_ID)[0]
- study_subject_lists = StudySubjectList.objects.filter(study=study, type=subject_list_type)
+ study_subject_lists = StudySubjectList.objects.filter(
+ study=study, type=subject_list_type)
if len(study_subject_lists) > 0:
study_subject_list = study_subject_lists[0]
subject_columns = study_subject_list.visible_subject_columns
@@ -46,29 +49,44 @@ def get_subject_columns(request, subject_list_type):
study_subject_columns = StudyColumns()
result = []
- add_column(result, "ND", "nd_number", study_subject_columns, "string_filter", study.columns)
- add_column(result, "Screening", "screening_number", study_subject_columns, "string_filter", study.columns)
- add_column(result, "First name", "first_name", subject_columns, "string_filter")
- add_column(result, "Last name", "last_name", subject_columns, "string_filter")
- add_column(result, "Social Security Number", "social_security_number", subject_columns, "string_filter")
+ add_column(result, "ND", "nd_number", study_subject_columns,
+ "string_filter", study.columns)
+ add_column(result, "Screening", "screening_number",
+ study_subject_columns, "string_filter", study.columns)
+ add_column(result, "First name", "first_name",
+ subject_columns, "string_filter")
+ add_column(result, "Last name", "last_name",
+ subject_columns, "string_filter")
+ add_column(result, "Social Security Number",
+ "social_security_number", subject_columns, "string_filter")
add_column(result, "Date of birth", "date_born", subject_columns, None)
- add_column(result, "Contact on", "datetime_contact_reminder", study_subject_columns, None, study.columns)
- add_column(result, "Last contact attempt", "last_contact_attempt", study_subject_list, None)
- add_column(result, "Referred by", "referral", study_subject_columns, "string_filter", study.columns)
+ add_column(result, "Contact on", "datetime_contact_reminder",
+ study_subject_columns, None, study.columns)
+ add_column(result, "Last contact attempt",
+ "last_contact_attempt", study_subject_list, None)
+ add_column(result, "Referred by", "referral",
+ study_subject_columns, "string_filter", study.columns)
add_column(result, "Health partner name", "health_partner_first_name", None, "string_filter",
add_param=study.columns.health_partner,
visible_param=study_subject_columns.health_partner)
add_column(result, "Health partner last name", "health_partner_last_name", None, "string_filter",
add_param=study.columns.health_partner,
visible_param=study_subject_columns.health_partner)
- add_column(result, "Location", "default_location", study_subject_columns, "location_filter", study.columns)
+ add_column(result, "Location", "default_location",
+ study_subject_columns, "location_filter", study.columns)
add_column(result, "Flying team location", "flying_team", study_subject_columns, "flying_team_filter",
study.columns)
add_column(result, "Deceased", "dead", subject_columns, "yes_no_filter")
- add_column(result, "Resigned", "resigned", study_subject_columns, "yes_no_filter", study.columns)
- add_column(result, "Postponed", "postponed", study_subject_columns, "yes_no_filter", study.columns)
- add_column(result, "Info sent", "information_sent", study_subject_columns, "yes_no_filter", study.columns)
- add_column(result, "Type", "type", study_subject_columns, "type_filter", study.columns)
+ add_column(result, "Resigned", "resigned",
+ study_subject_columns, "yes_no_filter", study.columns)
+ add_column(result, "Postponed", "postponed",
+ study_subject_columns, "yes_no_filter", study.columns)
+ add_column(result, "Excluded", "excluded",
+ study_subject_columns, "yes_no_filter", study.columns)
+ add_column(result, "Info sent", "information_sent",
+ study_subject_columns, "yes_no_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 visit_number in range(1, 9):
visit_key = "visit_" + str(visit_number)
@@ -104,9 +122,11 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
else:
order_direction = "-"
if order_column == "first_name":
- result = subjects_to_be_ordered.order_by(order_direction + 'subject__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')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'subject__last_name')
elif order_column == "nd_number":
result = subjects_to_be_ordered.order_by(order_direction + 'nd_number')
elif order_column == "referral":
@@ -117,40 +137,53 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
else:
pattern = column_filters[u'screening_number']
result = subjects_to_be_ordered.all()
- result = sorted(result, key=lambda t: t.sort_matched_screening_first(pattern, reverse=order_direction == '-'), reverse = order_direction == '-' )
+ result = sorted(result, key=lambda t: t.sort_matched_screening_first(
