diff --git a/smash/web/api_views/serialization_utils.py b/smash/web/api_views/serialization_utils.py
index 89e2c9c19c2eb5aa958a17165fe12d440b842c58..5f6cd27120fd039257378a8b3b83cedcc55b1d8e 100644
--- a/smash/web/api_views/serialization_utils.py
+++ b/smash/web/api_views/serialization_utils.py
@@ -10,6 +10,15 @@ def bool_to_yes_no(val):
return "NO"
+def bool_to_yes_no_null(val):
+ if val is None:
+ return "N/A"
+ if val:
+ return "YES"
+ else:
+ return "NO"
+
+
def flying_team_to_str(flying_team):
result = ""
if flying_team is not None:
diff --git a/smash/web/api_views/subject.py b/smash/web/api_views/subject.py
index c31d13903ab43b26fa7db0fd1f9c570d28e5cb5e..cd7b5ac5dd59429c1457ea3fd30d5f90a4b87c0a 100644
--- a/smash/web/api_views/subject.py
+++ b/smash/web/api_views/subject.py
@@ -1,12 +1,12 @@
import logging
-from django.urls import reverse
from django.db.models import Count, Case, When, Min, Max
from django.db.models import Q
from django.http import JsonResponse
+from django.urls import reverse
from web.api_views.serialization_utils import bool_to_yes_no, flying_team_to_str, location_to_str, add_column, \
- serialize_date, serialize_datetime, get_filters_for_data_table_request
+ serialize_date, serialize_datetime, get_filters_for_data_table_request, bool_to_yes_no_null
from web.models import StudySubject, Visit, Appointment, Subject, SubjectColumns, StudyColumns, Study, ContactAttempt
from web.models.constants import SUBJECT_TYPE_CHOICES, GLOBAL_STUDY_ID
from web.models.study_subject_list import SUBJECT_LIST_GENERIC, SUBJECT_LIST_NO_VISIT, SUBJECT_LIST_REQUIRE_CONTACT, \
@@ -73,12 +73,25 @@ def get_subject_columns(request, subject_list_type):
add_column(result, "Next of keen", "next_of_keen_name", subject_columns, "string_filter")
add_column(result, "Next of keen phone", "next_of_keen_phone", subject_columns, "string_filter")
add_column(result, "Next of keen address", "next_of_keen_address", subject_columns, "string_filter")
- add_column(result, "Brain donation agreement", "brain_donation_agreement", study_subject_columns, "yes_no_filter", study.columns)
+ add_column(result, "Brain donation agreement", "brain_donation_agreement", study_subject_columns, "yes_no_filter",
+ study.columns)
add_column(result, "Excluded", "excluded", study_subject_columns, "yes_no_filter", study.columns)
add_column(result, "Info sent", "information_sent", study_subject_columns, "yes_no_filter", study.columns)
+
+ add_column(result, "Visit 1 virus", "virus_test_1", study_subject_columns, "yes_no_null_filter", study.columns)
+ add_column(result, "Visit 1 virus date", "virus_test_1_updated", study_subject_columns, None, study.columns)
+ add_column(result, "Visit 2 virus", "virus_test_2", study_subject_columns, "yes_no_null_filter", study.columns)
+ add_column(result, "Visit 2 virus date", "virus_test_2_updated", study_subject_columns, None, study.columns)
+ add_column(result, "Visit 3 virus", "virus_test_3", study_subject_columns, "yes_no_null_filter", study.columns)
+ add_column(result, "Visit 3 virus date", "virus_test_3_updated", study_subject_columns, None, study.columns)
+ add_column(result, "Visit 4 virus", "virus_test_4", study_subject_columns, "yes_no_null_filter", study.columns)
+ add_column(result, "Visit 4 virus date", "virus_test_4_updated", study_subject_columns, None, study.columns)
+ add_column(result, "Visit 5 virus", "virus_test_5", study_subject_columns, "yes_no_null_filter", study.columns)
+ add_column(result, "Visit 5 virus date", "virus_test_5_updated", study_subject_columns, None, study.columns)
+
add_column(result, "Type", "type", study_subject_columns, "type_filter", study.columns)
add_column(result, "Edit", "edit", None, None, sortable=False)
- for visit_number in range(1, study.visits_to_show_in_subject_list+1):
+ for visit_number in range(1, study.visits_to_show_in_subject_list + 1):
visit_key = "visit_" + str(visit_number)
add_column(result, "Visit " + str(visit_number), visit_key, None, "visit_filter",
visible_param=study_subject_list.visits)
@@ -133,7 +146,8 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
else:
pattern = column_filters[u'screening_number']
result = subjects_to_be_ordered.all()
- result = sorted(result, key=lambda t: t.sort_matched_screening_first(pattern, reverse=order_direction == '-'), reverse = order_direction == '-' )
+ result = sorted(result, key=lambda t: t.sort_matched_screening_first(pattern, reverse=order_direction == '-'),
+ reverse=order_direction == '-')
elif order_column == "default_location":
result = subjects_to_be_ordered.order_by(order_direction + 'default_location')
elif order_column == "flying_team":
@@ -173,6 +187,26 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
elif str(order_column).startswith("visit_"):
visit_number = get_visit_number_from_visit_x_string(order_column)
result = order_by_visit(subjects_to_be_ordered, order_direction, visit_number)
+ elif order_column == "virus_test_1":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1')
+ elif order_column == "virus_test_2":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2')
+ elif order_column == "virus_test_3":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3')
+ elif order_column == "virus_test_4":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4')
+ elif order_column == "virus_test_5":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5')
+ elif order_column == "virus_test_1_updated":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_1_updated')
+ elif order_column == "virus_test_2_updated":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_2_updated')
+ elif order_column == "virus_test_3_updated":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_3_updated')
+ elif order_column == "virus_test_4_updated":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_4_updated')
+ elif order_column == "virus_test_5_updated":
+ result = subjects_to_be_ordered.order_by(order_direction + 'virus_test_5_updated')
else:
logger.warn("Unknown sort column: " + str(order_column))
return result
@@ -272,6 +306,31 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
result = result.filter(resigned=(value == "true"))
elif column == "endpoint_reached":
result = result.filter(endpoint_reached=(value == "true"))
+ elif column == "virus_test_1":
+ if value == "null":
+ result = result.filter(virus_test_1__isnull=True)
+ else:
+ result = result.filter(virus_test_1=(value == "true"))
