From 19c5528508c0ebe18cb719891a52d58fad440f52 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 26 May 2020 08:52:19 +0200
Subject: [PATCH] iga/igg status is imported from redcap
---
smash/db_scripts/create_dummy_data.py | 4 +
smash/web/api_views/subject.py | 40 ++++++
smash/web/forms/study_subject_forms.py | 19 +++
.../0171_configurationitem_serology.py | 35 ++++++
.../web/migrations/0172_auto_20200525_1246.py | 115 ++++++++++++++++++
smash/web/models/constants.py | 2 +
smash/web/models/study_columns.py | 40 ++++++
smash/web/models/study_subject.py | 51 ++++++++
smash/web/redcap_connector.py | 100 ++++++++++-----
9 files changed, 377 insertions(+), 29 deletions(-)
create mode 100644 smash/web/migrations/0171_configurationitem_serology.py
create mode 100644 smash/web/migrations/0172_auto_20200525_1246.py
diff --git a/smash/db_scripts/create_dummy_data.py b/smash/db_scripts/create_dummy_data.py
index 0e44344b..c197b510 100644
--- a/smash/db_scripts/create_dummy_data.py
+++ b/smash/db_scripts/create_dummy_data.py
@@ -433,6 +433,8 @@ class smashProvider(BaseProvider):
default_location.prefix)
virus_test_1 = choice([None, True, False], 1, p=[0.2, 0.3, 0.5])[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:
virus_test_1_updated = fake.date_between(start_date='-30d', end_date='-4d')
#inconclusive results have a date
@@ -448,6 +450,8 @@ class smashProvider(BaseProvider):
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_collection_date=virus_test_1_collection_date,
+ virus_test_1_iga_status=virus_iga_1,
+ virus_test_1_igg_status=virus_igg_1,
defaults={'default_location': default_location, 'type': type,
'screening_number': screening_number, 'study': study})
diff --git a/smash/web/api_views/subject.py b/smash/web/api_views/subject.py
index 5a8ff67a..57ed007f 100644
--- a/smash/web/api_views/subject.py
+++ b/smash/web/api_views/subject.py
@@ -105,6 +105,16 @@ def get_subject_columns(request, subject_list_type):
"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,
+ None, study.columns)
+ add_column(result,
+ "Visit {} IgG Status".format(virus_visit_number),
+ "virus_test_{}_igg_status".format(one_based_idx),
+ study_subject_columns,
+ None, study.columns)
add_column(result, "Type", "type", study_subject_columns, "type_filter", study.columns)
add_column(result, "Edit", "edit", None, None, sortable=False)
@@ -235,6 +245,26 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4_collection_date')
elif order_column == "virus_test_5_collection_date":
result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_collection_date')
+ elif order_column == "virus_test_1_iga_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1_iga_status')
+ elif order_column == "virus_test_1_igg_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1_igg_status')
+ elif order_column == "virus_test_2_iga_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2_iga_status')
+ elif order_column == "virus_test_2_igg_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2_igg_status')
+ elif order_column == "virus_test_3_iga_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3_iga_status')
+ elif order_column == "virus_test_3_igg_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3_igg_status')
+ elif order_column == "virus_test_4_iga_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4_iga_status')
+ elif order_column == "virus_test_4_igg_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4_igg_status')
+ elif order_column == "virus_test_5_iga_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_iga_status')
+ elif order_column == "virus_test_5_igg_status":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_igg_status')
else:
logger.warn("Unknown sort column: " + str(order_column))
return result
@@ -549,6 +579,16 @@ def serialize_subject(study_subject):
"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),
diff --git a/smash/web/forms/study_subject_forms.py b/smash/web/forms/study_subject_forms.py
index 39f2fb0e..18fbd7aa 100644
--- a/smash/web/forms/study_subject_forms.py
+++ b/smash/web/forms/study_subject_forms.py
@@ -41,6 +41,11 @@ class StudySubjectForm(ModelForm):
collection_date_field = 'virus_test_{}_collection_date'.format(one_based_idx)
self.fields[collection_date_field].label = 'Visit {} RT-PCR collection date'.format(virus_visit_number)
+ iga_field = 'virus_test_{}_iga_status'.format(one_based_idx)
