From 284f018b52ec06810ec8ffed994386ec2a2697df Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 17 Nov 2020 10:11:30 +0100
Subject: [PATCH] visit date column name is configurable
---
smash/web/importer/csv_tns_visit_import_reader.py | 14 ++++++++++++--
smash/web/migrations/0179_visitimportdata.py | 1 +
smash/web/models/etl/visit_import.py | 7 +++++++
.../importer/test_tns_csv_visit_import_reader.py | 9 +++++++++
4 files changed, 29 insertions(+), 2 deletions(-)
diff --git a/smash/web/importer/csv_tns_visit_import_reader.py b/smash/web/importer/csv_tns_visit_import_reader.py
index 9842573d..ec174b34 100644
--- a/smash/web/importer/csv_tns_visit_import_reader.py
+++ b/smash/web/importer/csv_tns_visit_import_reader.py
@@ -50,9 +50,12 @@ class TnsCsvVisitImportReader:
data = {}
for h, v in zip(headers, row):
data[h] = v
+
nd_number = self.get_study_subject_id(data)
+
study_subject = self.get_study_subject_by_id(nd_number)
- date = self.extract_date(data['dateofvisit'])
+
+ date = self.get_visit_date(data)
location = self.extract_location(data)
@@ -179,6 +182,12 @@ class TnsCsvVisitImportReader:
return result
+ def get_visit_date(self, data: dict) -> datetime:
+ try:
+ return TnsCsvVisitImportReader.extract_date(data[self.visit_import_data.visit_date_column_name])
+ except KeyError as e:
+ raise EtlException('Visit date is not defined') from e
+
def get_study_subject_by_id(self, nd_number: str) -> StudySubject:
study_subjects = StudySubject.objects.filter(nd_number=nd_number, study=self.visit_import_data.study)
if len(study_subjects) == 0:
@@ -199,7 +208,8 @@ class TnsCsvVisitImportReader:
except KeyError as e:
raise EtlException('Subject id is not defined') from e
- def extract_date(self, text: str) -> datetime:
+ @staticmethod
+ def extract_date(text: str) -> datetime:
# by default use day after tomorrow
result = datetime.datetime.now().replace(hour=9, minute=0) + datetime.timedelta(days=2)
diff --git a/smash/web/migrations/0179_visitimportdata.py b/smash/web/migrations/0179_visitimportdata.py
index 83d8d742..fece3e79 100644
--- a/smash/web/migrations/0179_visitimportdata.py
+++ b/smash/web/migrations/0179_visitimportdata.py
@@ -19,6 +19,7 @@ class Migration(migrations.Migration):
('import_worker', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='web.Worker', verbose_name='Worker used by importer')),
('study', models.ForeignKey(editable=False, on_delete=django.db.models.deletion.CASCADE, to='web.Study', verbose_name='Study')),
('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')),
],
),
]
diff --git a/smash/web/models/etl/visit_import.py b/smash/web/models/etl/visit_import.py
index d613677f..7247cc1f 100644
--- a/smash/web/models/etl/visit_import.py
+++ b/smash/web/models/etl/visit_import.py
@@ -31,3 +31,10 @@ class VisitImportData(models.Model):
null=False,
blank=False
)
+
+ visit_date_column_name = models.CharField(max_length=128,
+ verbose_name='Visit date column name',
+ default='dateofvisit',
+ 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 b5f56c80..a1b8f17b 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
@@ -170,6 +170,15 @@ class TestTnsCsvVisitReader(TestCase):
subject_id = TnsCsvVisitImportReader(self.visit_import_data).get_study_subject_id({'donor_id': 'x001'})
self.assertEqual('x001', subject_id)
+ def test_get_visit_date_by_invalid_id_column(self):
+ self.assertRaises(EtlException,
+ TnsCsvVisitImportReader(self.visit_import_data).get_visit_date,
+ {'invalid_date': '19901010'})
+
+ def test_get_visit_date_by_valid_id_column(self):
+ visit_date = TnsCsvVisitImportReader(self.visit_import_data).get_visit_date({'dateofvisit': '19901010'})
+ self.assertEqual(1990, visit_date.year)
+
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')
--
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