From bfb5ebcc1a806f7f2e4242e91359c1b46c2975ca Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 14 Apr 2020 14:16:17 +0200
Subject: [PATCH] list of subjects imported using new tns format
---
.../web/importer/csv_tns_subject_import_reader.py | 9 +++++++--
smash/web/tests/data/tns_subjects_import.csv | 4 ++--
.../test_tns_csv_subject_import_reader.py | 15 +++++++++++++++
.../importer/test_tns_csv_visit_import_reader.py | 1 -
4 files changed, 24 insertions(+), 5 deletions(-)
diff --git a/smash/web/importer/csv_tns_subject_import_reader.py b/smash/web/importer/csv_tns_subject_import_reader.py
index 638c798c..862bbb94 100644
--- a/smash/web/importer/csv_tns_subject_import_reader.py
+++ b/smash/web/importer/csv_tns_subject_import_reader.py
@@ -34,15 +34,18 @@ class TnsCsvSubjectImportReader(SubjectImportReader):
def add_data(self, study_subject, column_name, value):
# type: (StudySubject, str, str) -> None
- if column_name == "firstname":
+ if column_name == "firstname" or column_name == "sig_firstname":
study_subject.subject.first_name = self.get_new_value(study_subject.subject.first_name, column_name, value)
- elif column_name == "lastname":
+ elif column_name == "lastname" or column_name == "sig_lastname":
study_subject.subject.last_name = self.get_new_value(study_subject.subject.last_name, column_name, value)
elif column_name == "donor_id":
study_subject.screening_number = self.get_new_value(study_subject.screening_number, column_name, value)
elif column_name == "phonenr":
study_subject.subject.phone_number = self.get_new_value(study_subject.subject.phone_number, column_name,
value)
+ elif column_name == "representative":
+ study_subject.subject.next_of_keen_name = self.get_new_value(study_subject.subject.next_of_keen_name,
+ column_name, value)
elif column_name == "treatingphysician":
if value is not None and value != "":
value = "Treating physician: " + value
@@ -59,6 +62,8 @@ class TnsCsvSubjectImportReader(SubjectImportReader):
return new_value
if new_value is None or new_value == "":
return old_value
+ if old_value == new_value:
+ return new_value
logger.warn(
"Contradicting entries in csv file for column: " + column_name + "(" + new_value + "," + old_value +
"). Latest value will be used")
diff --git a/smash/web/tests/data/tns_subjects_import.csv b/smash/web/tests/data/tns_subjects_import.csv
index 4ae65947..05a910ed 100644
--- a/smash/web/tests/data/tns_subjects_import.csv
+++ b/smash/web/tests/data/tns_subjects_import.csv
@@ -1,4 +1,4 @@
donor_id;firstname;lastname;dateofbirth;phonenr;treatingphysician;sig_firstname;sig_lastname;representative
cov-000111;John;Doe;01/01/1977;555555;Gregory House;John;Doe;Mario Doe
-cov-222333;John2;Doe2;01/02/1977;621000000;Gregory House2;John 2;Doe 2;
-cov-444444;John2;Doe2;01/03/1977;691000000;Gregory House3;John 3;Doe 3;Elsa Doe
\ No newline at end of file
+cov-222333;John2;Doe2;01/02/1977;621000000;Gregory House2;John2;Doe2;
+cov-444444;John2;Doe2;01/03/1977;691000000;Gregory House3;John2;Doe2;Elsa Doe
\ No newline at end of file
diff --git a/smash/web/tests/importer/test_tns_csv_subject_import_reader.py b/smash/web/tests/importer/test_tns_csv_subject_import_reader.py
index a713f5b1..f81ec8f5 100644
--- a/smash/web/tests/importer/test_tns_csv_subject_import_reader.py
+++ b/smash/web/tests/importer/test_tns_csv_subject_import_reader.py
@@ -6,12 +6,20 @@ from django.test import TestCase
from web.importer import TnsCsvSubjectImportReader
from web.tests.functions import get_resource_path
+from web.importer import MsgCounterHandler
logger = logging.getLogger(__name__)
class TestTnsCsvSubjectReader(TestCase):
+ def setUp(self):
+ self.warning_counter = MsgCounterHandler()
+ logging.getLogger('').addHandler(self.warning_counter)
+
+ def tearDown(self):
+ logging.getLogger('').removeHandler(self.warning_counter)
+
def test_load_data(self):
filename = get_resource_path('tns_subjects_import.csv')
study_subjects = TnsCsvSubjectImportReader().load_data(filename)
@@ -29,3 +37,10 @@ class TestTnsCsvSubjectReader(TestCase):
self.assertEqual(1977, study_subject.subject.date_born.year)
self.assertIsNotNone(study_subject.study)
+ self.assertEqual(0, self.get_warnings_count())
+
+ def get_warnings_count(self):
+ if "WARNING" in self.warning_counter.level2count:
+ return self.warning_counter.level2count["WARNING"]
+ else:
+ return 0
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 ae7c1a04..44b62187 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
@@ -132,7 +132,6 @@ class TestTnsCsvSubjectReader(TestCase):
self.assertEquals(1, self.get_warnings_count())
-
def get_warnings_count(self):
if "WARNING" in self.warning_counter.level2count:
return self.warning_counter.level2count["WARNING"]
--
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