allow to import type from csv file

smash/web/importer/csv_subject_import_reader.py

@@ -5,7 +5,7 @@ from typing import List, Type, Tuple
 from django.db import models
 from django.db.models import Field
 
-from web.models import StudySubject, Subject, SubjectImportData, Language
+from web.models import StudySubject, Subject, SubjectImportData, Language, SubjectType
 from .etl_common import EtlCommon
 from .subject_import_reader import SubjectImportReader
 
@@ -56,16 +56,16 @@ class CsvSubjectImportReader(SubjectImportReader):
             value = self.get_value_for_foreign_field(field, value)
 
         if table == Subject:
-            old_val = getattr(study_subject.subject, field.name)
+            old_val = self.get_field_value(study_subject.subject, field)
             setattr(study_subject.subject, field.name, self.get_new_value(old_val, value))
         elif table == StudySubject:
-            old_val = getattr(study_subject, field.name)
+            old_val = self.get_field_value(study_subject, field)
             setattr(study_subject, field.name, self.get_new_value(old_val, value))
         else:
             logger.warning("Don't know how to handle column " + column_name + " with data " + value)
 
     @staticmethod
-    def get_value_for_foreign_field(field, value):
+    def get_value_for_foreign_field(field: Field, value: str):
         if field.related_model == Language:
             if value == "":
                 return None
@@ -74,10 +74,25 @@ class CsvSubjectImportReader(SubjectImportReader):
                 if language is None:
                     language = Language.objects.create(name=value)
                 return language
+        elif field.related_model == SubjectType:
+            subject_type = SubjectType.objects.filter(name=value).first()
+            if subject_type is None:
+                subject_type = SubjectType.objects.all().first()
+                logger.warning(
+                    "Subject type does not exist: '" + str(value) + "'. Changing to: '" + subject_type.name + "'")
+            return subject_type
         else:
             logger.warning("Don't know how to handle type " + str(field.related_model))
             return None
 
+    @staticmethod
+    def get_field_value(model_object: models.Model, field: Field):
+        # for foreign keys we need to check if the key id is not none, otherwise for not nullable fields exception
+        # would be raised
+        if field.get_internal_type() == "ForeignKey" and getattr(model_object, field.name + "_id") is None:
+            return None
+        return getattr(model_object, field.name)
+
     def get_table_and_field(self, column_name: str) -> Tuple[Type[models.Model], Field]:
         return self.mappings.get(column_name, (None, None))
 
@@ -86,7 +101,7 @@ class CsvSubjectImportReader(SubjectImportReader):
             if field.get_internal_type() == "CharField" or \
                     field.get_internal_type() == "DateField" or \
                     field.get_internal_type() == "TextField" or \
-                    (field.get_internal_type() == "ForeignKey" and field.related_model in (Language,)):
+                    (field.get_internal_type() == "ForeignKey" and field.related_model in (Language, SubjectType)):
                 found = False
                 for mapping in self.import_data.column_mappings.all():
                     if mapping.table_name == object_type._meta.db_table and field.name == mapping.column_name:

smash/web/tests/data/import_type.csv

+first_name,last_name,participant_id,type
+Piotr,Gawron,Cov-000001,PATIENT
+Piotr,Gawron,Cov-000002,CONTROL
+Piotr,Gawron,Cov-000003,
+Piotr,Gawron,Cov-000004,UNKNOWN

smash/web/tests/importer/test_csv_subject_import_reader.py

@@ -7,7 +7,8 @@ from django.test import TestCase
 from web.importer import CsvSubjectImportReader, MsgCounterHandler
 from web.models import SubjectImportData, EtlColumnMapping, StudySubject, Country
 from web.models.constants import COUNTRY_AFGHANISTAN_ID
-from web.tests.functions import get_resource_path, get_test_study, create_tns_column_mapping, create_location
+from web.tests.functions import get_resource_path, get_test_study, create_tns_column_mapping, create_location, \
+    get_control_subject_type, get_patient_subject_type
 
 logger = logging.getLogger(__name__)
 
@@ -60,6 +61,16 @@ class TestCsvReader(TestCase):
         self.assertIsNotNone(study_subjects[1].subject.default_written_communication_language)
         self.assertIsNone(study_subjects[2].subject.default_written_communication_language)
 
+    def test_load_type(self):
+        self.subject_import_data.filename = get_resource_path('import_type.csv')
+        study_subjects = CsvSubjectImportReader(self.subject_import_data).load_data()
+
+        self.assertEqual(4, len(study_subjects))
+        self.assertEqual(get_patient_subject_type(), study_subjects[0].type)
+        self.assertEqual(get_control_subject_type(), study_subjects[1].type)
+        self.assertIsNotNone(study_subjects[2].type)
+        self.assertIsNotNone(study_subjects[3].type)
+
     def test_load_data_for_tns(self):
         self.subject_import_data = SubjectImportData.objects.create(study=get_test_study(),
                                                                     date_format="%d/%m/%Y",