Merge branch 'release/v22.8.18'

portal/models/auth.py

@@ -362,11 +362,13 @@ def token_janitor():
             body=body)
         try:
             em.send_message()
+            db.session.add(em)
         except SMTPRecipientsRefused as exc:
             msg = ("Error sending site summary email to {}: "
                    "{}".format(sponsor_email, exc))
             current_app.logger.error(msg)
             for email in exc[0]:
                 error_emails.add(email)
 
+    db.session.commit()
     return list(error_emails)

portal/models/qb_status.py

@@ -198,6 +198,9 @@ def _indef_init(self):
         for q in qbs:
             if self._current_indef is not None:
                 raise RuntimeError("unexpected second indef qb")
+            if q.relative_start > self.as_of_date:
+                # Don't include if the consent date hasn't arrived
+                continue
             self._current_indef = q
 
     def indef_status(self):

portal/models/reporting.py

@@ -9,6 +9,7 @@
 
 from ..audit import auditable_event
 from ..cache import cache
+from ..database import db
 from ..date_tools import FHIR_datetime
 from ..trigger_states.models import TriggerStatesReporting
 from .app_text import MailResource, SiteSummaryEmail_ATMA, app_text
@@ -403,6 +404,7 @@ def generate_and_send_summaries(org_id):
                           body=summary_email.body)
         try:
             em.send_message()
+            db.session.add(em)
         except SMTPRecipientsRefused as exc:
             msg = ("Error sending site summary email to {}: "
                    "{}".format(staff_user.email, exc))
@@ -418,4 +420,5 @@ def generate_and_send_summaries(org_id):
             for email in exc[0]:
                 error_emails.add(email)
 
+    db.session.commit()
     return error_emails or None

portal/static/js/src/modules/TnthAjax.js

@@ -22,8 +22,8 @@ export default { /*global $ */
     },
     "sendRequest": function(url, method, userId, params, callback) {
         if (!url) { return false; }
-        var REQUEST_TIMEOUT_INTERVAL = 5000;
-        var defaultParams = {type: method ? method : "GET", url: url, attempts: 0, max_attempts: MAX_ATTEMPTS, contentType: "application/json; charset=utf-8", dataType: "json", sync: false, timeout: 5000, data: null, useWorker: false, async: true};
+        var REQUEST_TIMEOUT_INTERVAL = 5000; // default timed out at 5 seconds
+        var defaultParams = {type: method ? method : "GET", url: url, attempts: 0, max_attempts: MAX_ATTEMPTS, contentType: "application/json; charset=utf-8", dataType: "json", sync: false, timeout: REQUEST_TIMEOUT_INTERVAL, data: null, useWorker: false, async: true};
         params = params || defaultParams;
         params = $.extend({}, defaultParams, params);
         params.timeout = params.timeout || REQUEST_TIMEOUT_INTERVAL;
@@ -75,8 +75,8 @@ export default { /*global $ */
         }).fail(function(xhr) {
             if (params.attempts < params.max_attempts) {
                 (function(self, url, method, userId, params, callback) {
-                    setTimeout(function() {
-                        self.sendRequest(url, method, userId, params, callback);
+                    setTimeout(function () {
+                      self.sendRequest(url, method, userId, params, callback);
                     }, REQUEST_TIMEOUT_INTERVAL); //retry after 5 seconds
                 })(self, url, method, userId, params, callback);
             } else {

portal/static/js/src/profile.js

@@ -2994,7 +2994,8 @@ export default (function() {
                 var self = this, errorMessage = "";
                 $("#profileAuditLogTable").html(Utility.getLoaderHTML());
                 $("#profileAuditLogTable .loading-message-indicator").show();
-                this.modules.tnthAjax.auditLog(this.subjectId, {useWorker:true}, function(data) {
+                // set request times out at 5 minutes
+                this.modules.tnthAjax.auditLog(this.subjectId, {useWorker:true, timeout: 5 * 60 * 1000}, function(data) {
                     if (data.error) {
                         errorMessage = i18next.t("Error retrieving data from server");
                     }

portal/trigger_states/empro_states.py

@@ -24,10 +24,10 @@
 from ..models.questionnaire_bank import QuestionnaireBank
 from ..models.questionnaire_response import QuestionnaireResponse
 from ..models.observation import Observation
+from ..models.research_study import EMPRO_RS_ID
 from ..models.user import User
 from ..timeout_lock import TimeoutLock
 