+ elif column == "virus_test_2":
+ if value == "null":
+ result = result.filter(virus_test_2__isnull=True)
+ else:
+ result = result.filter(virus_test_2=(value == "true"))
+ elif column == "virus_test_3":
+ if value == "null":
+ result = result.filter(virus_test_3__isnull=True)
+ else:
+ result = result.filter(virus_test_3=(value == "true"))
+ elif column == "virus_test_4":
+ if value == "null":
+ result = result.filter(virus_test_4__isnull=True)
+ else:
+ result = result.filter(virus_test_4=(value == "true"))
+ elif column == "virus_test_5":
+ if value == "null":
+ result = result.filter(virus_test_5__isnull=True)
+ else:
+ result = result.filter(virus_test_5=(value == "true"))
elif column == "brain_donation_agreement":
result = result.filter(brain_donation_agreement=(value == "true"))
elif column == "postponed":
@@ -358,6 +417,7 @@ def types(request):
"types": data
})
+
def serialize_subject(study_subject):
location = location_to_str(study_subject.default_location)
flying_team = flying_team_to_str(study_subject.flying_team)
@@ -388,7 +448,7 @@ def serialize_subject(study_subject):
status = "SHOULD_BE_IN_PROGRESS"
else:
status = "UPCOMING"
-
+
appointment_types = ['{} ({})'.format(at.code, at.description) for at in visit.appointment_types.all()]
if len(appointment_types) == 0:
appointment_types = ['No appointment types set.']
@@ -436,6 +496,16 @@ def serialize_subject(study_subject):
"dead": bool_to_yes_no(study_subject.subject.dead),
"resigned": bool_to_yes_no(study_subject.resigned),
"endpoint_reached": bool_to_yes_no(study_subject.endpoint_reached),
+ "virus_test_1": bool_to_yes_no_null(study_subject.virus_test_1),
+ "virus_test_2": bool_to_yes_no_null(study_subject.virus_test_2),
+ "virus_test_3": bool_to_yes_no_null(study_subject.virus_test_3),
+ "virus_test_4": bool_to_yes_no_null(study_subject.virus_test_4),
+ "virus_test_5": bool_to_yes_no_null(study_subject.virus_test_5),
+ "virus_test_1_updated": study_subject.virus_test_1_updated,
+ "virus_test_2_updated": study_subject.virus_test_2_updated,
+ "virus_test_3_updated": study_subject.virus_test_3_updated,
+ "virus_test_4_updated": study_subject.virus_test_4_updated,
+ "virus_test_5_updated": study_subject.virus_test_5_updated,
"postponed": bool_to_yes_no(study_subject.postponed),
"brain_donation_agreement": bool_to_yes_no(study_subject.brain_donation_agreement),
"excluded": bool_to_yes_no(study_subject.excluded),
@@ -447,4 +517,4 @@ def serialize_subject(study_subject):
"id": study_subject.id,
"visits": serialized_visits,
}
- return result
\ No newline at end of file
+ return result
diff --git a/smash/web/forms/study_subject_forms.py b/smash/web/forms/study_subject_forms.py
index 2bc880780226734cfa1653501960eb47bc8138b0..1f75992f6793598ef7d2c760af61af98ab90ab09 100644
--- a/smash/web/forms/study_subject_forms.py
+++ b/smash/web/forms/study_subject_forms.py
@@ -36,6 +36,17 @@ class StudySubjectAddForm(StudySubjectForm):
self.study = get_study_from_args(kwargs)
super(StudySubjectAddForm, self).__init__(*args, **kwargs)
+ self.fields['virus_test_1'].widget.attrs['readonly'] = True
+ self.fields['virus_test_2'].widget.attrs['readonly'] = True
+ self.fields['virus_test_3'].widget.attrs['readonly'] = True
+ self.fields['virus_test_4'].widget.attrs['readonly'] = True
+ self.fields['virus_test_5'].widget.attrs['readonly'] = True
+ self.fields['virus_test_1_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_2_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_3_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_4_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_5_updated'].widget.attrs['readonly'] = True
+
prepare_study_subject_fields(fields=self.fields, study=self.study)
def save(self, commit=True):
@@ -128,6 +139,18 @@ class StudySubjectEditForm(StudySubjectForm):
self.fields['resigned'].disabled = was_resigned
self.fields['endpoint_reached'].disabled = endpoint_was_reached
+
+ self.fields['virus_test_1'].widget.attrs['readonly'] = True
+ self.fields['virus_test_2'].widget.attrs['readonly'] = True
+ self.fields['virus_test_3'].widget.attrs['readonly'] = True
+ self.fields['virus_test_4'].widget.attrs['readonly'] = True
+ self.fields['virus_test_5'].widget.attrs['readonly'] = True
+ self.fields['virus_test_1_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_2_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_3_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_4_updated'].widget.attrs['readonly'] = True
+ self.fields['virus_test_5_updated'].widget.attrs['readonly'] = True
+
prepare_study_subject_fields(fields=self.fields, study=self.study)
def clean(self):
@@ -181,6 +204,17 @@ def prepare_study_subject_fields(fields, study):
prepare_field(fields, study.columns, 'previously_in_study')
prepare_field(fields, study.columns, 'voucher_types')
+ prepare_field(fields, study.columns, 'virus_test_1')
+ prepare_field(fields, study.columns, 'virus_test_2')
+ prepare_field(fields, study.columns, 'virus_test_3')
+ prepare_field(fields, study.columns, 'virus_test_4')
+ prepare_field(fields, study.columns, 'virus_test_5')
+ prepare_field(fields, study.columns, 'virus_test_1_updated')
+ prepare_field(fields, study.columns, 'virus_test_2_updated')
+ prepare_field(fields, study.columns, 'virus_test_3_updated')
+ prepare_field(fields, study.columns, 'virus_test_4_updated')
+ prepare_field(fields, study.columns, 'virus_test_5_updated')
+
def validate_subject_screening_number(self, cleaned_data):
if self.study.columns.resign_reason:
diff --git a/smash/web/migrations/0159_configurationitem_email_items_for_redcap.py b/smash/web/migrations/0159_configurationitem_email_items_for_redcap.py
new file mode 100644
index 0000000000000000000000000000000000000000..f496a5a3f92489be49b66ac9dbac156eb07e46db
--- /dev/null
+++ b/smash/web/migrations/0159_configurationitem_email_items_for_redcap.py
@@ -0,0 +1,53 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.3 on 2017-04-04 09:43
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+from web.models.constants import 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, \
+ RED_CAP_SEX_FIELD_TYPE, RED_CAP_DATE_BORN_FIELD_TYPE, RED_CAP_ND_NUMBER_FIELD_TYPE, RED_CAP_VIRUS_FIELD_TYPE
+
+
+def create_item(apps, type, value, name):
+ # We can't import the ConfigurationItem model directly as it may be a newer
+ # version than this migration expects. We use the historical version.