+ pattern, reverse=order_direction == '-'), reverse=order_direction == '-')
elif order_column == "default_location":
- result = subjects_to_be_ordered.order_by(order_direction + 'default_location')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'default_location')
elif order_column == "flying_team":
- result = subjects_to_be_ordered.order_by(order_direction + 'flying_team')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'flying_team')
elif order_column == "dead":
- result = subjects_to_be_ordered.order_by(order_direction + 'subject__dead')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'subject__dead')
elif order_column == "resigned":
result = subjects_to_be_ordered.order_by(order_direction + 'resigned')
elif order_column == "information_sent":
- result = subjects_to_be_ordered.order_by(order_direction + 'information_sent')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'information_sent')
elif order_column == "health_partner_first_name":
- result = subjects_to_be_ordered.order_by(order_direction + 'health_partner__first_name')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'health_partner__first_name')
elif order_column == "health_partner_last_name":
- result = subjects_to_be_ordered.order_by(order_direction + 'health_partner__last_name')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'health_partner__last_name')
elif order_column == "social_security_number":
- result = subjects_to_be_ordered.order_by(order_direction + 'subject__social_security_number')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'subject__social_security_number')
elif order_column == "postponed":
result = subjects_to_be_ordered.order_by(order_direction + 'postponed')
+ elif order_column == "excluded":
+ result = subjects_to_be_ordered.order_by(order_direction + 'excluded')
elif order_column == "type":
result = subjects_to_be_ordered.order_by(order_direction + 'type')
elif order_column == "id":
result = subjects_to_be_ordered.order_by(order_direction + 'id')
elif order_column == "date_born":
- result = subjects_to_be_ordered.order_by(order_direction + 'subject__date_born')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'subject__date_born')
elif order_column == "datetime_contact_reminder":
- result = subjects_to_be_ordered.order_by(order_direction + 'datetime_contact_reminder')
+ result = subjects_to_be_ordered.order_by(
+ order_direction + 'datetime_contact_reminder')
elif order_column == "last_contact_attempt":
# noinspection SpellCheckingInspection
result = subjects_to_be_ordered.annotate(sort_contact_attempt=Max("contactattempt__datetime_when")).order_by(
order_direction + 'sort_contact_attempt')
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)
+ result = order_by_visit(subjects_to_be_ordered,
+ order_direction, visit_number)
else:
logger.warn("Unknown sort column: " + str(order_column))
return result
@@ -166,8 +199,10 @@ def filter_by_visit(result, visit_number, visit_type):
datetime_begin_filter = 'visit_' + str(visit_number) + '_datetime_begin'
datetime_end_filter = 'visit_' + str(visit_number) + '_datetime_end'
is_finished_filter = 'visit_' + str(visit_number) + '_is_finished'
- finished_appointments_filter = 'visit_' + str(visit_number) + '_finished_appointments'
- scheduled_appointments_filter = 'visit_' + str(visit_number) + '_scheduled_appointments'
+ finished_appointments_filter = 'visit_' + \
+ str(visit_number) + '_finished_appointments'
+ scheduled_appointments_filter = 'visit_' + \
+ str(visit_number) + '_scheduled_appointments'
# this is hack... instead of providing True/False value this field contain 1/0 value, the problem is that we need
# to provide aggregate function for the interacting parameter
@@ -179,11 +214,13 @@ def filter_by_visit(result, visit_number, visit_type):
# number of finished appointments
result = result.annotate(**{finished_appointments_filter: Count(Case(When(
- Q(visit__appointment__status=Appointment.APPOINTMENT_STATUS_FINISHED) & Q(visit__visit_number=visit_number),
+ Q(visit__appointment__status=Appointment.APPOINTMENT_STATUS_FINISHED) & Q(
+ visit__visit_number=visit_number),
then=1)))})
# number of scheduled appointments
result = result.annotate(**{scheduled_appointments_filter: Count(Case(When(
- Q(visit__appointment__status=Appointment.APPOINTMENT_STATUS_SCHEDULED) & Q(visit__visit_number=visit_number),
+ Q(visit__appointment__status=Appointment.APPOINTMENT_STATUS_SCHEDULED) & Q(
+ visit__visit_number=visit_number),
then=1)))})
# when visit starts
@@ -216,7 +253,8 @@ def filter_by_visit(result, visit_number, visit_type):
filter(**{datetime_end_filter + "__gt": get_today_midnight_date()}). \
filter(**{scheduled_appointments_filter: 0})
