Merge branch 'release/v23.2.6'

manage.py

@@ -771,6 +771,7 @@ def present_before_after_state(user_id, external_study_id, before_state):
             print(f"\t\t{item}")
             print(f"\t\t\t{modified_t[item][1]} ==> {modified_t[item][0]}")
 
+    return after_qnrs, after_timeline
 
 @app.cli.command()
 @click.option(
@@ -877,6 +878,10 @@ def preview_site_update(org_id, retired):
 
     # With new RP in place, cycle through patients, purge and
     # refresh timeline and QNR data, and report any diffs
+    total_qnrs, total_qnrs_assigned = 0, 0
+    total_qnrs_completed_b4, total_qnrs_completed_after = 0, 0
+    total_qbs_completed_b4, total_qbs_completed_after = 0, 0
+    patients_with_fewer_assigned = 0
     for patient in query:
         QuestionnaireResponse.purge_qb_relationship(
             subject_id=patient.id,
@@ -885,9 +890,36 @@ def preview_site_update(org_id, retired):
         )
         update_users_QBT(
             patient.id, research_study_id=0, invalidate_existing=True)
-        present_before_after_state(
+        after_qnrs, after_timeline = present_before_after_state(
             patient.id, patient.external_study_id, patient_state[patient.id])
-
+        total_qnrs += len(patient_state[patient.id]['qnrs'])
+        total_qbs_completed_b4 += len(
+            [1 for date_status in patient_state[patient.id]['timeline'].keys()
+             if date_status.endswith('Completed') and
+             not date_status.endswith('Partially Completed')])
+        total_qbs_completed_after += len(
+            [1 for date_status in after_timeline.keys()
+             if date_status.endswith('Completed') and
+             not date_status.endswith('Partially Completed')])
+        b4_total = sum(
+            [1 for qb_name in patient_state[patient.id]['qnrs'].values()
+             if qb_name[0] != "none of the above"])
+        total_qnrs_completed_b4 += b4_total
+        after_total = sum(
+            [1 for qb_name in after_qnrs.values()
+             if qb_name[0] != "none of the above"])
+        total_qnrs_completed_after += after_total
+        if b4_total != after_total:
+            patients_with_fewer_assigned += 1
+
+    print(f"{total_qnrs} QuestionnaireResponses for all patients in organization {org_id}")
+    print(organization.name)
+    print(f"  Patients in organization: {len(patient_state)}")
+    print(f"  Patients negatively affected by change: {patients_with_fewer_assigned}")
+    print(f"  Number of those QNRs assigned to a QB before RP change: {total_qnrs_completed_b4}")
+    print(f"  Number of those QNRs assigned to a QB after RP change: {total_qnrs_completed_after}")
+    print(f"  Number of QuestionnaireBanks completed before RP change: {total_qbs_completed_b4}")
+    print(f"  Number of QuestionnaireBanks completed after RP change: {total_qbs_completed_after}")
     # Restore organization to pre-test RPs
     db.session.delete(new_org_rp)
     db.session.commit()

portal/config/eproms/AppText.json

@@ -20,6 +20,11 @@
       "name": "IRONMAN patient privacy URL",
       "resourceType": "AppText"
     },
+    {
+      "custom_text": "{config[LR_ORIGIN]}/c/portal/truenth/asset/mail?version=latest&uuid=890f6204-2dc8-5a5c-617e-4933fab65353&editorUrl=true",
+      "name": "IRONMAN newsletter",
+      "resourceType": "AppText"
+    },
     {
       "custom_text": "{config[LR_ORIGIN]}/c/portal/truenth/asset/detailed?version=latest&uuid=a455d641-06cb-48b7-a4fd-ddc9fe98a921&editorUrl=true",
       "name": "IRONMAN patient terms and conditions URL",

portal/config/eproms/Organization.json

@@ -3784,34 +3784,6 @@
       },
       "resourceType": "Organization"
     },
-    {
-      "extension": [
-        {
-          "timezone": "Europe/Madrid",
-          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
-        },
-        {
-          "research_protocols": [
-			{"name": "IRONMAN v3"}
-          ],
-          "url": "http://us.truenth.org/identity-codes/research-protocol"
-        }
-      ],
-      "id": 146103,
-      "identifier": [
-        {
-          "system": "http://pcctc.org/",
-          "use": "secondary",
-          "value": "146-103"
-        }
-      ],
-      "language": "es_ES",
-      "name": "Hospital Universitario Virgen de la Victoria",
-      "partOf": {
-        "reference": "api/organization/29000"
-      },
-      "resourceType": "Organization"
-    },
     {
       "extension": [
         {
@@ -4110,7 +4082,8 @@
         },
         {
           "research_protocols": [
-			{"name": "IRONMAN v3"}
+            {"name": "IRONMAN v3", "retired_as_of": "2023-01-06T20:00:00Z"},
+            {"name": "IRONMAN v5"}
           ],
           "url": "http://us.truenth.org/identity-codes/research-protocol"
         }
@@ -4138,7 +4111,8 @@
         },
         {
           "research_protocols": [
-			{"name": "IRONMAN v3"}
+            {"name": "IRONMAN v3", "retired_as_of": "2023-01-06T20:00:00Z"},
+            {"name": "IRONMAN v5"}
           ],
           "url": "http://us.truenth.org/identity-codes/research-protocol"
         }