+ ConfigurationItem = apps.get_model("web", "ConfigurationItem")
+ item = ConfigurationItem.objects.create()
+ item.type = type
+ item.value = value
+ item.name = name
+ item.save()
+
+
+def configuration_items(apps, schema_editor):
+ create_item(apps, RED_CAP_LANGUAGE_4_FIELD_TYPE, "dm_language_4",
+ "Redcap field for language 4")
+ create_item(apps, RED_CAP_LANGUAGE_3_FIELD_TYPE, "dm_language_3",
+ "Redcap field for language 3")
+ create_item(apps, RED_CAP_LANGUAGE_2_FIELD_TYPE, "dm_language_2",
+ "Redcap field for language 2")
+ create_item(apps, RED_CAP_LANGUAGE_1_FIELD_TYPE, "dm_language_1",
+ "Redcap field for language 1")
+ create_item(apps, RED_CAP_MPOWER_ID_FIELD_TYPE, "dm_mpowerid",
+ "Redcap field for mPowerId")
+ create_item(apps, RED_CAP_DEAD_FIELD_TYPE, "dm_death",
+ "Redcap field for deceased")
+ create_item(apps, RED_CAP_SEX_FIELD_TYPE, "cdisc_dm_sex",
+ "Redcap field for sex")
+ create_item(apps, RED_CAP_DATE_BORN_FIELD_TYPE, "cdisc_dm_brthdtc",
+ "Redcap field for birth date")
+ create_item(apps, RED_CAP_ND_NUMBER_FIELD_TYPE, "cdisc_dm_usubjd",
+ "Redcap field for subject id")
+ create_item(apps, RED_CAP_VIRUS_FIELD_TYPE, "",
+ "Redcap field for virus test result")
+
+
+class Migration(migrations.Migration):
+ dependencies = [
+ ('web', '0158_configurationitem_email_items'),
+ ]
+
+ operations = [
+ migrations.RunPython(configuration_items),
+ ]
diff --git a/smash/web/migrations/0160_auto_20200415_1101.py b/smash/web/migrations/0160_auto_20200415_1101.py
new file mode 100644
index 0000000000000000000000000000000000000000..f00f970dcc844171d9c43b7743823b5e4b2772bb
--- /dev/null
+++ b/smash/web/migrations/0160_auto_20200415_1101.py
@@ -0,0 +1,115 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.5 on 2020-04-15 11:01
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0159_configurationitem_email_items_for_redcap'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_1',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 1 virus results'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_1_updated',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 1 virus results date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_2',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 2 virus results'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_2_updated',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 2 virus results date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_3',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 3 virus results'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_3_updated',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 3 virus results date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_4',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 4 virus results'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_4_updated',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 4 virus results date'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_5',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 5 virus results'),
+ ),
+ migrations.AddField(
+ model_name='studycolumns',
+ name='virus_test_5_updated',
+ field=models.BooleanField(default=False, verbose_name=b'Visit 5 virus results date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1',
+ field=models.NullBooleanField(choices=[(True, b'Yes'), (False, b'No'), (None, b'N/A')], default=None, editable=False, verbose_name=b'Visit 1 virus result'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_1_updated',
+ field=models.DateField(editable=False, null=True, verbose_name=b'Visit 1 virus result date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2',
+ field=models.NullBooleanField(choices=[(True, b'Yes'), (False, b'No'), (None, b'N/A')], default=None, editable=False, verbose_name=b'Visit 2 virus result'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_2_updated',
+ field=models.DateField(editable=False, null=True, verbose_name=b'Visit 2 virus result date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3',
+ field=models.NullBooleanField(choices=[(True, b'Yes'), (False, b'No'), (None, b'N/A')], default=None, editable=False, verbose_name=b'Visit 3 virus result'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_3_updated',
+ field=models.DateField(editable=False, null=True, verbose_name=b'Visit 3 virus result date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4',
+ field=models.NullBooleanField(choices=[(True, b'Yes'), (False, b'No'), (None, b'N/A')], default=None, editable=False, verbose_name=b'Visit 4 virus result'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_4_updated',
+ field=models.DateField(editable=False, null=True, verbose_name=b'Visit 4 virus result date'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5',
+ field=models.NullBooleanField(choices=[(True, b'Yes'), (False, b'No'), (None, b'N/A')], default=None, editable=False, verbose_name=b'Visit 5 virus result'),
+ ),
+ migrations.AddField(
+ model_name='studysubject',
+ name='virus_test_5_updated',
+ field=models.DateField(editable=False, null=True, verbose_name=b'Visit 5 virus result date'),