+ igg_field = 'virus_test_{}_igg_status'.format(one_based_idx)
+ self.fields[iga_field].label = 'Visit {} IgA status'.format(virus_visit_number)
+ self.fields[igg_field].label = 'Visit {} IgG status'.format(virus_visit_number)
+
for visit_number in range(1, 6):
disable_virus_test_field(self, visit_number)
self.update_virus_inconclusive_data(visit_number)
@@ -179,10 +184,14 @@ def disable_virus_test_field(self, visit_number):
test_result_column_name = 'virus_test_{}'.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)
+ test_igg_status_column_name = 'virus_test_{}_igg_status'.format(visit_number)
self.fields[test_result_column_name].widget.attrs['readonly'] = True
self.fields[test_result_column_name].widget.attrs['disabled'] = True
self.fields[test_result_date_column_name].widget.attrs['readonly'] = True
self.fields[test_collection_date_column_name].widget.attrs['readonly'] = True
+ self.fields[test_iga_status_column_name].widget.attrs['readonly'] = True
+ self.fields[test_igg_status_column_name].widget.attrs['readonly'] = True
def get_study_from_args(kwargs):
@@ -241,6 +250,16 @@ def prepare_study_subject_fields(fields, study):
prepare_field(fields, study.columns, 'virus_test_3_collection_date')
prepare_field(fields, study.columns, 'virus_test_4_collection_date')
prepare_field(fields, study.columns, 'virus_test_5_collection_date')
+ prepare_field(fields, study.columns, 'virus_test_1_iga_status')
+ prepare_field(fields, study.columns, 'virus_test_1_igg_status')
+ prepare_field(fields, study.columns, 'virus_test_2_iga_status')
+ prepare_field(fields, study.columns, 'virus_test_2_igg_status')
+ prepare_field(fields, study.columns, 'virus_test_3_iga_status')
+ prepare_field(fields, study.columns, 'virus_test_3_igg_status')
+ prepare_field(fields, study.columns, 'virus_test_4_iga_status')
+ prepare_field(fields, study.columns, 'virus_test_4_igg_status')
+ prepare_field(fields, study.columns, 'virus_test_5_iga_status')
+ prepare_field(fields, study.columns, 'virus_test_5_igg_status')
def validate_subject_screening_number(self, cleaned_data):
diff --git a/smash/web/migrations/0171_configurationitem_serology.py b/smash/web/migrations/0171_configurationitem_serology.py
new file mode 100644
index 00000000..824e5381
--- /dev/null
+++ b/smash/web/migrations/0171_configurationitem_serology.py
@@ -0,0 +1,35 @@
+# -*- 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_IGA_STATUS_FIELD_TYPE, RED_CAP_IGG_STATUS_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_IGA_STATUS_FIELD_TYPE, "",
+ "Redcap field for IgA status in the visit")
+ create_item(apps, RED_CAP_IGG_STATUS_FIELD_TYPE, "",
+ "Redcap field for IgG status in the visit")
+
+
+class Migration(migrations.Migration):
+ dependencies = [
+ ('web', '0170_auto_20200525_1126'),
+ ]
+
+ operations = [
+ migrations.RunPython(configuration_items),
+ ]
diff --git a/smash/web/migrations/0172_auto_20200525_1246.py b/smash/web/migrations/0172_auto_20200525_1246.py
new file mode 100644
index 00000000..0750d0a9
--- /dev/null
+++ b/smash/web/migrations/0172_auto_20200525_1246.py
@@ -0,0 +1,115 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.5 on 2020-05-25 12:46
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0171_configurationitem_serology'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_1_iga_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 1 virus IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_1_igg_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 1 virus IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_2_iga_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 2 virus IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_2_igg_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 2 virus IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_3_iga_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 3 virus IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_3_igg_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 3 virus IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_4_iga_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 4 virus IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_4_igg_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 4 virus IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_5_iga_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 5 virus IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_5_igg_status',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 