From 12aaacff59b7a7ec68fbf26634014e07f46096ab Mon Sep 17 00:00:00 2001
From: Amy Chen <achen2401@gmail.com>
Date: Thu, 22 Dec 2022 13:30:58 -0800
Subject: [PATCH 1/4] TN-3209 profile display styling fixes (#4271)

Co-authored-by: Amy Chen <clone@cesium.cirg.washington.edu>
---
 portal/static/less/eproms.less               |  2 +-
 portal/static/less/topnav.less               | 92 ++++++++++++++------
 portal/templates/portal_wrapper.html         | 31 ++++---
 portal/templates/profile/profile_macros.html | 26 +++---
 4 files changed, 98 insertions(+), 53 deletions(-)

diff --git a/portal/static/less/eproms.less b/portal/static/less/eproms.less
index 448851a857..0212bcf2f5 100644
--- a/portal/static/less/eproms.less
+++ b/portal/static/less/eproms.less
@@ -3960,7 +3960,7 @@ section.header {
     .choice {
       margin-bottom: 12px;
       display: flex;
-      flex-wrap: wrap;
+      align-items: flex-start;
       .text {
         margin-left: 8px;
       }
diff --git a/portal/static/less/topnav.less b/portal/static/less/topnav.less
index d9f5ce65c3..c7a2cd44fd 100644
--- a/portal/static/less/topnav.less
+++ b/portal/static/less/topnav.less
@@ -114,15 +114,35 @@
   max-width: 100%;
   background-color: @defaultBackgroundColor;
   background-image: url('../img/header_background.jpg');
-  height: 135px;
+  height: 136px;
   background-size: cover;
   margin: 0;
-  padding: 30px;
+  padding: 16px 24px;
 }
 #tnthNavMainContainer {
-  max-width: 720px;
   position: relative;
   margin: 0 auto;
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  #tnthLogo {
+    flex: 1;
+  }
+  #tnthTopLinks {
+    width: 35%;
+  }
+  .spacer {
+    width: 35%;
+  }
+  .text-container {
+    color: #FFF;
+    display: none;
+  }
+  @media (min-width: 992px) {
+    .text-container {
+      display: block;
+    }
+  }
 }
 #tnthNavXs {
   display: none;
@@ -178,14 +198,14 @@
 }
 @media (min-width: 699px) {
   #tnthNavXs {
-    min-height: 72px;
+    min-height: 86px;
+    padding: 16px;
   }
 }
 
 /** Logo **/
 #tnthLogo {
-  width: 500px;
-  margin: 4px auto;
+  margin: 16px auto;
   transition: margin 10ms ease-in;
   text-align: center;
 }
@@ -205,18 +225,23 @@
   }
 }
 #tnthTopLinks {
-  position: absolute;
-  top: 0;
-  left: 0;
+  line-height: 1.65;
+  white-space: normal;
 }
 