portal/config/eproms/ScheduledJob.json

@@ -19,13 +19,27 @@
       "id": 6,
       "kwargs": {
         "research_study_id": 1,
+        "run_dates": [15, 16, 17, 18, 19, 20, 21],
         "org_id": 20000
       },
       "name": "EMPRO site summary email",
       "resourceType": "ScheduledJob",
-      "schedule": "r 20 20 * *",
+      "schedule": "r 20 * * 1",
       "task": "send_questionnaire_summary"
     },
+    {
+      "active": false,
+      "args": null,
+      "kwargs": {
+        "org_id": 22000,
+        "newsletter": "IRONMAN newsletter",
+        "research_study_id": 0
+      },
+      "name": "Send Newsletter",
+      "resourceType": "ScheduledJob",
+      "schedule": "0 0 0 0 0",
+      "task": "send_newsletter"
+    },
     {
       "active": true,
       "args": null,

portal/models/message.py

@@ -2,15 +2,18 @@
 
 from datetime import datetime
 from flask import current_app
+from smtplib import SMTPRecipientsRefused
 from sqlalchemy.ext.hybrid import hybrid_property
 from textwrap import fill
 
 from flask_mail import Message, email_dispatched
 
+from .app_text import MailResource, app_text
 from ..audit import auditable_event
 from ..database import db
 from ..extensions import mail
-from .user import INVITE_PREFIX, User
+from .organization import OrgTree
+from .user import INVITE_PREFIX, User, patients_query
 
 
 def log_message(message, app):
@@ -198,3 +201,46 @@ def as_json(self):
             'body': self.body, 'sent_at': self.sent_at,
             'user_id': self.user_id}
         return d
+
+
+class Newsletter(object):
+    """Manages compiling newsletter content and sending out.
+    """
+
+    def __init__(self, org_id, research_study_id, content_key):
+        self.org_id = org_id
+        self.research_study_id = research_study_id
+        self.content_key = content_key
+
+    def transmit(self):
+        acting_user = User.query.filter_by(email='__system__').one()
+        resource_url = app_text(self.content_key)
+        requested_orgs = (
+            OrgTree().here_and_below_id(organization_id=self.org_id) if self.org_id
+            else None)
+        error_emails = []
+        for patient in patients_query(
+                acting_user=acting_user,
+                research_study_id=self.research_study_id,
+                requested_orgs=requested_orgs):
+            if not patient.email_ready()[0]:
+                continue
+            item = MailResource(resource_url, patient.locale_code)
+            msg = EmailMessage(
+                subject=item.subject,
+                body=item.body,
+                recipients=patient.email,
+                sender=current_app.config['MAIL_DEFAULT_SENDER'],
+                user_id=acting_user.id,
+                recipient_id=patient.id)
+            try:
+                msg.send_message()
+            except SMTPRecipientsRefused as exc:
+                current_app.logger.error(
+                    f"Error sending %s to %s: %s",
+                    self.content_key, patient.email, exc)
+                error_emails.append(patient.email)
+            db.session.add(msg)
+
+        db.session.commit()
+        return error_emails

portal/static/js/src/accountCreation.js

@@ -5,6 +5,10 @@ import SYSTEM_IDENTIFIER_ENUM from "./modules/SYSTEM_IDENTIFIER_ENUM.js";
 import OrgTool from "./modules/OrgTool.js";
 import ProcApp from "./modules/Procedures.js";
 import {CurrentUserObj} from "./mixins/CurrentUser.js";
+import {
+  REQUIRED_PI_ROLES,
+  REQUIRED_PI_ROLES_WARNING_MESSAGE,
+} from "./data/common/consts.js";
 
 (function() {
     var AccountCreationObj = window.AccountCreationObj = function (dependencies) { /*global $ tnthDates Utility*/
@@ -336,6 +340,17 @@ import {CurrentUserObj} from "./mixins/CurrentUser.js";
             }
         };
 
+        this.hasErrorText = function() {
+            var hasError = false;
+            $("#createProfileForm " + HELP_BLOCK_IDENTIFIER).each(function () {
+              if (hasError) {
+                return false;
+              }
+              hasError = $(this).text() !== "";
+            });
+            return hasError;
+        }
+
         this.__checkFields = function() {
 
             var hasError = false;
@@ -362,12 +377,7 @@ import {CurrentUserObj} from "./mixins/CurrentUser.js";
 