5 virus IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1_iga_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 1 IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1_igg_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 1 IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2_iga_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 2 IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2_igg_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 2 IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3_iga_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 3 IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3_igg_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 3 IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4_iga_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 4 IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4_igg_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 4 IgG status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5_iga_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 5 IgA status'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5_igg_status',
+ field=models.CharField(blank=True, max_length=255, null=True, verbose_name=b'Visit 5 IgG status'),
+ ),
+ ]
diff --git a/smash/web/models/constants.py b/smash/web/models/constants.py
index 498c9a6a..529d54fd 100644
--- a/smash/web/models/constants.py
+++ b/smash/web/models/constants.py
@@ -67,6 +67,8 @@ RED_CAP_ND_NUMBER_FIELD_TYPE = 'RED_CAP_ND_NUMBER_FIELD_TYPE'
RED_CAP_VIRUS_FIELD_TYPE = 'RED_CAP_VIRUS_FIELD_TYPE'
RED_CAP_KIT_ID_FIELD_TYPE = "RED_CAP_KIT_ID_FIELD_TYPE"
RED_CAP_SAMPLE_DATE_FIELD_TYPE = "RED_CAP_SAMPLE_DATE_FIELD_TYPE"
+RED_CAP_IGA_STATUS_FIELD_TYPE = "RED_CAP_IGA_STATUS_FIELD_TYPE"
+RED_CAP_IGG_STATUS_FIELD_TYPE = "RED_CAP_IGG_STATUS_FIELD_TYPE"
MAIL_TEMPLATE_CONTEXT_SUBJECT = 'S'
diff --git a/smash/web/models/study_columns.py b/smash/web/models/study_columns.py
index ac3954fa..858db85a 100644
--- a/smash/web/models/study_columns.py
+++ b/smash/web/models/study_columns.py
@@ -182,3 +182,43 @@ class StudyColumns(models.Model):
default=False,
verbose_name='Visit 5 virus collection date',
)
+ virus_test_1_iga_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 1 virus IgA status',
+ )
+ virus_test_1_igg_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 1 virus IgG status',
+ )
+ virus_test_2_iga_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 2 virus IgA status',
+ )
+ virus_test_2_igg_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 2 virus IgG status',
+ )
+ virus_test_3_iga_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 3 virus IgA status',
+ )
+ virus_test_3_igg_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 3 virus IgG status',
+ )
+ virus_test_4_iga_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 4 virus IgA status',
+ )
+ virus_test_4_igg_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 4 virus IgG status',
+ )
+ virus_test_5_iga_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 5 virus IgA status',
+ )
+ virus_test_5_igg_status = models.BooleanField(
+ default=False,
+ verbose_name='Visit 5 virus IgG status',
+ )
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index 99a0ebb8..a92c4c2c 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -263,6 +263,57 @@ class StudySubject(models.Model):
null=True,
)
+ virus_test_1_iga_status = models.CharField(max_length=255,
+ verbose_name='Visit 1 IgA status',
+ blank=True,
+ null=True,
+ )
+ virus_test_1_igg_status = models.CharField(max_length=255,
+ verbose_name='Visit 1 IgG status',
+ blank=True,
+ null=True,
+ )
+ virus_test_2_iga_status = models.CharField(max_length=255,
+ verbose_name='Visit 2 IgA status',
+ blank=True,
+ null=True,
+ )
+ virus_test_2_igg_status = models.CharField(max_length=255,
+ verbose_name='Visit 2 IgG status',
+ blank=True,
+ null=True,
+ )
+ virus_test_3_iga_status = models.CharField(max_length=255,
+ verbose_name='Visit 3 IgA status',
+ blank=True,
+ null=True,
+ )
+ virus_test_3_igg_status = models.CharField(max_length=255,
+ verbose_name='Visit 3 IgG status',
+ blank=True,
+ null=True,
+ )
+ virus_test_4_iga_status = models.CharField(max_length=255,
+ verbose_name='Visit 4 IgA status',
+ blank=True,
+ null=True,
+ )
+ virus_test_4_igg_status = models.CharField(max_length=255,
+ verbose_name='Visit 4 IgG status',
