Merge branch '330-mail-about-virus-test-results' into 'master'

Resolve "mail about virus test results"

Closes #330

See merge request NCER-PD/scheduling-system!245

smash/smash/settings.py

@@ -74,6 +74,7 @@ TEMPLATES = [
 
 CRON_CLASSES = [
     'web.views.kit.KitRequestEmailSendJob',
+    'web.views.virus_mail.KitRequestEmailSendJob',
     'web.redcap_connector.RedCapRefreshJob',
     'web.views.voucher.ExpireVouchersJob',
     'web.importer.exporter_cron_job.SubjectExporterCronJob',

smash/web/migrations/0165_configurationitem_email_virus.py

+# -*- 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 VIRUS_EMAIL_HOUR_CONFIGURATION_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, VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE, "",
+                "At what time a day email with updates about virus tests should be sent")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('web', '0164_configurationitem_email_items_for_redcap'),
+    ]
+
+    operations = [
+        migrations.RunPython(configuration_items),
+    ]

smash/web/models/constants.py

@@ -51,6 +51,7 @@ KIT_EMAIL_HOUR_CONFIGURATION_TYPE = "KIT_DAILY_EMAIL_HOUR_CONFIGURATION_TYPE"
 KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_TYPE = "KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_TYPE"
 KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE = "KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE"
 KIT_DAILY_EMAIL_TIME_FORMAT_TYPE = "KIT_DAILY_EMAIL_TIME_FORMAT_TYPE"
+VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE = "VIRUS_EMAIL_HOUR_CONFIGURATION_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'
@@ -64,6 +65,7 @@ RED_CAP_ND_NUMBER_FIELD_TYPE = 'RED_CAP_ND_NUMBER_FIELD_TYPE'
 RED_CAP_VIRUS_FIELD_TYPE = 'RED_CAP_VIRUS_FIELD_TYPE'
 RED_CAP_SAMPLE_DATE_FIELD_TYPE = "RED_CAP_SAMPLE_DATE_FIELD_TYPE"
 
+
 MAIL_TEMPLATE_CONTEXT_SUBJECT = 'S'
 MAIL_TEMPLATE_CONTEXT_APPOINTMENT = 'A'
 MAIL_TEMPLATE_CONTEXT_VISIT = 'V'

smash/web/redcap_connector.py

@@ -43,6 +43,7 @@ class RedcapSubject(object):
 
 class RedcapVisit(object):
     virus = None
+    virus_inconclusive = False
     visit_number = 0
 
 
@@ -218,6 +219,21 @@ class RedcapConnector(object):
                                 subject.virus_test_5 = visit.virus
                                 subject.virus_test_5_updated = datetime.datetime.now()
                                 subject.save()
+                            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()
+                            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()
+                            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()
+                            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()
+                            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()
+                                subject.save()
 
         return result
 
@@ -330,6 +346,8 @@ class RedcapConnector(object):
                         visit.virus = False
                     elif row.get(self.virus_field) == "Positive":
                         visit.virus = True
+                    elif row.get(self.virus_field) == "Inconclusive":
+                        visit.virus_inconclusive = True
                 if self.sample_date_field != "":
                     if row.get(self.sample_date_field) != "":
                         redcap_subject.visits.append(visit)

smash/web/views/virus_mail.py

+# coding=utf-8
+import datetime
+import logging
+
+import timeout_decorator
+from django_cron import CronJobBase, Schedule
+
+from web.models import ConfigurationItem
+from web.models.constants import VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE, \
+    CRON_JOB_TIMEOUT
+from ..models import StudySubject, Worker
+from ..smash_email import EmailSender
+
+logger = logging.getLogger(__name__)
+
+
+def get_subject_statistics():
+    date_from = datetime.datetime.now() - datetime.timedelta(days=1)
+
+    subjects_positive_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from, virus_test_1=True).count()
+    subjects_positive_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
+                                                           virus_test_2=True).count()
+    subjects_positive_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
+                                                           virus_test_3=True).count()
+    subjects_positive_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
+                                                           virus_test_4=True).count()
+    subjects_positive_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
+                                                           virus_test_5=True).count()
+
+    subjects_negative_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from,
+                                                          virus_test_1=False).count()
+    subjects_negative_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
+                                                           virus_test_2=False).count()
+    subjects_negative_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
+                                                           virus_test_3=False).count()
+    subjects_negative_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
+                                                           virus_test_4=False).count()
+    subjects_negative_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
+                                                           virus_test_5=False).count()
+
+    subjects_inconclusive_count = StudySubject.objects.filter(virus_test_1_updated__gt=date_from,
+                                                              virus_test_1__isnull=True).count()
+    subjects_inconclusive_count += StudySubject.objects.filter(virus_test_2_updated__gt=date_from,
+                                                               virus_test_2__isnull=True).count()
+    subjects_inconclusive_count += StudySubject.objects.filter(virus_test_3_updated__gt=date_from,
+                                                               virus_test_3__isnull=True).count()
+    subjects_inconclusive_count += StudySubject.objects.filter(virus_test_4_updated__gt=date_from,
+                                                               virus_test_4__isnull=True).count()
+    subjects_inconclusive_count += StudySubject.objects.filter(virus_test_5_updated__gt=date_from,
+                                                               virus_test_5__isnull=True).count()
+
+    return {"Positive": subjects_positive_count, "Negative": subjects_negative_count,
+            "Inconclusive": subjects_inconclusive_count,
+            "total": subjects_positive_count + subjects_negative_count + subjects_inconclusive_count}
+
+
+def create_statistic_email_content(data, title):
+    email_body = "<h1>" + title + "</h1>"
+
+    email_body += "In the past 24 hours " + str(data["total"]) + " donors were tested</br></br>"
+    for status in data:
+        if status != "total":
+            email_body += str(data[status]) + ' number of donors were tested ' + status + "</br>"
+
+    return email_body
+
+
+def send_mail(data):
+    title = "Virus test statistics"
+    email_body = create_statistic_email_content(data, title)
+
+    recipients = []
+    workers = Worker.objects.all()
+    for worker in workers:
+        if worker.user is not None:
+            if worker.user.is_active:
+                if worker.email is not None and worker.email != "":
+                    recipients.append(worker.email)
+    cc_recipients = []
+    logger.warn('Calling to send email')
+    EmailSender().send_email(title, email_body, ";".join(recipients), cc_recipients)
+
+
+class KitRequestEmailSendJob(CronJobBase):
+    RUN_AT = []
+
+    try:
+        times = ConfigurationItem.objects.get(
+            type=VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE).value.split(";")
+        for entry in times:
+            # TODO it's a hack assuming that we are in CEST
+            text = str((int(entry.split(":")[0]) + 22) % 24) + ":" + entry.split(":")[1]
+            RUN_AT.append(text)
+    except:
+        logger.error("Cannot fetch data about email hour")
+    schedule = Schedule(run_at_times=RUN_AT)
+    code = 'web.virus_daily_email'  # a unique code
+
+    @timeout_decorator.timeout(CRON_JOB_TIMEOUT)
+    def do(self):
+        data = get_subject_statistics()
+        send_mail(data)
+        return "mail sent"