-EMPRO_STUDY_ID = 1
 EMPRO_LOCK_KEY = "empro-trigger-state-lock-{user_id}"
 
 
@@ -317,7 +317,7 @@ def process_pending_actions(ts):
         # Withdrawn users should never receive reminders, nor staff
         # about them.
         qb_status = QB_Status(
-            user=patient, research_study_id=EMPRO_STUDY_ID, as_of_date=now)
+            user=patient, research_study_id=EMPRO_RS_ID, as_of_date=now)
         if qb_status.withdrawn_by(now):
             triggers = copy.deepcopy(ts.triggers)
             triggers['action_state'] = 'withdrawn'

portal/views/user.py

@@ -37,6 +37,7 @@
 from ..models.qb_timeline import QB_StatusCacheKey, invalidate_users_QBT
 from ..models.questionnaire_response import QuestionnaireResponse
 from ..models.relationship import Relationship
+from ..models.research_study import EMPRO_RS_ID
 from ..models.role import ROLE, Role
 from ..models.table_preference import TablePreference
 from ..models.url_token import url_token
@@ -962,8 +963,6 @@ def delete_user_consents(user_id):
       - ServiceToken: []
 
     """
-    from portal.trigger_states.empro_states import EMPRO_STUDY_ID
-
     current_app.logger.debug('delete user consent called w/: {}'.format(
         request.json))
     user = get_user(user_id, 'edit')
@@ -983,7 +982,7 @@ def delete_user_consents(user_id):
         abort(404, "matching user consent not found")
 
     audit_comment = 'Deleted consent agreement'
-    if research_study_id == EMPRO_STUDY_ID:
+    if research_study_id == EMPRO_RS_ID:
         audit_comment = 'Deleted EMPRO consent agreement'
     remove_uc.deleted = Audit(
         user_id=current_user().id, subject_id=user_id,

tests/test_assessment_status.py

@@ -406,7 +406,7 @@ def test_qnr_id_missing(self):
 
     def test_enrolled_in_metastatic(self):
         """metastatic should include baseline and indefinite"""
-        self.bless_with_basics(local_metastatic='metastatic')
+        self.bless_with_basics(local_metastatic='metastatic', setdate=now)
         user = db.session.merge(self.test_user)
 
         a_s = QB_Status(

tests/test_qb_timeline.py

@@ -559,6 +559,34 @@ def test_indef_change_before_start_rp_w_result(self):
         with pytest.raises(StopIteration):
             next(gen)
 
+    def test_indef_assignment_post_consent(self):
+        org = self.setup_org_qbs(rp_name='v3', include_indef=True)
+        org_id = org.id
+        back7, nowish = associative_backdate(
+            now=now, backdate=relativedelta(months=7))
+        self.consent_with_org(org_id=org_id, setdate=back7)
+        user = db.session.merge(self.test_user)
+
+        a_s = QB_Status(
+            user=user,
+            research_study_id=0,
+            as_of_date=nowish)
+        assert a_s.enrolled_in_classification('indefinite')
+
+    def test_indef_assignment_pre_consent(self):
+        org = self.setup_org_qbs(rp_name='v3', include_indef=True)
+        org_id = org.id
+        tomorrow, nowish = associative_backdate(
+            now=now, backdate=relativedelta(days=-1))
+        self.consent_with_org(org_id=org_id, setdate=tomorrow)
+        user = db.session.merge(self.test_user)
+
+        a_s = QB_Status(
+            user=user,
+            research_study_id=0,
+            as_of_date=nowish)
+        assert a_s.enrolled_in_classification('indefinite') is None
+
 
 class Test_QB_StatusCacheKey(TestCase):