+ blank=True,
+ null=True,
+ )
+ virus_test_5_iga_status = models.CharField(max_length=255,
+ verbose_name='Visit 5 IgA status',
+ blank=True,
+ null=True,
+ )
+ virus_test_5_igg_status = models.CharField(max_length=255,
+ verbose_name='Visit 5 IgG status',
+ blank=True,
+ null=True,
+ )
+
def sort_matched_screening_first(self, pattern, reverse=False):
if self.screening_number is None:
return None
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index 0bd62843..9e699cf9 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -17,7 +17,8 @@ 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, RED_CAP_SAMPLE_DATE_FIELD_TYPE, RED_CAP_KIT_ID_FIELD_TYPE
+ GLOBAL_STUDY_ID, RED_CAP_SAMPLE_DATE_FIELD_TYPE, RED_CAP_KIT_ID_FIELD_TYPE, RED_CAP_IGA_STATUS_FIELD_TYPE, \
+ RED_CAP_IGG_STATUS_FIELD_TYPE
from web.models.inconsistent_subject import InconsistentField, InconsistentSubject
from web.models.missing_subject import MissingSubject
@@ -47,6 +48,8 @@ class RedcapVisit(object):
virus_inconclusive = False
visit_number = 0
virus_collection_date = None
+ iga_status = None
+ igg_status = None
def different_string(string1, string2):
@@ -94,6 +97,8 @@ class RedcapConnector(object):
self.virus_field = ConfigurationItem.objects.get(type=RED_CAP_VIRUS_FIELD_TYPE).value
self.sample_kit_id_field = ConfigurationItem.objects.get(type=RED_CAP_KIT_ID_FIELD_TYPE).value
self.sample_date_field = ConfigurationItem.objects.get(type=RED_CAP_SAMPLE_DATE_FIELD_TYPE).value
+ self.iga_status_field = ConfigurationItem.objects.get(type=RED_CAP_IGA_STATUS_FIELD_TYPE).value
+ self.igg_status_field = ConfigurationItem.objects.get(type=RED_CAP_IGG_STATUS_FIELD_TYPE).value
self.study = Study.objects.get(id=GLOBAL_STUDY_ID)
@@ -230,46 +235,72 @@ class RedcapConnector(object):
smasch_appointment.visit.is_finished = True
smasch_appointment.visit.save()
if visit.virus is not None or visit.virus_inconclusive:
- changes = None
+ changes = []
if visit.visit_number == 1 and subject.virus_test_1 != visit.virus:
- changes = [('virus_test_1', visit.virus),
- ('virus_test_1_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_1', visit.virus),
+ ('virus_test_1_updated', datetime.datetime.now())])
if visit.visit_number == 2 and subject.virus_test_2 != visit.virus:
- changes = [('virus_test_2', visit.virus),
- ('virus_test_2_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_2', visit.virus),
+ ('virus_test_2_updated', datetime.datetime.now())])
if visit.visit_number == 3 and subject.virus_test_3 != visit.virus:
- changes = [('virus_test_3', visit.virus),
- ('virus_test_3_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_3', visit.virus),
+ ('virus_test_3_updated', datetime.datetime.now())])
if visit.visit_number == 4 and subject.virus_test_4 != visit.virus:
- changes = [('virus_test_4', visit.virus),
- ('virus_test_4_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_4', visit.virus),
+ ('virus_test_4_updated', datetime.datetime.now())])
if visit.visit_number == 5 and subject.virus_test_5 != visit.virus:
- changes = [('virus_test_5', visit.virus),
- ('virus_test_5_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_5', 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 = [('virus_test_1_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_1_updated', datetime.datetime.now())])
if visit.visit_number == 2 and subject.virus_test_2_updated is None and visit.virus_inconclusive:
- changes = [('virus_test_2_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_2_updated', datetime.datetime.now())])
if visit.visit_number == 3 and subject.virus_test_3_updated is None and visit.virus_inconclusive:
- changes = [('virus_test_3_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_3_updated', datetime.datetime.now())])
if visit.visit_number == 4 and subject.virus_test_4_updated is None and visit.virus_inconclusive:
- changes = [('virus_test_4_updated', datetime.datetime.now())]
+ changes.extend([('virus_test_4_updated', datetime.datetime.now())])
if visit.visit_number == 5 and subject.virus_test_5_updated is None and visit.virus_inconclusive:
- changes = [('virus_test_5_updated', datetime.datetime.now())]
-
- if visit.visit_number == 1 and not date_equals(subject.virus_test_1_collection_date , visit.virus_collection_date):
- changes = [('virus_test_1_collection_date', visit.virus_collection_date)]
- if visit.visit_number == 2 and subject.virus_test_2_collection_date != visit.virus_collection_date:
