From fe0fc30578e4006d06b835b0f487b9b2af04d1f0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 25 May 2020 14:06:23 +0200
Subject: [PATCH] date of virus collection is added automatically from redcap
---
smash/db_scripts/create_dummy_data.py | 4 +
smash/web/api_views/subject.py | 26 +++++-
smash/web/forms/study_subject_forms.py | 18 +++-
.../migrations/0168_rename_radcap_field.py | 37 ++++++++
.../web/migrations/0169_auto_20200525_1123.py | 40 +++++++++
.../web/migrations/0170_auto_20200525_1126.py | 40 +++++++++
smash/web/models/constants.py | 1 +
smash/web/models/study_columns.py | 20 +++++
smash/web/models/study_subject.py | 20 +++++
smash/web/redcap_connector.py | 90 ++++++++++++++-----
10 files changed, 266 insertions(+), 30 deletions(-)
create mode 100644 smash/web/migrations/0168_rename_radcap_field.py
create mode 100644 smash/web/migrations/0169_auto_20200525_1123.py
create mode 100644 smash/web/migrations/0170_auto_20200525_1126.py
diff --git a/smash/db_scripts/create_dummy_data.py b/smash/db_scripts/create_dummy_data.py
index b6a8ab53..0e44344b 100644
--- a/smash/db_scripts/create_dummy_data.py
+++ b/smash/db_scripts/create_dummy_data.py
@@ -437,13 +437,17 @@ class smashProvider(BaseProvider):
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:
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:
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')
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,
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 05a96565..5a8ff67a 100644
--- a/smash/web/api_views/subject.py
+++ b/smash/web/api_views/subject.py
@@ -95,9 +95,14 @@ def get_subject_columns(request, subject_list_type):
'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,
+ "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)
@@ -220,6 +225,16 @@ 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_updated')
elif order_column == "virus_test_5_updated":
result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_updated')
+ elif order_column == "virus_test_1_collection_date":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1_collection_date')
+ elif order_column == "virus_test_2_collection_date":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2_collection_date')
+ elif order_column == "virus_test_3_collection_date":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3_collection_date')
+ elif order_column == "virus_test_4_collection_date":
+ 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')
else:
logger.warn("Unknown sort column: " + str(order_column))
return result
@@ -529,6 +544,11 @@ def serialize_subject(study_subject):
"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,
+ "virus_test_1_collection_date": study_subject.virus_test_1_collection_date,
+ "virus_test_2_collection_date": study_subject.virus_test_2_collection_date,
+ "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,
"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 bf3a7844..39f2fb0e 100644
--- a/smash/web/forms/study_subject_forms.py
+++ b/smash/web/forms/study_subject_forms.py
@@ -34,8 +34,13 @@ class StudySubjectForm(ModelForm):
for one_based_idx, virus_visit_number in enumerate(virus_visit_numbers, 1):
field = 'virus_test_{}'.format(one_based_idx)
self.fields[field].label = 'Visit {} RT-PCR'.format(virus_visit_number)
+
date_field = 'virus_test_{}_updated'.format(one_based_idx)
- self.fields[date_field].label = 'Visit {} RT-PCR date'.format(virus_visit_number)
+ self.fields[date_field].label = 'Visit {} RT-PCR result date'.format(virus_visit_number)
+
+ 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)
+
for visit_number in range(1, 6):
disable_virus_test_field(self, visit_number)
self.update_virus_inconclusive_data(visit_number)
@@ -172,10 +177,12 @@ class StudySubjectEditForm(StudySubjectForm):
def disable_virus_test_field(self, visit_number):
test_result_column_name = 'virus_test_{}'.format(visit_number)
- test_date_column_name = 'virus_test_{}_updated'.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)
self.fields[test_result_column_name].widget.attrs['readonly'] = True
self.fields[test_result_column_name].widget.attrs['disabled'] = True
- self.fields[test_date_column_name].widget.attrs['readonly'] = True
+ self.fields[test_result_date_column_name].widget.attrs['readonly'] = True
+ self.fields[test_collection_date_column_name].widget.attrs['readonly'] = True
def get_study_from_args(kwargs):
@@ -229,6 +236,11 @@ def prepare_study_subject_fields(fields, study):
prepare_field(fields, study.columns, 'virus_test_3_updated')
prepare_field(fields, study.columns, 'virus_test_4_updated')
prepare_field(fields, study.columns, 'virus_test_5_updated')
+ prepare_field(fields, study.columns, 'virus_test_1_collection_date')
+ prepare_field(fields, study.columns, 'virus_test_2_collection_date')
+ 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')
def validate_subject_screening_number(self, cleaned_data):
diff --git a/smash/web/migrations/0168_rename_radcap_field.py b/smash/web/migrations/0168_rename_radcap_field.py
new file mode 100644
index 00000000..be1108a5
--- /dev/null
+++ b/smash/web/migrations/0168_rename_radcap_field.py