elif visit_type == "UPCOMING":
- result = result.filter(**{datetime_begin_filter + "__gt": get_today_midnight_date()})
+ result = result.filter(
+ **{datetime_begin_filter + "__gt": get_today_midnight_date()})
return result
@@ -242,6 +280,8 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
result = result.filter(resigned=(value == "true"))
elif column == "postponed":
result = result.filter(postponed=(value == "true"))
+ elif column == "excluded":
+ result = result.filter(excluded=(value == "true"))
elif column == "information_sent":
result = result.filter(information_sent=(value == "true"))
elif column == "health_partner_first_name":
@@ -249,7 +289,8 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
elif column == "health_partner_last_name":
result = result.filter(health_partner__last_name__icontains=value)
elif column == "social_security_number":
- result = result.filter(subject__social_security_number__icontains=value)
+ result = result.filter(
+ subject__social_security_number__icontains=value)
elif column == "default_location":
result = result.filter(default_location=value)
elif column == "flying_team":
@@ -273,14 +314,16 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
def subjects(request, type):
try:
- # id of the query from dataTable: https://datatables.net/manual/server-side
+ # id of the query from dataTable:
+ # https://datatables.net/manual/server-side
draw = int(request.GET.get("draw", "-1"))
start = int(request.GET.get("start", "0"))
length = int(request.GET.get("length", "10"))
order = int(request.GET.get("order[0][column]", "0"))
order_dir = request.GET.get("order[0][dir]", "asc")
- order_column = request.GET.get("columns[" + str(order) + "][data]", "last_name")
+ order_column = request.GET.get(
+ "columns[" + str(order) + "][data]", "last_name")
filters = get_filters_for_data_table_request(request)
@@ -289,7 +332,8 @@ def subjects(request, type):
count = all_subjects.count()
filtered_subjects = get_subjects_filtered(all_subjects, filters)
- ordered_subjects = get_subjects_order(filtered_subjects, order_column, order_dir, column_filters=dict(filters))
+ ordered_subjects = get_subjects_order(
+ filtered_subjects, order_column, order_dir, column_filters=dict(filters))
sliced_subjects = ordered_subjects[start:(start + length)]
result_subjects = sliced_subjects
@@ -323,7 +367,8 @@ def types(request):
def serialize_subject(study_subject):
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')
+ visits = Visit.objects.filter(
+ subject=study_subject).order_by('visit_number')
serialized_visits = []
for visit in visits:
if visit.datetime_begin < get_today_midnight_date():
@@ -355,8 +400,10 @@ def serialize_subject(study_subject):
"datetime_start": serialize_date(visit.datetime_begin),
"datetime_end": serialize_date(visit.datetime_end),
})
- contact_reminder = serialize_datetime(study_subject.datetime_contact_reminder)
- contact_attempts = ContactAttempt.objects.filter(subject=study_subject).order_by("-datetime_when")
+ contact_reminder = serialize_datetime(
+ study_subject.datetime_contact_reminder)
+ contact_attempts = ContactAttempt.objects.filter(
+ subject=study_subject).order_by("-datetime_when")
if len(contact_attempts) > 0:
last_contact_attempt = contact_attempts[0]
last_contact_attempt_string = serialize_datetime(last_contact_attempt.datetime_when) + "<br/>" + unicode(
@@ -385,6 +432,7 @@ def serialize_subject(study_subject):
"dead": bool_to_yes_no(study_subject.subject.dead),
"resigned": bool_to_yes_no(study_subject.resigned),
"postponed": bool_to_yes_no(study_subject.postponed),
+ "excluded": bool_to_yes_no(study_subject.excluded),
"information_sent": bool_to_yes_no(study_subject.information_sent),
"health_partner_first_name": health_partner_first_name,
"health_partner_last_name": health_partner_last_name,
diff --git a/smash/web/models/study_columns.py b/smash/web/models/study_columns.py
index 565ad55d..aae985a0 100644
--- a/smash/web/models/study_columns.py
+++ b/smash/web/models/study_columns.py
@@ -5,6 +5,7 @@ from web.models.constants import BOOL_CHOICES
class StudyColumns(models.Model):
+
class Meta:
app_label = 'web'
@@ -14,101 +15,103 @@ class StudyColumns(models.Model):
)
datetime_contact_reminder = models.BooleanField(
- default=True,
- verbose_name='Please make a contact on'
- )
+ default=True,
+ verbose_name='Please make a contact on'
+ )
type = models.BooleanField(
- default=True,
- verbose_name='Type'
- )
+ default=True,
+ verbose_name='Type'
+ )
default_location = models.BooleanField(
- default=True,
- verbose_name='Default appointment location',
- )
+ default=True,
+ verbose_name='Default appointment location',
+ )
flying_team = models.BooleanField(