- changes = [('virus_test_2_collection_date', visit.virus_collection_date)]
- if visit.visit_number == 3 and subject.virus_test_3_collection_date != visit.virus_collection_date:
- changes = [('virus_test_3_collection_date', visit.virus_collection_date)]
- if visit.visit_number == 4 and subject.virus_test_4_collection_date != visit.virus_collection_date:
- changes = [('virus_test_4_collection_date', visit.virus_collection_date)]
- if visit.visit_number == 5 and subject.virus_test_5_collection_date != visit.virus_collection_date:
- changes = [('virus_test_5_collection_date', visit.virus_collection_date)]
+ changes.extend([('virus_test_5_updated', datetime.datetime.now())])
+
+ if visit.visit_number == 1 and not date_equals(subject.virus_test_1_collection_date,
+ visit.virus_collection_date):
+ changes.extend([('virus_test_1_collection_date', visit.virus_collection_date)])
+ if visit.visit_number == 2 and not date_equals(subject.virus_test_2_collection_date,
+ visit.virus_collection_date):
+ changes.extend([('virus_test_2_collection_date', visit.virus_collection_date)])
+ if visit.visit_number == 3 and not date_equals(subject.virus_test_3_collection_date,
+ visit.virus_collection_date):
+ changes.extend([('virus_test_3_collection_date', visit.virus_collection_date)])
+ if visit.visit_number == 4 and not date_equals(subject.virus_test_4_collection_date,
+ visit.virus_collection_date):
+ changes.extend([('virus_test_4_collection_date', visit.virus_collection_date)])
+ if visit.visit_number == 5 and not date_equals(subject.virus_test_5_collection_date,
+ visit.virus_collection_date):
+ changes.extend([('virus_test_5_collection_date', visit.virus_collection_date)])
+
+ if visit.visit_number == 1 and subject.virus_test_1_iga_status != visit.iga_status:
+ changes.extend([('virus_test_1_iga_status', visit.iga_status)])
+ if visit.visit_number == 1 and subject.virus_test_1_igg_status != visit.igg_status:
+ changes.extend([('virus_test_1_igg_status', visit.igg_status)])
+ if visit.visit_number == 2 and subject.virus_test_2_iga_status != visit.iga_status:
+ changes.extend([('virus_test_2_iga_status', visit.iga_status)])
+ if visit.visit_number == 2 and subject.virus_test_2_igg_status != visit.igg_status:
+ changes.extend([('virus_test_2_igg_status', visit.igg_status)])
+ if visit.visit_number == 3 and subject.virus_test_3_iga_status != visit.iga_status:
+ changes.extend([('virus_test_3_iga_status', visit.iga_status)])
+ if visit.visit_number == 3 and subject.virus_test_3_igg_status != visit.igg_status:
+ changes.extend([('virus_test_3_igg_status', visit.igg_status)])
+ if visit.visit_number == 4 and subject.virus_test_4_iga_status != visit.iga_status:
+ changes.extend([('virus_test_4_iga_status', visit.iga_status)])
+ if visit.visit_number == 4 and subject.virus_test_4_igg_status != visit.igg_status:
+ changes.extend([('virus_test_4_igg_status', visit.igg_status)])
+ if visit.visit_number == 5 and subject.virus_test_5_iga_status != visit.iga_status:
+ changes.extend([('virus_test_5_iga_status', visit.iga_status)])
+ if visit.visit_number == 5 and subject.virus_test_5_igg_status != visit.igg_status:
+ changes.extend([('virus_test_5_igg_status', visit.igg_status)])
#
- if changes is not None:
+ if len(changes) > 0:
for field, new_value in changes:
old_value = getattr(subject, field)
description = u'{} changed from "{}" to "{}"'.format(field, old_value, new_value)
@@ -407,6 +438,11 @@ class RedcapConnector(object):
logger.warn("Invalid date: " + row.get(self.sample_date_field))
visit.virus_collection_date = None
+ if self.iga_status_field != "":
+ visit.iga_status = row.get(self.iga_status_field)
+ if self.igg_status_field != "":
+ visit.igg_status = row.get(self.igg_status_field)
+
if self.sample_kit_id_field != "":
if row.get(self.sample_kit_id_field) != "":
redcap_subject.visits.append(visit)
@@ -486,6 +522,12 @@ class RedcapConnector(object):
if self.sample_date_field != "":
result['fields[' + str(field_number) + ']'] = self.sample_date_field
field_number += 1
+ if self.iga_status_field != "":
+ result['fields[' + str(field_number) + ']'] = self.iga_status_field
+ field_number += 1
+ if self.igg_status_field != "":
+ result['fields[' + str(field_number) + ']'] = self.igg_status_field
+ field_number += 1
return result
def get_language(self, name):
--
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