added backup documentation and workup script

compose/production/postgres/maintenance/_sourced/constants.sh

@@ -1,5 +1,4 @@
 #!/usr/bin/env bash
 
-
 BACKUP_DIR_PATH='/backups'
 BACKUP_FILE_PREFIX='backup'

compose/production/postgres/maintenance/_sourced/countdown.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 
-
 countdown() {
     declare desc="A simple countdown. Source: https://superuser.com/a/611582"
     local seconds="${1}"

compose/production/postgres/maintenance/_sourced/messages.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 
-
 message_newline() {
     echo
 }

compose/production/postgres/maintenance/backup

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 
-
 ### Create a database backup.
 ###
 ### Usage:
@@ -16,7 +15,6 @@ working_dir="$(dirname ${0})"
 source "${working_dir}/_sourced/constants.sh"
 source "${working_dir}/_sourced/messages.sh"
 
-
 message_welcome "Backing up the '${POSTGRES_DB}' database..."
 
 

config/urls.py

@@ -28,7 +28,7 @@
     path('labs/', include('osler.labs.urls')),
     path('inventory/', include('osler.inventory.urls')),
     path('surveys/', include('osler.surveys.urls')),
-    # path('datadashboard/', include('osler.datadashboard.urls')),
+    #path('datadashboard/', include('osler.datadashboard.urls')),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 # API URLS

docs/conf.py

@@ -3,13 +3,10 @@
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-
 # -- Path setup --------------------------------------------------------------
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-
 import os
 import datetime
 import sys

docs/technical-reference/makingBackups.rst

@@ -0,0 +1,26 @@
+Creating Backups and Copy to Host
+======================================================================
+
+Create Backups
+----------------------------------------------------------------------
+
+To create a backup of the postgres container, use the command:
+    ::
+
+        docker-compose -f production.yml (exec |run --rm) postgres backup
+
+If you are on windows and the above command doesn't work, delete the headings in the script files you are calling, rebuild and run the server, and then use the command:
+    ::
+
+        docker exec -it llemr_postgres_1 /bin/bash usr/local/bin/backup
+
+Note: If you want to view all of the backups you have created in the postgres container, replace backup with backups in the above commands
+
+
+Copy to Host
+----------------------------------------------------------------------
+
+This command will copy the backups you have created to your local machine:
+    ::
+
+        docker cp llemr_postgres_1:./backups .

osler/workup/scripts/workup_date_checker.py

@@ -0,0 +1,45 @@
+"""
+Script that identifies all workups whose encounter date differs from the written_datetime by more than 7 days 
+and for each of these workups print the patient name, author name, the written_datetime, and the encounter date
+
+Instructions for running this script are located in (PUT THE PLACE THAT I PUT THE DOC FILE IN) [note: I need to make docs for this]
+"""
+
+from osler.workup.models import Workup
+from datetime import datetime
+
+NAME = 'django.core.management.commands.shell'
+
+def days_between(d1, d2):
+    '''computes number of days between two date objects'''
+    delta = d2 - d1
+    return abs(delta.days)
+
+
+def get_returned_workups(n):
+    '''check if written_date differs from encounter_date by more than n days for each workup'''
+    all_workups = Workup.objects.all()
+    returned_workups = []
+    for workup in all_workups:
+        if days_between(workup.encounter.clinic_day, datetime.date(workup.written_datetime)) >= n:
+            returned_workups.append(workup)
+    return returned_workups
+
+
+def print_returned_workups(returned_workups):
+    '''for each workup in returned_workups, print the patient name, author name, written_datetime, and the encounter date'''
+    print("All workups whose encounter date differs from the written_datetime by more than 7 days: ")
+    for i, workup in enumerate(returned_workups):
+        st1 = f"Workup {i} | Patient name: {workup.patient.name()}, Author name: {workup.signer}, Date "
+        st2 = f"written: {datetime.date(workup.written_datetime)}, Encounter date: {workup.encounter.clinic_day}"
+        print(st1 + st2)
+
+
+def out_of_date_workup_finder():
+    returned_workups = get_returned_workups(7)
+    print_returned_workups(returned_workups)
+    return returned_workups
+
+
+if __name__ == NAME:
+    out_of_date_workup_finder()

osler/workup/tests/test_scripts.py

@@ -0,0 +1,31 @@
+from django.test import TestCase
+from osler.workup.models import Workup
+from osler.workup.scripts import workup_date_checker
+from .factories import WorkupFactory
+import datetime
+
+class testScripts(TestCase):
+
+    fixtures = ['workup', 'core']
+
+    def test_workup_date_checker(self):
+        d1 = datetime.datetime(2019, 4, 13)
+        d2 = datetime.datetime.now() - datetime.timedelta(days=2)
+        d3 = datetime.datetime(2018, 4, 4)
+
+        workup_one = WorkupFactory()
+        workup_two = WorkupFactory()
+        workup_three = WorkupFactory()
+
+        workup_one.written_datetime = d1
+        workup_two.written_datetime = d2
+        workup_three.written_datetime = d3
+
+        workup_one.save()
+        workup_two.save()
+        workup_three.save()
+
+        expected_returned_workups = [workup_one, workup_three]
+        assert workup_date_checker.out_of_date_workup_finder() == expected_returned_workups
+
+