+ ),
+ ]
diff --git a/smash/web/models/constants.py b/smash/web/models/constants.py
index e83ddc83fa6dc4ea020850952d9fb151f97ab3d4..b512e714efac9136e8c4d9d9bc048f77d065458f 100644
--- a/smash/web/models/constants.py
+++ b/smash/web/models/constants.py
@@ -10,6 +10,11 @@ SEX_CHOICES = (
(SEX_CHOICES_MALE, 'Male'),
(SEX_CHOICES_FEMALE, 'Female'),
)
+BOOL_CHOICES_WITH_NONE = (
+ (True, 'Yes'),
+ (False, 'No'),
+ (None, 'N/A'),
+)
SUBJECT_TYPE_CHOICES_CONTROL = 'C'
SUBJECT_TYPE_CHOICES_PATIENT = 'P'
SUBJECT_TYPE_CHOICES = {
@@ -47,6 +52,17 @@ KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_TYPE = "KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_
KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE = "KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE"
KIT_DAILY_EMAIL_TIME_FORMAT_TYPE = "KIT_DAILY_EMAIL_TIME_FORMAT_TYPE"
+RED_CAP_LANGUAGE_4_FIELD_TYPE = 'RED_CAP_LANGUAGE_4_FIELD_TYPE'
+RED_CAP_LANGUAGE_3_FIELD_TYPE = 'RED_CAP_LANGUAGE_3_FIELD_TYPE'
+RED_CAP_LANGUAGE_2_FIELD_TYPE = 'RED_CAP_LANGUAGE_2_FIELD_TYPE'
+RED_CAP_LANGUAGE_1_FIELD_TYPE = 'RED_CAP_LANGUAGE_1_FIELD_TYPE'
+RED_CAP_MPOWER_ID_FIELD_TYPE = 'RED_CAP_MPOWER_ID_FIELD_TYPE'
+RED_CAP_DEAD_FIELD_TYPE = 'RED_CAP_DEAD_FIELD_TYPE'
+RED_CAP_SEX_FIELD_TYPE = 'RED_CAP_SEX_FIELD_TYPE'
+RED_CAP_DATE_BORN_FIELD_TYPE = 'RED_CAP_DATE_BORN_FIELD_TYPE'
+RED_CAP_ND_NUMBER_FIELD_TYPE = 'RED_CAP_ND_NUMBER_FIELD_TYPE'
+RED_CAP_VIRUS_FIELD_TYPE = 'RED_CAP_VIRUS_FIELD_TYPE'
+
MAIL_TEMPLATE_CONTEXT_SUBJECT = 'S'
MAIL_TEMPLATE_CONTEXT_APPOINTMENT = 'A'
MAIL_TEMPLATE_CONTEXT_VISIT = 'V'
diff --git a/smash/web/models/study_columns.py b/smash/web/models/study_columns.py
index 7d20b3913d40a71f72fc0b70327a20084e83a158..d2e769ca52216cf9560933ec89d9902f3092220e 100644
--- a/smash/web/models/study_columns.py
+++ b/smash/web/models/study_columns.py
@@ -12,69 +12,69 @@ class StudyColumns(models.Model):
)
datetime_contact_reminder = models.BooleanField(
- default=True,
- verbose_name='Please make a contact on'
- )
+ default=True,
+ verbose_name='Please make a contact on'
+ )
type = models.BooleanField(
- default=True,
- verbose_name='Type'
- )
+ default=True,
+ verbose_name='Type'
+ )
default_location = models.BooleanField(
- default=True,
- verbose_name='Default appointment location',
- )
+ default=True,
+ verbose_name='Default appointment location',
+ )
flying_team = models.BooleanField(
- default=True,
- verbose_name='Default flying team location (if applicable)',
- )
+ default=True,
+ verbose_name='Default flying team location (if applicable)',
+ )
screening_number = models.BooleanField(
- default=True,
- verbose_name='Screening number',
- )
+ default=True,
+ verbose_name='Screening number',
+ )
nd_number = models.BooleanField(
- default=True,
- verbose_name='ND number',
- )
+ default=True,
+ verbose_name='ND number',
+ )
mpower_id = models.BooleanField(
- default=True,
- verbose_name='MPower ID'
- )
+ default=True,
+ verbose_name='MPower ID'
+ )
comments = models.BooleanField(
- default=True,
- verbose_name='Comments'
- )
+ default=True,
+ verbose_name='Comments'
+ )
referral = models.BooleanField(
- default=True,
- verbose_name='Referred by'
- )
+ default=True,
+ verbose_name='Referred by'
+ )
diagnosis = models.BooleanField(
- default=True,
- verbose_name='Diagnosis'
- )
+ default=True,
+ verbose_name='Diagnosis'
+ )
year_of_diagnosis = models.BooleanField(
- default=True,
- verbose_name='Year of diagnosis (YYYY)'
- )
+ default=True,
+ verbose_name='Year of diagnosis (YYYY)'
+ )
information_sent = models.BooleanField(
- default=True,
- verbose_name='Information sent',
- )
+ default=True,
+ verbose_name='Information sent',
+ )
pd_in_family = models.BooleanField(
- default=True,
- verbose_name='PD in family',
- )
+ default=True,
+ verbose_name='PD in family',
+ )
resigned = models.BooleanField(
- default=True,
- verbose_name='Resigned',
- )
+ default=True,
+ verbose_name='Resigned',
+ )
resign_reason = models.BooleanField(
- default=True,
- verbose_name='Resign reason'
- )
+ default=True,
+ verbose_name='Resign reason'
+ )
excluded = models.BooleanField(default=False, verbose_name='Excluded')
@@ -83,41 +83,82 @@ class StudyColumns(models.Model):
resign_reason = models.BooleanField(default=True, verbose_name='Endpoint reached comments')
referral_letter = models.BooleanField(
- default=False,
- verbose_name='Referral letter'
- )
+ default=False,
+ verbose_name='Referral letter'
+ )
health_partner = models.BooleanField(
- default=False,
- verbose_name='Health partner'
- )
+ default=False,
+ verbose_name='Health partner'
+ )
health_partner_feedback_agreement = models.BooleanField(
- default=False,
- verbose_name='Agrees to give information to referral'
- )
+ default=False,
+ verbose_name='Agrees to give information to referral'
+ )
screening = models.BooleanField(
- default=False,
- verbose_name='Screening'
- )
+ default=False,
+ verbose_name='Screening'
+ )
previously_in_study = models.BooleanField(
- default=False,
- verbose_name='Previously in PDP study',
- )
+ default=False,
+ verbose_name='Previously in PDP study',
+ )
voucher_types = models.BooleanField(