             /* finally check fields to make sure there isn't error, e.g. due to validation error */
               if (!hasError) {
-                $("#createProfileForm " + HELP_BLOCK_IDENTIFIER).each(function() {
-                    if (hasError) {
-                        return false;
-                    }
-                    hasError = ($(this).text() !== "");
-                });
+                hasError = this.hasErrorText();
             }
 
             if (hasError) {
@@ -379,11 +389,20 @@ import {CurrentUserObj} from "./mixins/CurrentUser.js";
             return hasError;
         };
 
+
+        this.isRoleChecked = function(role) {
+            if (!role) return false;
+            return $(`#createProfileForm .input-role[data-role='${role}']`).is(
+              ":checked"
+            );
+        };
+
         this.initFieldEvents = function() {
             let self = this;
             Utility.convertToNumericField($("#date, #year, #phone, #altPhone"));
 
             $("#createProfileForm [required]").on("change", function() {
+                if (self.hasErrorText()) return;
                 $("#updateProfile").attr("disabled", false);
                 setTimeout(function() { self.clearError(); }, 600);
             });
@@ -396,6 +415,44 @@ import {CurrentUserObj} from "./mixins/CurrentUser.js";
             $("#createProfileForm input[type='checkbox']").on("change", function() {
                 $(this).closest(".profile-section").find(HELP_BLOCK_IDENTIFIER).text("").removeClass("error-message");
             });
+
+            $("#createProfileForm .input-role").on("change", function() {
+                // PI role checked
+                var primaryInvestatorRoleChecked = self.isRoleChecked(
+                  "primary_investigator"
+                );
+
+                if (!primaryInvestatorRoleChecked) {
+                    $(this)
+                    .closest(".profile-section")
+                    .find(HELP_BLOCK_IDENTIFIER)
+                    .text("")
+                    .removeClass("error-message");
+                    $("#updateProfile").attr("disabled", false);
+                    return;
+                }
+                var requiredRolesChecked = REQUIRED_PI_ROLES.filter((role) =>
+                  self.isRoleChecked(role)
+                ).length > 0;
+
+                if (!requiredRolesChecked) {
+                  $(this)
+                    .closest(".profile-section")
+                    .find(HELP_BLOCK_IDENTIFIER)
+                    .html(REQUIRED_PI_ROLES_WARNING_MESSAGE)
+                    .addClass("error-message");
+                  $("#updateProfile").attr("disabled", true);
+                } else {
+                  $(this)
+                    .closest(".profile-section")
+                    .find(HELP_BLOCK_IDENTIFIER)
+                    .html("")
+                    .addClass("error-message");
+                  $("#updateProfile").attr("disabled", false);
+                }
+
+
+            });
         };
 
         this.setDefaultRoles = function() {

portal/static/js/src/data/common/consts.js

@@ -2,9 +2,27 @@ export var EPROMS_MAIN_STUDY_ID = 0;
 export var EPROMS_SUBSTUDY_ID = 1;
 export var EPROMS_SUBSTUDY_SHORT_TITLE = "EMPRO";
 export var EPROMS_SUBSTUDY_TITLE = i18next.t("IRONMAN EMPRO study");
-export var EMPRO_TRIGGER_PROCCESSED_STATES = ["processed", "triggered", "resolved"];
-export var EMPRO_TRIGGER_UNPROCCESSED_STATES = ["due", "inprocess", "unstarted"];
+export var EMPRO_TRIGGER_PROCCESSED_STATES = [
+  "processed",
+  "triggered",
+  "resolved",
+];
+export var EMPRO_TRIGGER_UNPROCCESSED_STATES = [
+  "due",
+  "inprocess",
+  "unstarted",
+];
 export var EPROMS_SUBSTUDY_QUESTIONNAIRE_IDENTIFIER = "ironman_ss";
 export var EMPRO_POST_TX_QUESTIONNAIRE_IDENTIFIER = "ironman_ss_post_tx";
 //pre-existing translated text
-export var DEFAULT_SERVER_DATA_ERROR = i18next.t("Error retrieving data from server");
+export var DEFAULT_SERVER_DATA_ERROR = i18next.t(
+  "Error retrieving data from server"
+);
+export var REQUIRED_PI_ROLES = ["staff", "staff_admin", "clinician"];
+export var REQUIRED_PI_ROLES_WARNING_MESSAGE =
+  i18next.t(`<p>An account with a Primary Investigator role must also have at least ONE of the following roles:</p>
+            <ul>
+                <li><b>Staff</b></li>
+                <li><b>Admin Staff</b></li>
+                <li><b>Clinician</b></li>
+            </ul>`);