From f1b52d9adee522d224631c0670e1c3c762600087 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 17 Nov 2020 10:42:32 +0100
Subject: [PATCH] visit_number column is configurable
visit_number is computed properly based on the redcap_first_visit_number configuration option
---
.../importer/csv_tns_visit_import_reader.py | 11 ++++++++--
smash/web/migrations/0179_visitimportdata.py | 1 +
smash/web/models/etl/visit_import.py | 16 ++++++++++-----
.../test_tns_csv_visit_import_reader.py | 20 +++++++++++++++++++
4 files changed, 41 insertions(+), 7 deletions(-)
diff --git a/smash/web/importer/csv_tns_visit_import_reader.py b/smash/web/importer/csv_tns_visit_import_reader.py
index 7cf94cfa..525a15a1 100644
--- a/smash/web/importer/csv_tns_visit_import_reader.py
+++ b/smash/web/importer/csv_tns_visit_import_reader.py
@@ -59,8 +59,7 @@ class TnsCsvVisitImportReader:
location = self.extract_location(data)
- visit_number = data['visit_id']
- visit_number = int(visit_number) + 1
+ visit_number = self.get_visit_number(data)
for i in range(1, visit_number, 1):
if Visit.objects.filter(subject=study_subject, visit_number=i).count() == 0:
@@ -247,6 +246,14 @@ class TnsCsvVisitImportReader:
result += "<p><font " + style + ">Number of raised warnings: <b>" + str(self.warning_count) + "</b></font></p>"
return result
+ def get_visit_number(self, data: dict) -> int:
+ try:
+ visit_number = data[self.visit_import_data.visit_number_column_name]
+ visit_number = int(visit_number) + (1 - self.visit_import_data.study.redcap_first_visit_number)
+ return visit_number
+ except KeyError as e:
+ raise EtlException('Visit number is not defined') from e
+
def remove_bom(line):
if type(line) == str:
diff --git a/smash/web/migrations/0179_visitimportdata.py b/smash/web/migrations/0179_visitimportdata.py
index e802ed85..4064c8d2 100644
--- a/smash/web/migrations/0179_visitimportdata.py
+++ b/smash/web/migrations/0179_visitimportdata.py
@@ -21,6 +21,7 @@ class Migration(migrations.Migration):
('subject_id_column_name', models.CharField(blank=False, default='donor_id', max_length=128, null=False,verbose_name='Subject id column name')),
('visit_date_column_name', models.CharField(blank=False, default='dateofvisit', max_length=128, null=False,verbose_name='Visit date column name')),
('location_column_name', models.CharField(blank=False, default='adressofvisit', max_length=128, null=False,verbose_name='Location column name')),
+ ('visit_number_column_name', models.CharField(blank=False, default='visit_id', max_length=128, null=False,verbose_name='Visit number column name')),
],
),
]
diff --git a/smash/web/models/etl/visit_import.py b/smash/web/models/etl/visit_import.py
index adb76494..528dd997 100644
--- a/smash/web/models/etl/visit_import.py
+++ b/smash/web/models/etl/visit_import.py
@@ -39,8 +39,14 @@ class VisitImportData(models.Model):
blank=False
)
location_column_name = models.CharField(max_length=128,
- verbose_name='Location column name',
- default='adressofvisit',
- null=False,
- blank=False
- )
+ verbose_name='Location column name',
+ default='adressofvisit',
+ null=False,
+ blank=False
+ )
+ visit_number_column_name = models.CharField(max_length=128,
+ verbose_name='Visit number column name',
+ default='visit_id',
+ null=False,
+ blank=False
+ )
diff --git a/smash/web/tests/importer/test_tns_csv_visit_import_reader.py b/smash/web/tests/importer/test_tns_csv_visit_import_reader.py
index 3995fce3..8cac00af 100644
--- a/smash/web/tests/importer/test_tns_csv_visit_import_reader.py
+++ b/smash/web/tests/importer/test_tns_csv_visit_import_reader.py
@@ -17,6 +17,9 @@ logger = logging.getLogger(__name__)
class TestTnsCsvVisitReader(TestCase):
def setUp(self):
appointment_type = create_appointment_type(code="SAMPLE_2")
+ study = get_test_study()
+ study.redcap_first_visit_number = 0
+ study.save()
self.visit_import_data = VisitImportData.objects.create(study=get_test_study(),
appointment_type=appointment_type,
import_worker=create_worker())
@@ -169,6 +172,23 @@ class TestTnsCsvVisitReader(TestCase):
self.assertEqual('x001', location.name)
self.assertEqual(1, self.get_warnings_count())
+ def test_get_visit_number_by_invalid_id_column(self):
+ self.assertRaises(EtlException,
+ TnsCsvVisitImportReader(self.visit_import_data).get_visit_number, {'invalid_id': '1'})
+
+ def test_get_visit_number_by_valid_id_column(self):
+ self.visit_import_data.study.redcap_first_visit_number = 0
+ self.visit_import_data.study.save()
+ visit_number = TnsCsvVisitImportReader(self.visit_import_data).get_visit_number({'visit_id': '1'})
+ # normalized visit number is from 1
+ self.assertEqual(2, visit_number)
+
+ def test_get_visit_number_by_valid_id_column_started_from_one(self):
+ self.visit_import_data.study.redcap_first_visit_number = 1
+ self.visit_import_data.study.save()
+ visit_number = TnsCsvVisitImportReader(self.visit_import_data).get_visit_number({'visit_id': '1'})
+ self.assertEqual(1, visit_number)
+
def test_get_study_subject_by_id_for_existing_subject(self):
reader = TnsCsvVisitImportReader(self.visit_import_data)
study_subject = StudySubject.objects.get(nd_number='cov-000111')
--
GitLab