@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+from web.models.constants import RED_CAP_SAMPLE_DATE_FIELD_TYPE, RED_CAP_KIT_ID_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', '0167_auto_20200428_1110'),
+ ]
+
+ operations = [
+ migrations.RunSQL(
+ "update web_configurationitem set type = '" + RED_CAP_KIT_ID_FIELD_TYPE + "' where type = '" + RED_CAP_SAMPLE_DATE_FIELD_TYPE + "';"),
+ migrations.RunSQL(
+ "update web_configurationitem set name = 'Redcap field for sample kit id in the visit' where type = '" + RED_CAP_KIT_ID_FIELD_TYPE + "';"),
+ migrations.RunPython(configuration_items),
+
+ ]
diff --git a/smash/web/migrations/0169_auto_20200525_1123.py b/smash/web/migrations/0169_auto_20200525_1123.py
new file mode 100644
index 00000000..ecc26be1
--- /dev/null
+++ b/smash/web/migrations/0169_auto_20200525_1123.py
@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.5 on 2020-05-25 11:23
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0168_rename_radcap_field'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1_collection_date',
+ field=models.DateField(blank=True, null=True, verbose_name=b'Visit 1 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2_collection_date',
+ field=models.DateField(blank=True, null=True, verbose_name=b'Visit 2 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3_collection_date',
+ field=models.DateField(blank=True, null=True, verbose_name=b'Visit 3 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4_collection_date',
+ field=models.DateField(blank=True, null=True, verbose_name=b'Visit 4 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5_collection_date',
+ field=models.DateField(blank=True, null=True, verbose_name=b'Visit 5 virus collection date'),
+ ),
+ ]
diff --git a/smash/web/migrations/0170_auto_20200525_1126.py b/smash/web/migrations/0170_auto_20200525_1126.py
new file mode 100644
index 00000000..4f70a352
--- /dev/null
+++ b/smash/web/migrations/0170_auto_20200525_1126.py
@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.5 on 2020-05-25 11:26
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0169_auto_20200525_1123'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_1_collection_date',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 1 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_2_collection_date',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 2 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_3_collection_date',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 3 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_4_collection_date',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 4 virus collection date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_5_collection_date',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 5 virus collection date'),
+ ),
+ ]
diff --git a/smash/web/models/constants.py b/smash/web/models/constants.py
index 51e7a70b..498c9a6a 100644
--- a/smash/web/models/constants.py
+++ b/smash/web/models/constants.py
@@ -65,6 +65,7 @@ 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_KIT_ID_FIELD_TYPE = "RED_CAP_KIT_ID_FIELD_TYPE"
RED_CAP_SAMPLE_DATE_FIELD_TYPE = "RED_CAP_SAMPLE_DATE_FIELD_TYPE"
diff --git a/smash/web/models/study_columns.py b/smash/web/models/study_columns.py
index d2e769ca..ac3954fa 100644
--- a/smash/web/models/study_columns.py
+++ b/smash/web/models/study_columns.py
@@ -162,3 +162,23 @@ class StudyColumns(models.Model):
default=False,
verbose_name='Visit 5 virus results date',
)
+ virus_test_1_collection_date = models.BooleanField(
+ default=False,
+ verbose_name='Visit 1 virus collection date',
+ )
+ virus_test_2_collection_date = models.BooleanField(
+ default=False,
+ verbose_name='Visit 2 virus collection date',
+ )
+ virus_test_3_collection_date = models.BooleanField(
+ default=False,
+ verbose_name='Visit 3 virus collection date',
+ )
+ virus_test_4_collection_date = models.BooleanField(
+ default=False,
+ verbose_name='Visit 4 virus collection date',
+ )
+ virus_test_5_collection_date = models.BooleanField(
+ default=False,
+ verbose_name='Visit 5 virus collection date',
+ )
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index d802d8de..99a0ebb8 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -242,6 +242,26 @@ class StudySubject(models.Model):
blank=True,
null=True,
)
+ virus_test_1_collection_date = models.DateField(verbose_name='Visit 1 virus collection date',
+ blank=True,
+ null=True,
+ )
+ virus_test_2_collection_date = models.DateField(verbose_name='Visit 2 virus collection date',
+ blank=True,
+ null=True,
+ )
+ virus_test_3_collection_date = models.DateField(verbose_name='Visit 3 virus collection date',
+ blank=True,
+ null=True,
+ )
+ virus_test_4_collection_date = models.DateField(verbose_name='Visit 4 virus collection date',
+ blank=True,
+ null=True,
+ )
+ virus_test_5_collection_date = models.DateField(verbose_name='Visit 5 virus collection date',
+ blank=True,
+ null=True,
+ )
def sort_matched_screening_first(self, pattern, reverse=False):
if self.screening_number is None:
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index 01ada9e9..0bd62843 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -11,12 +11,13 @@ from django.conf import settings
