diff --git a/smash/smash/local_settings.py.template b/smash/smash/local_settings.py.template
index 652a544a7cbe0200a79bf08391d99e85743fc7fd..6a6d9320b67791836ca102e1869c0c1189b1e366 100644
--- a/smash/smash/local_settings.py.template
+++ b/smash/smash/local_settings.py.template
@@ -6,6 +6,8 @@ DEBUG = True
WSGI_APPLICATION = 'smash.wsgi.application'
+IMPORTER_USER = 'admin' #username
+
EMAIL_USE_TLS = False
EMAIL_USE_SSL = False
EMAIL_HOST = 'smtp.uni.lu'
diff --git a/smash/web/importer/csv_tns_visit_import_reader.py b/smash/web/importer/csv_tns_visit_import_reader.py
index ae9501c06abab72ef192b80056a2fb23e3aa1d11..4ba9eef37c2421d48809ee469bb39c379d0307f4 100644
--- a/smash/web/importer/csv_tns_visit_import_reader.py
+++ b/smash/web/importer/csv_tns_visit_import_reader.py
@@ -10,7 +10,7 @@ import pytz
from django.conf import settings
from warning_counter import MsgCounterHandler
-from web.models import StudySubject, Study, Visit, Appointment, AppointmentType, Location, AppointmentTypeLink, Subject
+from web.models import StudySubject, Study, Visit, Appointment, AppointmentType, Location, AppointmentTypeLink, Subject, User, Worker, Provenance
from web.models.constants import GLOBAL_STUDY_ID
CSV_DATE_FORMAT = "%d/%m/%Y"
@@ -33,6 +33,16 @@ class TnsCsvVisitImportReader:
self.processed_count = 0
self.warning_count = 0
+ self.importer_user = None
+
+ importer_user_name = getattr(settings, "IMPORTER_USER", None)
+ if importer_user_name is not None:
+ user = User.objects.filter(username=importer_user_name)
+ if user is None:
+ logger.warn("User does not exist: " + importer_user_name)
+ else:
+ self.importer_user = Worker.objects.filter(user=user)
+
def load_data(self, filename):
warning_counter = MsgCounterHandler()
logging.getLogger('').addHandler(warning_counter)
@@ -80,22 +90,74 @@ class TnsCsvVisitImportReader:
if len(visits) > 0:
logger.debug("Visit for subject " + nd_number + " already exists. Updating")
visit = visits[0]
- visit.datetime_begin = date
- visit.datetime_end = date + datetime.timedelta(days=14)
+
+ changes = [('datetime_begin', date),
+ ('datetime_end', date + datetime.timedelta(days=14))]
+
+ for field, new_value in changes:
+ old_value = getattr(visit, field)
+ if old_value == new_value:
+ continue
+ description = u'{} changed from "{}" to "{}"'.format(field, old_value, new_value)
+ p = Provenance(modified_table=Visit._meta.db_table,
+ modified_table_id=visit.id,
+ modification_author=self.importer_user,
+ previous_value=old_value,
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field,
+ )
+ setattr(visit, field, new_value)
+ p.save()
+ visit.save()
else:
visit = Visit.objects.create(subject=study_subject, visit_number=visit_number,
datetime_begin=date,
datetime_end=date + datetime.timedelta(days=14))
- visit.save()
+ visit.save()
+ #visit does not have id until .save() is done
+ for field in Visit._meta.get_fields():
+ if field.get_internal_type() == "CharField" or field.get_internal_type() == "DateField" or field.get_internal_type() is "BooleanField":
+ new_value = getattr(visit, field.name)
+ if new_value is not None and new_value != "":
+ description = u'{} changed from "{}" to "{}"'.format(field, '', new_value)
+ p = Provenance(modified_table=Visit._meta.db_table,
+ modified_table_id=visit.id,
+ modification_author=self.importer_user,
+ previous_value='',
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field,
+ )
+ p.save()
+
result.append(visit)
appointments = Appointment.objects.filter(visit=visit, appointment_types=self.appointment_type)
if len(appointments) > 0:
logger.debug("Appointment for subject " + nd_number + " already set. Updating")
appointment = appointments[0]
- appointment.length = 60
- appointment.datetime_when = date
- appointment.location = location
+
+ #(field, new_value)
+ changes = [('length', 60),
+ ('datetime_when', date),
+ ('location', location)]
+
+ for field, new_value in changes:
+ old_value = getattr(appointment, field)
+ if old_value == new_value:
+ continue