- default=True,
- verbose_name='Default flying team location (if applicable)',
- )
+ default=True,
+ verbose_name='Default flying team location (if applicable)',
+ )
screening_number = models.BooleanField(
- default=True,
- verbose_name='Screening number',
- )
+ default=True,
+ verbose_name='Screening number',
+ )
nd_number = models.BooleanField(
- default=True,
- verbose_name='ND number',
- )
+ default=True,
+ verbose_name='ND number',
+ )
mpower_id = models.BooleanField(
- default=True,
- verbose_name='MPower ID'
- )
+ default=True,
+ verbose_name='MPower ID'
+ )
comments = models.BooleanField(
- default=True,
- verbose_name='Comments'
- )
+ default=True,
+ verbose_name='Comments'
+ )
referral = models.BooleanField(
- default=True,
- verbose_name='Referred by'
- )
+ default=True,
+ verbose_name='Referred by'
+ )
diagnosis = models.BooleanField(
- default=True,
- verbose_name='Diagnosis'
- )
+ default=True,
+ verbose_name='Diagnosis'
+ )
year_of_diagnosis = models.BooleanField(
- default=True,
- verbose_name='Year of diagnosis (YYYY)'
- )
+ default=True,
+ verbose_name='Year of diagnosis (YYYY)'
+ )
information_sent = models.BooleanField(
- default=True,
- verbose_name='Information sent',
- )
+ default=True,
+ verbose_name='Information sent',
+ )
pd_in_family = models.BooleanField(
- default=True,
- verbose_name='PD in family',
- )
+ default=True,
+ verbose_name='PD in family',
+ )
resigned = models.BooleanField(
- default=True,
- verbose_name='Resigned',
- )
+ default=True,
+ verbose_name='Resigned',
+ )
resign_reason = models.BooleanField(
- default=True,
- verbose_name='Resign reason'
- )
+ default=True,
+ verbose_name='Resign reason'
+ )
+
+ excluded = models.BooleanField(default=False, verbose_name='Excluded')
referral_letter = models.BooleanField(
- default=False,
- verbose_name='Referral letter'
- )
+ default=False,
+ verbose_name='Referral letter'
+ )
health_partner = models.BooleanField(
- default=False,
- verbose_name='Health partner'
- )
+ default=False,
+ verbose_name='Health partner'
+ )
health_partner_feedback_agreement = models.BooleanField(
- default=False,
- verbose_name='Agrees to give information to referral'
- )
+ default=False,
+ verbose_name='Agrees to give information to referral'
+ )
screening = models.BooleanField(
- default=False,
- verbose_name='Screening'
- )
+ default=False,
+ verbose_name='Screening'
+ )
previously_in_study = models.BooleanField(
- default=False,
- verbose_name='Previously in PDP study',
- )
+ default=False,
+ verbose_name='Previously in PDP study',
+ )
voucher_types = models.BooleanField(
- default=False,
- verbose_name='Voucher types',
- )
+ default=False,
+ verbose_name='Voucher types',
+ )
vouchers = models.BooleanField(
- default=False,
- verbose_name='Vouchers',
- )
+ default=False,
+ verbose_name='Vouchers',
+ )
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index e6242553..dc7cedb0 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -32,6 +32,11 @@ class StudySubject(models.Model):
self.finish_all_visits()
self.finish_all_appointments()
+ def mark_as_excluded(self):
+ self.excluded = True
+ self.finish_all_visits()
+ self.finish_all_appointments()
+
subject = models.ForeignKey("web.Subject",
verbose_name='Subject',
editable=False,
@@ -161,6 +166,15 @@ class StudySubject(models.Model):
blank=True,
verbose_name='Resign reason'
)
+ excluded = models.BooleanField(
+ verbose_name='Excluded',
+ default=False,
+ editable=True
+ )
+ exclude_reason = models.TextField(max_length=2000,
+ blank=True,
+ verbose_name='Exclude reason'
+ )
def sort_matched_screening_first(self, pattern, reverse=False):
parts = self.screening_number.split(';')
diff --git a/smash/web/tests/models/test_study_subject.py b/smash/web/tests/models/test_study_subject.py
index f91762f3..50a850a5 100644
--- a/smash/web/tests/models/test_study_subject.py
+++ b/smash/web/tests/models/test_study_subject.py
@@ -24,6 +24,21 @@ class SubjectModelTests(TestCase):
self.assertEquals(
Appointment.APPOINTMENT_STATUS_CANCELLED, appointment_status)
+ def test_mark_as_excluded(self):
+ subject = create_study_subject()
+ visit = create_visit(subject)
+ appointment = create_appointment(visit)
+
+ subject.mark_as_excluded()
+ appointment_status = Appointment.objects.filter(id=appointment.id)[
+ 0].status
+ visit_finished = Visit.objects.filter(id=visit.id)[0].is_finished
+
+ self.assertTrue(subject.excluded)
+ self.assertTrue(visit_finished)
+ self.assertEquals(
+ Appointment.APPOINTMENT_STATUS_CANCELLED, appointment_status)
+
def test_check_nd_number_regex(self):
# delete everything
StudySubject.objects.all().delete()
--
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