 /** Buttons **/
 .tnth-btn-group {
   position: relative;
-  display: inline-block;
-  vertical-align: middle; // match .btn alignment given font-size hack above
+  display: flex;
+  flex-direction: column;
+  align-items: center;
   margin-left: 0.2em;
 }
+@media (min-width: 786px) {
+  .tnth-btn-group {
+    flex-direction: row;
+  }
+}
 .tnth-nav-btn {
   display: inline-block;
   height: inherit;
@@ -237,11 +262,20 @@
   }
 }
 #tnthUserBtn {
-padding: 0 6px;
+  padding: 0 6px;
+  display: flex;
+  align-items: center;
+  .menu-text {
+    display: inline-block;
+    margin-right: 4px;
+  }
+  .profile-img {
+    margin-left: 12px;
+  }
 }
 @media (min-width: 992px) {
   #tnthUserBtn {
-    padding: 0 14px 0 0;
+    padding: 0 16px 0 0;
     height: inherit;
   }
 }
@@ -353,6 +387,23 @@ padding: 0 6px;
 .welcome-text {
   display: block;
   margin: 0.2em 0;
+  white-space: normal;
+  word-break: break-word;
+  .prompt {
+    display: inline-block;
+  }
+}
+@media (min-width: 992px) {
+  .welcome-text {
+    .prompt {
+      display: block;
+    }
+  }
+}
+@media (min-width: 1600px) {
+  .welcome-text {
+    white-space: nowrap;
+  }
 }
 @media all and (-ms-high-contrast: none),(-ms-high-contrast: active) {
   /* IE10+ */
@@ -446,7 +497,7 @@ padding: 0 6px;
 #tnthNavXs {
   display: block;
 }
-@media (min-width: 768px) {
+@media (min-width: 992px) {
   #tnthNavMain {
     display: block;
   }
@@ -460,19 +511,8 @@ padding: 0 6px;
   }
 }
 @media (min-width: 992px) {
-  #tnthNavMainContainer {
-    max-width: 940px;
-  }
   #tnthNavWrapper img {
     margin: 0 0.5em;
-    vertical-align: middle;
-  }
-}
-@media (min-width: 1220px) {
-  #tnthNavMainContainer {
-    max-width: 100%;
-  }
-  .welcome-text {
-    display: inline-block;
+    vertical-align: top;
   }
 }
diff --git a/portal/templates/portal_wrapper.html b/portal/templates/portal_wrapper.html
index 0b2b5dad1e..81003c420a 100644
--- a/portal/templates/portal_wrapper.html
+++ b/portal/templates/portal_wrapper.html
@@ -50,14 +50,6 @@
 <div id="tnthNavWrapper">
     <div id="tnthNavMain">
         <div id="tnthNavMainContainer">
-            <div id="tnthLogo">
-                {% if enable_links %}<a href="{{PORTAL}}">{% endif %}
-                    <img class="tnth-topnav-wordmark" src="{{PORTAL}}/{{config.BANNER_LOGOS['desktop']}}" alt="{{_('TrueNTH logo')}}"/>
-                {% if enable_links %}</a>{% endif %}
-                {% if branded_logos %}
-                    <img src="{{ branded_logos[0] }}" alt="{{_('brand logo')}}"></img>
-                {% endif %}
-            </div>
             <div id="tnthTopLinks">
                 <div class="tnth-btn-group">
                     {% if user %}
@@ -100,24 +92,35 @@
                         </ul>
                         {% endif %}
                          <button id="tnthUserBtn" type="button" class="tnth-nav-btn tnth-white tnth-dropdown-toggle" data-toggle="tnth-dropdown">
-                            {% if enable_links %}&nbsp;&nbsp; {{ _("MENU") }} <i class="fa fa-bars"></i>{% endif %}
+                            {% if enable_links %}<span class="menu-text">{{ _("MENU") }}</span> <i class="fa fa-bars"></i>{% endif %}
                             <img class="profile-img" src="{{movember_profile}}" width="50" height="50" alt="{{_('Profile image')}}"/>
+                         </button>
+                         <div class="text-container">
                             {% if user.current_encounter().auth_method != 'url_authenticated' %}
-                                <span class="welcome-text portal-weak-auth-hide"><em>{{ _("Welcome") }}</em>{% if user.display_name != "Anonymous" %}, {{ user.display_name }}{% endif %}</span>
+                                <span class="welcome-text portal-weak-auth-hide"><span class="prompt"><em>{{ _("Welcome") }}</em></span>{% if user.display_name != "Anonymous" %} {{ user.display_name }}{% endif %}</span>
                             {% endif %}
-                            {% if config.DEBUG_TIMEOUTS %}({{ expires_in }} seconds remaining){% endif %}
-                         </button>
-                            {% elif login_url %}<ul class="tnth-dropdown-menu" role="menu"><li><a href="{{ login_url }}">{{ _("Log In to TrueNTH") }}</a></li></ul>
+                            {% if config.DEBUG_TIMEOUTS %}<span class="debug-text">({{ expires_in }} seconds remaining)</span>{% endif %}