+ description = u'{} changed from "{}" to "{}"'.format(field, old_value, new_value)
+ p = Provenance(modified_table=Appointment._meta.db_table,
+ modified_table_id=appointment.id,
+ modification_author=self.importer_user,
+ previous_value=old_value,
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field,
+ )
+ setattr(appointment, field, new_value)
+ p.save()
appointment.save()
else:
appointment = Appointment.objects.create(visit=visit, length=60, datetime_when=date,
@@ -103,6 +165,23 @@ class TnsCsvVisitImportReader:
if self.appointment_type is not None:
AppointmentTypeLink.objects.create(appointment_id=appointment.id,
appointment_type=self.appointment_type)
+
+ appointment.save()
+ #appointment does not have id until .save() is done
+ for field in Appointment._meta.get_fields():
+ if field.get_internal_type() == "CharField" or field.get_internal_type() == "DateField" or field.get_internal_type() is "BooleanField":
+ new_value = getattr(appointment, field.name)
+ if new_value is not None and new_value != "":
+ description = u'{} changed from "{}" to "{}"'.format(field, '', new_value)
+ p = Provenance(modified_table=Appointment._meta.db_table,
+ modified_table_id=appointment.id,
+ modification_author=self.importer_user,
+ previous_value='',
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field,
+ )
+ p.save()
self.processed_count += 1
except:
self.problematic_count += 1
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index a2af5169ca07e21bf5bce8098b152dbd53122891..01ada9e9c12d07b945679485dbcd6aa6dc870d7e 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -11,7 +11,7 @@ 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
+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, \
@@ -86,6 +86,16 @@ class RedcapConnector(object):
self.study = Study.objects.get(id=GLOBAL_STUDY_ID)
+ self.importer_user = None
+
+ importer_user_name = getattr(settings, "IMPORTER_USER", None)
+ if importer_user_name is not None:
+ user = User.objects.filter(username=importer_user_name)
+ if user is None:
+ logger.warn("User does not exist: " + importer_user_name)
+ else:
+ self.importer_user = Worker.objects.filter(user=user)
+
def find_missing(self):
pid = self.get_project_id()
redcap_version = self.get_redcap_version()
@@ -196,43 +206,53 @@ class RedcapConnector(object):
status=Appointment.APPOINTMENT_STATUS_SCHEDULED)
for smasch_appointment in smasch_appointments:
smasch_appointment.mark_as_finished()
- smasch_appointment.visit.is_finished = True
- smasch_appointment.visit.save()
+ if 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')
+ 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:
- subject.virus_test_1 = visit.virus
- subject.virus_test_1_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_2 = visit.virus
- subject.virus_test_2_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_3 = visit.virus
- subject.virus_test_3_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_4 = visit.virus
- subject.virus_test_4_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_5 = visit.virus
- subject.virus_test_5_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_1_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_2_updated = datetime.datetime.now()
- subject.save()
+ changes = [('virus_test_2_updated', datetime.datetime.now())]
if visit.visit_number == 3 and subject.virus_test_3_updated is None and visit.virus_inconclusive:
- subject.virus_test_3_updated = datetime.datetime.now()
- subject.save()
+ changes = [('virus_test_3_updated', datetime.datetime.now())]
if visit.visit_number == 4 and subject.virus_test_4_updated is None and visit.virus_inconclusive:
- subject.virus_test_4_updated = datetime.datetime.now()
- subject.save()
+ 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:
- subject.virus_test_5_updated = datetime.datetime.now()
+ changes = [('virus_test_5_updated', datetime.datetime.now())]
+ #
+ 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)
+ setattr(subject, field, new_value)
+ p.save()
subject.save()
return result