From 2f6ee01fb9250926847130eede02d48a59afb323 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 16 Apr 2020 16:17:27 +0200
Subject: [PATCH] there must be date in the visit to mark is as finished when
importing from redcap
---
...onfigurationitem_email_items_for_redcap.py | 33 +++++++++++++++++++
smash/web/models/constants.py | 1 +
smash/web/redcap_connector.py | 17 +++++++---
3 files changed, 47 insertions(+), 4 deletions(-)
create mode 100644 smash/web/migrations/0164_configurationitem_email_items_for_redcap.py
diff --git a/smash/web/migrations/0164_configurationitem_email_items_for_redcap.py b/smash/web/migrations/0164_configurationitem_email_items_for_redcap.py
new file mode 100644
index 00000000..efa3e50f
--- /dev/null
+++ b/smash/web/migrations/0164_configurationitem_email_items_for_redcap.py
@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.3 on 2017-04-04 09:43
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+from web.models.constants import RED_CAP_SAMPLE_DATE_FIELD_TYPE
+
+
+def create_item(apps, type, value, name):
+ # We can't import the ConfigurationItem model directly as it may be a newer
+ # version than this migration expects. We use the historical version.
+ ConfigurationItem = apps.get_model("web", "ConfigurationItem")
+ item = ConfigurationItem.objects.create()
+ item.type = type
+ item.value = value
+ item.name = name
+ item.save()
+
+
+def configuration_items(apps, schema_editor):
+ create_item(apps, RED_CAP_SAMPLE_DATE_FIELD_TYPE, "",
+ "Redcap field for sample date in the visit")
+
+
+class Migration(migrations.Migration):
+ dependencies = [
+ ('web', '0163_study_redcap_first_visit_number'),
+ ]
+
+ operations = [
+ migrations.RunPython(configuration_items),
+ ]
diff --git a/smash/web/models/constants.py b/smash/web/models/constants.py
index b512e714..049ea707 100644
--- a/smash/web/models/constants.py
+++ b/smash/web/models/constants.py
@@ -62,6 +62,7 @@ RED_CAP_SEX_FIELD_TYPE = 'RED_CAP_SEX_FIELD_TYPE'
RED_CAP_DATE_BORN_FIELD_TYPE = 'RED_CAP_DATE_BORN_FIELD_TYPE'
RED_CAP_ND_NUMBER_FIELD_TYPE = 'RED_CAP_ND_NUMBER_FIELD_TYPE'
RED_CAP_VIRUS_FIELD_TYPE = 'RED_CAP_VIRUS_FIELD_TYPE'
+RED_CAP_SAMPLE_DATE_FIELD_TYPE = "RED_CAP_SAMPLE_DATE_FIELD_TYPE"
MAIL_TEMPLATE_CONTEXT_SUBJECT = 'S'
MAIL_TEMPLATE_CONTEXT_APPOINTMENT = 'A'
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index 8329ef60..df68598c 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -16,7 +16,7 @@ from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, \
REDCAP_BASE_URL_CONFIGURATION_TYPE, CRON_JOB_TIMEOUT, RED_CAP_LANGUAGE_4_FIELD_TYPE, RED_CAP_LANGUAGE_3_FIELD_TYPE, \
RED_CAP_LANGUAGE_2_FIELD_TYPE, RED_CAP_LANGUAGE_1_FIELD_TYPE, RED_CAP_MPOWER_ID_FIELD_TYPE, RED_CAP_DEAD_FIELD_TYPE, \
RED_CAP_SEX_FIELD_TYPE, RED_CAP_DATE_BORN_FIELD_TYPE, RED_CAP_ND_NUMBER_FIELD_TYPE, RED_CAP_VIRUS_FIELD_TYPE, \
- GLOBAL_STUDY_ID
+ GLOBAL_STUDY_ID, RED_CAP_SAMPLE_DATE_FIELD_TYPE
from web.models.inconsistent_subject import InconsistentField, InconsistentSubject
from web.models.missing_subject import MissingSubject
@@ -81,6 +81,7 @@ class RedcapConnector(object):
self.language_4_field = ConfigurationItem.objects.get(type=RED_CAP_LANGUAGE_4_FIELD_TYPE).value
self.m_power_id_field = ConfigurationItem.objects.get(type=RED_CAP_MPOWER_ID_FIELD_TYPE).value
self.virus_field = ConfigurationItem.objects.get(type=RED_CAP_VIRUS_FIELD_TYPE).value
+ self.sample_date_field = ConfigurationItem.objects.get(type=RED_CAP_SAMPLE_DATE_FIELD_TYPE).value
self.study = Study.objects.get(id=GLOBAL_STUDY_ID)
@@ -187,6 +188,7 @@ class RedcapConnector(object):
result.append(inconsistent_subject)
if appointment_type_to_finish is not None:
for visit in red_cap_subject.visits:
+
smasch_visits = Visit.objects.filter(visit_number=visit.visit_number, subject=subject)
smasch_appointments = Appointment.objects.filter(visit__in=smasch_visits,
appointment_types=appointment_type_to_finish,
@@ -328,7 +330,9 @@ class RedcapConnector(object):
visit.virus = False
elif row.get(self.virus_field) == "Positive":
visit.virus = True
- redcap_subject.visits.append(visit)
+ if self.sample_date_field != "":
+ if row.get(self.sample_date_field) != "":
+ redcap_subject.visits.append(visit)
result.append(redcap_subject)
for i in range(1, 9):
query_data = self.get_subject_query_data()
@@ -342,13 +346,15 @@ class RedcapConnector(object):
for redcap_subject in result:
if redcap_subject.nd_number == nd_number:
visit = RedcapVisit()
- visit.visit_number = i
+ 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
elif row.get(self.virus_field) == "Positive":
visit.virus = True
- redcap_subject.visits.append(visit)
+ if self.sample_date_field != "":
+ if row.get(self.sample_date_field) != "":
+ redcap_subject.visits.append(visit)
return result
@@ -397,6 +403,9 @@ class RedcapConnector(object):
if self.virus_field != "":
result['fields[' + str(field_number) + ']'] = self.virus_field
field_number += 1
+ if self.sample_date_field != "":
+ result['fields[' + str(field_number) + ']'] = self.sample_date_field
+ field_number += 1
return result
def get_language(self, name):
--
GitLab