- default=False,
- verbose_name='Voucher types',
- )
+ default=False,
+ verbose_name='Voucher types',
+ )
vouchers = models.BooleanField(
- default=False,
- verbose_name='Vouchers',
- )
+ default=False,
+ verbose_name='Vouchers',
+ )
brain_donation_agreement = models.BooleanField(
- default=False,
- verbose_name='Brain donation agreement',
- )
+ default=False,
+ verbose_name='Brain donation agreement',
+ )
+
+ virus_test_1 = models.BooleanField(
+ default=False,
+ verbose_name='Visit 1 virus results',
+ )
+ virus_test_2 = models.BooleanField(
+ default=False,
+ verbose_name='Visit 2 virus results',
+ )
+ virus_test_3 = models.BooleanField(
+ default=False,
+ verbose_name='Visit 3 virus results',
+ )
+ virus_test_4 = models.BooleanField(
+ default=False,
+ verbose_name='Visit 4 virus results',
+ )
+ virus_test_5 = models.BooleanField(
+ default=False,
+ verbose_name='Visit 5 virus results',
+ )
+ virus_test_1_updated = models.BooleanField(
+ default=False,
+ verbose_name='Visit 1 virus results date',
+ )
+ virus_test_2_updated = models.BooleanField(
+ default=False,
+ verbose_name='Visit 2 virus results date',
+ )
+ virus_test_3_updated = models.BooleanField(
+ default=False,
+ verbose_name='Visit 3 virus results date',
+ )
+ virus_test_4_updated = models.BooleanField(
+ default=False,
+ verbose_name='Visit 4 virus results date',
+ )
+ virus_test_5_updated = models.BooleanField(
+ default=False,
+ verbose_name='Visit 5 virus results date',
+ )
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index 22a5b0b8fe77518abb0092587531f0b715413633..d802d8debb0e5d87dc0a54756bc9152349855cd9 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -1,23 +1,25 @@
# coding=utf-8
import logging
import re
-from django.db import models
-from web.models import VoucherType, Appointment, Location, Visit, Provenance
-from web.models.constants import BOOL_CHOICES, SUBJECT_TYPE_CHOICES, FILE_STORAGE
+from django.db import models
from django.db.models.signals import post_save
from django.dispatch import receiver
+from web.models import VoucherType, Appointment, Location, Visit, Provenance
+from web.models.constants import BOOL_CHOICES, SUBJECT_TYPE_CHOICES, FILE_STORAGE, BOOL_CHOICES_WITH_NONE
+
logger = logging.getLogger(__name__)
-class StudySubject(models.Model):
+class StudySubject(models.Model):
class Meta:
app_label = 'web'
@property
def provenances(self):
- return Provenance.objects.filter(modified_table=StudySubject._meta.db_table, modified_table_id=self.id).order_by('-modification_date')
+ return Provenance.objects.filter(modified_table=StudySubject._meta.db_table,
+ modified_table_id=self.id).order_by('-modification_date')
def finish_all_visits(self):
visits = Visit.objects.filter(subject=self, is_finished=False)
@@ -168,9 +170,9 @@ class StudySubject(models.Model):
default=None,
)
brain_donation_agreement = models.BooleanField(
- default=False,
- verbose_name='Brain donation agreement',
- )
+ default=False,
+ verbose_name='Brain donation agreement',
+ )
resigned = models.BooleanField(
verbose_name='Resigned',
@@ -196,42 +198,84 @@ class StudySubject(models.Model):
editable=True
)
endpoint_reached_reason = models.TextField(max_length=2000,
- blank=True,
- verbose_name='Endpoint reached comments'
- )
+ blank=True,
+ verbose_name='Endpoint reached comments'
+ )
+
+ virus_test_1 = models.NullBooleanField(choices=BOOL_CHOICES_WITH_NONE,
+ verbose_name='Visit 1 virus result',
+ default=None
+ )
+ virus_test_2 = models.NullBooleanField(choices=BOOL_CHOICES_WITH_NONE,
+ verbose_name='Visit 2 virus result',
+ default=None
+ )
+ virus_test_3 = models.NullBooleanField(choices=BOOL_CHOICES_WITH_NONE,
+ verbose_name='Visit 3 virus result',
+ default=None
+ )
+ virus_test_4 = models.NullBooleanField(choices=BOOL_CHOICES_WITH_NONE,
+ verbose_name='Visit 4 virus result',
+ default=None
+ )
+ virus_test_5 = models.NullBooleanField(choices=BOOL_CHOICES_WITH_NONE,
+ verbose_name='Visit 5 virus result',
+ default=None
+ )
+ virus_test_1_updated = models.DateField(verbose_name='Visit 1 virus result date',
+ blank=True,
+ null=True,
+ )
+ virus_test_2_updated = models.DateField(verbose_name='Visit 2 virus result date',
+ blank=True,
+ null=True,
+ )
+ virus_test_3_updated = models.DateField(verbose_name='Visit 3 virus result date',
+ blank=True,
+ null=True,
+ )
+ virus_test_4_updated = models.DateField(verbose_name='Visit 4 virus result date',
+ blank=True,
+ null=True,
+ )
+ virus_test_5_updated = models.DateField(verbose_name='Visit 5 virus result date',
+ blank=True,
+ null=True,
+ )
def sort_matched_screening_first(self, pattern, reverse=False):
- if self.screening_number is None:
- return None
-
- parts = self.screening_number.split(';')
- matches, reminder = [], []
-
- try:
- for part in parts:
- chunks = part.strip().split('-')
- if len(chunks) == 2:
- letter, number = chunks
- try:
- tupl = (letter, int(number))
- except ValueError: #better than isdigit because isdigit fails with negative numbers and others
- tupl = (letter, number)
- else:
- logger.warn('There are {} chunks in some parts of this screening_number: |{}|.'.format(