from django.forms.models import model_to_dict
from django_cron import CronJobBase, Schedule
-from web.models import ConfigurationItem, StudySubject, Language, AppointmentType, Appointment, Visit, Study, Provenance, Worker, User
+from web.models import ConfigurationItem, StudySubject, Language, AppointmentType, Appointment, Visit, Study, \
+ Provenance, Worker, User
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
+ GLOBAL_STUDY_ID, RED_CAP_SAMPLE_DATE_FIELD_TYPE, RED_CAP_KIT_ID_FIELD_TYPE
from web.models.inconsistent_subject import InconsistentField, InconsistentSubject
from web.models.missing_subject import MissingSubject
@@ -45,6 +46,7 @@ class RedcapVisit(object):
virus = None
virus_inconclusive = False
visit_number = 0
+ virus_collection_date = None
def different_string(string1, string2):
@@ -55,6 +57,14 @@ def different_string(string1, string2):
return string1.strip() != string2.strip()
+def date_equals(date1, date2):
+ if date1 is None and date2 is None:
+ return True
+ if date1 is None or date2 is None:
+ return False
+ return date1.strftime("%Y-%m-%d") == date2.strftime("%Y-%m-%d")
+
+
class RedcapConnector(object):
def __init__(self):
self.token = None
@@ -82,6 +92,7 @@ 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_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.study = Study.objects.get(id=GLOBAL_STUDY_ID)
@@ -199,7 +210,6 @@ 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,
@@ -207,28 +217,35 @@ class RedcapConnector(object):
for smasch_appointment in smasch_appointments:
smasch_appointment.mark_as_finished()
if smasch_appointment.visit.is_finished != True:
- description = u'{} changed from "{}" to "{}"'.format('is_finished', smasch_appointment.visit.is_finished, True)
+ description = u'{} changed from "{}" to "{}"'.format('is_finished',
+ smasch_appointment.visit.is_finished,
+ True)
p = Provenance(modified_table=Visit._meta.db_table,
- modified_table_id=smasch_appointment.visit.id,
- modification_author=self.importer_user,
- previous_value=smasch_appointment.visit.is_finished,
- new_value=True,
- modification_description=description,
- modified_field='is_finished')
+ modified_table_id=smasch_appointment.visit.id,
+ modification_author=self.importer_user,
+ previous_value=smasch_appointment.visit.is_finished,
+ new_value=True,
+ modification_description=description,
+ modified_field='is_finished')
smasch_appointment.visit.is_finished = True
smasch_appointment.visit.save()
if visit.virus is not None or visit.virus_inconclusive:
changes = None
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 = [('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 = [('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 = [('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 = [('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 = [('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())]
if visit.visit_number == 2 and subject.virus_test_2_updated is None and visit.virus_inconclusive:
@@ -239,18 +256,30 @@ class RedcapConnector(object):
changes = [('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)]
+
#
if changes is not None:
for field, new_value in changes:
old_value = getattr(subject, field)
description = u'{} changed from "{}" to "{}"'.format(field, old_value, new_value)
p = Provenance(modified_table=StudySubject._meta.db_table,
- modified_table_id=subject.id,
- modification_author=self.importer_user,
- previous_value=old_value,
- new_value=new_value,
- modification_description=description,
- modified_field=field)
+ modified_table_id=subject.id,
+ modification_author=self.importer_user,
+ previous_value=old_value,
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field)
setattr(subject, field, new_value)
p.save()
subject.save()
@@ -369,7 +398,17 @@ class RedcapConnector(object):
elif row.get(self.virus_field) == "Inconclusive":
visit.virus_inconclusive = True
if self.sample_date_field != "":
- if row.get(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":
+ try:
+ visit.virus_collection_date = datetime.datetime.strptime(row.get(self.sample_date_field),
+ "%Y-%m-%d")
+ except ValueError:
+ logger.warn("Invalid date: " + row.get(self.sample_date_field))
+ visit.virus_collection_date = None
+
+ if self.sample_kit_id_field != "":
+ if row.get(self.sample_kit_id_field) != "":
redcap_subject.visits.append(visit)
result.append(redcap_subject)
for i in range(1, 9):
@@ -390,8 +429,8 @@ class RedcapConnector(object):
visit.virus = False
elif row.get(self.virus_field) == "Positive":
visit.virus = True
- if self.sample_date_field != "":
- if row.get(self.sample_date_field) != "":
+ if self.sample_kit_id_field != "":
+ if row.get(self.sample_kit_id_field) != "":
redcap_subject.visits.append(visit)
return result
@@ -441,6 +480,9 @@ class RedcapConnector(object):
if self.virus_field != "":
result['fields[' + str(field_number) + ']'] = self.virus_field
field_number += 1
+ if self.sample_kit_id_field != "":
+ result['fields[' + str(field_number) + ']'] = self.sample_kit_id_field
+ field_number += 1
if self.sample_date_field != "":
result['fields[' + str(field_number) + ']'] = self.sample_date_field
field_number += 1
--
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