+                        </div>
+                        {% elif login_url %}<ul class="tnth-dropdown-menu" role="menu"><li><a href="{{ login_url }}">{{ _("Log In to TrueNTH") }}</a></li></ul>
                         <button type="button" class="tnth-nav-btn tnth-white tnth-dropdown-toggle" data-toggle="tnth-dropdown">{{ _("Welcome") }}</button>
                     {% endif %}
                 </div>
             </div>
+            <div id="tnthLogo">
+                {% if enable_links %}<a href="{{PORTAL}}">{% endif %}
+                    <img class="tnth-topnav-wordmark" src="{{PORTAL}}/{{config.BANNER_LOGOS['desktop']}}" alt="{{_('TrueNTH logo')}}"/>
+                {% if enable_links %}</a>{% endif %}
+                {% if branded_logos %}
+                    <img src="{{ branded_logos[0] }}" alt="{{_('brand logo')}}"></img>
+                {% endif %}
+            </div>
+            <div class="spacer"></div>
         </div>
     </div>
     <div id="tnthNavXs">
         <div class="tnth-container-fluid">
             <div class="tnth-navbar-header">
-                <div class="tnth-white tnth-navbar-toggle tnth-nav-btn {% if not user %}tnth-navbar-no-profile{% endif %}">{{ _("MENU") }} <img src="{{movember_profile}}" width="45" height="45" class="profile-img" alt="{{_('Profile image')}}" /></div>
+                <div class="tnth-white tnth-navbar-toggle tnth-nav-btn {% if not user %}tnth-navbar-no-profile{% endif %}"><span class="menu-text">{{ _("MENU") }}</span> <img src="{{movember_profile}}" width="45" height="45" class="profile-img" alt="{{_('Profile image')}}" /></div>
                 {% if enable_links %}<a id="tnthLogoXs" href="{{PORTAL}}" title="{{ _('Return to TrueNTH home') }}">{% endif %}
                 <img src="{{PORTAL}}/{{config.BANNER_LOGOS['mobile']}}" alt="{{_('TrueNTH logo')}}"/>
                 {% if enable_links %}</a>{% endif %}
diff --git a/portal/templates/profile/profile_macros.html b/portal/templates/profile/profile_macros.html
index 24282dd3cb..04c0ce87af 100644
--- a/portal/templates/profile/profile_macros.html
+++ b/portal/templates/profile/profile_macros.html
@@ -931,18 +931,20 @@ <h5 class="muted" v-show="!isSubStudyTriggersResolved()">{{_("Actions Required (
                             v-if="item.type == 'boolean'">
                         <!-- open-choice (checkboxes) type answer -->
                         <div class="choices answer" v-if="item.type == 'open-choice'">
-                            <div class="choice" v-for="option in item.option">
-                                <input
-                                    type="checkbox"
-                                    :code="option.valueCoding.code"
-                                    :class="{other: /other/gi.test(option.valueCoding.display)}"
-                                    :dataType="item.type"
-                                    :linkId="item.linkId"
-                                    :value="option.valueCoding.display"
-                                    @change="onResponseChangeFieldEvent"
-                                >
-                                <span class="text" v-text="option.valueCoding.display"></span>
-                                <textarea
+                            <div v-for="option in item.option">
+                                <div class="choice">
+                                    <input
+                                        type="checkbox"
+                                        :code="option.valueCoding.code"
+                                        :class="{other: /other/gi.test(option.valueCoding.display)}"
+                                        :dataType="item.type"
+                                        :linkId="item.linkId"
+                                        :value="option.valueCoding.display"
+                                        @change="onResponseChangeFieldEvent"
+                                    >
+                                    <span class="text" v-text="option.valueCoding.display"></span>
+                                </div>
+                                 <textarea
                                     class="form-control addl-text other-text"
                                     dataType="string"
                                     :code="option.valueCoding.code"