- len(chunks), self.screening_number))
- tupl = (part.strip(), None)
- if pattern is not None and pattern in part:
- matches.append(tupl)
- else:
- reminder.append(tupl)
- except: #if the format is not the expected format
- matches = parts
-
- return matches + sorted(reminder, reverse=reverse)
+ if self.screening_number is None:
+ return None
+
+ parts = self.screening_number.split(';')
+ matches, reminder = [], []
+
+ try:
+ for part in parts:
+ chunks = part.strip().split('-')
+ if len(chunks) == 2:
+ letter, number = chunks
+ try:
+ tupl = (letter, int(number))
+ except ValueError: # better than isdigit because isdigit fails with negative numbers and others
+ tupl = (letter, number)
+ else:
+ logger.warn('There are {} chunks in some parts of this screening_number: |{}|.'.format(
+ len(chunks), self.screening_number))
+ tupl = (part.strip(), None)
+ if pattern is not None and pattern in part:
+ matches.append(tupl)
+ else:
+ reminder.append(tupl)
+ except: # if the format is not the expected format
+ matches = parts
+
+ return matches + sorted(reminder, reverse=reverse)
@staticmethod
def check_nd_number_regex(regex_str, study):
- nd_numbers = StudySubject.objects.filter(study=study).exclude(nd_number__isnull=True).exclude(nd_number__exact='').all().values_list('nd_number', flat=True)
+ nd_numbers = StudySubject.objects.filter(study=study).exclude(nd_number__isnull=True).exclude(
+ nd_number__exact='').all().values_list('nd_number', flat=True)
regex = re.compile(regex_str)
for nd_number in nd_numbers:
if regex.match(nd_number) is None:
@@ -239,21 +283,20 @@ class StudySubject(models.Model):
return True
def can_schedule(self):
- return not any([self.resigned, self.excluded, self.endpoint_reached, self.subject.dead])
+ return not any([self.resigned, self.excluded, self.endpoint_reached, self.subject.dead])
@property
def status(self):
- if self.subject.dead:
- return 'Deceased'
- elif self.resigned:
- return 'Resigned'
- elif self.excluded:
- return 'Excluded'
- elif self.endpoint_reached:
- return 'Endpoint Reached'
- else:
- return 'Normal'
-
+ if self.subject.dead:
+ return 'Deceased'
+ elif self.resigned:
+ return 'Resigned'
+ elif self.excluded:
+ return 'Excluded'
+ elif self.endpoint_reached:
+ return 'Endpoint Reached'
+ else:
+ return 'Normal'
def __str__(self):
return "%s %s" % (self.subject.first_name, self.subject.last_name)
@@ -261,12 +304,13 @@ class StudySubject(models.Model):
def __unicode__(self):
return "%s %s" % (self.subject.first_name, self.subject.last_name)
-#SIGNALS
+
+# SIGNALS
@receiver(post_save, sender=StudySubject)
def set_as_resigned_or_excluded_or_endpoint_reached(sender, instance, **kwargs):
- if instance.excluded:
- instance.mark_as_excluded()
- if instance.resigned:
- instance.mark_as_resigned()
- if instance.endpoint_reached:
- instance.mark_as_endpoint_reached()
\ No newline at end of file
+ if instance.excluded:
+ instance.mark_as_excluded()
+ if instance.resigned:
+ instance.mark_as_resigned()
+ if instance.endpoint_reached:
+ instance.mark_as_endpoint_reached()
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
index 4e1da4fa683708eb0a6c28dc46c7ae214622f143..793e0fa221ee88c8daffcd67d08c95d069bf7498 100644
--- a/smash/web/redcap_connector.py
+++ b/smash/web/redcap_connector.py
@@ -1,43 +1,24 @@
# coding=utf-8
import cStringIO
+import datetime
import json
import logging
-import pycurl
import certifi
+import pycurl
import timeout_decorator
+from django.conf import settings
+from django.forms.models import model_to_dict
from django_cron import CronJobBase, Schedule
-from django.forms.models import model_to_dict
-from web.models.constants import GLOBAL_STUDY_ID
-from web.models import ConfigurationItem, StudySubject, Language, Study, StudyRedCapColumns
+from web.models import ConfigurationItem, StudySubject, Language, AppointmentType, Appointment, Visit
from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, \
- REDCAP_BASE_URL_CONFIGURATION_TYPE, CRON_JOB_TIMEOUT
+ 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, \
+ RED_CAP_SEX_FIELD_TYPE, RED_CAP_DATE_BORN_FIELD_TYPE, RED_CAP_ND_NUMBER_FIELD_TYPE, RED_CAP_VIRUS_FIELD_TYPE
from web.models.inconsistent_subject import InconsistentField, InconsistentSubject
from web.models.missing_subject import MissingSubject
-RED_CAP_LANGUAGE_4_FIELD = 'dm_language_4'
-
-RED_CAP_LANGUAGE_3_FIELD = 'dm_language_3'
-
-RED_CAP_LANGUAGE_2_FIELD = 'dm_language_2'
-
-RED_CAP_LANGUAGE_1_FIELD = 'dm_language_1'
-
-# noinspection SpellCheckingInspection
-RED_CAP_MPOWER_ID_FIELD = 'dm_mpowerid'
-
-RED_CAP_DEAD_FIELD = 'dm_death'
-
-# noinspection SpellCheckingInspection
-RED_CAP_SEX_FIELD = 'cdisc_dm_sex'
-
-# noinspection SpellCheckingInspection
-RED_CAP_DATE_BORN_FIELD = 'cdisc_dm_brthdtc'
-
-# noinspection SpellCheckingInspection
-RED_CAP_ND_NUMBER_FIELD = 'cdisc_dm_usubjd'
-
logger = logging.getLogger(__name__)
@@ -52,12 +33,18 @@ class RedcapSubject(object):
def __init__(self):
self.languages = []
+ self.visits = []
def add_language(self, language):
if language is not None:
self.languages.append(language)
+class RedcapVisit(object):