From 7eb4db411a093007170a450ff6d931f60f264000 Mon Sep 17 00:00:00 2001
From: pbugni <pbugni@u.washington.edu>
Date: Thu, 29 Dec 2022 19:43:40 -0800
Subject: [PATCH 2/4] default 5 year expiration on user_consents coming into
 play (#4278) (#4281)

* default 5 year expiration on user_consents coming into play, unexpectedly.
the use of user_consents.expired is not being managed and erroneously hiding consent rows.  delete checks against this column as hot fix for now.

* migration to restore timelines for patients with a user_consent that has since expired (according to the defunct user_consents.expires field)
---
 portal/migrations/versions/17060aa3c9d6_.py | 71 +++++++++++++++++++++
 portal/models/user.py                       |  5 +-
 2 files changed, 73 insertions(+), 3 deletions(-)
 create mode 100644 portal/migrations/versions/17060aa3c9d6_.py

diff --git a/portal/migrations/versions/17060aa3c9d6_.py b/portal/migrations/versions/17060aa3c9d6_.py
new file mode 100644
index 0000000000..572a5968e8
--- /dev/null
+++ b/portal/migrations/versions/17060aa3c9d6_.py
@@ -0,0 +1,71 @@
+"""Clean up user_consents.expires issue
+
+Revision ID: 17060aa3c9d6
+Revises: 2aa8089588bf
+Create Date: 2022-12-28 05:08:10.714337
+
+"""
+from alembic import op
+from datetime import datetime
+import sqlalchemy as sa
+from sqlalchemy.orm import sessionmaker
+
+from portal.models.qb_timeline import update_users_QBT
+from portal.models.questionnaire_response import QuestionnaireResponse
+from portal.models.research_study import BASE_RS_ID
+from portal.models.role import ROLE
+from portal.models.user import User, unchecked_get_user
+from portal.models.user_consent import UserConsent
+
+# revision identifiers, used by Alembic.
+revision = '17060aa3c9d6'
+down_revision = '2aa8089588bf'
+
+SessionMaker = sessionmaker()
+
+
+def upgrade():
+    """ The user_consents table has an expires field, given a default value
+    of 5 years from the moment any user_content row is generated, and never
+    touched again.
+
+    Once user_consents.expires is eclipsed by current time, the user's
+    timeline is incorrectly purged, as they no longer have a valid consent
+    on file.  This field isn't being used as originally intended, and the
+    QuestionnaireBank logic handles the end of a study correctly, thus
+    user_consents.expires should be removed.
+
+    But first, we need to restore timeline status for all users having
+    passed the point of expiration.
+    """
+    session = SessionMaker(bind=op.get_bind())
+    sys_user = User.query.filter_by(email='__system__').one()
+
+    # Obtain a list of patients for whom their consent has expired
+    now = datetime.utcnow()
+    query = UserConsent.query.filter(UserConsent.expires < now).with_entities(
+        UserConsent.user_id).distinct().order_by(UserConsent.user_id)
+    for row in session.execute(query):
+        user_id = row[0]
+        user = unchecked_get_user(user_id, allow_deleted=True)
+        if user.deleted_id or not user.has_role(ROLE.PATIENT.value):
+            continue
+
+        # Code modifications in place ignore expires, force a QB timeline
+        # full rebuild
+        QuestionnaireResponse.purge_qb_relationship(
+            subject_id=user_id,
+            research_study_id=BASE_RS_ID,
+            acting_user_id=sys_user.id)
+
+        update_users_QBT(
+            user_id,
+            research_study_id=BASE_RS_ID,
+            invalidate_existing=True)
+
+        print(f"Restored timeline for {user_id}")
+
+
+def downgrade():
+    # no downgrade for this migration
+    pass
diff --git a/portal/models/user.py b/portal/models/user.py
index c5baeb526e..c51fb0baed 100644
--- a/portal/models/user.py
+++ b/portal/models/user.py
@@ -429,10 +429,9 @@ def all_consents(self):
     @property
     def valid_consents(self):
         """Access to consents that have neither been deleted or expired"""
-        now = datetime.utcnow()
         return [
             c for c in self._consents
-            if c.expires > now and c.deleted_id is None]
+            if c.deleted_id is None]
 
     @hybrid_property
     def clinicians(self):
@@ -2212,7 +2211,7 @@ def patients_query(
         consent_query = UserConsent.query.filter(and_(
             UserConsent.deleted_id.is_(None),
             UserConsent.research_study_id == research_study_id,
-            UserConsent.expires > datetime.utcnow()))
+        ))
         consented_users = [
             u.user_id for u in consent_query if u.staff_editable]
 

From 049225eacf9642589a14b43066c8387645a92cd6 Mon Sep 17 00:00:00 2001
From: Lars Gohr <elgohr@users.noreply.github.com>
Date: Tue, 10 Jan 2023 22:07:52 +0100
Subject: [PATCH 3/4] Updated elgohr/Publish-Docker-Github-Action to a
 supported version (v5) (#4282)

elgohr/Publish-Docker-Github-Action@master is not supported anymore
---
 .github/workflows/build-deliver.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-deliver.yaml b/.github/workflows/build-deliver.yaml
index 8e56a020af..a717402cf3 100644
--- a/.github/workflows/build-deliver.yaml
+++ b/.github/workflows/build-deliver.yaml
@@ -17,7 +17,7 @@ jobs:
 
       - name: Publish to GitHub Container Registry
         # TODO: pin to hash
-        uses: elgohr/Publish-Docker-Github-Action@master
+        uses: elgohr/Publish-Docker-Github-Action@v5
         with:
           name: ${{ github.repository }}
           registry: ghcr.io

From 559414b45cc5cec8d65495244438973f3f4d0059 Mon Sep 17 00:00:00 2001
From: Ivan Cvitkovic <ivanc@uw.edu>
Date: Tue, 10 Jan 2023 13:09:16 -0800
Subject: [PATCH 4/4]  Remove version pin for
 elgohr/Publish-Docker-Github-Action

---
 .github/workflows/build-deliver.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-deliver.yaml b/.github/workflows/build-deliver.yaml
index a717402cf3..06d5daf379 100644
--- a/.github/workflows/build-deliver.yaml
+++ b/.github/workflows/build-deliver.yaml
@@ -17,7 +17,7 @@ jobs:
 
       - name: Publish to GitHub Container Registry
         # TODO: pin to hash
-        uses: elgohr/Publish-Docker-Github-Action@v5
+        uses: elgohr/Publish-Docker-Github-Action@main
         with:
           name: ${{ github.repository }}
           registry: ghcr.io