+ virus = None
+ visit_number = 0
+
+
def different_string(string1, string2):
if string1 is None:
string1 = ""
@@ -83,6 +70,28 @@ class RedcapConnector(object):
for language in languages:
self.language_by_name[language.name.lower()] = language
+ self.date_born_field = ConfigurationItem.objects.get(type=RED_CAP_DATE_BORN_FIELD_TYPE).value
+ self.sex_field = ConfigurationItem.objects.get(type=RED_CAP_SEX_FIELD_TYPE).value
+ self.nd_number_field = ConfigurationItem.objects.get(type=RED_CAP_ND_NUMBER_FIELD_TYPE).value
+ self.dead_field = ConfigurationItem.objects.get(type=RED_CAP_DEAD_FIELD_TYPE).value
+ self.language_1_field = ConfigurationItem.objects.get(type=RED_CAP_LANGUAGE_1_FIELD_TYPE).value
+ self.language_2_field = ConfigurationItem.objects.get(type=RED_CAP_LANGUAGE_2_FIELD_TYPE).value
+ self.language_3_field = ConfigurationItem.objects.get(type=RED_CAP_LANGUAGE_3_FIELD_TYPE).value
+ self.language_4_field = ConfigurationItem.objects.get(type=RED_CAP_LANGUAGE_4_FIELD_TYPE).value
+ self.m_power_id_field = ConfigurationItem.objects.get(type=RED_CAP_MPOWER_ID_FIELD_TYPE).value
+ self.virus_field = ConfigurationItem.objects.get(type=RED_CAP_VIRUS_FIELD_TYPE).value
+
+ self.date_born_field = ""
+ self.sex_field = ""
+ self.nd_number_field = "donor_id"
+ self.dead_field = ""
+ self.language_1_field = ""
+ self.language_2_field = ""
+ self.language_3_field = ""
+ self.language_4_field = ""
+ self.m_power_id_field = ""
+ self.virus_field = "sarscov2_status"
+
def find_missing(self):
pid = self.get_project_id()
redcap_version = self.get_redcap_version()
@@ -157,6 +166,13 @@ class RedcapConnector(object):
self.add_inconsistent(inconsistent)
def find_inconsistent(self):
+ appointment_type_code_to_finish = getattr(settings, "IMPORT_APPOINTMENT_TYPE", None)
+ appointment_type_to_finish = None
+ if appointment_type_code_to_finish is not None:
+ appointment_types = AppointmentType.objects.filter(code=appointment_type_code_to_finish)
+ if len(appointment_types) > 0:
+ appointment_type_to_finish = appointment_types[0]
+
pid = self.get_project_id()
redcap_version = self.get_redcap_version()
@@ -173,9 +189,41 @@ class RedcapConnector(object):
if red_cap_subject is not None:
url = self.create_redcap_link(pid, redcap_version, subject)
- subject = self.create_inconsistency_subject(red_cap_subject, subject, url)
- if subject is not None:
- result.append(subject)
+
+ inconsistent_subject = self.create_inconsistency_subject(red_cap_subject, subject, url)
+ if inconsistent_subject is not None:
+ result.append(inconsistent_subject)
+ if appointment_type_to_finish is not None:
+ for visit in red_cap_subject.visits:
+ smasch_visits = Visit.objects.filter(visit_number=visit.visit_number, subject=subject)
+ smasch_appointments = Appointment.objects.filter(visit__in=smasch_visits,
+ appointment_types=appointment_type_to_finish,
+ 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 visit.virus is not 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()
+ 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()
+ 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()
+ 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()
+ 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()
return result
@@ -228,7 +276,7 @@ class RedcapConnector(object):
@staticmethod
def create_inconsistency_subject(red_cap_subject, study_subject, url):
- #func dict
+ # func dict
field_checks = {
'sex': RedcapConnector.check_sex_consistency,
'date_born': RedcapConnector.check_birth_date_consistency,
@@ -239,14 +287,14 @@ class RedcapConnector(object):
fields = []
- #get fields which are true from redcap columns
- fields_to_check = [k for k,v in model_to_dict(study_subject.study.redcap_columns).iteritems() if v is True]
+ # get fields which are true from redcap columns
+ fields_to_check = [k for k, v in model_to_dict(study_subject.study.redcap_columns).iteritems() if v is True]
for field_to_check in fields_to_check:
field = field_checks[field_to_check](red_cap_subject, study_subject)
if field is not None:
fields.append(field)
-
+
result = None
if len(fields) > 0:
result = InconsistentSubject.create(smash_subject=study_subject, url=url, fields=fields)
@@ -257,20 +305,66 @@ class RedcapConnector(object):
subject.nd_number + "&page=demographics"
def get_red_cap_subjects(self):
- query_data = {
+ query_data = self.get_subject_query_data()
+ data = self.execute_query(query_data)
+ result = []
+ for row in data:
+ if isinstance(row, dict):
+ redcap_subject = RedcapSubject()
+ redcap_subject.nd_number = row.get(self.nd_number_field)
+ if self.date_born_field != "":
+ redcap_subject.date_born = row.get(self.date_born_field)
+ if self.sex_field != "":
+ redcap_subject.sex = row.get(self.sex_field)
+ if self.dead_field != "":
+ redcap_subject.dead = (row.get(self.dead_field).lower() == "yes")
+ if self.m_power_id_field != "":
+ redcap_subject.mpower_id = row.get(self.m_power_id_field)
+ if self.language_1_field != "" and row.get(self.language_1_field):
+ redcap_subject.add_language(self.get_language(row.get(self.language_1_field)))
+ if self.language_2_field != "" and row[self.language_2_field]:
+ redcap_subject.add_language(self.get_language(row.get(self.language_2_field)))
+ if self.language_3_field != "" and row[self.language_3_field]:
+ redcap_subject.add_language(self.get_language(row.get(self.language_3_field)))
+ if self.language_4_field != "" and row[self.language_4_field]:
+ redcap_subject.add_language(self.get_language(row.get(self.language_4_field)))
+ visit = RedcapVisit()
+ visit.visit_number = 1
+ if self.virus_field != "":
+ if row.get(self.virus_field) == "Negative":
+ visit.virus = False
+ elif row.get(self.virus_field) == "Positive":
+ visit.virus = True
+ redcap_subject.visits.append(visit)
+ result.append(redcap_subject)
+ for i in range(2, 10):
+ query_data = self.get_subject_query_data()
+ query_data["events[0]"] = "visit_" + str(i) + "_arm_1"
+ data = self.execute_query(query_data)
+ if isinstance(data, dict):
+ break
+ for row in data:
+ if isinstance(row, dict):
+ nd_number = row.get(self.nd_number_field)
+ for redcap_subject in result:
+ if redcap_subject.nd_number == nd_number:
+ visit = RedcapVisit()
+ visit.visit_number = i
+ if self.virus_field != "":
+ if row.get(self.virus_field) == "Negative":
+ visit.virus = False
+ elif row.get(self.virus_field) == "Positive":
+ visit.virus = True
+ redcap_subject.visits.append(visit)
+
+ return result
+
+ def get_subject_query_data(self):
+ result = {
'token': self.token,
'content': 'record',
'format': 'json',
'type': 'flat',
- 'fields[0]': RED_CAP_DATE_BORN_FIELD,
- 'fields[1]': RED_CAP_SEX_FIELD,
- 'fields[2]': RED_CAP_ND_NUMBER_FIELD,
- 'fields[3]': RED_CAP_DEAD_FIELD,
- 'fields[4]': RED_CAP_LANGUAGE_1_FIELD,
- 'fields[5]': RED_CAP_LANGUAGE_2_FIELD,
- 'fields[6]': RED_CAP_LANGUAGE_3_FIELD,
- 'fields[7]': RED_CAP_LANGUAGE_4_FIELD,
- 'fields[8]': RED_CAP_MPOWER_ID_FIELD,
'events[0]': 'visit_1_arm_1',
'rawOrLabel': 'label',
'rawOrLabelHeaders': 'raw',
@@ -279,24 +373,37 @@ class RedcapConnector(object):
'exportDataAccessGroups': 'false',
'returnFormat': 'json'
}
- data = self.execute_query(query_data)
- result = []
- for row in data:
- redcap_subject = RedcapSubject()
- redcap_subject.nd_number = row[RED_CAP_ND_NUMBER_FIELD]
- redcap_subject.date_born = row[RED_CAP_DATE_BORN_FIELD]
- redcap_subject.sex = row[RED_CAP_SEX_FIELD]
- redcap_subject.dead = (row[RED_CAP_DEAD_FIELD].lower() == "yes")
- redcap_subject.mpower_id = row[RED_CAP_MPOWER_ID_FIELD]
- if row[RED_CAP_LANGUAGE_1_FIELD]:
- redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_1_FIELD]))
- if row[RED_CAP_LANGUAGE_2_FIELD]:
- redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_2_FIELD]))
- if row[RED_CAP_LANGUAGE_3_FIELD]:
- redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_3_FIELD]))
- if row[RED_CAP_LANGUAGE_4_FIELD]:
- redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_4_FIELD]))
- result.append(redcap_subject)
+ field_number = 0
+ if self.date_born_field != "":
+ result['fields[' + str(field_number) + ']'] = self.date_born_field
+ field_number += 1
+ if self.sex_field != "":
+ result['fields[' + str(field_number) + ']'] = self.sex_field
+ field_number += 1
+ if self.nd_number_field != "":
+ result['fields[' + str(field_number) + ']'] = self.nd_number_field
+ field_number += 1
+ if self.dead_field != "":
+ result['fields[' + str(field_number) + ']'] = self.dead_field
+ field_number += 1
+ if self.language_1_field != "":
+ result['fields[' + str(field_number) + ']'] = self.language_1_field
+ field_number += 1
+ if self.language_2_field != "":
+ result['fields[' + str(field_number) + ']'] = self.language_2_field
+ field_number += 1
+ if self.language_3_field != "":
+ result['fields[' + str(field_number) + ']'] = self.language_3_field
+ field_number += 1
+ if self.language_4_field != "":
+ result['fields[' + str(field_number) + ']'] = self.language_4_field
+ field_number += 1
+ if self.m_power_id_field != "":
+ result['fields[' + str(field_number) + ']'] = self.m_power_id_field
+ field_number += 1
+ if self.virus_field != "":
+ result['fields[' + str(field_number) + ']'] = self.virus_field
+ field_number += 1
return result
def get_language(self, name):
diff --git a/smash/web/static/js/smash.js b/smash/web/static/js/smash.js
index 2f2846523db2447089e98c1c7f08de6accf1aff3..fecda37d4b7560d1b16fd9ee768119189ea9138c 100644
--- a/smash/web/static/js/smash.js
+++ b/smash/web/static/js/smash.js
@@ -300,6 +300,9 @@ function createTable(params) {
$(tableElement).find('tfoot div[name="yes_no_filter"]').each(function () {
$(this).html('<select style="width:60px" ><option value selected="selected">---</option><option value="true">YES</option><option value="false">NO</option></select>');
});
+ $(tableElement).find('tfoot div[name="yes_no_null_filter"]').each(function () {
+ $(this).html('<select style="width:60px" ><option value selected="selected">---</option><option value="true">YES</option><option value="false">NO</option><option value="null">N/A</option></select>');
+ });
$(tableElement).find('tfoot div[name="integer_filter"]').each(function () {
var options = '<option value selected="selected">---</option>';
for (var i = 1; i <= 8; i++) {